gebhart/patrepeval huggingface dataset:
Isotropic inverse-problem approach for two-dimensional phase unwrapping (2015)

In this paper, we propose a new technique for two-dimensional phase unwrapping. The unwrapped phase is found as the solution of an inverse problem that consists in the minimization of an energy functional. The latter includes a weighted data-fidelity term that favors sparsity in the error between the true and wrapped phase differences, as well as a regularizer based on higher-order total-variation. One desirable feature of our method is its rotation invariance, which allows it to unwrap a much larger class of images compared to the state of the art. We demonstrate the effectiveness of our method through several experiments on simulated and real data obtained through the tomographic phase microscope. The proposed method can enhance the applicability and outreach of techniques that rely on quantitative phase evaluation.
Fluorescent Calixarene Scaffolds for NO Detection in Protic Media (2019)

We present the first fluorescent water-soluble conjugated calixarene scaffolds that are capable of NO gas detection. Two different scaffolds, one based on a 5,5'-bicalixarene structure and its isomer bearing two distantly conjugated calixarene moieties, were synthesized. While the fluorescence of both isomers is quenched upon either passing of NO gas or generating it in situ from diethylamine NONOate, the bicalixarene-based scaffold showed a significantly stronger response. We also present an example of a dye encapsulation strategy to achieve the detection of NO at longer wavelengths than in the parent calixarene host. Finally, a conjugated polymer bearing a 5,5'-bicalixarene scaffold has also been prepared and demonstrated enhanced sensitivity compared to the monomer due to the molecular wire effect.
Towards a Parsimonious Pathway Model of Modifiable and Mediating Risk Factors Leading to Diabetes Risk (2021)

Modifiable risk factors are of interest for chronic disease prevention. Few studies have assessed the system of modifiable and mediating pathways leading to diabetes mellitus. We aimed to develop a pathway model for Diabetes Risk with modifiable Lifestyle Risk factors as the start point and Physiological Load as the mediator. As there are no standardised risk thresholds for lifestyle behaviour, we derived a weighted composite for Lifestyle Risk. Physiological Load was based on an index using clinical thresholds. Sociodemographics are non-modifiable risk factors and were specified as covariates. We used structural equation modeling to test the model, first using 2014/2015 data from the Indonesian Family Life Survey. Next, we fitted a smaller model with longitudinal data (2007/2008 to 2014/2015), given limited earlier data. Both models showed the indirect effects of Lifestyle Risk on Diabetes Risk via the mediator of Physiological Load, whereas the direct effect was only supported in the cross-sectional analysis. Specifying Lifestyle Risk as an observable, composite variable incorporates the cumulative effect of risk behaviour and differentiates this study from previous studies assessing it as a latent construct. The parsimonious model groups the multifarious risk factors and illustrates modifiable pathways that could be applied in chronic disease prevention efforts.
Predicting HIV Pre-exposure Prophylaxis Efficacy for Women using a Preclinical Pharmacokinetic-Pharmacodynamic In Vivo Model (2017)

The efficacy of HIV pre-exposure prophylaxis (PrEP) relies on adherence and may also depend on the route of HIV acquisition. Clinical studies of systemic tenofovir disoproxil fumarate (TDF) PrEP revealed reduced efficacy in women compared to men with similar degrees of adherence. To select the most effective PrEP strategies, preclinical studies are critically needed to establish correlations between drug concentrations (pharmacokinetics [PK]) and protective efficacy (pharmacodynamics [PD]). We utilized an in vivo preclinical model to perform a PK-PD analysis of systemic TDF PrEP for vaginal HIV acquisition. TDF PrEP prevented vaginal HIV acquisition in a dose-dependent manner. PK-PD modeling of tenofovir (TFV) in plasma, female reproductive tract tissue, cervicovaginal lavage fluid and its intracellular metabolite (TFV diphosphate) revealed that TDF PrEP efficacy was best described by plasma TFV levels. When administered at 50 mg/kg, TDF achieved plasma TFV concentrations (370 ng/ml) that closely mimicked those observed in humans and demonstrated the same risk reduction (70%) previously attained in women with high adherence. This PK-PD model mimics the human condition and can be applied to other PrEP approaches and routes of HIV acquisition, accelerating clinical implementation of the most efficacious PrEP strategies.
Ab initiomolecular dynamics: Analytically continued energy functionals and insights into iterative solutions (1992)

