gebhart/patrepeval huggingface dataset:
Antitumoral properties and reduced toxicity of LPS targeted to macrophages via normal or mannosylated liposomes. (1990)

Neo-mannosylated liposomes have been prepared by coupling a mannose derivative bearing a hydrophilic spacer arm to preformed large unilamellar liposomes containing 4-(p-maleimidophenyl) butyryl-phosphatidylethanolamine. Lipopolysaccharide (LPS) was encapsulated in normal or neo-mannosylated liposomes; the neo-mannosylated vesicles showed specificity for the in vitro activation to toxicity of macrophages only in the case of differentiated macrophages presenting mannose receptors at their surface. In vivo, LPS entrapped in neo-mannosylated vesicles showed a reduced toxicity for animals hypersensitive to LPS. Moreover targeting of LPS to tissue macrophages with neo-mannosylated liposomes induced regression of experimental solid tumors in mice (EMT6 sarcoma, 3LL carcinoma) and was effective on lung metastases.
Real-time observation of postprandial hepatic glucose metabolism with interleaved 2H Metabolic Imaging and 13C-MRS at 7 T (2023)

The liver takes a central role in the regulation of glucose homeostasis by storing glucose in the fed state and releasing it during food abstinence. As a consequence, the liver is critically involved in glucose homeostasis disorders. We propose a novel non-invasive approach combining Deuterium Metabolic Imaging (DMI) with 13 C-MRS at 7 T to dynamically map hepatic glucose metabolism. Preliminary results support technical feasibility and provide first insights into distinct hepatic glucose profiles in patients with dysregulated glucose homeostasis. The proposed approach may open new avenues for a better understanding of pathophysiology of glucose dysregulation and development of targeted treatments.
Correlation between barrier height and band offsets in metal/Si1−xGex/Si heterostructures (1998)

The variation of barrier height with the band gap in the metal/heterojunction systems is related to how the Fermi level position varies with respect to band edges. If the Fermi level is pinned by the interface states its movement will also correspond to the movement of the neutrality level at the interface. Metal/Si1−xGex/Si heterostructures (0⩽x⩽0.24) for both n- and p-type substrates were studied to understand the relation between Schottky barrier, Fermi level movement, and the band gap variations. It was shown that a correlation exists between Schottky barrier height variation and band-offset values ΔEc and ΔEv. For n-type substrate, measured barrier height differences are almost the same as the band offsets in the conduction band ΔEc. For p-type substrates they were found to be slightly smaller than ΔEv. This shows that Fermi level position relative to the conduction band edge does not change with band gap variation.
All-optical wavelength shifting of subcarrier channels using difference-frequency-generation in a PPLN (2001)

Summary form only given. It may be critical for future networks to provide wavelength shifting and subcarrier modulation to ensure high-throughput performance. Wavelength shifting is important because it enables wavelength reuse, contention resolution and efficient use of the wavelength domain. Similarly, subcarrier modulation is important for data grooming, bandwidth allocation flexibility, control/header information transportation, and access networks. In this paper, we demonstrate and characterize all-optical wavelength shifting of subcarrier channels in a periodically poled lithium niobate (PPLN) structure.
Mass Measurements of C-terminally Truncated α-Crystallins from Two-dimensional Gels Identify Lp82 as a Major Endopeptidase in Rat Lens (2002)

