gebhart/patrepeval huggingface dataset:
Challenges and perspectives of metaproteomic data analysis (2017)

In nature microorganisms live in complex microbial communities. Comprehensive taxonomic and functional knowledge about microbial communities supports medical and technical application such as fecal diagnostics as well as operation of biogas plants or waste water treatment plants. Furthermore, microbial communities are crucial for the global carbon and nitrogen cycle in soil and in the ocean. Among the methods available for investigation of microbial communities, metaproteomics can approximate the activity of microorganisms by investigating the protein content of a sample. Although metaproteomics is a very powerful method, issues within the bioinformatic evaluation impede its success. In particular, construction of databases for protein identification, grouping of redundant proteins as well as taxonomic and functional annotation pose big challenges. Furthermore, growing amounts of data within a metaproteomics study require dedicated algorithms and software. This review summarizes recent metaproteomics software and addresses the introduced issues in detail.
Generalized fuzzy c-means clustering strategies using L/sub p/ norm distances (2000)

Fuzzy c-means (FCM) is a useful clustering technique. Modifications of FCM using L/sub 1/ norm distances increase robustness to outliers. Object and relational data versions of FCM clustering are defined for the more general case where the L/sub p/ norm (p/spl ges/1) or semi-norm (0<p<1) is used as the measure of dissimilarity. We give simple (though computationally intensive) alternating optimization schemes for all object data cases of p>0 in order to facilitate the empirical examination of the object data models. Both object and relational approaches are included in a numerical study.
Multiresidue method for the analysis of multiclass pesticides in agricultural products by gas chromatography-tandem mass spectrometry (2002)

A multiresidue method is described for determining 55 organophosphorus and organochlorinated compounds and pyrethroids commonly used in crop protection. Pesticide residues are extracted from samples with a mixture of ethyl acetate and sodium sulfate, obtaining a final preconcentration of I mg sample (ml extract)(-1). No additional clean-up steps are necessary. Analysis is performed by gas chromatography by using a combination of positive chemical ionisation (PCI) and electron impact (EI) ionisation modes and tandem mass spectrometry (GC-PCI/EI-MS-MS). Good sensitivity and selectivity of the method are obtained with limits of detection (LODs) ranging from 0.07 to 4.21 microg kg(-1) in all the cases, except for methamidophos, permethrin, cypermethrin and difenconazol. Average recoveries between 52 and 114% are obtained and good linearity is observed in the studied ranges (r > or = 0.994). The RSD values are < or = 29% in all the cases. The method has been applied to the analysis of 178 vegetable samples, as a part of the monitoring programme of the Association of Producers and Exporters of Fruits and Vegetables of Almería (COEXPHAL) and quality control systems applied during the assays have demonstrated a good performance and stability with time.
Asynchronous asymmetrical write termination (AAWT) for a low power STT-MRAM (2014)

Spin Transfer Torque (STT) memory is an emerging and promising non-volatile storage technology. However, the high write current is still a major challenge which leads to a huge power consumption of the memory. Due to an inherent torque asymmetry of the Magnetic Tunnel Junction (MTJ) device employed in STT memories, the switching time between parallel to anti-parallel and anti-parallel to parallel magnetization is significantly different. Hence, the write latencies for writing `0' and `1' are also considerably different. In this paper, we propose a technique called Asynchronous Asymmetrical Write Termination (AAWT) which utilizes this asymmetrical behavior to terminate the write operations asynchronously and as a result significantly reduces the write power consumption. Furthermore, we present two different AAWT implementations to determine the actual write termination times. The first one makes use of a clock signal and the second one employs a self-timing approach based on an internal delay element. As shown by our experimental results, AAWT can reduce the total write energy by 30% in average with a negligible area overhead.
Automated Search for Causal Relations: Theory and Practice (2018)

Department of Philosophy technical report
Cancer immunoediting: antigens, mechanisms, and implications to cancer immunotherapy (2013)

