gebhart/patrepeval huggingface dataset:
Photonic nanostructures for advanced light trapping in thin crystalline silicon solar cells (2014)

We report on the fabrication, integration, and simulation, both optical and optoelectrical, of two-dimensional photonic nanostructures for advanced light trapping in thin crystalline silicon (c-Si) solar cells. The photonic nanostructures are fabricated by the combination of various lithography (nanoimprint, laser interference, and hole mask colloidal) and etching (dry plasma and wet chemical) techniques. The nanopatterning possibilities thus range from periodic to random corrugations and from inverted nanopyramids to high aspect ratio profiles. Optically, the nanopatterning results in better performance than the standard pyramid texturing, showing a more robust behavior with respect to light incidence angle. Electrically, wet etching results in higher minority carrier lifetimes compared to dry etching. From the integration of the photonic nanostructures into a micron-thin c-Si solar cell certain factors limiting the efficiencies are identified. More precisely: (a) the parasitic absorption is limiting the short circuit current, (b) the conformality of thin-film coatings on the nanopatterned surface is limiting the fill factor, and (c) the material damage from dry etching is limiting the open circuit voltage. From optical simulations, the optimal pattern parameters are identified. From optoelectrical simulations, cell design considerations are discussed, suggesting to position the junction on the opposite side of the nanopattern.
Replication Data for: Entropic Control of HD Exchange Rates over Dilute Pd-in-Au Alloy Nanoparticle Catalysts (2021)

The data underlying this published work have been made publicly available in this repository as part of the IMASC Data Management Plan. This work was supported as part of the Integrated Mesoscale Architectures for Sustainable Catalysis (IMASC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012573.
Dietary sequestration of defensive steroids in nuchal glands of the Asian snake Rhabdophis tigrinus (2007)

The Asian snake Rhabdophis tigrinus possesses specialized defensive glands on its neck that contain steroidal toxins known as bufadienolides. We hypothesized that R. tigrinus does not synthesize these defensive steroids but instead sequesters the toxins from toads it consumes as prey. To test this hypothesis, we conducted chemical analyses on the glandular fluid from snakes collected in toad-free and toad-present localities. We also performed feeding experiments in which hatchling R. tigrinus were reared on controlled diets that either included or lacked toads. We demonstrate that the cardiotonic steroids in the nuchal glands of R. tigrinus are obtained from dietary toads. We further show that mothers containing high levels of bufadienolides can provision their offspring with toxins. Hatchlings had bufadienolides in their nuchal glands only if they were fed toads or were born to a dam with high concentrations of these compounds. Because geographic patterns in the availability of toxic prey are reflected in the chemical composition of the glandular fluid, snakes in toad-free regions are left undefended by steroidal toxins. Our findings confirm that the sequestration of dietary toxins underlies geographic variation in antipredatory behavior in this species and provide a unique example of sequestered defensive compounds in a specialized vertebrate structure.
A Novel Approach to Quantify G-Protein-Coupled Receptor Dimerization Equilibrium Using Bioluminescence Resonance Energy Transfer (2013)

Along with other resonance energy transfer techniques, bioluminescence resonance energy transfer (BRET) has emerged as an important method for demonstrating protein-protein interactions in cells. In the field of G-protein-coupled receptors, including chemokine receptors, BRET has been widely used to investigate homo- and heterodimerization, a feature of their interactions that is emerging as integral to function and regulation. While demonstrating the existence of dimers for a given receptor proved to be fairly straightforward, quantitative comparisons of different receptors or mutants are nontrivial because of inevitable variations in the expression of receptor constructs. The uncontrollable parameters of the cellular expression machinery make amounts of transfected DNA extremely poor predictors for the expression levels of BRET donor and acceptor receptor constructs, even in relative terms. In this chapter, we show that properly accounting for receptor expression levels is critical for quantitative interpretation of BRET data. We also provide a comprehensive account of expected responses in all types of BRET experiments and propose a framework for uniform and accurate quantitative treatment of these responses. The framework allows analysis of both homodimer and heterodimer BRET data. The important caveats and obstacles for quantitative treatment are outlined, and the utility of the approach is illustrated by its application to the homodimerization of wild-type (WT) and mutant forms of the chemokine receptor CXCR4.
Influenza A Viruses Lacking Sialidase Activity Can Undergo Multiple Cycles of Replication in Cell Culture, Eggs, or Mice (2000)