We present a new method for performing finite-temperature ab initio total-energy calculations at long length scales, which we demonstrate with a dynamics calculation of 50 \AA{}-long phonon modes in silicon. The method involves both a prescription for the analytic continuation of tradional fermionic energy functionals into the space of nonorthonormal single-particle orbitals (speeding convergence to the minimum) and insights into the common computational physics problem of solving by iterative refinement for the state of a complex system as a function of a continuous external parameter.
Tumor Necrosis Factor Receptor-associated Protein 1 (TRAP1) Mutation and TRAP1 Inhibitor Gamitrinib-triphenylphosphonium (G-TPP) Induce a Forkhead Box O (FOXO)-dependent Cell Protective Signal from Mitochondria (2015)

TRAP1 (tumor necrosis factor receptor-associated protein 1), a mitochondrial Hsp90 family chaperone, has been identified as a critical regulator of cell survival and bioenergetics in tumor cells. To discover novel signaling networks regulated by TRAP1, we generated Drosophila TRAP1 mutants. The mutants successfully developed into adults and produced fertile progeny, showing that TRAP1 is dispensable in development and reproduction. Surprisingly, mutation or knockdown of TRAP1 markedly enhanced Drosophila survival under oxidative stress. Moreover, TRAP1 mutation ameliorated mitochondrial dysfunction and dopaminergic (DA) neuron loss induced by deletion of a familial Parkinson disease gene PINK1 (Pten-induced kinase 1) in Drosophila. Gamitrinib-triphenylphosphonium, a mitochondria-targeted Hsp90 inhibitor that increases cell death in HeLa and MCF7 cells, consistently inhibited cell death induced by oxidative stress and mitochondrial dysfunction induced by PINK1 mutation in mouse embryonic fibroblast cells and DA cell models such as SH-SY5Y and SN4741 cells. Additionally, gamitrinib-triphenylphosphonium also suppressed the defective locomotive activity and DA neuron loss in Drosophila PINK1 null mutants. In further genetic analyses, we showed enhanced expression of Thor, a downstream target gene of transcription factor FOXO, in TRAP1 mutants. Furthermore, deletion of FOXO almost nullified the protective roles of TRAP1 mutation against oxidative stress and PINK1 mutation. These results strongly suggest that inhibition of the mitochondrial chaperone TRAP1 generates a retrograde cell protective signal from mitochondria to the nucleus in a FOXO-dependent manner.
STAP-2 positively regulates FcεRI-mediated basophil activation and basophil-dependent allergic inflammatory reactions (2019)

Basophils are an important cell type in the regulation of Th2 immune responses. Recently, we revealed that signal-transducing adaptor protein-2 (STAP-2) negatively regulates mast cell activation via FcεRI. However, the role of STAP-2 in basophil maturation and activation remained unclear. In this study, we demonstrated the normal development of basophils in STAP-2-deficient (STAP-2-/-) mice. We also demonstrated in vitro normal basophil differentiation and FcεRI expression in STAP-2-/- mice, suggesting that STAP-2 is dispensable for basophil maturation. Using bone marrow-derived cultured basophils (BMBs), we showed that degranulation and cytokine production of STAP-2-/- BMBs were lower than those of wild-type (WT) BMBs upon stimulation with IgE/Ag. In accordance with the reduction of degranulation and cytokine production, phosphorylation of several signal molecules such as Lyn, PLC-γ2 and Erk was reduced in STAP-2-/- BMBs after stimulation via FcεRI. Finally, it was observed that IgE-dependent chronic allergic inflammation of STAP-2-/- mice was significantly inhibited compared with WT mice. Taken together, we conclude that STAP-2 is an adaptor molecule that positively regulates FcεRI-mediated basophil activation and basophil-dependent allergic inflammatory reactions.
Synthesis and cytotoxic activity of 1,2,3-triazoles derived from 2,3-seco-dihydrobetulin via a click chemistry approach (2021)