Accumulated data from animal models and human cancer patients strongly support the concept that the immune system can identify and control nascent tumor cells in a process called cancer immunosurveillance. In addition, the immune system can also promote tumor progression through chronic inflammation, immunoselection of poorly immunogenic variants, and suppressing antitumor immunity. Together, the dual host-protective and tumor-promoting actions of immunity are referred to as cancer immunoediting. The current framework of cancer immunoediting is a dynamic process comprised of three distinct phases: elimination, equilibrium, and escape. Recently, we demonstrated that immunoselection by CD8(+) T cells of tumor variants lacking strong tumor-specific antigens represents one mechanism by which cancer cells escape tumor immunity and points toward the future of personalized cancer therapy.
Limited proteolysis of human low-molecular-mass kininogen by tissue kallikrein. Isolation and characterization of the heavy and the light chains (1985)

The limited proteolysis of human low-molecular-mass kininogen by kallikrein from tissue sources has been studied. Porcine pancreatic kallikrein applied in catalytic amounts split the kininogen molecule (apparent mass 68 kDa) with the release of lysyl-bradykinin (1 kDa). This generated a nicked kininogen molecule with a heavy chain and light chain interconnected via disulfide bridging. Following reductive cleavage of the disulfide bonds, the heavy chain of apparent mass 62 kDa was isolated by preparative sodium dodecyl sulfate electrophoresis, and the light chain of 5 kDa by reversed-phase high-performance liquid chromatography. The light chain was found to be composed of 38 amino acids with a single half-cystine residue. Amino-terminal sequence analysis revealed that the light chain is derived from the carboxy terminus of the kininogen molecule [Lottspeich et al. (1984) Eur. J. Biochem. 142, 227-232]. Immunological characterization of the isolated L chain indicated that it harbours antigenic site(s) unique for low-Mr kininogen as well as sites common to high-Mr and low-Mr kininogen.
Abstract 2277: Anti-tumor effect of an apoptosis-targeting peptide-conjugated heparin derivative in breast cancer xenografts (2010)

Abstract Anti-tumor effect of an apoptosis-targeting peptide-conjugated heparin derivative in breast cancer xenografts. Sang Mun Bae1, Jong-Ho Kim1, Kai Wang1, Sungwoo Chung2, Youngro Byun2, Byung-Heon Lee1, In-San Kim1 and Rang-Woon Park1 1Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea 2College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Abstract Angiogenesis, the development of new blood vessels, is an essential process during tumor growth and metastasis. In the process of tumor angiogenesis, tumor cells secret various angiogenic growth factors such as vascular endothelial growth factor (VEGF), fibroblast growth factor basic (bFGF), platelet-derived endothelial cell growth factor (PDGF), insulin-like growth factors (IGF-1 and IGF-2) and scatter factors, which are potential targets for development of angiogenesis inhibitor and depend on heparin sulfate for their biological functions. Angiogenic endothelial cells are a central challenge for therapeutic intervention since its easy accessibility. Recently, researchers have sought to develop angiogenesis inhibitor for tumor therapy since tumor cannot grow without blood-supplied oxygen and nutrients. Heparan sulfate is located in cell surface and in the extracellular matrix and plays pivotal regulatory roles in growth factor. For this reason, heparin has been highlighted as a growth factor inhibitory therapeutic agent beyond its anticoagulant indications. In a previous study, we reported new angiogenesis inhibitor, low molecular weight heparin derivative (heparin-taurocholic acid conjugate; HT), showed delay of in vivo tumor growth in MDA-MB231 human breast cancer. In this study, we sought to design a new angiogenesis inhibitor targeting tumor tissue by introducing the actively targeting moiety, tumor homing peptide, to previously developed HT. Here, we evaluate the inhibitory effect of HT-Apopep by in vivo antitumor efficacy and show the body distribution image of HT-Apopep in tumor-bearing mice. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2277.
Genetically encoded light-up RNA aptamers and their applications for imaging and biosensing (2020)

Intracellular small ligands and biomacromolecules are playing crucial roles not only as executors but also as regulators. It is essential to develop tools to investigate their dynamics to interrogate their functions and reflect the cellular status. Light-up RNA aptamers are RNA sequences that can bind with their cognate nonfluorescent fluorogens and greatly activate their fluorescence. The emergence of genetically encoded light-up RNA aptamers has provided fascinating tools for studying intracellular small ligands and biomacromolecules owing to their high fluorescence activation degree and facile programmability. Here we review the burgeoning field of light-up RNA aptamers. We first briefly introduce light-up RNA aptamers with a focus on the photophysical properties of the fluorogens. Then design strategies of genetically encoded light-up RNA aptamer based sensors including turn-on, signal amplification and ratiometric rationales are emphasized.
Radioimmunotheranostic Pair Based on the Anti-HER2 Monoclonal Antibody: Influence of Chelating Agents and Radionuclides on Biological Properties (2021)

