gebhart/patrepeval huggingface dataset:
Supervoxel-Based Segmentation of Mitochondria in EM Image Stacks With Learned Shape Features (2011)

It is becoming increasingly clear that mitochondria play an important role in neural function. Recent studies show mitochondrial morphology to be crucial to cellular physiology and synaptic function and a link between mitochondrial defects and neuro-degenerative diseases is strongly suspected. Electron microscopy (EM), with its very high resolution in all three directions, is one of the key tools to look more closely into these issues but the huge amounts of data it produces make automated analysis necessary. State-of-the-art computer vision algorithms designed to operate on natural 2-D images tend to perform poorly when applied to EM data for a number of reasons. First, the sheer size of a typical EM volume renders most modern segmentation schemes intractable. Furthermore, most approaches ignore important shape cues, relying only on local statistics that easily become confused when confronted with noise and textures inherent in the data. Finally, the conventional assumption that strong image gradients always correspond to object boundaries is violated by the clutter of distracting membranes. In this work, we propose an automated graph partitioning scheme that addresses these issues. It reduces the computational complexity by operating on supervoxels instead of voxels, incorporates shape features capable of describing the 3-D shape of the target objects, and learns to recognize the distinctive appearance of true boundaries. Our experiments demonstrate that our approach is able to segment mitochondria at a performance level close to that of a human annotator, and outperforms a state-of-the-art 3-D segmentation technique.
PON Coexistence Interference Avoidance with Cross-Layer Design (2022)

We propose a dynamic bandwidth allocation (DBA) mechanism with cross-layer design for multiple PON coexistence. Interfering ONUs are scheduled outside transmission timeslots of possible victim ONUs. Simulation results show salient performance in interference avoidance.
The Role of Cell-Free Plasma DNA in Patients with Cardiorenal Syndrome Type 1 (2021)

Our study explores the premise of cfDNA as a marker for apoptosis and inflammation in CRS type 1 patients. cfDNA could potentially serve as an index for noninvasive monitoring of tissue damage and apoptosis in patients with AKI induced by AHF.
Projected Multi-Agent Consensus Equilibrium (PMACE) with Application to Ptychography (2023)

Multi-Agent Consensus Equilibrium (MACE) formulates an inverse imaging problem as a balance among multiple update agents such as data-fitting terms and denoisers. However, each such agent operates on a separate copy of the full image, leading to redundant memory use and slow convergence when each agent affects only a small subset of the full image. In this paper, we extend MACE to Projected Multi-Agent Consensus Equilibrium (PMACE), in which each agent updates only a projected component of the full image, thus greatly reducing memory use for some applications.We describe PMACE in terms of an equilibrium problem and an equivalent fixed point problem and show that in most cases the PMACE equilibrium is not the solution of an optimization problem. To demonstrate the value of PMACE, we apply it to the problem of ptychography, in which a sample is reconstructed from the diffraction patterns resulting from coherent X-ray illumination at multiple overlapping spots. In our PMACE formulation, each spot corresponds to a separate data-fitting agent, with the final solution found as an equilibrium among all the agents. Our results demonstrate that the PMACE reconstruction algorithm generates more accurate reconstructions at a lower computational cost than existing ptychography algorithms when the spots are sparsely sampled.
Finding ECM-friendly curves through a study of Galois properties (2013)

We prove some divisibility properties of the cardinality of elliptic curve groups modulo primes. These proofs explain the good behavior of certain parameters when using Montgomery or Edwards curves in the setting of the elliptic curve method (ECM) for integer factorization. The ideas behind the proofs help us to find new infinite families of elliptic curves with good division properties increasing the success probability of ECM.
Model Order Reduction for Rotating Electrical Machines (2017)

The simulation of electric rotating machines is both computationally expensive and memory intensive. To overcome these costs, model order reduction techniques can be applied. The focus of this contribution is especially on machines that contain non-symmetric components. These are usually introduced during the mass production process and are modeled by small perturbations in the geometry (e.g., eccentricity) or the material parameters. While model order reduction for symmetric machines is clear and does not need special treatment, the non-symmetric setting adds additional challenges. An adaptive strategy based on proper orthogonal decomposition is developed to overcome these difficulties. Equipped with an a posteriori error estimator the obtained solution is certified. Numerical examples are presented to demonstrate the effectiveness of the proposed method.
Crocin, a natural molecule with potentially beneficial effects against skin ageing (2018)

Results could designate this molecule as a promising skin ageing prevention cosmetic agent. Of note, some of these effects could be mediated by protein O-glycosylation and interaction of crocin with osidic receptors of keratinocytes.
Cold Shock Response of Leuconostoc mesenteroides SY1 Isolated from Kimchi (2005)

