gebhart/patrepeval huggingface dataset:
Different murine-derived feeder cells alter the definitive endoderm differentiation of human induced pluripotent stem cells (2018)

The crosstalk between cells is important for differentiation of cells. Murine-derived feeder cells, SNL76/7 feeder cells (SNLs) or mouse primary embryonic fibroblast feeder cells (MEFs) are widely used for culturing undifferentiated human induced pluripotent stem cells (hiPSCs). It is still unclear whether different culture conditions affect the induction efficiency of definitive endoderm (DE) differentiation from hiPSCs. Here we show that the efficiency of DE differentiation from hiPSCs cultured on MEFs was higher than that of hiPSCs cultured on SNLs. The qPCR, immunofluorescent and flow cytometry analyses revealed that the expression levels of mRNA and/or proteins of the DE marker genes, SOX17, FOXA2 and CXCR4, in DE cells differentiated from hiPSCs cultured on MEFs were significantly higher than those cultured on SNLs. Comprehensive RNA sequencing and molecular network analyses showed the alteration of the gene expression and the signal transduction of hiPSCs cultured on SNLs and MEFs. Interestingly, the expression of non-coding hXIST exon 4 was up-regulated in hiPSCs cultured on MEFs, in comparison to that in hiPSCs cultured on SNLs. By qPCR analysis, the mRNA expression of undifferentiated stem cell markers KLF4, KLF5, OCT3/4, SOX2, NANOG, UTF1, and GRB7 were lower, while that of hXIST exon 4, LEFTY1, and LEFTY2 was higher in hiPSCs cultured on MEFs than in those cultured on SNLs. Taken together, our finding indicated that differences in murine-feeder cells used for maintenance of the undifferentiated state alter the expression of pluripotency-related genes in hiPSCs by the signaling pathways and affect DE differentiation from hiPSCs, suggesting that the feeder cells can potentiate hiPSCs for DE differentiation.
To generate a photonic nanojet outside a high refractive index microsphere illuminated by a Gaussian beam (2022)

A non-resonant, concentrated, narrow beam of light emerging from an illuminated microlens is called a photonic nanojet (PNJ). According to currently prevailing opinion, microspheres and microcylinders are only able to generate a PNJ in their exterior when their refractive index ns (or refractive index contrast) is less than 2. In this Letter we demonstrate that a PNJ can emerge from a microsphere even when ns > 2: first by employing the laws of geometrical optics for a divergent light source; then, by using ray transfer matrix analysis, a mathematical condition for the Gaussian beam (GB) outside the high ns microsphere is derived. The PNJ outside the microsphere with ns = 2.5 is simulated using Generalized Lorenz-Mie theory (GLMT), by using a front focused GB source. The simulated difference between front and back focusing on the dependence of ns is confirmed experimentally by Raman imaging. By opening the PNJ field for high refractive index materials, we believe this work will be a nucleus for new ideas in the field and enable new PNJ applications.
Design of slot waveguide for ultra-violet light based on atomic layer deposition (2019)

We unveil parameter sets to achieve a low loss single mode waveguide operating at UV wavelengths. The proposed design that is compatible with atomic layer deposition technology is expected to have potential applications in integrated-photonics based UV sensing.
PD-L1 expression and tumor mutational burden are independent biomarkers in most cancers (2019)

Funding was provided by Foundation Medicine Inc., the Johns Hopkins Bloomberg-Kimmel Institute for Cancer Immunotherapy, the Viragh Foundation, the National Cancer Institute Specialized Program of Research Excellence (SPORE) in Gastrointestinal Cancers (P50 CA062924), the NIH Center Core Grant (P30 CA006973), the Norman & Ruth Rales Foundation, and the Conquer Cancer Foundation.
Biochemical and Pharmacological Characterization of a Depressant Insect Toxin from the Venom of the Scorpion <i>Buthacus arenicola</i> (1997)