The oncogene HER2 is an important molecular target in oncology because it is associated with aggressive disease and the worst prognosis. The development of non-invasive imaging techniques and target therapies using monoclonal antibodies is a rapidly developing field. Thus, this work proposes the study of the radioimmunotheranostic pair, [<sup>111</sup>In]In-DTPA-trastuzumab and [<sup>177</sup>Lu]Lu-DOTA-trastuzumab, evaluating the influence of the chelating agents and radionuclides on the biological properties of the radioimmunoconjugates (RICs). The trastuzumab was immunoconjugated with the chelators DTPA and DOTA and radiolabeled with [<sup>111</sup>In]InCl<sub>3</sub> and [<sup>177</sup>Lu]LuCl<sub>3</sub>, respectively. The stability of the RICs was evaluated in serum, and the immunoreactive and internalization fractions were determined in SK-BR-3 breast cancer cells. The in vivo pharmacokinetics and dosimetry quantification and the ex vivo biodistribution were performed in normal and SK-BR-3 tumor-bearing mice. The data showed that there was no influence of the chelating agents and radionuclides on the immunoreactive and internalization fractions of RICs. In contrast, they influenced the stability of RICs in serum, as well as the pharmacokinetics, dosimetry and biodistribution profiles. Therefore, the results showed that the nature of the chelating agent and radionuclide could influence the biological properties of the radioimmunotheranostic pair.
Evaluating Corrosion Effects on the Stainless Steel Components of the SAVY-4000/Hagan Nuclear Material Storage Containers (2018)

Surveillance of vented, stainless-steel Hagan and SAVY-4000 storage containers with some plutonium materials has revealed evidence of corrosion inside the container. There are ~3000 items stored in Hagan containers and ~600 items currently stored in SAVY-4000 containers at TA -55. The Hagan is made of 304L steel, while the SAVY-4000 is made of 316L and should be less susceptible to corrosion. Given the relatively thin body wall of these containers (nominally 0.762 millimeters), it is essential to understand the effects of corrosion on the lifetime of the containers to ensure worker safety. Studies are being conducted on both container types to determine the relative susceptibility of the two containers to corrosion. This paper describes the potential cause of corrosion, the extent of corrosion, and types of corrosion observed, along with the results of accelerated aging experiments. The combined results of the surveillance and lifetime extension studies establish a technical basis for extending the design life of the stainless steel components of the SAVY-4000 container from 5 years to 15 years.
Syntheses of Siderophore–Drug Conjugates Using a Convergent Thiol–Maleimide System (2012)

Three siderophore-drug conjugates (sideromycins) were synthesized by preparation of a maleimide linked derivative of the siderophore desferrioxamine B and reacting the corresponding Ga(3+)-complex with freshly prepared thiol-containing antibiotics: loracarbef, ciprofloxacin and nadifloxacin. The conjugates and their synthetic precursors were tested against a broad panel of bacteria and were found to display Gram-positive selective, growth inhibitory activity (µM) indicating that this approach is suitable for the convergent synthesis and screening of novel sideromycins.
Plasma‐assisted heparin conjugation on electrospun poly(l‐lactide) fibrous scaffolds (2013)

Heparin conjugation on poly(L-lactide) fibrous scaffolds fabricated by electrospinning was accomplished by surface functionalization with amine (-NH2) groups using a sequential treatment with Ar-NH3 and H2 plasmas. The density of the incorporated -NH2 groups was determined by combining a chemical derivatization method with X-ray photoelectron spectroscopy. The time of Ar-NH3 plasma treatment significantly affected the N/C, -NH2 /N, and -NH2 /C fractions, whereas the plasma power, Ar-NH3 gas composition, and time of H2 plasma treatment only influenced the -NH2 /N and -NH2 /C fractions. Scaffold surface functionalization by -NH2 groups significantly increased the amount of covalently bonded heparin compared to a hydrolysis method. The function of immobilized heparin was confirmed by the decrease of platelet attachment during the exposure of the scaffolds to blood from Sprague-Dawley rats. In vitro experiments with bovine aorta endothelial cells demonstrated that heparin conjugation enhanced cell infiltration through the fibrous scaffolds, regardless of the amount of covalently immobilized heparin.
Effect of chloride ions on adsorption of cadmium from a landfill leachate (1991)