Low-temperature adaptation and cryoprotection were studied in Leuconostoc mesenteroides SY1, a strain isolated from Kimchi. L. mesenteroides SY1 cells grown in exponential growth phase at 30C were exposed to 15°C, 10°C, and 5°C for 2, 4, and 6 h, respectively, and then frozen at -70°C for 24 h. Survival ratio was measured after the cells were thawed. The freezing-thawing cycles were repeated four times. Preadapted cells survived better than non-adapted control cells, and the highest survival ratio (96%) was observed for cells preadapted for 2 h at 5°C, whereas control cells showed only 22%. The 2D gel showed that two proteins (spots A and B) were induced in cells preadapted at lower temperatures. Spots A and B have the same molecular weight (7 kDa), but the pi was 4.6 for spot A and 4.3 for spot B. The first 29 and 15 amino acid sequences from spots A and B were determined, and they were identical, except for one amino acid. A csp gene was cloned, and nucleotide sequencing confirmed that the gene encoded spot A cold shock protein.
Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA compete for the same binding surface (2008)

ssDNA-binding proteins are key components of the machinery that mediates replication, recombination, and repair. Prokaryotic ssDNA-binding proteins share a conserved DNA-binding fold and an acidic C-terminal tail. It has been proposed that in the absence of ssDNA, the C-terminal tail contacts the ssDNA-binding cleft, therefore predicting that the binding of ssDNA and the C-terminal tail is mutually exclusive. Using chemical cross-linking, competition studies, and NMR chemical-shift mapping, we demonstrate that: (i) the C-terminal peptide of the gene 2.5 protein cross-links to the core of the protein only in the absence of ssDNA, (ii) the cross-linked species fails to bind to ssDNA, and (iii) a C-terminal peptide and ssDNA bind to the same overall surface of the protein. We propose that the protection of the DNA-binding cleft by the electrostatic shield of the C-terminal tail observed in prokaryotic ssDNA-binding proteins, ribosomal proteins, and high-mobility group proteins is an evolutionarily conserved mechanism. This mechanism prevents random binding of charged molecules to the nucleic acid-binding pocket and coordinates nucleic acid-protein and protein-protein interactions.
Ready routes to key myo-inositol component of GPIs employing microbial arene oxidation or Ferrier reaction (1998)

Z. J. Jia, L. Olsson and B. Fraser-Reid, J. Chem. Soc., Perkin Trans. 1, 1998, 631 DOI: 10.1039/A800282G
Self-catalyzed growth of Ga(Al)As nanowires for solar cells on silicon (2015)

poster
Uncertainty of PIV/PTV based pressure, using velocity uncertainty (2021)

Pressure reconstruction from velocity measurements using particle image velocimetry (PIV) and particle tracking velocimetry (PTV) has drawn significant attention as it can provide instantaneous pressure fields without altering the flow. Previous studies have found that the accuracy of the calcualted pressure field depends on several factors including the accuarcy of the velocity measurement, the spatiotemporal resolutions, the method for calculating pressure-gradient, the algorithm for pressure-gradient integration, the pressure boundary condition, etc. Therefore, it is critical and challenging to quantify the uncertainty of the reconstructed pressure field. The recent development of the uncertainty quantification algorithms for PIV and PTV allows for the local and instantaneous uncertainty estimation of velocity measurement, which can be used to infer the pressure uncertainty. In this study, we introduce a framework that propagates the standard velocity uncertainty defined as the standard deviation of the velocity error distribution through the pressure reconstruction process to obtain the uncertainty of the pressure field. The uncertainty propagations through the calculation of the pressure-gradient and the pressure-gradient integration were modeled as linear transformations, which can reproduce the effects of the spatiotemporal resolutions, the numerical schemes, the integration algorithms, and the pressure boundary condition on the accuracy of the resulting pressure fields. The proposed uncertainty estimation approach also considers the effect of the spatiotemporal and componentwise correlation of the velocity errors in common PIV/PTV measurements on the pressure uncertainty.
High-Throughput Activity Assay for Screening Inhibitors of the SARS-CoV-2 Mac1 Macrodomain (2021)

Macrodomains are a class of conserved ADP-ribosylhydrolases expressed by viruses of pandemic concern, including coronaviruses and alphaviruses. Viral macrodomains are critical for replication and virus-induced pathogenesis; therefore, these enzymes are a promising target for antiviral therapy. However, no potent or selective viral macrodomain inhibitors currently exist, in part due to the lack of a high-throughput assay for this class of enzymes. Here we developed a high-throughput ADP-ribosylhydrolase assay using the SARS-CoV-2 macrodomain Mac1. We performed a pilot screen that identified dasatinib and dihydralazine as ADP-ribosylhydrolase inhibitors. Importantly, dasatinib inhibits SARS-CoV-2 and MERS-CoV Mac1 but not the closest human homologue, MacroD2. Our study demonstrates the feasibility of identifying selective inhibitors based on ADP-ribosylhydrolase activity, paving the way for the screening of large compound libraries to identify improved macrodomain inhibitors and to explore their potential as antiviral therapies for SARS-CoV-2 and future viral threats.
The Induction of Cytolytic T Lymphocytes with Purified Plasma Membranes (1978)