A depressant toxin active on insects, Buthacus arenicola IT2, was isolated from the venom of the North African scorpion B. arenicola and its structural and pharmacological properties were investigated. B. arenicola IT2 is a single polypeptide of 61 amino acid residues, including 8 half-cystines but no methionine and histidine, with a molecular mass of 6835 Da. Its amino acid sequence is 79-95% identical to other depressant toxins from scorpions. When injected into the cockroach Blatella germanica, B. arenicola IT2 induced a slow depressant flaccid paralysis with a LD50 of 175 ng. B. arenicola IT2 has two non-interacting binding sites in cockroach neuronal membranes: one of high affinity (Kd1 = 0.11 +/- 0.04 nM) and low capacity (Bmax1 = 2.2 +/- 0.6 pmol/mg), and one of low affinity (Kd2 = 24 +/- 7 nM) and high capacity (Bmax2 = 226 +/- 92 pmol/mg). Its binding to these two sites was completely inhibited by Leiurus quinquestriatus quinquestriatus IT2, a depressant toxin from L. quinquestriatus quinquestriatus. Reciprocal-binding experiments between B. arenicola IT2 and the excitatory insect-toxin A. australis Hector IT revealed competition between the two toxins for the high-affinity sites of B. arenicola IT2. B. arenicola IT2 has a higher affinity than L. quinquestriatus hebraeus IT2, a depressant toxin from L. quinquestriatus hebraeus. Thus, B. arenicola IT2 represents an interesting tool to study the receptor site for depressant toxins on insect sodium channels.
Haemodynamic responses to obstructive sleep apnoeas in premenopausal women (1999)

Obstructive apnoeas in women were associated with marked blood pressure changes, similar to those previously reported in men. While respiratory events improved slightly in the luteal phase, blood pressure responses to these events increased by approximately 100%. Thus, the menstrual cycle has discordant effects on the respiratory and cardiovascular effects of OSA in women.
Incremental Model Predictive Control Exploiting Time-Delay Estimation for a Robot Manipulator (2022)

This article proposes a new incremental model predictive control (IMPC) strategy, which allows for constrained control of a robot manipulator, while the resulting incremental model is derived without a concrete mathematical system model. First, to reduce dependence on the nominal model of robot manipulators, the continuous-time nonlinear system model is approximated by an incremental system using the time-delay estimation (TDE). Then, based on the incremental system, the tracking IMPC is designed in the framework of MPC without terminal ingredients. Thus, compared with existing MPC methods, the nominal mathematical model is not required. Moreover, we investigate reachable reference trajectories and confirm the local input-to-state stability (ISS) of IMPC, considering the bounded TDE error as the disturbance of the incremental system. For reachable reference trajectories, the local ISS of IMPC is analyzed using the continuity of the value function, and the cumulative error bound is not overconservative. Finally, several real-time experiments are conducted to verify the effectiveness of IMPC. Experimental results show that the system can achieve optimal control performance while guaranteeing that input and state constraints are not violated.
Diagnostic TR-FRET assays for detection of antibodies in patient samples (2023)

Serological assays are important diagnostic tools for surveying exposure to the pathogen, monitoring immune response post vaccination, and managing spread of the infectious agent among the population. Current serological laboratory assays are often limited because they require the use of specialized laboratory technology and/or work with a limited number of sample types. Here, we evaluate an alternative by developing time-resolved Förster resonance energy transfer (TR-FRET) homogeneous assays that exhibited exceptional versatility, scalability, and sensitivity and outperformed or matched currently used strategies in terms of sensitivity, specificity, and precision. We validated the performance of the assays measuring total immunoglobulin G (IgG) levels; antibodies against severe acute respiratory syndrome coronavirus (SARS-CoV) or Middle Eastern respiratory syndrome (MERS)-CoV spike (S) protein; and SARS-CoV-2 S and nucleocapsid (N) proteins and applied it to several large sample sets and real-world applications. We further established a TR-FRET-based ACE2-S competition assay to assess the neutralization propensity of the antibodies. Overall, these TR-FRET-based serological assays can be rapidly extended to other antigens and are compatible with commonly used plate readers.
Chord recognition using measures of fit, chord templates and filtering methods (2009)

