gebhart/patrepeval huggingface dataset:
Revealing anisotropic properties of cornea at different intraocular pressures using optical coherence elastography (2016)

In this study we have evaluated the elastic anisotropy of porcine corneas with increasing intraocular pressures (IOPs) using a noncontact optical coherence elastography (OCE) technique. A focused air-pulse induced low amplitude (≤10 μm) elastic waves in fresh porcine corneas (n=9) in situ in the whole eye-globe configuration. A phase-stabilized swept source optical coherence elastography (PhS-SSOCE) system imaged the propagation of the elastic wave in different stepped radial directions. A closed-loop feedback system was utilized to artificially manipulate the IOP, and OCE measurements were repeated while the IOP was increased in 5 mmHg increments from 15 to 30 mmHg. The OCE measurements demonstrated that the elastic anisotropy of the cornea became more pronounced at higher IOPs, and that there were distinct radial angles of higher and lower stiffness. The presented noncontact OCE method was capable of detecting and assessing the corneal elastic anisotropy as a function of IOP. Due to the noninvasive nature and small amplitude of the elastic wave, this method may be able to provide additional information about corneal health and integrity in vivo.
Fast Embedded Video Compression Using Cache-Based Zerotree Processing (1998)

Publication in the conference proceedings of EUSIPCO, Rhodes, Greece, 1998
Secondary Photocrosslinking of Injectable Shear‐Thinning Dock‐and‐Lock Hydrogels (2013)

Shear-thinning hydrogels are useful in numerous applications, including as injectable carriers that act as scaffolds to support cell and drug therapies. Here, we describe the engineering of a self-assembling Dock-and-Lock (DnL) system that forms injectable shear-thinning hydrogels using molecular recognition interactions that also possess photo-triggerable secondary crosslinks. These DnL hydrogels are fabricated from peptide-modified hyaluronic acid (HA) and polypeptide precursors, can self-heal immediately after shear induced flow, are cytocompatible, and can be stabilized through light-initiated radical polymerization of methacrylate functional groups to tune gel mechanics and erosion kinetics. Secondary crosslinked hydrogels retain self-adhesive properties and exhibit cooperative physical and chemical crosslinks with moduli as high as ∼10 times larger than moduli of gels based on physical crosslinking alone. The extent of reaction and change in properties are dependent on whether the methacrylate is incorporated either at the terminus of the peptide or directly to the HA backbone. Additionally, the gel erosion can be monitored through an incorporated fluorophore and physical-chemical gels remain intact in solution over months, whereas physical gels that are not covalently crosslinked erode completely within days. Mesenchymal stem cells exhibit increased viability when cultured in physical- chemical gels, compared with those cultured in gels based on physical crosslinks alone. The physical properties of these DnL gels may be additionally tuned by adjusting component compositions, which allows DnL gels with a wide range of physical properties to be constructed for use.
Isolation and Characterization of a High Affinity Peptide Inhibitor of ClC-2 Chloride Channels (2009)

The ClC protein family includes voltage-gated chloride channels and chloride/proton exchangers. In eukaryotes, ClC proteins regulate membrane potential of excitable cells, contribute to epithelial transport, and aid in lysosomal acidification. Although structure/function studies of ClC proteins have been aided greatly by the available crystal structures of a bacterial ClC chloride/proton exchanger, the availability of useful pharmacological tools, such as peptide toxin inhibitors, has lagged far behind that of their cation channel counterparts. Here we report the isolation, from Leiurus quinquestriatus hebraeus venom, of a peptide toxin inhibitor of the ClC-2 chloride channel. This toxin, GaTx2, inhibits ClC-2 channels with a voltage-dependent apparent K(D) of approximately 20 pm, making it the highest affinity inhibitor of any chloride channel. GaTx2 slows ClC-2 activation by increasing the latency to first opening by nearly 8-fold but is unable to inhibit open channels, suggesting that this toxin inhibits channel activation gating. Finally, GaTx2 specifically inhibits ClC-2 channels, showing no inhibitory effect on a battery of other major classes of chloride channels and voltage-gated potassium channels. GaTx2 is the first peptide toxin inhibitor of any ClC protein. The high affinity and specificity displayed by this toxin will make it a very powerful pharmacological tool to probe ClC-2 structure/function.
Methods for treating glassware surfaces using zinc-containing corrosion protection agents. (2003)

