gebhart/patrepeval huggingface dataset:
Aspects of Flexographic Print Quality and Relationship to some Printing Parameters (2008)

Flexographic printing is a common printing method in the packaging field. The printing method is characterized primarily by the flexible printing plate and the low viscosity inks which make it suitable for use on almost any substrate. The object of this study was to obtain further knowledge of the some important mechanisms of flexographic printing and how they influence the print quality. The thesis deals with printing primarily on board and liner but also on newsprint with water-borne ink using a full-scale flexographic central impression (CI) printing press. Several printing trials have been performed with a focus on the chemical interaction between the ink and substrate and the physical contact between the ink-covered printing plate and the substrate. Multicolour printing exposes the substrate to water from the water-containing ink. The emphasis was to investigate the relation between print quality and water-uptake of the paper surface with heat and water. Printing trials was carried out on substrates possessing a hydrophobic, and also a rather hydrophilic surface using a regular commercial water-borne ink. The favorable effect which water or surfactant solution had on the hydrophobic substrate with regard to print mottle could depend on its surface compressibility in combination with the hydrophobic nature of its surface that could affect the wetting properties. Conventional printing involves physical contact between plate and ink and between ink and substrate. A method for measuring the dynamic nip pressure using thin load cells is presented. Print quality was influenced by the plate material. A correction procedure taking into account the size of the sensor was developed in order to estimate the maximum dynamic pressure in the printing nip. An attempt was made to identify essential mechanical and chemical parameters, and also geometrical properties of the plate that affected print quality. Laboratory printing trials were carried out and a multivariate analysis was applied for evaluation of print quality data. The impact of the plate properties on print quality was evident. The essential properties of the plate that influence print quality were the small-scale roughness and long-scale roughness.
Automated comparative protein structure modeling with SWISS‐MODEL and Swiss‐PdbViewer: A historical perspective (2009)

SWISS-MODEL pioneered the field of automated modeling as the first protein modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-MODEL Repository, it provides a fully integrated sequence to structure analysis and modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative protein modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper.
ASCOT: a text mining-based web-service for efficient search and assisted creation of clinical trials (2012)

Clinical trials are mandatory protocols describing medical research on humans and among the most valuable sources of medical practice evidence. Searching for trials relevant to some query is laborious due to the immense number of existing protocols. Apart from search, writing new trials includes composing detailed eligibility criteria, which might be time-consuming, especially for new researchers. In this paper we present ASCOT, an efficient search application customised for clinical trials. ASCOT uses text mining and data mining methods to enrich clinical trials with metadata, that in turn serve as effective tools to narrow down search. In addition, ASCOT integrates a component for recommending eligibility criteria based on a set of selected protocols.
Cement Design Based on Cement Mechanical Response (1998)

Summary The disappearance of cement bond log response as a result of variations of downhole conditions has been observed in numerous wells. This observation has led to concern about the loss of proper zonal isolation. Stresses induced in the cement, through deformation of the cemented casing resulting from the variation of down-hole conditions, are the cause of this damage. We present an analysis of the mechanical response of set cement in a cased wellbore to quantify this damage and determine the key controlling parameters. The results show that the thermo-elastic properties of the casing, cement, and formation play a significant role. The type of failure, either cement debonding or cement cracking, is a function of the nature of the downhole condition variations. This analysis allows us to propose appropriate cement mechanical properties to avoid cement failure and debonding. We show that the use of high compressive strength cement is not always the best solution and, in some cases, flexible cements are preferred.
Magnetic domains in thin epitaxial Co/Au(111) films (1990)

The formation of magnetic domains in thin epitaxial Co/Au(111) films is investigated. Three-monolayer films are shown to decay into out-of-plane domains of micron size. We find a smooth transition from out-of-plane to in-plane magnetization at a crossover thickness of 4.5 layers and determine that the domain size depends linearly on film thickness below crossover.
Relationship between Antimalarial Activity and Heme Alkylation for Spiro- and Dispiro-1,2,4-Trioxolane Antimalarials (2008)