This study examines possible formation of neutral and negative complex ions between trace quantities of cadmium (Cd) and chloride ions (Cl − ). Experiments were first performed for the adsorption of Cd, from 2 to 10 mg/L, onto kaolinite in a soil suspension from a landfill leachate. A companion set of experiments was performed involving Cd, also from 2 to 10 mg/L, onto kaolinite in a soil suspension from a pure solution. By comparing the results from these two sets of experiments, it was apparent that there were constituents in the leachate which interfered with the adsorption of cadmium onto kaolinite. With the use of thermodynamic equilibrium calculations, it is seen that the chloride ions could account for some of the interference. Further experiments involving adsorption of Cd, from 5 to 80 μg/L, in the presence of Cl − , at 1000 mg/L, indicate that there is less adsorption of Cd than in an experiment involving [Formula: see text] at pH values from 4 to 5. This result is in agreement with the thermodynamic equilibrium calculations. Additional experimental results of adsorption of Cd at 80 μg/L for pH values of from 2 to 9 indicate that the apparent Cd – Cl complex formation interferes with the precipitation of Cd as Cd(OH) 2 and is in agreement with those obtained from predicted thermodynamic equilibrium. The study demonstrates that if accurate and precise predictions of Cd transport are required, detailed aqueous hydrogeochemistry studies may be important and necessary. Key words: adsorption, cadmium, leachate, speciation, cadmium–chloride complexes, thermodynamic equilibrium.
Ambient Nitrogen Reduction to Ammonia Electrocatalyzed by Bimetallic PdRu Porous Nanostructures (2018)

Electrochemical nitrogen fixation provides an attractive route for ammonia production with a convenient and sustainable manner. The design and development of active electrocatalysts with high yield and Faradaic efficiency for catalytic nitrogen reduction to ammonia remain a great challenge at present. Herein, we demonstrated efficient electrochemical synthesis of ammonia on three-dimensional bimetallic PdRu porous nanostructures (PdRu BPNs), which were synthesized by a very rapid reduction route. The PdRu BPNs can provide sufficient active sites to react with target species and enhance the interaction between active sites and the adsorbed nitrogen species. As such, the PdRu BPNs achieved a high activity with a NH3 yield of 25.92 μg h–1 mgcat–1 in acidic solution, which was superior to that of monometallic Pd and Ru nanostructures. This study offers a facile synthetic strategy for the rational design and development of porous metallic nanostructures as efficient electrocatalysts for electrochemical ammonia production at ambient conditions.
Fast developing of a Natural Language Interface for a Portuguese WordNet: Leveraging on Sentence Embeddings (2019)

We describe how a natural language interface can be developed for a wordnet with a small set of handcrafted templates, leveraging on sentence embeddings.The proposed approach does not use rules for parsing natural language queries but experiments showed that the embeddings model is tolerant enough for correctly predicting relation types that do not match known patterns exactly.It was tested with OpenWordNet-PT, for which this method may provide an alternative interface, with benefits also on the curation process.
Self-Separation of Sublimation-Grown AlN with AlSiN Buffer Layer (2013)

AlN was grown by a sublimation method on 6H-SiC. We found the grown AlN layer is easily separated from the substrate when Si powder is added to the AlN source powder. The formation of AlSiN layer with the Si content of 15% at the AlN/6H-SiC interface was confirmed by energy-dispersive X-ray spectroscopy (EDS) and X-ray diffraction (XRD). This AlSiN layer causes the separation of AlN.
Ectopic Bone Formation Is Enhanced in Senescent Animals Implanted with Embryonic Cells (1988)

