gebhart/patrepeval huggingface dataset:
Self-assembled liposomal nanoparticles in photodynamic therapy (2013)

Photodynamic therapy (PDT) employs the combination of non-toxic photosensitizers (PS) together with harmless visible light of the appropriate wavelength to produce reactive oxygen species that kill unwanted cells. Because many PS are hydrophobic molecules prone to aggregation, numerous drug delivery vehicles have been tested to solubilize these molecules, render them biocompatible and enhance the ease of administration after intravenous injection. The recent rise in nanotechnology has markedly expanded the range of these nanoparticulate delivery vehicles beyond the well-established liposomes and micelles. Self-assembled nanoparticles are formed by judicious choice of monomer building blocks that spontaneously form a well-oriented 3-dimensional structure that incorporates the PS when subjected to the appropriate conditions. This self-assembly process is governed by a subtle interplay of forces on the molecular level. This review will cover the state of the art in the preparation and use of self-assembled liposomal nanoparticles within the context of PDT.
Design and Synthesis of Visible Isotope-Coded Affinity Tags for the Absolute Quantification of Specific Proteins in Complex Mixtures (2004)

Identification of proteins in complex mixtures by mass spectrometry is most useful when quantitative data is also obtained. We recently introduced isotope-coded affinity tags (ICAT reagents) for the relative quantification of proteins present in two or more biological samples. In this report, we describe a new generation of ICAT reagents that contain the following additional features: (1) a visible tag that allows the electrophoretic position of tagged peptides during separation to be easily monitored; (2) a photocleavable linker that allows most of the tag to be removed prior to mass spectrometric analysis; (3) an isotope tag that contains carbon-13 and nitrogen-15 atoms instead of deuterium to ensure precise comigration of light and heavy tagged peptides by reverse-phase HPLC. These reagents contain an iodoacetyl group that selectively reacts with peptide cysteine residues. Peptide modification chemistry is also reported that allows tagging of peptides that are devoid of cysteine. The synthesis of these visible isotope-coded affinity tags (VICAT reagents), and their reaction with peptides are described in this report. VICAT reagents containing a carbon-14 visible probe or an NBD fluorophore are described. These reagents are most useful for the determination of the absolute quantity of specific target proteins in complex protein mixtures such as serum or cell lysates.
The Effects of Intracellular Calcium Depletion on Insulin Signaling in 3T3-L1 Adipocytes (2002)

We have examined the requirement for intracellular calcium (Ca(2+)) in insulin signal transduction in 3T3-L1 adipocytes. Using the Ca(2+) chelator 1,2- bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid, sodium (BAPTA-AM), we find both augmentation and inhibition of insulin signaling phenomena. Pretreatment of cells with 50 microM BAPTA-AM did not affect tyrosine phosphorylation of insulin receptor substrate (IRS)1/2 or insulin receptor (IR)beta. The decreased mobility of IRS1 normally observed after chronic stimulation with insulin, due to serine phosphorylation, was completely eliminated by Ca(2+) chelation. Correlating with decreased insulin-induced serine phosphorylation of IRS1, phosphotyrosine-mediated protein-protein interactions involving p85, IRS1, IRbeta, and phosphotyrosine-specific antibody were greatly enhanced by pretreatment of cells with BAPTA-AM. As a result, insulin-mediated, phosphotyrosine-associated PI3K activity was also enhanced. BAPTA-AM pretreatment inhibited other insulin-induced phosphorylation events including phosphorylation of Akt, MAPK (ERK1 and 2) and p70 S6K. Phosphorylation of Akt on threonine-308 was more sensitive to Ca(2+) depletion than phosphorylation of Akt on serine-473 at the same insulin dose (10 nM). In vitro 3'-phosphatidylinositol-dependent kinase 1 activity was unaffected by BAPTA-AM. Insulin-stimulated insulin-responsive glucose transporter isoform translocation and glucose uptake were both inhibited by calcium depletion. In summary, these data demonstrate a positive role for intracellular Ca(2+) in distal insulin signaling events, including initiation/maintenance of Akt phosphorylation, insulin-responsive glucose transporter isoform translocation, and glucose transport. A negative role for Ca(2+) is also indicated in proximal insulin signaling steps, in that, depletion of intracellular Ca(2+) blocks IRS1 serine/threonine phosphorylation and enhances insulin-stimulated protein-protein interaction and PI3K activity.
The construction of supramolecular systems (2019)