Molecular chaperone activity of lens alpha-crystallins is reduced by loss of the C terminus. The purpose of this experiment was to 1) determine the cleavage sites produced in vitro by ubiquitous m-calpain and lens-specific Lp82 on alpha-crystallins, 2) identify alpha-crystallin cleavage sites produced in vivo during maturation and cataract formation in rat lens, and 3) estimate the relative activities of Lp82 and m-calpain by appearance of protease-specific cleavage products in vivo. Total soluble protein from young rat lens was incubated with recombinant m-calpain or Lp82 and 2 mM Ca2+. Resulting fragmented alpha-crystallins were separated by two-dimensional gel electrophoresis. Eluted alpha-crystallin spots were analyzed by mass spectrometry. Cleavage sites on insoluble alpha-crystallins were determined similarly in mature rat lens nucleus and in cataractous rat lens nucleus induced by selenite. In vitro proteolysis of alphaA-crystallin by Lp82 and m-calpain produced unique cleavage sites by removing 5 and 11 residues, respectively, from the C terminus. In vivo, the protease-specific truncations removing 5 and 11 residues from alphaA were both found in maturing lens, whereas only the truncation removing 5 residues was found in cataractous lens. Other truncation sites, common to both calpain isoforms, resulted from the removal of 8, 10, 16, 17, and 22 residues from the C terminus of alphaA. Using uniquely truncated alphaA-crystallins as in vivo markers, Lp82 and m-calpain were both found to be active during normal maturation of rat lens, whereas Lp82 seemed especially active during selenite cataract formation. These C-terminal truncations decrease chaperone activity of alpha-crystallins, possibly leading to the observed increases in insoluble proteins during aging and cataract. The methodology that allowed accurate mass measurements of proteins eluted from 2D gels should be useful to examine rapidly other post-translational modifications.
Preparation, Separation, and Conformational Analysis of Differentially Sulfated Heparin Octasaccharide Isomers Using Ion Mobility Mass Spectrometry (2012)

Heparin is a linear sulfated polysaccharide widely used in medicine because of its anticoagulant properties. The various sulfation and/or acetylation patterns on heparin impart different degrees of conformational change around the glycosidic bonds and subsequently alter its function as an anticoagulant, anticancer, or antiviral drug. Characterization of these structures is important for eventual elucidation of its function but presents itself as an analytical challenge due to the inherent heterogeneity of the carbohydrates. Heparin octasaccharide structural isomers of various sulfation patterns were investigated using ion mobility mass spectrometry (IMMS). In addition to distinguishing the isomers, we report the preparation and tandem mass spectrometry analysis for multiple sulfated or acetylated oligosaccharides. Herein, our data indicate that heparin octasaccharide isomers were separated on the basis of their structural conformations in the ion mobility cell. Subsequent to this separation, isomers were further distinguished using product ions resulting from tandem mass spectrometry. Overall, IMMS analysis was used to successfully characterize and separate individual isomers and subsequently measure their conformations.
Ultrasensitive, background‐free single copy DNA detection: Benchmarking performance using HPV infected cell lines and tissue biopsies (2012)

In situ hybridization (ISH), immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) are common detection methods in biology. For high copy number targets, they perform well, but for single‐copy targets, sensitivity is often lacking. Chromosomal hybridizations require large probes (~100 kilobases) to obtain sufficient signal. At times, the desired target is not large enough for hybridization with probes of this size. We describe a method for single‐molecule detection wherein a probe contains multiple copies of a signaling moiety, like a fluorescent molecule, or an enzyme, like alkaline phosphatase, linked to a single binding molecule, like streptavidin. The small construct size allows efficient labeling of permeabilized cells. Cell lines and tissues infected with HPV, the disease‐causing agent of cervical cancer, were used to benchmark the method, employing biotinylated, probes specific to HPV subtypes. Using cell lines of known HPV DNA copy number, single copy detection per cell was demonstrated. The integrated copies of HPV16 in SiHa cells and chromosome spreads appear as punctate loci, as expected. Also, detection of the repressed p53 protein in HPV‐infected cells and tissue biopsies was demonstrated. The new method increases the overall sensitivity of FISH, ISH and IHC by roughly an order of magnitude and thus should prove applicable to the detection of cancer and infectious agents.
Homogeneous cobalt electrocatalysts for solar driven hydrogen evolution from water (2011)