The reaction of spiro- and dispiro-1,2,4-trioxolane antimalarials with heme has been investigated to provide further insight into the mechanism of action for this important class of antimalarials. A series of trioxolanes with various antimalarial potencies was found to be unreactive in the presence of Fe(III) hemin, but all were rapidly degraded by reduced Fe(II) heme. The major reaction product from the heme-mediated degradation of biologically active trioxolanes was an alkylated heme adduct resulting from addition of a radical intermediate. Under standardized reaction conditions, a correlation (R2 = 0.88) was found between the extent of heme alkylation and in vitro antimalarial activity, suggesting that heme alkylation may be related to the mechanism of action for these trioxolanes. Significantly less heme alkylation was observed for the clinically utilized artemisinin derivatives compared to the equipotent trioxolanes included in this study.
Specific Targeting of Brain Tumors with an Optical/Magnetic Resonance Imaging Nanoprobe across the Blood-Brain Barrier (2009)

Nanoparticle-based platforms have drawn considerable attention for their potential effect on oncology and other biomedical fields. However, their in vivo application is challenged by insufficient accumulation and retention within tumors due to limited specificity to the target, and an inability to traverse biological barriers. Here, we present a nanoprobe that shows an ability to cross the blood-brain barrier and specifically target brain tumors in a genetically engineered mouse model, as established through in vivo magnetic resonance and biophotonic imaging, and histologic and biodistribution analyses. The nanoprobe is comprised of an iron oxide nanoparticle coated with biocompatible polyethylene glycol-grafted chitosan copolymer, to which a tumor-targeting agent, chlorotoxin, and a near-IR fluorophore are conjugated. The nanoprobe shows an innocuous toxicity profile and sustained retention in tumors. With the versatile affinity of the targeting ligand and the flexible conjugation chemistry for alternative diagnostic and therapeutic agents, this nanoparticle platform can be potentially used for the diagnosis and treatment of a variety of tumor types.
Anisotropic Organic Materials (2001)

The use of electroabsorption (EA) spectroscopy and pyroelectric investigations by the laser intensity modulation method (LIMM) for the characterization of nonlinear optical (NLO) polymer systems is demonstrated. EA spectroscopy may be used to evaluate basic parameters of NLO chromophores and their polar order. The influence of the rotational mobility of the chromophores on the EA spectra and the application of this effect to characterize the relaxation of the chromophores is shown. EA spectroscopy may be applied to determine in situ the electric field in the electrooptic active layer of multi layer polymer stacks. Pyroelectric LIMM measurements are applied to characterize the polarization profile in double layer polymer systems.
Evolution of Snake Venom Disintegrins by Positive Darwinian Selection (2008)

PII-disintegrins, cysteine-rich polypeptides broadly distributed in the venoms of geographically diverse species of vipers and rattlesnakes, antagonize the adhesive functions of beta(1) and beta(3) integrin receptors. PII-disintegrins evolved in Viperidae by neofunctionalization of disintegrin-like domains of duplicated PIII-snake venom hemorrhagic metalloproteinase (SVMP) genes recruited into the venom proteome before the radiation of the advanced snakes. Minimization of the gene (loss of introns and coding regions) and the protein structures (successive loss of disulfide bonds) underpins the postduplication divergence of disintegrins. However, little is known about the underlying genetic mechanisms that have generated the structural and functional diversity among disintegrins. Phylogenetic inference and maximum likelihood-based codon substitution approaches were used to analyze the evolution of the disintegrin family. The topology of the phylogenetic tree does not parallel that of the species tree. This incongruence is consistent with that expected for a multigene family undergoing a birth-and-death process in which the appearance and disappearance of loci are being driven by selection. Cysteine and buried residues appear to be under strong purifying selection due to their role in maintaining the active conformation of disintegrins. Divergence of disintegrins is strongly influenced by positive Darwinian selection causing accelerated rate of substitution in a substantial proportion of surface-exposed disintegrin residues. Global and lineage-specific sites evolving under diversifying selection were identified. Several sites are located within the integrin-binding loop and the C-terminal tail, two regions that form a conformational functional epitope. Arginine-glycine-aspartic acid (RGD) was inferred to represent the ancestral integrin-recognition motif, which emerged from the subgroup of PIII-SVMPs bearing the RDECD sequence. The most parsimonious nucleotide substitution model required for the emergence of all known disintegrin's integrin inhibitory motifs from an ancestral RGD sequence involves a minimum of three mutations. The adaptive advantage of the emergence of motifs targeting beta(1) integrins and the role of positively selected sites located within nonfunctional disintegrin regions appear to be difficult to rationalize in the context of a predator-prey arms race. Perhaps, this represents a consequence of the neofunctionalization potential of the disintegrin domain, a feature that may underlie its recruitment into the venom proteome followed by its successful transformation into a toxin.
Kalman-filter-based algorithms of spectrometric data correction-Part I: an iterative algorithm of deconvolution (1997)