Influenza A viruses possess both hemagglutinin (HA), which is responsible for binding to the terminal sialic acid of sialyloligosaccharides on the cell surface, and neuraminidase (NA), which contains sialidase activity that removes sialic acid from sialyloligosaccharides. Interplay between HA receptor-binding and NA receptor-destroying sialidase activity appears to be important for replication of the virus. Previous studies by others have shown that influenza A viruses lacking sialidase activity can undergo multiple cycles of replication if sialidase activity is provided exogenously. To investigate the sialidase requirement of influenza viruses further, we generated a series of sialidase-deficient mutants. Although their growth was less efficient than that of the parental NA-dependent virus, these viruses underwent multiple cycles of replication in cell culture, eggs, and mice. To understand the molecular basis of this viral growth adaptation in the absence of sialidase activity, we investigated changes in the HA receptor-binding affinity of the sialidase-deficient mutants. The results show that mutations around the HA receptor-binding pocket reduce the virus's affinity for cellular receptors, compensating for the loss of sialidase. Thus, sialidase activity is not absolutely required in the influenza A virus life cycle but appears to be necessary for efficient virus replication.
Effect of Implementing a Standardized Shoulder Dystocia Documentation Form on Quality of Delivery Notes (2016)

Use of a mandatory shoulder dystocia documentation form is associated with significant improvement in the comprehensiveness of delivering provider narrative notes and may encourage more complete and accurate charting. Such improvements can allow for more complete and accurate explanation of events to patients and better demonstrate adherence to standards of care in the management of shoulder dystocia and may improve litigation defensibility.
The dynamics of image denoising viewed as damped elastic deformation (2009)

Diffusion-type algorithms have been integrated successfully into the toolbox of image processing. We introduce a new more flexible and powerful family of parabolic-hyperbolic partial differential equations (PDEs) that somewhat resembles the structure of the parabolic diffusion equation, but incorporates the second order derivative in time. It is instructive intuitively to consider in this context the dynamics of image processing as the deformation of an `elastic sheet'. Indeed, our parabolic-hyperbolic PDE models elastic deformation. This analogy between a well-known physical system and process on one hand, and the dynamics of an image processing scheme on the other hand, contributes interesting and important insight about images and their processing. We explore and demonstrate the capabilities and advantages afforded by the application of the proposed family of equations in image enhancement, and highlight the importance of incorporating the second derivative in time. The problem of computational complexity is addressed, and efficient numeric schemes are also presented.
p73-Dependent Apoptosis through Death Receptor: Impairment by Human Cytomegalovirus Infection (2005)

The discovery of p73, a p53-related protein with various isotypes resulting from different promoter usage or splicing events, provided new insights into regulation of neurogenesis and tumorigenesis. Among p73 isoforms described thus far, TA-truncated molecules (DeltaN) appeared as key proteins according to their antagonistic activity against transcription factor activity of p53 family members. We previously showed that infection by human cytomegalovirus (HCMV) induced drug resistance and altered p53- and p73-dependent apoptosis of infected cells through accumulation of DeltaN-p73alpha. In accordance with the ability of p53 to induce apoptosis through death receptors, we asked whether p73 activation could compensate for p53 deficiency. We showed that p73 transcriptional activity sensitized cells to apoptosis through death receptors in a caspase-dependent pathway. Expression of the death-inducing signaling complex (DISC) proteins was unchanged, whereas p73 activation through either cisplatin treatment or ectopic overexpression induced up-regulation of Fas transcription and expression at cell surface. According to its ability to flood cells with DeltaN-p73alpha, HCMV inhibited p73-dependent Fas-mediated apoptosis, gaining an additional trick to favor its survival in the host cell. Owing to the involvement of p53- and p73-dependent death receptor signaling in development of the central nervous system, immune surveillance of neural cells, and sensitivity of tumors to drugs, our previous and present data prompt us to consider stabilization of DeltaN-p73alpha by HCMV as a possible mechanism in impairment of embryogenesis and in tumorigenesis.
Cellular Localization of Estrogen Receptor Beta Messenger Ribonucleic Acid in Cynomolgus Monkey Reproductive Organs (1999)