In search of new cytotoxic derivatives based on the lupane scaffold, the seco-lupane azides were coupled with a number of alkynes under the 1,3-dipolar cycloaddition (CuAAC) conditions to afford 1,2,3-triazoles. Phenylalkynes having different substituents at the para position were used as starting materials. Similarly, coupling of the seco-lupane thiocyanate with sodium azide gave 5-thiotetrazole. The cytotoxicity of thirteen derivatives were investigated, as well as the effect of substituents in the phenyl ring on the activity of 1,2,3-triazoles. Limited activity was observed for some of these products. Most of the studied compounds were inactive in cancer cell lines and healthy fibroblasts. Triazole 46 exhibited cytotoxic activity against CEM and MCF-7 cancer cell lines, however, it was also toxic to normal human BJ fibroblasts. Two other derivatives – triazole 45 and tetrazole 49 – exhibited low cytotoxicity. Compound 49 showed good selectivity towards tumor cell lines compared to normal fibroblasts. This compound did not affect the growth of normal human fibroblasts and therefore has a wide therapeutic window.
Multidetector-row CT with a 64-row amorphous silicon flat panel detector (2007)

A unique 64-row flat panel (FP) detector has been developed for sub-second multidetector-row CT (MDCT). The intent was to explore the image quality achievable with relatively inexpensive amorphous silicon (a-Si) compared to existing diagnostic scanners with discrete crystalline diode detectors. The FP MDCT system is a bench-top design that consists of three FP modules. Each module uses a 30 cm x 3.3 cm a-Si array with 576 x 64 photodiodes. The photodiodes are 0.52 mm x 0.52 mm, which allows for about twice the spatial resolution of most commercial MDCT scanners. The modules are arranged in an overlapping geometry, which is sufficient to provide a full-fan 48 cm diameter scan. Scans were obtained with various detachable scintillators, e.g. ceramic Gd<sub>2</sub>O<sub>2</sub>S, particle-in-binder Gd<sub>2</sub>O<sub>2</sub>S:Tb and columnar CsI:Tl. Scan quality was evaluated with a Catphan-500 performance phantom and anthropomorphic phantoms. The FP MDCT scans demonstrate nearly equivalent performance scans to a commercial 16-slice MDCT scanner at comparable 10 - 20 mGy/100mAs doses. Thus far, a high contrast resolution of 15 lp/cm and a low contrast resolution of 5 mm @ 0.3 % have been achieved on 1 second scans. Sub-second scans have been achieved with partial rotations. Since the future direction of MDCT appears to be in acquiring single organ coverage per scan, future efforts are planned for increasing the number of detector rows beyond the current 64- rows.
Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair (2012)

Signaling pathways depend on regulatory protein-protein interactions; controlling these interactions in cells has important applications for reengineering biological functions. As many regulatory proteins are modular, considerable progress in engineering signaling circuits has been made by recombining commonly occurring domains. Our ability to predictably engineer cellular functions, however, is constrained by complex crosstalk observed in naturally occurring domains. Here we demonstrate a strategy for improving and simplifying protein network engineering: using computational design to create orthogonal (non-crossreacting) protein-protein interfaces. We validated the design of the interface between a key signaling protein, the GTPase Cdc42, and its activator, Intersectin, biochemically and by solving the crystal structure of the engineered complex. The designed GTPase (orthoCdc42) is activated exclusively by its engineered cognate partner (orthoIntersectin), but maintains the ability to interface with other GTPase signaling circuit components in vitro. In mammalian cells, orthoCdc42 activity can be regulated by orthoIntersectin, but not wild-type Intersectin, showing that the designed interaction can trigger complex processes. Computational design of protein interfaces thus promises to provide specific components that facilitate the predictable engineering of cellular functions.
The Delta Tree: An Object-Centered Approach to Image-Based Rendering (1996)

This paper introduces the delta tree, a data structure that represents an object using a set of reference images. It also describes an algorithm for generating arbitrary re-projections of an object by traversing its delta tree. Delta trees are an efficient representation in terms of both storage and rendering performance. Each node of a delta tree stores an image taken from a point on a sampling sphere that encloses the object. Each image is compressed by discarding pixels that can be reconstructed by warping its ancestor’s images to the node’s viewpoint. The partial image stored at each node is divided into blocks and represented in the frequency domain. The rendering process generates an image at an arbitrary viewpoint by traversing the delta tree from a root node to one or more of its leaves. A subdivision algorithm selects only the required blocks from the nodes along the path. For each block, only the frequency components necessary to reconstruct the final image at an appropriate sampling density are used. This frequency selection mechanism handles both antialiasing and level-of-detail within a single framework. A complex scene is initially rendered by compositing images generated by traversing the delta trees of its components. Once the reference views of a scene are rendered once in this manner, the entire scene can be reprojected to an arbitrary viewpoint by traversing its own delta tree. Our approach is limited to generating views of an object from outside the object’s convex hull. In practice we work around this problem by subdividing objects to render views from within the convex hull. 1.
An efficient domain decomposition method for 3-D finite element analysis of nonlinear electric machine problems (2013)