This series of two papers aims to present the different solutions of the problem of improving the resolution of spectrometric measurements via numerical processing of spectrometric data subject both to systematic instrumental errors and to random measurement errors. It is assumed that the model of the spectrometric data has the form of a convolution-type equation of the first kind. The method for improving the resolution consists in numerically solving this equation using the acquired data. In this first paper of the series, an algorithm of correction is proposed which is based on the iterative use of the Kalman filter incorporating a non-negativity constraint. Its applicability to the problem of correction is assessed not only from a purely metrological point of view (accuracy, resolution) but also with respect to its suitability for implementation as a VLSI processor dedicated to measuring systems. For this latter reason a time-invariant model of the data and a steady-state version of the Kalman filter is used. The efficiency of this approach to correction is demonstrated using both synthetic and real-world data.
Finding Strongly Knit Clusters in Social Networks (2008)

Social networks are ubiquitous. The discovery of closely knit clusters in these networks is of fundamental and practical interest. Existing clustering criteria are limited in that clusters typically do not overlap, all vertices are clustered, and/or external sparsity is ignored. We introduce a new criterion that overcomes these limitations by combining internal density with external sparsity in a natural way. This paper explores combinatorial properties of internally dense and externally sparse clusters. A simple algorithm is given for provably finding such clusters assuming a sufficiently large gap between internal density and external sparsity. Experimental results show that the algorithm is able to identify over 90% of the clusters in real graphs, assuming conditions on external sparsity.
Expression of a<i>Mycobacterium tuberculosis</i>Arabinomannan Antigen In Vitro and In Vivo (2001)

The outermost layer of Mycobacterium tuberculosis contains two major polysaccharides, arabinomannan (AM) and glucan (GC). We studied the in vitro and in vivo expression of an M. tuberculosis AM antigen using monoclonal antibody (MAb) 9d8 (2a), an isotype-switched variant of the immunoglobulin G3 (IgG3) MAb 9d8. MAb 9d8 had been previously shown to bind M. tuberculosis AM and the M. tuberculosis surface. Our in vitro experiments showed that MAb 9d8(2a) bound strongly to whole-cell M. tuberculosis Erdman but not to the CDC 1551 strain grown in medium for an extended period. However, AM antigen was detected in the culture supernatant of both strains, and its concentration increased in a time-dependent manner. The detection of AM antigen from both strains was decreased in the presence of Tween 80. In mice infected with M. tuberculosis Erdman, AM antigen accumulated in organ homogenates concomitant to an increase in bacterial organ burden and an increase in IgG and IgM titer to AM. These results (i) indicate that the surface expression of AM during in vitro growth changes with culture age, is strain dependent, and is affected by the presence of Tween 80 in the culture media; (ii) show that AM is produced by bacteria growth in vivo; and (iii) demonstrate that the amount of in vivo-detected AM can be dependent on the number of bacteria in the infected organ.
Fluorescent proteins as tools to aid protein production (2005)