Ectopic bone formation induced by the subcutaneous implantation of demineralized bone matrix (DBM) is very significantly reduced in older Fischer 344 rats. Cells originating from calvaria of 20-day-old embryo donors were introduced into cylinders of DBM sealed at the ends with a Millipore filter or collagen sponges prior to subcutaneous implantation. Cells within the chambers had access to vascular channels that could penetrate through the interstices of the DBM. After four weeks of implantation in 26-month-old rats, the cylinders were full of bone. This bone was assessed by histologic techniques, by calcium and bone gamma-carboxyglutamic acid (gla) protein (BGP) concentrations, and by alkaline phosphatase activity. Cylinders to which no cells were added produced no bone. Bone marrow cells enclosed in similar cylinders or injected weekly at the implantation site also enhanced new bone formation but to a much lesser extent. Embryonic muscle cells formed large amounts of cartilage and less bone. Fibroblasts were inactive in this system. Prior treatment of the DBM with trypsin inhibited the myoblast response but not that of calvaria cells.
Acetylcholine receptors of cultured muscle cells demonstrated with ferritin-α-bungarotoxin conjugates (1974)

ABSTRACT α-Bungarotoxin-ferritin conjugates were used to visualize by freeze-fracture and thin-section electron microscopy toxin-binding sites, presumably acetylcholine (ACh) receptors, in membranes of muscle cells grown in tissue culture. Toxin conjugated to ferritin by a glutaraldehyde reaction and purified by column chromatography in a buffer of high ionic strength remains active in blocking the effect of iontophoretically applied ACh. The potency of the conjugates was decreased 5–10 times compared to native α-bungarotoxin. Toxin-ferritin conjugates were identified in small clusters which were not uniformly distributed over the surface membrane. Binding was inhibited by preincubation in D-tubocurare or unconjugated toxin. The relation of the clusters to the non-uniform distribution of ACh sensitivity and α-bungarotoxin binding on cultured muscle fibres is discussed.
SOFTWARE ENGINEERING DAYS: USING A VIDEO GAME PLATFORM TO TEACH COLLABORATIVE SOFTWARE DEVELOPMENT (2019)

This paper describes the implementation and assessment of a multi-day engineering design activity for Software Engineering students. This activity required students to work in teams of 16 to develop and implement four sub-systems of a digital spaceship. The Unity video game engine with a custom "spaceship sandbox" were used to drive student intrinsic motivation for the task, and to limit the complexity of the spaceship implementation. &#x0D; Student feedback of the activity was captured through a survey given immediately following the second day of the activity, and through a focus group conducted with four students later in the term. The feedback on the activity was largely positive, with teamwork, collaboration, and the software to accomplish it (Git) as major learning outcomes identified by students. Several improvements are planned for the fall 2019 version of the activity based on both instructor observation and student feedback.&#x0D;
A quality‐checked and physics‐constrained deep learning method to estimate material basis images from single‐kV contrast‐enhanced chest CT scans (2023)

The Deep-En-Chroma network provides a new pathway to estimating the clinically relevant material basis images from single-kV CT data and the Deep-QC module to inform end-users of the accuracy of the DL material basis images in practice.
Improving Multiprocessor Performance with Coarse-Grain Coherence Tracking (2005)

To main coherence in conventional shared-memory multiprocessor systems, processors first check other proessors' caches before obtaining data from memory. This coherence checking adds latency to memory requests and leads to large amounts of interconnect traffic in broadcast-based systems. Our results for a set of commercial, scientific and multiprogrammed workloads show that on average 67% (and up to 94%) of broadcasts are unnecessary. Coarse-Grain Coherence Tracking is a new technique that supplements a conventional coherence mechanism and optimizes the performance of coherence enforcement. The Coarse-Grain Coherence mechanism monitors the coherence status of large regions of memory, and uses that information to avoid unnecessary broadcasts. Coarse-Grain Coherence Tracking is shown to eliminate 55-97% of the unnecessary broadcasts, and improve performance by 8.8% on average (and up to 21.7%).
Hexagonality and Stacking Sequence Dependence of Etching Properties in Cl<sub>2</sub>-O<sub>2</sub>-SiC System (2010)

Thermal etching of hexagonal (4H-, 6H-, 8H- and 10H-), rhombohedral (15R- and 21R-), and cubic (3C-) SiC Si-faces was performed between 900 and 1000oC in a mixed gas of chlorine (Cl2) and oxygen (O2). In the case of well oriented Si-faces, the 3C-SiC (111) substrate was etched fastest in polytypes. The etching rate in the dislocation-free area depended on the hexagonality. Etch pits with definite shapes appeared, which depend on the type of dislocation and crystal structures. On the basis of these results, etching properties are discussed.