This paper presents an efficient method for chord transcription of music signals. A succession of chroma vectors is calculated from the signal in order to extract the musical content of the piece over time. We introduce a set of chord templates for several types of chords (major, minor, dominant seventh, ...): different chord models taking into account one or more harmonics of the notes of the chord are considered. In order to fit the chroma vectors to the chord templates, we analytically calculate a scale parameter. The detected chord over a frame is the one minimizing a measure of fit between a rescaled chroma vector and the chord templates. Several popular measures in the probability and signal processing field are considered for our task. In order to take into account the time-persistence, we perform a post-processing filtering over the recognition criteria which quickly smooths the results and corrects random errors. The system is evaluated on the 13 Beatles albums and compared to the state-of-the-art. Results show that our method outperforms state-of-the-art methods but more importantly is significantly faster.
Rapid and transient calcium response in acquired granulocytic or monocytic phenotype of promyelocytic human leukemia HL-60 cells (2008)

3424 Calcium flux is a well established type of signal transduction in cells, elicited by a large number of mediators binding to their respective target receptors. Changes in intracellular calcium levels result in a plethora of effects including changes in gene transcription and post-transcriptional modifications that can lead to cell activation or suppression.  Utilizing the ability of promyelocytic human leukemia HL-60 cells to undergo in vitro differentiation into the granulocytic or monocytic phenotype and the measurement of intracellular response of Fluo-4 loaded cells by a microcapillary flow cytometer, we demonstrated that as expected, A23187 and ionomycin, known pharmacological stimuli, resulted in sharp increases in intracellular calcium response. We then found that FMLP, SDF-1α and ATP elicited a rapid and transient intracellular calcium mobilization in both undifferentiated and granulocytic or monocytic differentiated cells, with ATP being the most efficacious stimulant. In contrast, LPS, known to be potent activator of macrophages, did not cause a rapid and transient increase in intracellular calcium level at the concentration of 1 ug/mL i.e. up to 100-fold the concentration normally required for maximal biological effects.  Thus, the results obtained in this study were consistent with and extended the previous studies of activation of macrophages for tumor cytotoxicity (Johnson & Torres, 1985, Johnston & Kitagawa, 1985 and Wright et al., 1985), suggesting that the importance of intracellular calcium mobilization as a second messenger in macrophages and granulocytes in response to stimuli.
Effect of a Size-Dependent Equilibrium Potential on Nano-LiFePO<sub>4</sub>Particle Interactions (2015)

Several electrode materials, such as LiFePO4, have a thermodynamic driving force toward phase separation. However, phase separation inside the electrode particles can be suppressed when the particles are nanosized. In this case, each individual particle remains monophasic, but phase separation can occur between particles via Li redistribution. Here, we investigate the dynamics of Li redistribution when the equilibrium potential is size dependent. We perform simulations of the charge-discharge cycle in a two-particle cell and in a 65-particle agglomerate. The difference in particle equilibrium potentials can lead to an asymmetry between lithiation and delithiation of an electrode, in which the order of transformation of the particles during lithiation and delithiation is reversed. This effect is more significant at low currents but almost negligible at high currents.
Federated learning and differential privacy for medical image analysis (2022)

The artificial intelligence revolution has been spurred forward by the availability of large-scale datasets. In contrast, the paucity of large-scale medical datasets hinders the application of machine learning in healthcare. The lack of publicly available multi-centric and diverse datasets mainly stems from confidentiality and privacy concerns around sharing medical data. To demonstrate a feasible path forward in medical image imaging, we conduct a case study of applying a differentially private federated learning framework for analysis of histopathology images, the largest and perhaps most complex medical images. We study the effects of IID and non-IID distributions along with the number of healthcare providers, i.e., hospitals and clinics, and the individual dataset sizes, using The Cancer Genome Atlas (TCGA) dataset, a public repository, to simulate a distributed environment. We empirically compare the performance of private, distributed training to conventional training and demonstrate that distributed training can achieve similar performance with strong privacy guarantees. We also study the effect of different source domains for histopathology images by evaluating the performance using external validation. Our work indicates that differentially private federated learning is a viable and reliable framework for the collaborative development of machine learning models in medical image analysis.
Sesquiterpenoids from the Formosan Soft Coral Lemnalia flava (2011)