Fluorescent proteins are genetically encoded, highly versatile reporters useful for monitoring various aspects of recombinant protein production. In addition to the widely popular green fluorescent protein (GFP) from Aequorea victoria, a variety of other fluorescent proteins have been discovered that display a wide range of spectral properties. Synthetic variants have also been developed to overcome limitations associated with their wild-type counterparts. Having a large repertoire of fluorescent proteins with diverse traits opens new opportunities for rapid monitoring and optimization of recombinant protein production.
Agile Development of Platform Independent Model in Model Driven Architecture (2010)

Along with the growing software market in recent years, business requirements are changing more rapidly and the complexity of enterprise applications is growing continuously. An ideal goal is to encapsulate these requirements into a high-level abstraction, which can be used to drive large-scale adaptation of the underlying software implementation. Model Driven Engineering (MDE) is one of the enabling techniques that support this objective. One of the important parts in this process is the creation of Platform Independent Model (PIM). There are several approaches on this matter. However there is still the absence of clear documentation on the methods especially when the purpose is aimed for generic PIMs in a specific domain. This article introduces an approach to developing PIMs by using UML, OCL and promotes agility by applying agile modeling for this purpose. A practical example will be demonstrated.
Intra-Islet Somatostatin Regulates Glucagon Release via Type 2 Somatostatin Receptors in Rats (2003)

Exogenously administered somatostatin (SST) inhibits secretion of insulin and glucagon. Furthermore, it is hypothesized that islet SST regulates glucagon secretion by a local action. A number of studies utilizing SST antibodies have been performed to test this hypothesis, and their results have been conflicting. Five subtypes of SST receptor (SSTR1–5) mediate the effect of SST on target cells. In rodents, SST inhibits the release of glucagon, but not that of insulin, via SSTR2. A novel SSTR2-selective antagonist, DC-41-33, was synthesized recently. We have investigated the effects of this antagonist on arginine-stimulated glucagon and insulin release in batch incubations of isolated rat islets, perifused isolated rat islets, and isolated perfused rat pancreas. In batch incubations at 3.3 mmol/l glucose, DC-41-33 increased glucagon release in a dose-dependent manner. At the maximum dose tested (2 μmol/l), DC-41-33 enhanced the glucagon response by 4.3- to 5-fold. Similarly, this compound increased arginine-induced glucagon release in perifused islets at 3.3 mmol/l glucose (2.8-fold) and perfused pancreas at 3.3 and 5.5 mmol/l glucose (2.5- and 2.3-fold, respectively). In the two latter experimental systems, DC-41-33 had no significant effect on insulin release. In conclusion, our results strongly support the hypothesis that islet SST inhibits glucagon secretion via a local action.
Recombinant antibodies: a novel approach to cancer diagnosis and therapy (2000)

Recombinant antibodies and their fragments currently represent over 30% of all biological proteins undergoing clinical trials for diagnosis and therapy. These reagents dominate the cancer-targeting field, as highlighted by the recent approval of the first engineered therapeutic antibodies by the Food and Drugs Administration (FDA). Last year, important advances have been made in the design, selection and production of recombinant antibodies. The natural immune repertoire and somatic cell affinity maturation has been superseded by large antibody display libraries and rapid molecular evolution strategies. These novel libraries and selection methods have enabled the rapid isolation of high-affinity cancer targeting and antiviral antibodies, the latter capable of redirecting viruses for gene therapy applications. In alternative strategies for cancer diagnosis and therapy, recombinant antibody fragments have been fused to radioisotopes, drugs, toxins, enzymes and biosensor surfaces. Antibody-directed cancer pre-targeting followed by prodrug activation (ADEPT) has proved a most promising therapeutic strategy. Multi-specific antibodies have been effective for cytotoxic T-cell recruitment and antibody-fusion proteins have delivered enhanced immunotherapeutic and vaccination strategies. The new millennium is indeed an exciting time for the design, selection and formulation of a range of new antibody-based products for cancer diagnosis and therapy.
Catalytic Conversion of Biomass to Monofunctional Hydrocarbons and Targeted Liquid-Fuel Classes (2008)