Subcellular fractions were demonstrated to be effective in stimulating primary and secondary allogeneic CTL responses. 5' nucleotidase activity was used to assess purification of plasma membranes and stimulating activity was found to co-purify with the plasma membrane fraction of the cell. Electron micrographs of these purified plasma membranes showed the majority of the material to be in the form of vesicles of relatively heterogeneous size. The cytolytic T lymphocytes generated by incubation with purified plasma membranes demonstrated immunologic specificity.
The future of software engineering (2010)

This paper argues that the essential point of software engineering is not to (semi-automatically) improve the quality of software, but rather to help human problem solvers to improve the quality of software. This paper argues that this essential point of software engineering research has been forgotten, and that without regaining that perspective, significant progress is not likely.
Tuning structural parameters for the optimization of drug delivery performance of cyclodextrin-based nanosponges (2016)

In light of the recent development of new soft materials, nanostructured self-assembled systems have attracted attention in a variety of technological fields of high social impact. Cyclodextrin nanosponges (CDNS) represent a new and highly versatile class of cross-linked cyclodextrin (CD)-based nanoporous polymers. Their intriguing properties, including safety, biodegradability, negligible toxicity, marked swelling behavior, superior inclusion capability with respect to native CD, are the bases for potential for applications in drug delivery, tissue engineering and regenerative medicine. Areas covered: We report on the state-of-art concerning a detailed characterization of structural and dynamical features of CDNS explored by the combined use of different and complementary techniques, such as Fourier transform infrared absorption in attenuated total reflectance geometry (FTIR-ATR) and Raman spectroscopies, and high resolution magic angle spinning (HR-MAS) NMR spectroscopy. The ambitious objective is to furnish an exhaustive survey of the role played by hydrophobic and hydrophilic groups within the cross-linked network, in dry and swollen states, in determining the macroscopic functional features of CDNS. Expert opinion: The reported results may significantly contribute in the rational design and optimization of new stimuli-responsive systems exhibiting tunable inclusion/release properties, adapted to the therapeutic demands of pathology.
Color from colorless nanomaterials: Bragg reflectors made of nanoparticles (2009)

We report herein on a facile and reproducible approach to prepare mesoporous nanoparticle-based distributed Bragg reflectors (DBRs) from a diverse group of metal oxide nanoparticles including SiO2, TiO2, SnO2, and Sb:SnO2. The films prepared, regardless of the composition, and following dispersion and process engineering, demonstrate uniform color and high optical quality over large areas. Not only do the prepared NP DBRs possess high reflectivity but also significant mesoporosity, which opens up the opportunity for introduction of a variety of materials into the pores creating new opportunities in optical and optoelectronic devices. In addition, what also must be highlighted are the added-value properties to the above characteristic of the individual NP materials comprising the DBR such as the electrical conductivity and optical transparency of ATO or the photoconductivity of SnO2, which enable new opportunities in a broad range of fields.
Reactivity patterns of nitrogen electrophiles with certain charge-delocalized six-membered chelate rings (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactivity patterns of nitrogen electrophiles with certain charge-delocalized six-membered chelate ringsChristian J. Hipp and Daryle H. BuschCite this: Inorg. Chem. 1973, 12, 4, 894–896Publication Date (Print):April 1, 1973Publication History Published online1 May 2002Published inissue 1 April 1973https://pubs.acs.org/doi/10.1021/ic50122a037https://doi.org/10.1021/ic50122a037research-articleACS PublicationsRequest reuse permissionsArticle Views74Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Persistence of Post-COVID Lung Parenchymal Abnormalities during the Three-Month Follow-Up (2021)

This is the first study from Southeast Asia that identified post-COVID lung parenchymal abnormalities in patients who had no pre-existing lung disease highlighting the importance of timely recognition and treatment of this entity that might lead to fatal outcome.
Pushing the envelope of pervasive access (2005)

This paper presents the design and implementation of the Puma middleware system. Puma enables pervasive access to Web applications from a wide range of clients. In addition to traditional, browser-equipped client devices such as laptops and PDAs, Puma supports the use of peer collaboration tools such as instant messengers, SMS devices, email clients and telephones. While those collaboration tools were initially intended for free-form interaction between people, Puma leverages them for structured interaction between people and computers in order to offer more flexibility, convenience and intimacy to end users. In addition to user-initiated, or pull-based, interactions, Puma allows an application to proactively push an interaction to a user, in a manner sensitive to the application's needs and the user's current context. Architecturally, Puma employs various Modality Bots to mediate between application servers and heterogeneous clients. The Modality Bots also serve as the initial point of contact for application-initiated interactions. As an experiment, Puma has been used to mobilize the human tasks application, which supports the creation, processing, and management of the manual steps in business processes.
An Investigation of Form Compensation in Fabricating Microlens Arrays by Ultra-Precision Fast-Tool-Servo Technology (2006)