Towards the bigger picture of developing modular solns. for photoelectrochem. water splitting, catalytic proton&#13;\nredn. mediated by cobalt bis(iminopyridine) complexes has been explored in buffered aq. media over a broad&#13;\nrange of pH conditions. The extremely rapid rates of electrocatalytic hydrogen evolution exhibited by firstgeneration&#13;\ncatalysts will be discussed in conjunction with the performance of second-generation&#13;\nelectrocatalysts. Details of electrochem. and photochem. mechanistic studies, kinetic competency, and the&#13;\neffects of reaction medium on H_2 evolution will also be presented.
A MOS-controlled triac device (1978)

A merged device - an insulated-gate triac - has been developed and modeled for analysis and design using a circuit analysis program combining MOS and bipolar capabilities. Applications include crosspoint switches, power control and microprocessor interface.
Performance Demonstration of a Burst-Mode EDFA for Packetized Radio-over-Fiber Signal Transmission (2014)

Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. Shiraiwa, A. Kanno, Y. Awaji, N. Wada, and T. Kawanishi, "Performance Demonstration of a Burst-Mode EDFA for Packetized Radio-over-Fiber Signal Transmission," in CLEO: 2014, OSA Technical Digest (online) (Optica Publishing Group, 2014), paper JTu4A.58. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Parallel Force/Position Control of an Epicardial Parallel Wire Robot (2016)

Gene therapies for heart failure have emerged in recent years, yet they lack an effective method for minimally invasive, uniform delivery. To address this need we developed a minimally invasive parallel wire robot for epicardial interventions. Accurate and safe interventions using this device require control of force in addition to injector position. Accounting for the nonidealities of the device design, however, yields nonlinear and underconstrained statics. This work solves these equations and demonstrates the efficacy of using this information in a parallel control scheme, which is shown to provide superior positioning compared to a position-only controller.
The Foundational data initiative for Parkinson’s disease (FOUNDIN-PD): enabling efficient translation from genetic maps to mechanism (2021)

Abstract The FOUNdational Data INitiative for Parkinson’s Disease (FOUNDIN-PD) is an international collaboration producing fundamental resources for Parkinson’s disease (PD). FOUNDIN-PD generated a multi-layered molecular dataset in a cohort of induced pluripotent stem cell (iPSC) lines differentiated to dopaminergic (DA) neurons, a major affected cell type in PD. The lines were derived from the Parkinson’s Progression Markers Initiative study including participants with PD carrying monogenic PD ( SNCA ) variants, variants with intermediate effects and variants identified by genome-wide association studies and unaffected individuals. We generated genetic, epigenetic, regulatory, transcriptomic, and longitudinal cellular imaging data from iPSC-derived DA neurons to understand molecular relationships between disease associated genetic variation and proximate molecular events. These data reveal that iPSC-derived DA neurons provide a valuable cellular context and foundational atlas for modelling PD genetic risk. We have integrated these data into a FOUNDIN-PD data browser ( https://www.foundinpd.org ) as a resource for understanding the molecular pathogenesis of PD.
SU‐FF‐J‐68: First Clinical Results of An Adaptive Off‐Line Radiation Scheme Using Cone‐Beam CT Scans for Treatment of Prostate Cancer (2006)

Purpose: We developed an adaptive scheme for prostate cancer radiotherapy based on kV cone‐beam‐CT (CBCT) images that are obtained on the machine during the first six treatment days. The aim of this scheme is to improve knowledge of the average prostate position and average rectum shape and safely reduce the PTV margin. Method and Materials: CBCT‐scans, acquired our on Elekta Synergy systems, were first matched on the planning CT scan using the pelvic bones. Automatic grey‐value matching was then used to match the prostates of the CBCT‐scans to the prostate of the planning CT scan. The mean of the obtained translations and rotations was used to move the prostate of the planning CT scan to its average position. Subsequently, the rectal wall was delineated in the CBCT‐scans, and coordinates of corresponding points of the 7 rectums were averaged to obtain the average rectal wall. Based on average prostate and rectum a new IMRT treatment plan was made with a reduced PTV margin of 7 mm. Weekly CBCT‐scans were made to verify that the new PTV encompasses the prostate. Results: So far, 16 patients were successfully treated with our adaptive treatment scheme. For 85% of the CBCT‐scans a successful grey‐value match was obtained, the other scans were discarded. For 88 out of 89 verification scans the prostate was inside the PTV. The mean dose received by the rectum reduced on average by 7.6%, and the equivalent uniform dose (a=12) by 1.5%. Conclusion: This is the first routine clinical application of soft tissue image guidance for the prostate using kV CBCT. Contrary to adaptive schemes that use implanted markers, our method is non‐invasive and improves localization of both prostate and rectum. Conflict of Interest: Elekta, Inc financially supported part of this study.
Plasma Electrolytic Polished Patient-Specific Orbital Implants in Clinical Use—A Technical Note (2023)