The dual-primal finite element tearing and interconnecting (FETI-DP) method is combined with the Newton-Raphson method to expand the capability and improve the efficiency of three-dimensional finite element analysis (FEA) of nonlinear electromechanical and electric machine problems. Despite its modeling capability and high degree of accuracy, FEA has high computational complexity, especially for nonlinear analysis. The FETI-DP method is a robust domain decomposition method, which is a suitable choice for improving the efficiency of large-scale 3-D nonlinear FEA. The FETI-DP method decomposes the original large-scale problem into multiple subdomains, which can then be handled by parallel computing techniques so that the total computation time is reduced significantly. Linear and nonlinear regions are separated using the FETI-DP method. This further improves simulation efficiency and flexibility. Cubic splines and relaxation techniques are adopted to ensure stable and fast convergence of the Newton-Raphson method.
Human myelin DM-20 proteolipid protein deletion defined by cDNA sequence (1987)

Using a myelin proteolipid protein (PLP) cDNA as probe, a homologous 2 Kb cDNA was isolated from a human retinal cDNA library. This clone, designated pDM-20, contained all of the coding sequence of PLP except for 105 bp of sequence which encodes amino acids 116 to 150 of PLP. This in frame deletion resulting in the absence of 35 amino acids from intact PLP would reduce the molecular weight by 4385, resulting in a protein of the size of DM-20, the second major proteolipid of CNS myelin. The finding is also in agreement with the evidence from preliminary sequencing of bovine DM-20 protein which indicated the deletion of residues 100-140. Homologies between DNA sequences at the 5' and 3' ends of the DM-20 deletion and the donor and acceptor slicing consensus sequences, respectively, are suggestive that PLP and DM-20 transcripts are derived from a single PLP gene by alternate splicing. The DM-20 deletion comprises a strongly positively charged hydrophilic segment which is believed to be orientated cytoplasmically. The availability of probes capable of distinguishing PLP and DM-20 mRNAs will enable the elucidation of temporal and spatial control of their expression in the CNS.
Topographical localization of lipofuscin pigment in the brain of the aged fat-tailed dwarf lemur(Cheirogaleus Medius) and grey lesser mouse lemur(Microcebus Murinus): Comparison to iron localization (1999)

The present study was undertaken to explore the distribution of lipofuscin in the brain of cheirogaleids by autofluorescence and compare it to other studies of iron distribution. Aged dwarf (Cheirogaleus medius) and mouse (Microcebus murinus) lemurs provide a reliable model for the study of normal and pathological cerebral aging. Accumulation of lipofuscin, an age pigment derived by lipid peroxidation, constitutes the most reliable cytological change correlated with neuronal aging. Brain sections of four aged (8-15 year old) and 3 young (2-3 year old) animals were examined. Lipofuscin accumulation was observed in the aged animals but not in the young ones. Affected regions include the hippocampus (granular and pyramidal cells), where no iron accumulation was observed, the olfactory nucleus and the olfactory bulb (mitral cells), the basal forebrain, the hypothalamus, the cerebellum (Purkinje cells), the neocortex (essentially in the pyramidal cells), and the brainstem. Even though iron is known to catalyse lipid oxidation, our data indicate that iron deposits and lipofuscin accumulation are not coincident. Different biochemical and morphological cellular compartments might be involved in iron and lipofuscin deposition. The nonuniform distribution of lipofuscin indicates that brain structures are not equally sensitive to the factors causing lipofuscin accumulation. The small size, the rapid maturity, and the relatively short life expectancy of the cheirogaleids make them a good model system in which to investigate the mechanisms of lipofuscinogenesis in primates.
Differential roles of inflammatory cells in induced osteogenesis (1976)

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Construction of Reference Standards for Blood Pressure 24-h Patterns (1990)