Microlens arrays are widely used as critical components in a large number of photonics and telecommunication products. The increasing demand for high-tech products provides an expanding room for the development of the micro-fabrication technology. This study presents a tool compensation for correcting the form error of fabricated microlenses in ultra-precision machining with fast-tool-servo (FTS) system. After presentation of optimal cutting conditions deduced on the basis of cutting experiments of microlens arrays, a tool radius compensation method will be proposed and evaluated in this paper. This methodology makes use of form measurement data from a Form Talysurf system to modify the C program employed in the software of ultra-precision machining FTS system – SOP. The form error was successfully reduced after implementation of tool compensation.
Evaluation of NH2-Terminus Gastrins in Gastrinoma Syndrome* (1986)

Forty-six patients with the gastrinoma syndrome were divided into 2 categories: 1) benign sporadic gastrinoma (n = 30), and 2) gastrinoma with metastases to liver (n = 16). Thirteen of the 46 patients had multiple endocrine neoplasia type I syndrome. Serum gastrin levels in patients fasted overnight were determined by RIA using antisera directed toward the NH2- and COOH-terminals of heptadecapeptide gastrin (G17) and the NH2-terminus of the triacontatetrapeptide (G34). These results were compared with findings in 50 normal subjects. In the normal subjects, the mean COOH-terminal gastrin-17 level was higher [65 +/- 8 (+/- SEM) pg/ml] than the NH2-terminal gastrin-17 level (11 +/- 0.2 pg/ml) and lower than the NH2-terminal gastrin-34 level (134 +/- 20 pg/ml). The levels of NH2-terminal gastrin-17 were higher in patients with metastatic disease than in those with benign gastrinoma, whereas the COOH-terminal gastrin-17 and the NH2-terminal gastrin-34 levels were similarly high in both groups. The mean ratio of NH2-terminal gastrin-17 to COOH-terminal gastrin-17 was less than 1 in normal subjects (0.22 +/- 0.02) and benign gastrinoma patients (0.2 +/- 0.04), and it was 2.2 +/- 0.41 in the patients with metastatic gastrinoma. An NH2 to COOH gastrin-17 ratio greater than 1 was found in 13 of 16 patients with metastatic gastrinoma, but in none of the patients with benign gastrinoma or normal subjects. Similar results were found in multiple endocrine neoplasia type I patients with benign and metastatic disease. A high NH2 to COOH gastrin-17 ratio is suggestive of metastatic gastrinoma. In 4 patients with metastatic gastrinoma, the NH2 to COOH gastrin-17 ratio fell in parallel with the response to chemotherapy.
Plasmonic enhancement of electroluminescence (2018)

Here plasmonic effect specifically on electroluminescence (EL) is studied in terms of radiative and nonradiative decay rates for a dipole near a metal spherical nanoparticle (NP). Contribution from scattering is taken into account and is shown to play a decisive role in EL enhancement owing to pronounced size-dependent radiative decay enhancement and weak size effect on non-radiative counterpart. Unlike photoluminescence where local incident field factor mainly determines the enhancement possibility and level, EL enhancement is only possible by means of quantum yield rise, EL enhancement being feasible only for an intrinsic quantum yield Q0 &amp;lt; 1. The resulting plasmonic effect is independent of intrinsic emitter lifetime but is exclusively defined by the value of Q0, emission spectrum, NP diameter and emitter-metal spacing. For 0.1&amp;lt; Q0 &amp;lt; 0.25, Ag nanoparticles are shown to enhance LED/OLED intensity by several times over the whole visible whereas Au particles feature lower effect within the red-orange range only. Independently of positive effect on quantum yield, metal nanoparticles embedded in an electroluminescent device will improve its efficiency at high currents owing to enhanced overall recombination rate which will diminish manifestation of Auger processes. The latter are believed to be responsible for the known undesirable efficiency droop in semiconductor commercial quantum well based LEDs at higher current. For the same reason plasmonics can diminish quantum dot photodegradation from Auger process induced non-radiative recombination and photoionization thus opening a way to avoid negative Auger effects in emerging colloidal semiconductor LEDs.
Absolute Konfiguration des Cancerostaticums S()-Isophosphamid (1980)

Struktur/Wirkung-Beziehungen bei chiralen Arzneimitteln lassen sich nur dann untersuchen, wenn die absolute Konfiguration bekannt ist. Die linksdrehende Form des Cancerostaticums Isophosphamid hat nach der Röntgen-Strukturanalyse S-Konfiguration.