A treatment system corrosion protection agents, esp. corrosion protection agents comprising zinc-contg. materials, is used for treating glassware for example dishes and glasses, with reduced surface corrosion. Such a domestic, institutional, industrial, and/or com. method of reducing glassware surface corrosion in an automatic dishwashing appliance comprises the step of contacting a glassware surface with a corrosion protection agent comprising: (a) an effective amt. of a zinc-contg. layered material; and (b) optionally, an adjunct ingredient. [on SciFinder(R)]
Optical-Layer Traffic Grooming in Flexible Grid WDM Networks (2011)

In this paper, we introduce an electronic traffic grooming (E-Grooming) technique, and propose a novel bit rate and protocol independent optical-layer traffic grooming (O-Grooming) technique for OFDM-based flexible grid WDM networks. We introduce a novel routing, wavelength assignment, subcarrier assignment, and spectrum allocation (RWSSA) problem for the first time. An effective polynomial-time heuristic algorithms is proposed to address the RWSSA problem in OGrooming capable flexible grid networks. The performance of the proposed E-Grooming and O-Grooming techniques are evaluated with transparent flexible grid networks. Simulation results show that traffic grooming in flexible grid networks improve spectral efficiency compared to transparent networks. In addition to bit rate and protocol transparent, the O-Grooming technique is cost and energy efficient compared to the E-Grooming technique while marginally sacrificing the spectral efficiency.
Signal-to-noise characterization of time-gated intensifiers used for wide-field time-domain FLIM (2009)

Time-gated imaging using gated optical intensifiers provides a means to realize high speed fluorescence lifetime imaging (FLIM) for the study of fast events and for high throughput imaging. We present a signal-to-noise characterization of CCD-coupled micro-channel plate gated intensifiers used with this technique and determine the optimal acquisition parameters (intensifier gain voltage, CCD integration time and frame averaging) for measuring mono-exponential fluorescence lifetimes in the shortest image acquisition time for a given signal flux. We explore the use of unequal CCD integration times for different gate delays and show that this can improve the lifetime accuracy for a given total acquisition time.
A novel framework for fast scene matching in consumer image collections (2010)

The widespread utilization of digital visual media has motivated many research efforts towards efficient search and retrieval from large photo collections. Traditionally, SIFT feature-based methods have been widely used for matching photos taken at particular locations or places of interest. These methods are very time-consuming due to the complexity of the features and the large number of images typically contained in the image database being searched. In this paper, we propose a fast approach to matching images captured at particular locations or places of interest by selecting representative images from an image collection that have the best chance of being successfully matched by using SIFT, and relying on only these representative images for efficient scene matching. We present a unified framework incorporating a set of discriminative features that can effectively select the images containing signature elements of particular locations from a large number of images. The proposed approach produces an order of magnitude improvement in computational time for matching similar scenes in an image collection using SIFT features. The experimental results demonstrate the efficiency of our approach compared to the traditional SIFT, PCA-SIFT, and SURF-based approaches.
Bifunctional Short Hairpin RNA (bi-shRNA): Design and Pathway to Clinical Application (2012)

The discovery of RNA interference (RNAi) engendered great excitement and raised expectations regarding its potential applications in biomedical research and clinical usage. Over the ensuing years, expanded understanding of RNAi and preliminary results from early clinical trials tempered enthusiasm with realistic appraisal resulting in cautious optimism and a better understanding of necessary research and clinical directions. As a result, data from more recent trials are beginning to show encouraging positive clinical outcomes. The capability of delivering a pharmacologically effective dose to the target site while avoiding adverse host reactions still remains a challenge although the delivery technology continues to improve. We have developed a novel vector-driven bifunctional short hairpin RNA (bi-shRNA) technology that harnesses both cleavage-dependent and cleavage-independent RISC loading pathways to enhance knockdown potency. Consequent advantages provided by the bi-shRNA include a lower effective systemic dose than comparator siRNA/shRNA to minimize the potential for off-target side effects, due to its ability to induce both a rapid (inhibition of protein translation) and delayed (mRNA cleavage and degradation) targeting effect depending on protein and mRNA kinetics, and a longer duration of effectiveness for clinical applications. Here, we provide an overview of key molecular methods for the design, construction, quality control, and application of bi-shRNA that we believe will be useful for others interested in utilizing this technology.
A peptide-based fluorescence resonance energy transfer assay for <i>Bacillus anthracis</i> lethal factor protease (2002)