Four new nardosinane-type sesquiterpenoids, flavalins E-H (1-4) and two new nornardosinane-type norsesquiterpenoids, flavalins I (5) and J (6), along with five known compounds (7-11) have been isolated from a Formosan soft coral Lemnalia flava. The structures of these compounds were elucidated on the basis of their spectroscopic data. Moreover, the absolute configuration of 10 was further determined by Mosher's method.
Nanocrystalline mesoporous palladium activated tin oxide thin films as room-temperature hydrogen gas sensors (2007)

A unique nanocrystalline, mesoporous PdO-SnO(2) film exhibiting high sensitivity and selectivity to hydrogen gas at room temperature has been developed.
Controlled growth of silicon particles via plasma pulsing and their application as battery material (2021)

Abstract The use of silicon nanoparticles for lithium-ion batteries requires a precise control over both their average size and their size distribution. Particles larger than the generally accepted critical size of 150 nm fail during lithiation because of excessive swelling, while very small particles (&lt;10 nm) inevitably lead to a poor first cycle coulombic efficiency because of their excessive specific surface area. Both mechanisms induce irreversible capacity losses and are detrimental to the anode functionality. In this manuscript we describe a novel approach for enhanced growth of nanoparticles to ∼20 nm using low-temperature flow-through plasma reactors via pulsing. Pulsing of the RF power leads to a significant increase in the average particle size, all while maintaining the particles well below the critical size for stable operation in a lithium-ion battery anode. A zero-dimensional aerosol plasma model is developed to provide insights into the dynamics of particle agglomeration and growth in the pulsed plasma reactor. The accelerated growth correlates with the shape of the particle size distribution in the afterglow, which is in turn controlled by parameters such as metastable density, gas and electron temperature. The accelerated agglomeration in each afterglow phase is followed by rapid sintering of the agglomerates into single-crystal particles in the following plasma-on phase. This study highlights the potential of non-thermal plasma reactors for the synthesis of functional nanomaterials, while also underscoring the need for better characterization of their fundamental parameters in transient regimes.
Viability of using CIPN as a delayed neutron detector (2011)

Abstract Not Provided
Inter-regional correlation estimators for functional magnetic resonance imaging (2020)

Functional magnetic resonance imaging (fMRI) functional connectivity between brain regions is often computed using parcellations defined by functional or structural atlases. Typically, some kind of voxel averaging is performed to obtain a single temporal correlation estimate per region pair. However, several estimators can be defined for this task, with various assumptions and degrees of robustness to local noise, global noise, and region size. In this paper, we systematically present and study the properties of 9 different functional connectivity estimators taking into account the spatial structure of fMRI data, based on a simple fMRI data spatial model. These include 3 existing estimators and 6 novel estimators. We demonstrate the empirical properties of the estimators using synthetic, animal, and human data, in terms of graph structure, repeatability and reproducibility, discriminability, dependence on region size, as well as local and global noise robustness. We prove analytically the link between regional intra-correlation and inter-region correlation, and show that the choice of estimator has a strong influence on inter-correlation values.
Auger effect in yellow light emitters based on InGaN–AlGaN–GaN quantum wells (2016)

Abstract The Auger effect and its impact on the internal quantum efficiency (IQE) of yellow light emitters based on silicon-doped InGaN–AlGaN–GaN quantum wells are investigated by power dependence measurement and using an ABC model. Photoluminescence intensity recorded as a function of excitation power density follows a linear dependence up to a threshold P T that depends on the design of the sample. Above this threshold, the variation of the intensity becomes sublinear, which is characteristic of the onset of Auger recombination processes. After extracting the evolution of IQE with pump power from the experimental data, we use a modified ABC modeling that includes the residual n-type doping to estimate the contribution of different recombination channels. We find that the Auger effect dominates in the high-excitation regime. In addition, we find that intercalating an AlGaN-strain-compensating layer reduces not only the coefficient of nonradiative recombination rates but also reduces the onset of Auger recombination.
Adrenocorticotropin Acutely Regulates Pregnenolone Sulfate Production by the Human Adrenal In Vivo and In Vitro (2017)