This technical note describes the technique of plasma electrolytic polishing on orbital patient-specific implants and demonstrates clinical handling and use by the insertion of a plasma electrolytic polished orbital implant into a patient.
Independent parallel lithography using the atomic force microscope (1996)

Independent parallel features have been lithographically patterned with a 2×1 array of individually controlled cantilevers using an atomic force microscope. Control of the individual cantilevers was achieved with an integrated piezoelectric actuator in feedback with a piezoresistive sensor. Patterns were formed on 〈100〉 single crystal silicon by using a computer controlled tip voltage to locally enhance the oxidation of the silicon. Using the piezoresistor directly as a force sensor, parallel images can be simultaneously acquired in the constant force mode. A discussion of electrostatic forces due to applied tip voltages, hysteresis characteristics of the actuator, and the cantilever system is also presented.
Endophilin-A Deficiency Induces the Foxo3a-Fbxo32 Network in the Brain and Causes Dysregulation of Autophagy and the Ubiquitin-Proteasome System (2016)

Endophilin-A, a well-characterized endocytic adaptor essential for synaptic vesicle recycling, has recently been linked to neurodegeneration. We report here that endophilin-A deficiency results in impaired movement, age-dependent ataxia, and neurodegeneration in mice. Transcriptional analysis of endophilin-A mutant mice, complemented by proteomics, highlighted ataxia- and protein-homeostasis-related genes and revealed upregulation of the E3-ubiquitin ligase FBXO32/atrogin-1 and its transcription factor FOXO3A. FBXO32 overexpression triggers apoptosis in cultured cells and neurons but, remarkably, coexpression of endophilin-A rescues it. FBXO32 interacts with all three endophilin-A proteins. Similarly to endophilin-A, FBXO32 tubulates membranes and localizes on clathrin-coated structures. Additionally, FBXO32 and endophilin-A are necessary for autophagosome formation, and both colocalize transiently with autophagosomes. Our results point to a role for endophilin-A proteins in autophagy and protein degradation, processes that are impaired in their absence, potentially contributing to neurodegeneration and ataxia.
Theoretical Analysis of Grating Lobe Intensity (1986)

Grating lobe intensity is theoretically analyzed for electronic scanner array design. An analytical expression of the intensity is derived by taking the effect of aberrations and array element directivity on grating lobe formation into account. The intensity obtained using the derived expression is compared with computer simulation results, whereby it is seen that their dependences on acoustic parameters agree well with each other.
Heterogeneous Biomedical Database Integration using a Hybrid Strategy: A P53 Cancer Research Database (2006)

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html .)
Size control and luminescence properties of Eu2+:LiCaAlF6 particles prepared by femtosecond pulsed laser ablation (2017)