Self-assembly must be transformed into multistep synthesis to create complex structures
Giant Random Telegraph Signals in Nanoscale Floating-Gate Devices (2007)

The magnitude of a random telegraph signal (RTS) in nanoscale floating-gate devices has been experimentally investigated as a function of carrier concentration. Discrete current switching, which is caused by a single trap, has been found to be almost one order of magnitude higher with respect to what was predicted by the classical theory of carrier number and correlated mobility fluctuations. Nevertheless, the trap signature well fits the typical SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> trap spectroscopy. In addition, the rigid shift between the transfer curves related to filled- and empty-trap state, together with the normalized current fluctuation dependence on the channel carrier density, suggests that a pure number fluctuation is the correct theoretical interpretative framework. Thus, we propose a possible physical explanation for such a giant RTS on the basis of a quasi-1-D current filamentation.
Objectively Measured Sedentary Time, Physical Activity, and Metabolic Risk (2008)

These findings highlight the importance of decreasing sedentary time, as well as increasing time spent in physical activity, for metabolic health.
Synthesis of phenylquinoxaline oligomers containing pendant electron‐donating and electron‐withdrawing groups (2005)

Abstract A series of extended 6‐substituted quinoxaline AB monomer mixtures, 2‐(4‐fluorophenyl)‐3‐[4‐(4‐hydroxyphenoxy)phenyl]‐6‐substituted quinoxaline and 3‐(4‐fluorophenyl)‐2‐[4‐(4‐hydroxyphenoxy)phenyl]‐6‐substituted quinoxaline, were prepared and polymerized to afford phenylquinoxaline oligomers. High‐molecular‐weight polymers could not be obtained because of the formation of cyclic oligomers. On the basis of matrix‐assisted laser desorption/ionization time‐of‐flight analysis and molecular modeling results, the formation of a cyclic dimer could be a favorable process resulting in low‐molecular‐weight oligomers. They were completely soluble and amorphous, with glass‐transition temperatures varying from 165 to 266 °C, and they had thermooxidative stability, with samples displaying 5% weight loss temperatures of 419–511 °C in nitrogen. The thermal properties of the monomers and resultant polymers dramatically depended on the polarity of the substituents. The monomers and resultant oligomers displayed high fluorescence in tetrahydrofuran solutions and N ‐methyl‐2‐pyrrolidinone solutions, respectively. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6465–6479, 2005
Therapeutic efficacy and dose‐limiting toxicity of auger‐electron vs. beta emitters in radioimmunotherapy with internalizing antibodies: Evaluation of 125I‐ vs. 131I‐labeled CO17‐1A in a human colorectal cancer model (1998)

Recent clinical results suggest that higher anti-tumor efficacy may be achieved with internalizing monoclonal antibodies (MAbs) at lower toxicity when labeled with Auger-electron, as compared to conventional β-emitters. The aim of our study was to compare the toxicity and anti-tumor efficacy of the 125I-labeled internalizing MAb, CO17-1A, with its 131I-labeled form in a human colon cancer model in nude mice. Biodistribution studies were performed in nude mice bearing s.c. human colon cancer xenografts. For therapy, the mice were injected either with unlabeled 125I- or 131I-labeled CO17-1A at equitoxic doses. Control groups were left untreated, were given a radiolabeled isotype-matched irrelevant antibody or a tumor-specific, but noninternalizing antibody. The maximum tolerated activities (MTD) of 131I- and 125I-CO17-1A without artificial support were 300 μCi and 3 mCi, respectively. Myelotoxicity was dose-limiting; bone marrow transplantation allowed for an increase of the MTD to 400 μCi of 131I-17-1A, whereas the MTD of 125I-17-1A with bone marrow support had not been reached at 5 mCi. Whereas no significant therapeutic effects were seen with unlabeled CO17-1A, tumor growth was retarded with 131I-CO17-1A. With the 125I-label, however, therapeutic results were clearly superior. In contrast, no significant difference was observed in the therapeutic efficacy of the 131I- vs. 125I-labeled, noninternalizing antibodies. Our data indicate a superiority of Auger-electron emitters, such as 125I, as compared to therapy with conventional β-emitters with internalizing antibodies. The lower toxicity of Auger emitters may be due to the short path length of their low-energy electrons, which can reach the nuclear DNA only if the antibody is internalized (as is the case in antigen-expressing tumor tissue, but not in the stem cells of the red marrow). Int. J. Cancer 76:738–748, 1998.© 1998 Wiley-Liss, Inc.
Networked Swept-Source Raman Sensors (2021)