P. Cugini, G. Leone, L. Di Palma, P. Battisti, D. W. Wilson, T. Kawasaki, K. Tamura, F. Halberg, G. Cornelissen, Construction of Reference Standards for Blood Pressure 24-h Patterns, Journal of the Royal Statistical Society. Series D (The Statistician), Vol. 39, No. 3, Special Issue: Health of Inner Cities and Urban Areas (2) (1990), pp. 285-299
Advances in Fiber Technologies for Subsea Systems (2023)

This paper will provide a view of several future Space Division Multiplexing (SDM) approaches to support more transmission paths within a subsea cable and their effects on the practicalities of submarine system manufacturing and deployment.
Digital microfluidics and delivery of molecular payloads with magnetic porous silicon chaperones (2007)

Digital microfluidics involves the manipulation of molecules and materials in discrete packages. This paper reviews our work using amphiphilic magnetic microparticles constructed from porous silicon. An individual porous particle can be used to carry a nanomole or smaller quantities of a reagent, and assemblies of the particles can encapsulate and transport microliter droplets of liquid containing inorganic, organic, or biological molecules. The tracking and identification of each particle can be accomplished with spectral labels that are encoded into the particles during their synthesis. When used to chaperone liquid droplets, the labels can identify the separate droplets prior to mixing and also the combined droplets after mixing. Magnetic iron oxide nanoparticles encapsulated in the porous matrix allow the manipulation of the particles or whole droplet assemblies with a magnetic field, and they also allow heating of the particle's payload by means of an externally applied RF field. Examples of organic, inorganic, and biomolecular addition reactions, catalytic reactions, and thermolysis reactions are described.
Viscosities for R22 alternatives and their mixtures with a lubricant oil. (1994)

Viscosities for pure liquid refrigerants HFC32, HFC125, HFC134a, and HFC143a, as well as their mixtures with a synthetic polyolester lubricant oil, have been measured.Measurements for the refrigerant/lubricant mixtures were made over a temperature range from 20 to 8CPC and a range of oil mass fractions from 0.5 to 1.A modified capillary tube method was used for all measurements.The accuracy of measured viscosities is estimated to be 1.2% and 1.8% for pure refrigerants and for refrigerant/ oil mixtures, respectively.Correlations for calculating the viscosity of saturated liquid refrigerants were developed.A method has also been proposed to calculate viscosities of refrigerant/ oil mixtures on the basis of pure component data alone.
Synthesis of [(tmeda)LiCH2PMe2Li(tmeda)CH2PMe2](tmeda = tetramethyl-ethylenediamine) and of a binuclear zirconocene phosphine functionalized ketene complex, [(η-C5H5)2ClZr(PMe2CHCO)ZrCl(η-C5H5)2](both structurally characterized), the latter via carbonylation of ‘[(η-C5H5)2ZrCl(CH2PMe2)]’ (1984)

Reaction of [(tmeda)L[graphic omitted]Me2], (1), or (tmeda tetramethylethylenediamine) with [(η-C5H5)2ZrCl2] in tetrahydrofuran at –78 °C yields [(η-C5H5)2Zr(CH2PMe2)n, Cl2 –n]n= 1, (2), n= 2, (3); carbonylation of (2) affords exclusively a novel binuclear ketene complex, [(η-C5H5)2ClZ[graphic omitted]Cl(η-C5H5)2], (4), which in the crystal form possesses a Zr–P linkage [2.724(5)Å].
Folded-cavity resonators as key elements for optical filtering and low-voltage electroabsorption modulation (2006)

Folded-cavity (FC) resonators, which are based on shallow-etched ridge waveguides combined with four deeply etched turning mirrors, are designed and fabricated. The device consists of a resonant FC and a bus waveguide coupled to it through a directional coupler. Optical passive filters, based on this technology, exhibit quality factors in the excess of 5000, with a low insertion loss of 5 dB (including the input coupling loss to a fiber) and more than 15-dB extinction at resonance. When the filter is combined with an electroabsorption active region and is designed to operate in the overcoupled regime, a low-voltage/high-extinction-ratio resonant modulation becomes feasible. The resonant modulator exhibits a low insertion loss (greater than 22-dB extinction at resonance) and offers a low-voltage operation. A change in the applied voltage by 0.7 V (close to the critically coupled conditions) leads to a transmission change of more than 16 dB. Open eye diagrams at 12 Gb/s are presented. To decrease the insertion loss, multiple material bangaps are further monolithically integrated across the wafer by utilizing the quantum-well-intermixing techniques