We have fabricated Eu2+:LiCaAlF6 (Eu:LiCAF) nanoparticles via a dry pulsed laser ablation process using femtosecond laser pulses. The particle size was controlled by adjusting the laser fluence. The crystallographic orientation and chemical composition were preserved in all particles. The typical luminescence peak of Eu:LiCAF crystals at approximately 370 nm was observed in both the PL and X-ray induced luminescence (XL) spectra. The temporal PL profiles of all deposited particles exhibited fast-decay components in addition to the slow-decay components observed in the profile of the bulk crystal. Smaller particles had shorter decay times than larger particles. The fast-decay component of particles with a mean diameter of less than 0.36 μm (∼40 ns) was at least one order of magnitude shorter than the decay time of the bulk crystal (∼1700 ns). Even in the temporal XL profile, all deposited particles showed shorter decay times than the bulk decay time. We attribute these fast-decay components to defects on the particle surface. To confirm the defect level, we investigated the thermally stimulated luminescence of the deposited particles. In addition to an emission peak at approximately 540 K, which was also observed in the spectrum of the bulk crystal, an emission peak corresponding to surface defects at approximately 700 K was observed in the spectrum of the particles.
Extracellular matrix controls myosin light chain phosphorylation and cell contractility through modulation of cell shape and cytoskeletal prestress (2004)

The mechanism by which vascular smooth muscle (VSM) cells modulate their contractility in response to structural cues from extracellular matrix remains poorly understood. When pulmonary VSM cells were cultured on increasing densities of immobilized fibronectin (FN), cell spreading, myosin light chain (MLC) phosphorylation, cytoskeletal prestress (isometric tension in the cell before vasoagonist stimulation), and the active contractile response to the vasoconstrictor endothelin-1 all increased in parallel. In contrast, MLC phosphorylation did not increase when suspended cells were allowed to bind FN-coated microbeads (4.5-microm diameter) or cultured on micrometer-sized (30 x 30 microm) FN islands surrounded by nonadhesive regions that support integrin binding but prevent cell spreading. Cell spreading and MLC phosphorylation also both decreased in parallel when the mechanical compliance of flexible FN substrates was raised. MLC phosphorylation was inhibited independently of cell shape when cytoskeletal prestress was dissipated using a myosin ATPase inhibitor in fully spread cells, whereas it increased to maximal levels when microtubules were disrupted using nocodazole in cells adherent to FN but not in suspended cells. These data demonstrate that changes in cell-extracellular matrix (ECM) interactions modulate smooth muscle cell contractility at the level of biochemical signal transduction and suggest that the mechanism underlying this regulation may involve physical interplay between ECM and the cytoskeleton, such that cell spreading and generation of cytoskeletal tension feed back to promote MLC phosphorylation and further increase tension generation.
Complexity Estimation of the H.264 Coded Video Bitstreams (2005)

The emerging H.264 video coding standard offers a flexible coding algorithm for use in a range of applications from broadcast TV to low bitrate mobile applications. The flexibility comes with complexity. The H.264 video coding algorithm is complex and requires substantial amount of resources for encoding and decoding. The resources required to decode an H.264 video varies depending upon the encoding options used. Understanding the resources required to play the video at the receiver is especially important for mobile devices with limited amount of resources. In this paper, we present an overview of the H.264 video coding standard, complexity analysis of H.264 video, and its implications for resource management and adaptive coding for mobile devices. We examine high level bitstream characteristics and its suitability for estimating the bitstream complexity and receiver resource consumption. We show that high level metrics can be used to estimate receiver resource consumption with reasonable accuracy.
Life on biomembranes viewed with the atomic force microscope. (1997)

Since its invention in 1986, the atomic force microscope (AFM) has become one of the most widely used near-field microscopes. Surfaces of hard samples are imaged almost routinely with atomic resolution. Soft biological surfaces, however, are still challenging. In this brief review, the AFM technique is introduced to the experimental biologist. We discuss recent data on imaging molecular structures of biomembranes, and give detailed information on the application of the AFM with three representative examples. One is imaging plasma membrane turnover of transformed renal epithelial cells during migration in vivo, another is visualizing a cloned and isolated potassium channel usually located in kidney, and a third is imaging macromolecular pore complexes of the nuclear envelope of aldosterone-sensitive kidney cells and of Xenopus laevis oocytes. The review ends with the conclusion that nuclear pores can serve as birthday candles on a Guglhupf.