It is imperative to develop more efficient processes for conversion of biomass to liquid fuels, such that the cost of these fuels would be competitive with the cost of fuels derived from petroleum. We report a catalytic approach for the conversion of carbohydrates to specific classes of hydrocarbons for use as liquid transportation fuels, based on the integration of several flow reactors operated in a cascade mode, where the effluent from the one reactor is simply fed to the next reactor. This approach can be tuned for production of branched hydrocarbons and aromatic compounds in gasoline, or longer-chain, less highly branched hydrocarbons in diesel and jet fuels. The liquid organic effluent from the first flow reactor contains monofunctional compounds, such as alcohols, ketones, carboxylic acids, and heterocycles, that can also be used to provide reactive intermediates for fine chemicals and polymers markets.
The interaction of bride of sevenless with sevenless is conserved between Drosophila virilis and Drosophila melanogaster. (1993)

An inductive interaction between the sevenless (sev) transmembrane tyrosine kinase receptor and the bride of sevenless (boss) transmembrane ligand is required for the development of the R7 photoreceptor neuron in the compound eye of Drosophila melanogaster. The boss protein is proposed to contain a large N-terminal extracellular domain, seven transmembrane segments, and a C-terminal cytoplasmic tail. The boss protein from Drosophila virilis (bossvir) retains strong amino acid identity with loss from D. melanogaster (bossmel): 73% identity in the N-terminal extracellular domain and 91% identity in the seven-transmembrane domain, including the cytoplasmic tail. By using P-element-mediated DNA transformation, the bossmel and bossvir genes were shown to rescue the D. melanogaster boss1 mutation. The expression of bossvir protein in D. melanogaster is indistinguishable from that of bossmel protein. Noncoding sequences which may regulate boss expression were identified based on their conservation during evolution. The predicted sev protein from D. virilis (sevvir) was previously shown to be 63% identical to sev from D. melanogaster (sevmel). A chimeric gene, (sevvir/mel), encoding the extracellular domain of sevvir and the cytoplasmic domain of sevmel rescues the D. melanogaster sevd2 mutation through interaction with either bossvir or bossmel.
Relevance feedback with a small number of relevance judgements (2000)

The use of incremental relevance feedback and document clustering were investigated in an relevance feedback environment in which the number of relevance judgements was quite small. Through experiments on the TREC collection, the incremental relevance feedback approach was found not to improve the overall search effectiveness. The clustering approach was found to be promising, although it sometimes over-focuses on a particular topic in a query and ignores the others. To overcome this problem, a query-biased clustering algorithm was developed and shown to be effective.
Demonstration of Functional Similarity of Proposed Biosimilar ABP 501 to Adalimumab (2016)

Similarity in biofunctional activity is a critical component of the totality of evidence required for demonstration of biosimilarity. The functional similarity demonstrated for ABP 501 comprehensively assesses the known mechanisms of action of adalimumab, supporting the conclusion that ABP 501, adalimumab (US), and adalimumab (EU) are likely to be clinically similar.
Microsoft Access 97/Visual Basic ステップバイステップ (1997)

１ データベースの処理を自動化する（ウィザードからはじめる；Ｖｉｓｕａｌ Ｂａｓｉｃでアプリケーションをカスタマイズする ほか） ２ Ｖｉｓｕａｌ Ｂａｓｉｃでプログラムを作成する（独自の関数を作成する；コードをモニタしてデバッグする ほか） ３ 独自のアプリケーションを作成する（ダイアログボックスで情報を収集する；アプリケーションを実行する ほか） ４ データとオブジェクトに取り組む（オブジェクトとコレクションを探求する；Ｖｉｓｕａｌ Ｂａｓｉｃでカスタマイズする ほか）