Abstract Background Dehydroepiandrosterone sulfate (DHEAS) is the most abundant steroid in human circulation, and adrenocorticotropic hormone (ACTH) is considered the major regulator of its synthesis. Pregnenolone sulfate (PregS) and 5-androstenediol-3-sulfate (AdiolS) have recently emerged as biomarkers of adrenal disorders. Objective To define the relative human adrenal production of Δ5-steroid sulfates under basal and cosyntropin-stimulated conditions. Methods Liquid chromatography-tandem mass spectrometry was used to quantify three unconjugated and four sulfated Δ5-steroids in (1) paired adrenal vein (AV) and mixed venous serum samples (21 patients) and (2) cultured human adrenal cells both before and after cosyntropin stimulation, (3) microdissected zona fasciculata (ZF) and zona reticularis (ZR) from five human adrenal glands, and (4) a reconstituted in vitro human 17α-hydroxylase/17,20-lyase/(P450 17A1) system. Results Of the steroid sulfates, PregS had the greatest increase after cosyntropin stimulation in the AV (32-fold), whereas DHEAS responded modestly (1.8-fold). PregS attained concentrations comparable to those of DHEAS in the AV after cosyntropin stimulation (AV DHEAS/PregS, 24 and 1.3 before and after cosyntropin, respectively). In cultured adrenal cells, PregS demonstrated the sharpest response to cosyntropin, whereas DHEAS responded only modestly (21-fold vs 1.8-fold higher compared with unstimulated cells at 3 hours, respectively). Steroid analyses in isolated ZF and ZR showed similar amounts of PregS and 17α-hydroxypregnenolone in both zones, whereas DHEAS and AdiolS were higher in ZR (P &amp;lt; 0.05). Conclusion Our studies demonstrated that unlike DHEAS, PregS displayed a prominent acute response to cosyntropin. PregS could be used to interrogate the acute adrenal response to ACTH stimulation and as a biomarker in various adrenal disorders.
Predict+Optimize Problem in Renewable Energy Scheduling (2022)

Predict+Optimize frameworks integrate forecasting and optimization to address real-world challenges such as renewable energy scheduling, where variability and uncertainty are critical factors. This paper benchmarks solutions from the IEEE-CIS Technical Challenge on Predict+Optimize for Renewable Energy Scheduling, focusing on forecasting renewable production and demand and optimizing energy cost. The competition attracted 49 participants in total. The top-ranked method employed stochastic optimization using LightGBM ensembles, and achieved at least a 2% reduction in energy costs compared to deterministic approaches, demonstrating that the most accurate point forecast does not necessarily guarantee the best performance in downstream optimization. The published data and problem setting establish a benchmark for further research into integrated forecasting-optimization methods for energy systems, highlighting the importance of considering forecast uncertainty in optimization models to achieve cost-effective and reliable energy management. The novelty of this work lies in its comprehensive evaluation of Predict+Optimize methodologies applied to a real-world renewable energy scheduling problem, providing insights into the scalability, generalizability, and effectiveness of the proposed solutions. Potential applications extend beyond energy systems to any domain requiring integrated forecasting and optimization, such as supply chain management, transportation planning, and financial portfolio optimization.
Table S1 from MFF Regulation of Mitochondrial Cell Death Is a Therapeutic Target in Cancer (2023)

&lt;p&gt;MFF1 synthetic peptides used in this study&lt;/p&gt;
Supplementary Figure S2 from ERBB3-Independent Activation of the PI3K Pathway in EGFR-Mutant Lung Adenocarcinomas (2023)

&lt;p&gt;Supplementary Figure S2. Development of lung adenocarcinomas in mice lacking ERBB3.&lt;/p&gt;
Synchrotron radiation based cross-sectional scanning photoelectron microscopy and spectroscopy of n-ZnO:Al/p-GaN:Mg heterojunction (2013)

Al-doped ZnO (AZO) deposited by radio frequency co-sputtering is formed on epitaxial Mg-doped GaN template at room temperature to achieve n-AZO/p-GaN heterojunction. Alignment of AZO and GaN bands is investigated using synchrotron radiation based cross-sectional scanning photoelectron microscopy and spectroscopy on the nonpolar side-facet of a vertically c-axis aligned heterostructure. It shows type-II band configuration with valence band offset of 1.63 ± 0.1 eV and conduction band offset of 1.61 ± 0.1 eV, respectively. Rectification behavior is clearly observed, with a ratio of forward-to-reverse current up to six orders of magnitude when the bias is applied across the p-n junction.