Raman spectroscopy with large-area, spectrally-selective detectors and tunable lasers enables distributed chemical sensing where excitation light can be delivered via optical datacom networks. Distributed sensing over 100’s of meters and multiple locations is demonstrated.
CPG3D: Cross-Modal Priors Guided 3D Object Reconstruction (2023)

Three-dimensional reconstruction is a multimedia technology widely used in computer-aided modeling and 3D animation. Nevertheless, it is still hard for reconstruction methods to overcome the 3D geometry missing and the object occlusion in the single-view images. In this article, we propose a novel method (CPG3D) for reconstructing high-quality 3D shapes from a single image under the guidance of prior knowledge. Using the single-view image as the query, prior knowledge is collected from public 3D datasets, which can compensate for missing 3D geometries and assist the 3D reconstruction network to high fidelity results. Our method consists of three parts: 1) Cross-modal 3D shape retrieval module: This part retrieves related 3D shapes based on 2D images. Here, we apply the pre-trained model to guarantee the correlation between the retrieved 3D shape and the input image. 2) Multimodal information fusion module: We propose a multimodal attention mechanism to handle the information fusing of 2D visual and 3D structural information; 3) Three-dimensional reconstruction module: We propose a novel encoder-decoder network for 3D shape reconstruction. Specifically, we employ the skip connection operation to link the target image's visual information with the 3D model's structural information to enhance the prediction of 3D details. During training, we employ two carefully designed loss functions to lead the multimodal learning to obtain proper modal features. On the ShapeNet and Pix3D datasets, the final experimental results reveal that our method notably increases reconstruction quality and outperforms SOTA methods.
ChemInform Abstract: Organic Reactions Mediated by Tetrachlorosilane (2014)

Abstract Review: [107 refs.
Abstract 3302: Antisense oligonucleotide depletion of the mitotic kinesin Eg5 by direct delivery to the brain could be a useful strategy for treating glioma tumors. (2013)