A fluorescence resonance energy transfer assay has been developed for monitoring Bacillus anthracis lethal factor (LF) protease activity. A fluorogenic 16-mer peptide based on the known LF protease substrate MEK1 was synthesized and found to be cleaved by the enzyme at the anticipated site. Extension of this work to a fluorogenic 19-mer peptide, derived, in part, from a consensus sequence of known LF protease targets, produced a much better substrate, cleaving approximately 100 times more efficiently. This peptide sequence was modified further on resin to incorporate donor/quencher pairs to generate substrates for use in fluorescence resonance energy transfer-based appearance assays. All peptides cleaved at similar rates with signal/background ranging from 9-16 at 100% turnover. One of these substrates, denoted (Cou)Consensus(K(QSY-35)GG)-NH(2), was selected for additional assay optimization. A plate-based assay requiring only low nanomolar levels of enzyme was developed for screening and inhibitor characterization.
Secretion of a malarial histidine-rich protein (Pf HRP II) from Plasmodium falciparum-infected erythrocytes. (1986)

Plasmodium falciparum-infected erythrocytes (IRBCs) synthesize several histidine-rich proteins (HRPs) that accumulate high levels of [3H]histidine but very low levels of amino acids such as [3H]isoleucine or [35S]methionine. We prepared a monoclonal antibody which reacts specifically with one of these HRPs (Pf HRP II) and studied the location and synthesis of this protein during the parasite's intracellular growth. With the knob-positive Malayan Camp strain of P. falciparum, the monoclonal antibody identified a multiplet of protein bands with major species at Mr 72,000 and 69,000. Pf HRP II synthesis began with immature parasites (rings) and continued through the trophozoite stage. The Mr 72,000 band of Pf HRP II, but not the faster moving bands of the multiplet, was recovered as a water-soluble protein from the culture supernatant of intact IRBCs. Approximately 50% of the total [3H]histidine radioactivity incorporated into the Mr 72,000 band was extracellular between 2 and 24 h of culture. Immunofluorescence and cryothin-section immunoelectron microscopy localized Pf HRP II to several cell compartments including the parasite cytoplasm, as concentrated "packets" in the host erythrocyte cytoplasm and at the IRBC membrane. Our results provide evidence for an intracellular route of transport for a secreted malarial protein from the parasite through several membranes and the host cell cytoplasm.
Association of Cross-Reactive Antibodies Targeting Peptidyl-Arginine Deiminase 3 and 4 with Rheumatoid Arthritis-Associated Interstitial Lung Disease (2014)

The prevalence and extent of ILD was markedly higher among RA patients with anti-PAD3/4 cross-reactive antibodies, even after accounting for relevant confounders, particularly among ever smokers. These findings may suggest etiopathologic mechanisms of RA-ILD, and their clinical utility for predicting ILD warrants additional study.
Multiple Graph Kernel Fusion Prediction of Drug Prescription (2019)

We present an end-to-end interpretable deep architecture that predicts the success of drug prescription based on multiple graph kernel fusion using a graphical representation of electronic health records. We formulate the predictive model as a binary graph classification problem with a set of graph kernels proposed to capture different aspects of graph structures through deep neural networks. Results using the Taiwanese National Health Insurance Research Database demonstrate that our approach outperforms current start-of-the-art models on accuracy and interpretability. The approach is in preliminary deployment.
Efficient rendering of heterogeneous polydisperse granular media (2016)