There is now evidence that the recently identified estrogen receptor (ER) beta is more widely distributed in the body than is ER-alpha. In order to gain more information about the role of ER-beta in reproduction, we have investigated by in situ hybridization the localization of mRNA expression of this ER subtype in adult monkey reproductive organs. In the pituitary gland of animals of both sexes, in both the anterior and intermediate lobes, a large number of cells were positive. No specific signal was observed in the posterior lobe. In the ovary, granulosa cells in primary and growing follicles highly expressed ER-beta mRNA. The theca interna cells were also strongly labeled. In some corpora lutea, the luteal cells were strongly labeled, while in other ones, the signal was weak. A hybridization signal was also detected in the ovarian surface epithelium. In the uterus, ER-beta mRNA was found in high concentration in glandular epithelial cells and stromal cells of the endometrium, while weaker labeling was consistently observed in smooth muscle cells. In the mammary gland, labeling was detected in the epithelial cells of acini and interlobular ducts as well as stromal cells. In the testis, specific labeling was detected in the seminiferous epithelium whereas the interstitial Leydig cells were unlabeled. Although it was not possible to clearly identify all the positive cell types, it appears that Sertoli cells as well as the vast majority of germinal cells express ER-beta mRNA. In the prostate, the secretory epithelial cells exhibited a specific autoradiographic reaction while the stromal cells did not show mRNA expression. The epithelial cells of the prostatic urethra showed a strong labeling. No hybridization signal was detected in the seminal vesicles. It then appears quite clear that ER-beta is expressed in a cell-specific manner in all the monkey reproductive organs studied. In the female, the wide distribution of these receptors in the ovary and uterus suggests that ER-beta may play an important role in the mediation of the known effects of estrogen in reproduction functions. In the male testis and prostate, ER-beta has been found in cells that contain very little or no ER-alpha. The role of circulating or locally produced estrogens in the male reproductive system remains to be clarified.
The Present (2012)

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Notes on Some Questions in Mathematical Physics and Quantum Information (2014)

This is a set of notes on some unrelated topics in mathematical physics, at varying levels of detail. First, I consider certain questions relating to the decay of correlation functions in matrix product states, in particular those generated by quantum expanders. This is discussed in relation to recent results of Brandao and Horodecki on area laws on systems with exponentially decaying correlation function\cite{areaexp}. Second, I consider some difficulties in trying to construct a tensor product state (or PEPS) describing a two-dimensional fermionic system with non-vanishing Hall conductance. Third, I present some relations between the theory of almost commuting matrices and that of vector bundles, making the connection between the classifications more explicit. Fourth, I present an open question about quantum channels, and some partial results.
Exchange Protein Directly Activated by Cyclic AMP Increases Melanoma Cell Migration by a Ca2+-Dependent Mechanism (2010)

Melanoma has a poor prognosis due to its strong metastatic ability. Although Ca(2+) plays a major role in cell migration, little is known about the role of Ca(2+) in melanoma cell migration. We recently found that the exchange protein directly activated by cyclic AMP (Epac) increases melanoma cell migration via a heparan sulfate-related mechanism. In addition to this mechanism, we also found that Epac regulates melanoma cell migration by a Ca(2+)-dependent mechanism. An Epac agonist increased Ca(2+) in several different melanoma cell lines but not in melanocytes. Ablation of Epac1 with short hairpin RNA inhibited the Epac agonist-induced Ca(2+) elevation, suggesting the critical role of Epac1 in Ca(2+) homeostasis in melanoma cells. Epac-induced Ca(2+) elevation was negated by the inhibition of phospholipase C (PLC) and inositol triphosphate (IP(3)) receptor. Furthermore, Epac-induced cell migration was reduced by the inhibition of PLC or IP(3) receptor. These data suggest that Epac activates Ca(2+) release from the endoplasmic reticulum via the PLC/IP(3) receptor pathway, and this Ca(2+) elevation is involved in Epac-induced cell migration. Actin assembly was increased by Epac-induced Ca(2+), suggesting the involvement of actin in Epac-induced cell migration. In human melanoma specimens, mRNA expression of Epac1 was higher in metastatic melanoma than in primary melanoma, suggesting a role for Epac1 in melanoma metastasis. In conclusion, our findings reveal that Epac is a potential target for the suppression of melanoma cell migration, and, thus, the development of metastasis.
Characterization of a freestanding AlN substrate prepared by hydride vapor phase epitaxy (2008)