Abstract To date, all approved chemotherapeutic agents which target the mitotic cell division interfere with spindle microtubule dynamics, leading to mitotic arrest and apoptosis. While effective, these drugs are subject to resistance mechanisms and they are also associated with a variety of side effects, including neurotoxicity. Their use in treating nervous system tumors is therefore not warranted. One strategy to target mitosis, without damaging microtubules in non-dividing neurons, would be to inhibit key mitotic components, such as the mitotic kinesin Eg5, which is required for establishing a normal bipolar mitotic spindle. We have shown that glioblastoma cells depleted for Eg5 arrest in the next mitosis. After a prolonged arrest, they may slip out and become multinucleated, which will likely prevent further successful divisions or they may go into apoptosis. Further, mitotic arrest and induction of apoptosis in Eg5 depleted glioblastoma cells occur independent of p53, Rb-signalling and the PI3K-pathway suggesting that Eg5 is a potential therapeutic target for glioblastoma patients with different underlying genetic abnormalities We have also tested the clinical feasibility of using a cell cycle targeting antisense oligonucleotide based therapy delivered directly to the central nervous system (CNS) as a novel treatment for glioblastoma tumors. This work has demonstrated that intraventricular administration of ASOs can efficiently target cells in the CNS and be delivered to glioma-initiating neural stem cells transplanted into the cortex of naïve mice as well as to glioblastoma tumors in a genetically predisposed mouse model. This strategy is therefore a potential route of administration for treating glioblastoma tumors which originate in the CNS. Direct targeting of mitotic components in the brain should have a limited toxicity to non-cycling neurons and as a benefit, as long as the blood-brain barrier is intact direct CNS delivery should have minimal dose-limiting toxicity outside of the CNS. Ongoing studies will determine the effect of Eg5 inhibition on glioblastoma growth in vivo. Citation Format: Cecilia C. Krona, Jihane Boubaker, Dinorah Friedmann-Morvinski, Alex Wong, Melissa McAlonis-Downes, Erich Koller, Aneeza S. Kim, Gene Hung, Frank Rigo, Seung Chun, Benjamin Vitre, Frank Bennett, Inder Verma, Don W. Cleveland. Antisense oligonucleotide depletion of the mitotic kinesin Eg5 by direct delivery to the brain could be a useful strategy for treating glioma tumors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3302. doi:10.1158/1538-7445.AM2013-3302
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts (2009)

We report the extended database and data mining resources newly released in the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes and transcripts, and consists of two main views and six sub-databases. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs. 'Navigation search' is an extended search system that enables complicated searches by combining 16 different search options. HEAT is a data mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. H-InvDB now has web service APIs of SOAP and REST to allow the use of H-InvDB data in programs, providing the users extended data accessibility.
Distributed Control of Autonomous Swarms by Using Parallel Simulated Annealing Algorithm (2006)

In early work of the authors, it was shown that Gibbs sampler based sequential annealing algorithm could be used to achieve self-organization in swarm vehicles based only on local information. However, long travelling time presents barriers to implement the algorithm in practice. In this paper we study a popular acceleration approach, the parallel annealing algorithm, and its convergence properties. We first study the convergence and equilibrium properties of the synchronous parallel sampling algorithm. A special example based on a battle field scenario is then studied. Sufficient conditions that the synchronous algorithm leads to desired configurations (global minimizers) are derived. While the synchronized algorithm reduces travelling time, it also raises delay and communication cost dramatically, in order to synchronize moves of a large group of vehicles. An asynchronous version of the parallel sampling algorithm is then proposed to solve the problem. Convergence properties of the asynchronous algorithm are also investigated
Ag and Si particles sintering technology for SiC power device (2019)

Ag sintering technology is one of the best candidates for SiC die attach because of good mechanical and thermal properties at high temperature. However cracks propagates into SiC dies or DBC substrates at thermal fatigue test at more than 200 °C because Ag is too hard for die attach materials and 10ppm/ °C of CTE mismatch between SiC dies and Ag layers is too big. Therefore a development of low CTE sinterng materials is dispensable for SiC power device operated at high temperature. In this study, a method to coat Si particles with Ag layer at room and its sintering properties are researched. Si particles with $\varphi 30\mu m$ and Ag flakes with $\varphi 5\mu m$ are prepared and Si-20,40 and 60 vol%Ag particles are produced by utilizing high-speed 3D motion of a patented 3D Ball Millproducted by Nagao System Inc.. It is revealed that their Si particles after the ball milling are almost covered by Ag layer except for Si-20vol.%Ag particles and furthermore the coated particles are crushed to 5pm by SEM observation. Their Si-Ag particles are mixed with a solvent to formulate into pastes. These Si-Ag pastes are printed onto Ag electroplated Cu plats, and then the bonding experiments are carried out at temperatures of250°C for 60 min without pressure at air atmosphere. It is revealed that some Ag layers are jointed on the surface of Si particles and others are delaminated by FE-SEM observation. Si particles are connected via Ag layers on their surface. The strength between Ag layer and Si particles must be improved in order to adopt Ag-Si sintering paste to die-attach technology..
On new current signatures and adaptive test technique combination (2004)