We address the challenge of efficiently rendering massive assemblies of grains within a forward path-tracing framework. Previous approaches exist for accelerating high-order scattering for a limited, and static, set of granular materials, often requiring scene-dependent precomputation. We significantly expand the admissible regime of granular materials by considering heterogeneous and dynamic granular mixtures with spatially varying grain concentrations, pack rates, and sizes. Our method supports both procedurally generated grain assemblies and dynamic assemblies authored in off-the-shelf particle simulation tools. The key to our speedup lies in two complementary aggregate scattering approximations which we introduced to jointly accelerate construction of short and long light paths. For low-order scattering, we accelerate path construction using novel grain scattering distribution functions (GSDF) which aggregate intra-grain light transport while retaining important grain-level structure. For high-order scattering, we extend prior work on shell transport functions (STF) to support dynamic, heterogeneous mixtures of grains with varying sizes. We do this without a scene-dependent precomputation and show how this can also be used to accelerate light transport in arbitrary continuous heterogeneous media. Our multi-scale rendering automatically minimizes the usage of explicit path tracing to only the first grain along a light path, or can avoid it completely, when appropriate, by switching to our aggregate transport approximations. We demonstrate our technique on animated scenes containing heterogeneous mixtures of various types of grains that could not previously be rendered efficiently. We also compare to previous work on a simpler class of granular assemblies, reporting significant computation savings, often yielding higher accuracy results.
A Lipid-Modified Estrogen Derivative that Treats Breast Cancer Independent of Estrogen Receptor Expression through Simultaneous Induction of Autophagy and Apoptosis (2011)

It is a challenge to develop a universal single drug that can treat breast cancer at single- or multiple-stage complications, yet remains nontoxic to normal cells. The challenge is even greater when breast cancer-specific, estrogen-based drugs are being developed that cannot act against multistaged breast cancer complications owing to the cells differential estrogen receptor (ER) expression status and their possession of drug-resistant and metastatic phenotypes. We report here the development of a first cationic lipid-conjugated estrogenic derivative (ESC8) that kills breast cancer cells independent of their ER expression status. This ESC8 molecule apparently is nontoxic to normal breast epithelial cells, as well as to other noncancer cells. ESC8 induces apoptosis through an intrinsic pathway in ER-negative MDA-MB-231 cells. In addition, ESC8 treatment induces autophagy in these cells by interfering with the mTOR activity. This is the first example of an estrogen structure-based molecule that coinduces apoptosis and autophagy in breast cancer cells. Further in vivo study confirms the role of this molecule in tumor regression. Together, our results open new perspective of breast cancer chemotherapy through a single agent, which could provide the therapeutic benefit across all stages of breast cancer.
Stoichiometric Synthesis of Pure MFe<sub>2</sub>O<sub>4</sub>(M = Mg, Co, and Ni) Spinel Ferrites from Tailored Layered Double Hydroxide (Hydrotalcite-Like) Precursors (2004)

In this paper a novel synthetic route of pure MFe2O4 (M = Mg, Co, and Ni) spinel ferrites is reported. The key feature of this method is using a single molecular precursor. The pure spinel ferrites can be obtained by calcination of tailored hydrotalcite-like layered double hydroxides (LDHs) of the type [M1-X-YFe2+YFe3+X(OH)2]X+(SO42-)X/2·mH2O (M = Mg, Co, and Ni) precursors at 900 °C for 2 h, in which the molar ratio of M2+/(Fe2+ + Fe3+) is adjusted to the same value as that in single spinel ferrite itself. The structural characteristics of the as-synthesized LDHs and their resulting calcined products are obtained by powder X-ray diffraction (XRD), chemical analysis, Fourier transform infrared spectroscopy (FT-IR), simultaneous thermogravimetric and differential thermal analysis (TG-DTA), and Mössbauer spectroscopy. The saturation magnetizations of the materials produced by calcinations of LDHs are higher than those of the spinel ferrites produced by the conventional ceramic and wet chemical routes, although the compositions of the materials are similar. The major advantage of the new method is that it affords uniform distribution of all metal cations on an atomic level in the LDH precursors; hence, the formation of spinel ferrites starting from the LDHs requires a much lower temperature and shorter time, leading to a lower chance of side-reactions occurring.
Atomic (Scanning) Force Microscopy in Cardiovascular Research (1996)