Abstract A thick AlN layer was grown on a (111)Si starting substrate at 1230 ºC by hydride vapor phase epitaxy (HVPE). A 112‐μm‐thick freestanding AlN substrate was successfully prepared by removing the Si substrate using a chemical etchant. The AlN substrate was transparent with a smooth (0001) surface. Immersion of the AlN substrate in an aqueous KOH solution revealed that the AlN layer grown on the (111)Si substrate predominately has Al‐polarity. Owing to improvement of crystalline quality by thick layer growth, a near‐band‐edge (NBE) emission could be obtained at 5.92 eV in the room‐temperature photoluminescence (PL) spectrum taken at the top surface of the AlN substrate. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Temperature-activated transition of positronium from self-trapped to delocalized state inCaF2 (2007)

Temperature dependence of the momentum distribution of positronium (Ps) in $\mathrm{Ca}{\mathrm{F}}_{2}$ single crystal has been investigated in a temperature range from $10\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}297\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. Temperature activated transition of Ps from the stable self-trapped state to the metastable delocalized state has been observed. The self-trapping barrier height and the under-barrier tunnel self-trapping rate have been determined to be $0.17\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ and $2.9\ifmmode\times\else\texttimes\fi{}{10}^{10}\phantom{\rule{0.3em}{0ex}}{\mathrm{s}}^{\ensuremath{-}1}$, respectively, and an important role of the under-barrier tunneling has been demonstrated. The bottom of the delocalized Ps band is $6.6\phantom{\rule{0.3em}{0ex}}\mathrm{meV}$ higher in energy than the ground self-trapped state. The observed effective mass of the delocalized Ps is considerably larger than the free Ps mass in vacuum.
A 0.9 V low-power reconfigurable successive approximation ADC for integrated sensors (2013)

In this paper, a reconfigurable successive approximation analog-to-digital converter with selectable resolutions ranging from 7 to 10 bits is presented. The circuit is implemented in IBM CMOS 0.13 μm technology, and operates with a 0.9 V supply. The simulated effective number of bits (ENOB) ranges from 6.66 to 9.75, while the simulated power consumption during a continuous conversion ranges from 194 nW (7 bits) to 418 nW (10 bits) at a sampling rate of 50 kS/s.
Light‐Induced Modular Ligation of Conventional RAFT Polymers (2012)

Making light work of RAFT conjugation: a non-activated RAFT agent at the end of RAFT polymers can readily be coupled with ortho-quinodimethanes (photoenols) in a photo-triggered Diels-Alder reaction under mild conditions without catalyst. The method is universal and opens the door for the conjugation of a large number of RAFT-prepared polymers with photoenol-functionalized (macro)molecules. (RAFT=reversible addition-fragmentation chain transfer.).
Dopamine D1AReceptors and Renin Release in Rat Juxtaglomerular Cells (1997)