This paper proposes new current signatures for test purposes. It estimates their capabilities in the detection of additional current caused by weak resistive active and passive defects, when used separately and in combination with other current-based test techniques. Estimation results based in part on actual I/sub DDQ/ measurements show that current-based test technique combinations allow reliable detection of smaller current deltas and offsets. The extra margin provided by these combinations can also be used to reduce the yield losses associated to current-based test techniques by applying these test techniques more conservatively while keeping the same detection capabilities. The cost of adding a second set of I/sub DDQ/ test patterns can be greatly reduced if part of an adaptive test strategy.
Studio dei meccanismi molecolari della citoprotezione indotta dal forskolin (2011)

I dati quantitativi ottenuti, da saggi con forskolino dimostrano una stimolazione lineare della sintesi proteica rispetto alle concentrazioni utilizzate. Il fattore di trascrizione elF4B è risultato avere un ruolo chiave nell’inizio della biosintesi proteica nelle cellule umane in coltura trattate (HEK293) e quindi un possibile ruolo neuroprotettivo da valutare con successive sperimentazioni.
Geographical and Energy Aware Routing: a recursive data dissemination protocol for wireless sensor networks (2002)

Future sensor networks will be composed of a large number of densely deployed sensors/actuators. A key feature of such networks is that their nodes are untethered and unattended. Consequently, energy efficiency is an important design consideration for these networks. Motivated by the fact that sensor network queries may often be geographical, we design and evaluate an energy efficient routing algorithm that propagates a query to the appropriate geographical region, without flooding. The proposed Geographic and Energy Aware Routing (GEAR) algorithm uses energy aware neighbor selection to route a packet towards the target region and Recursive Geographic Forwarding or Restricted Flooding algorithm to disseminate the packet inside the destination region. We evaluate the GEAR protocol using simulation. We find that, especially for non-uniform traffic distribution, GEAR exhibits noticeably longer network lifetime than non-energyaware geographic routing algorithms. 1
Characterization of Two Transposon Mutants from Haemophilus influenzae Type b with Altered Lipooligosaccharide Biosynthesis (1996)

Two isogenic mutants of Haemophilus influenzae type b (Hib) strain A2 were prepared by random m-Tn3(Cm) insertions into the 7.4-kb lsg (lipooligosaccharide synthesis genes) region of Hib DNA, which consists of seven complete and one partial open reading frame (orfs). Compared to the parent A2 strain which produces a complex mixture of lipooligosaccharides (LOS), the mutant strains 281.25 and 276.4 produced only a few LOS species. The precise locations of transposon insertions into the lsg loci of these mutants were determined (base 3546 in orf 4 for strain 281.25 and base 4402 in orf 5 for strain 276.4), and the effects of these mutations on LOS biosynthesis and epitope expression were evaluated. When the O-deacylated LOS were analyzed by mass spectrometry, both strains contained major LOS species of M(r) 2601, 2439, and 2277, which consisted of a common heptose trisaccharide core structure [Hep3(PEA)Kdo(P)-lipid A, where Hep is L-glycero-D-manno-heptose, Kdo is 3-deoxy-D-manno-octulosonic acid, and PEA is phosphoethanolamine] and four, three, or two hexoses, respectively. These species represent the smallest components of the wild-type LOS mixture. The major LOS oligosaccharide obtained from the strain 281.25 by mild acid hydrolysis was dephosphorylated and shown by composition analysis, methylation analysis, mass spectrometry, and 2D NMR studies to be a triantennary structure consisting of a heptose trisaccharide core with two glucose disaccharide branches: Hep alpha 1 --> (Glc beta 1 --> 4Glc alpha 1 --> 3) 2Hep alpha 1 --> (Glc beta 1 --> 4Glc beta 1 --> 4)3Hep alpha 1 --> anhydroKdo. Unlike the parent A2 strain, mutant strain 281.25 cannot add galactoses to the branches of this octasaccharide. Strain 276.4 is similarly deficient, except that it can still utilize a minor biosynthetic pathway leading to the addition of sialyl-N-acetyllactosamine.