The promise of atomic (scanning) force microscopy (AFM) for cardiovascular research is enormous. The AFM images by using a sharp cantilever tip to sense the repulsive and attractive forces between the tip and the sample surface. The force of interaction is kept constant while raster scanning, resulting in images of the surface contours with molecular and, on hard inorganic surfaces, even atomic resolution. Movement of the cantilever in the Z plane is detected by a laser beam reflected off the cantilever to a photodiode system, a piezotube allows an X and Y raster, and a three-dimensional image results. Its capabilities include: (1) the three-dimensional imaging of membranes and biomolecules with molecular and submolecular resolution; (2) such imaging not only of dry specimens but of specimens in a physiologic solution, thereby allowing the investigation of dynamic processes in both viable biomolecules and living cells; (3) the sensing of charge and intermolecular interaction forces; (4) the chemical or biochemical modification of the cantilever tip, which allows the identification of specific structures and the measurement of specific interactions (e.g., a ligand-receptor interaction); (5) nanometer control of the position and force of the cantilever, which, in turn, allows the physical manipulation of biomolecules, the dissection of biological structures (e.g., the separation of one gap junctional hemichannel from its neighbor, thereby revealing normally inaccessible surfaces), the delivery of ligands, drugs, or other materials to specific locations, and the precise measurement of interacting forces at specific sites; and (6) the modification of the apparatus by adding complementary methodologies (e.g., magnetic resonance imaging, fluorescence microscopy, confocal microscopy, and perhaps electrophysiology). AFM, however, is only now being applied to biological research, many technical and methodologic problems exist, and a number of them are considered in this review. Little work has been done in cardiovascular research and the purpose of this review is to introduce this new and exciting approach to investigation.
Ultrasonic Rapid Manufacturing of Layered Objects (2000)

Abstract The Ultrasonic Rapid Manufacturing process is a new non-thermal rapid prototyping technique for layered fabrication of metallic or multiple-material products. The process introduced in this paper employs ultrasonic welding and contour cutting of thin material foils. Its laboratory implementation, automation and integration, and parameter optimization are described first. Next, a numerical FEA simulation of the static and dynamic stress/strain field, based on experimental calibration of the friction coefficient between the welded surfaces, is established and found in agreement with laboratory strain data. Last, the technical advantages of the process, including fabrication of dense, full-strength functional solid metal parts, multiple-material composites, and active parts with embedded intelligent components and electronic, mechatronic, optic and fluidic structures, are examined in the manufacturing industry.
Privacy-Preserving Method for Temporarily Linking/Revoking Pseudonym Certificates in VANETs (2018)

Vehicular communication (V2X) technologies are expected to become increasingly common in the future. Although they enable improvements on transportation safety and efficiency, the large scale deployment of V2X requires addressing some challenges. In particular, to prevent abuse by drivers and by the system itself, V2X architectures must: (1) ensure the authenticity of messages, which is usually accomplished by means of digital certification; and (2) preserve the privacy of honest users, so owners of non-revoked certificates cannot be easily identified or tracked by eavesdroppers. A promising design to address these requirements is the Security Credential Management System (SCMS), which is currently among the main candidates for protecting V2X communications in the United States. Even though SCMS provides efficient, scalable and privacy-preserving mechanisms for managing V2X-oriented certificates, in this paper we show that it can be further enhanced. Namely, we present two birthday attacks against SCMS's certificate revocation process, both of which degrade the system's security as time passes and more certificates are revoked. We then describe an alternative design to prevent such security degradation with minimal computational overhead. In complement to these security gains, we also describe a mechanism for improving the flexibility of revocation, allowing certificates (as well as their owner's privacy) to be temporarily revoked in an efficient manner. This functionality is useful, for example, to implement suspension mechanisms or to aid in investigations by law-enforcement authorities.