Two dopamine D1-like receptors have been cloned from mammals, the D1 and D5 receptors, also known as D1A and D1B receptors, respectively, in rodents. Although D1-like receptors are known to stimulate renin release, the receptor subtype mediating this action has not been determined. We investigated D1 receptor subtype expression in rat juxtaglomerular cells obtained after enzymatic dispersion of kidney cortex and differential centrifugation. Juxtaglomerular cells in primary culture were immunocytochemically 85% to 95% renin positive. These cells expressed the D1A but not the D1B receptor (mRNA and protein). D1-like receptor function was demonstrated by a concentration-dependent stimulation of cAMP production by dopamine (n = 5-9 per group). Fenoldopam, a D1-like receptor agonist, also caused a concentration-dependent increase in cAMP production and renin secretion that was blocked by the selective D1-like receptor antagonist SCH23390 (n = 4-13 per group). Although the D1 ligands do not distinguish between the cloned D1-like receptors, the actions of fenoldopam were due to occupancy of the D1A receptor: (1) the D1B receptor, the only other mammalian D1-like receptor, is not expressed in juxtaglomerular cells; (2) antisense but not sense D1A oligonucleotides completely blocked the stimulatory effect of fenoldopam on cAMP production and renin secretion. We conclude that there is selective dopamine receptor gene expression in juxtaglomerular cells; the dopamine receptor subtype linked to the stimulation of cAMP and renin secretion in juxtaglomerular cells is the D1A subtype.
Adiabatic transfer scheme of light between strongly coupled photonic crystal nanocavities (2013)

Ultra-high-quality factor photonic crystal nanocavities are attracting much attention because they can confine light into an ultra-small region and enable strong interaction between light and matter. One important step toward the realization of quantum information processing with cavity quantum electrodynamics approaches is a robust method that transfers photons among such cavities. We propose and theoretically investigate a scheme to transfer photons between strongly coupled, distant photonic crystal nanocavities by an adiabatic change in the cavity characteristics in the time domain. Adding one intermediate nanocavity for control allows efficient light transfer between objective nanocavities. Because our scheme utilizes adiabatic transfer, its operation is robust for both the control parameters and the control timing.
Development of Compact 473nm Laser Using Intra-Cavity SHG with Short-PPSLT (2007)

Combination of intra-cavity SHG and passively-Q-switching demonstrated on 473 nm quasi-four-level Nd:YAG laser. Periodically-poled MgO:SLT was inserted into the 10 mm length cavity of passively-Q-switched Cr:Nd:YAG laser. A longitudinally pumping with 4 W laser diode shows beam quality of M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ap1. The output energy of 29 muJ and pulse duration of 3.1 ns were obtained.
Traffic Load Balancing Among Brokers at the IoT Application Layer (2017)

At the Internet of Things (IoT) application layer, a physical phenomenon, which is sensed by a server (i.e., an IoT device), is defined as an IoT resource. In this paper, we propose to cache popular IoT resources in brokers, which are considered as the application layer middleware nodes. Caching popular resources in the brokers is to move the traffic loads (for delivering the up-to-date contents of the resources) from the servers (which host these popular resources) to the brokers, thus reducing the energy consumption of the servers. However, many brokers may be geographically distributed in the network and caching popular resources in nearby brokers may result in unbalanced traffic loads among the brokers, and may thus dramatically increase the average delay of the brokers in delivering the contents of their cached popular resources to clients. To reduce the average delay among the brokers, we propose to re-cache/re-allocate the popular resources from heavily loaded brokers into lightly loaded brokers in order to balance the traffic loads among brokers. We formulate the popular resource re-caching problem as an optimization problem, which is proven to be NP-hard. We design the latency aware popular resource re-caching (LEARN) algorithm to efficiently solve the problem, and demonstrate the performance of LEARN via simulations.
Internet-Based Education in Confocal and Widefield Fluorescence Microscopy (2004)

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.
Improved Segmentation of Focal Cortical Dysplasia Lesions on MRI Using Expansion Towards Cortical Boundaries (2006)

Focal cortical dysplasia (FCD), a malformation of cortical development, is an important cause of intractable epilepsy. On magnetic resonance images (MRI), FCD lesions are difficult to distinguish from healthy cortex and defining their spatial extent is challenging. We previously introduced a method to segment FCD lesions on MRI, relying on a 3D deformable model driven by MR features of FCD. In the present paper, we propose to improve our approach by adding a second evolution step which expands the result towards the cortical boundaries. A quantitative evaluation was performed in 18 FCD patients by comparison with manually traced lesion labels. The proposed approach achieved a strong agreement with the manual labels and substantially improved the results obtained with our previous method.