gebhart/patrepeval huggingface dataset:
Handling of biological cells using fluid integrated circuit (2003)

Studies are made of methods of cell handling using dielectrophoretic (DEP) force in a novel device called a fluid-integrated-circuit (FIC), where all cell-handling components are integrated onto one substrate with a photolithography technique. Cell passages and driving electrodes can be fabricated in arbitrary two-dimensional shape, allowing great flexibility in its design. Through an analytical study it was found that a careful tailoring of a field pattern is essential in realizing cell motions. Methods for detailed field analysis are developed and used to design cell-handling components. One is the FIC cell shift register, a device in which cells are stored and electrostatically transported one-by-one, just as bits are shifted in TTL shift registers. The other is the FIC cell deflector, where the cell fed from the inlet can be dielectrophoretically deflected to either of the bifurcating branches.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Hamster embryo cells transformed by herpes simplex virus: reactions with adeno-associated satellite virus (AAV) and its adenovirus helpers. (1977)

We have studied the reactions of hamster embryo cells transformed by ultraviolet-inactivated herpes simplex type 2 (333-8-9 T cells) to infections with adeno-associated satellite virus (AAV) and its adenovirus helpers. Resident HSV structural antigens were not detectable in early or late passage of 333-8-9 T cells. AAV structural antigens were not detected in these cells unless the cells were coinfected with a helper adenovirus. In early passage 333-8-9 T cells were permissive to infections with simian adenovirus SV15 whereas normal hamster cell line LSH was nonpermissive. In some late passages of 333-8-9 T cells infections with SV15 adenovirus led to the production of viruslike particles whose morphology was identical with reoviruses.
Adhesive Bonding of III-V Dies to Processed SOI Using BCB for Photonic Applications (2006)

The bonding process of InP/InGaAsP dies to processed SOI using DVS-bis-BenzoCycloButene was developed. Surface preparation and the degree of planarization of bonding layers thinner than 300nm were optimized. Bonding strength and bonding quality was assessed, which shows to be sufficient for post-bonding processing. The heterogeneous integration of active photonic devices fabricated in this bonding layer on top of the SOI photonic layer is described.
Combustion efficiency tables (1991)

This valuable handbook is packed with combusion efficiency tables based on the ASME/ANSI Power Test Code 4.1. Each table clearly illustrates how different variables impact combustion and follows an easy-to-use format. A variety of costs can be calculated using this book, such as performance deficiency costs, and there are dozens of practical methods including the heat loss efficiency method, the imput-output method, carbon monoxide and combustibles measurement methods. There are also procedures for properly inspecting and adjusting the boiler, and a general survey of heat recovery equipment.
Advances in Therapeutic Drug Monitoring of Atypical Antipsychotic Drugs (2004)

The introduction in clinical practice of new antipsychotic drugs neurologically safer and with a broader spectrum of efficacy than “classical” neuroleptics has brought about significant improvement in the therapy of schizophrenic patients. These second-generation antipsychotics usually called “atypical” antipsychotics, have several therapeutical features in common, such as their effectiveness against the negative symptoms of schizophrenia and the advantage of not causing severe extrapyramidal symptoms and hyperprolactinemia. The therapeutic drug monitoring of patients treated with atypical antipsychotics is however, still advisable. In many cases, it can avoid the onset of side and toxic effects due to high plasma levels of the drug caused by overdose or interactions with other drugs. Furthermore, monitoring can significantly improve the patients compliance, thus leading to higher treatment efficacy. The pharmacological properties of the most widely used atypical antipsychotics (clozapine, olanzapine, risperidone and quetiapine) will be treated herein with particular attention paid to metabolism, side effects and pharmacokinetics. The analytical methods suitable for the therapeutical drug monitoring of these drugs will also be discussed, in terms of sensitivity, selectivity and usefulness in clinical settings. Other recent atypical agents (ziprasidone, aripiprazole, iloperidone, sertindole and zotepine) will be described as well. Keywords: therapeutic drug monitoring, atypical antipsychotics, pharmacological profile, analytical methods, plasma sample pre-treatment
Two-dimensional scanning realized by an asymmetry fiber cantilever driven by single piezo bender actuator for optical coherence tomography (2009)

We develop a fiber based probe that is capable of two-dimensional scanning applicable in optical coherence tomography (OCT). Based on the resonance of the fiber cantilever with asymmetry structure which has two distinguished resonant frequencies in orthogonal directions, Lissajous pattern is produced suitable for two-dimensional scanning upon a sample. Orthogonal resonances of the fiber cantilever are simultaneously excited by single piezo bender actuator with one driving signal consisting of two components corresponding to above-mentioned two resonant frequencies. By integrating a backward-placed two-dimensional position sensitive detector (PSD) into the probe, real-time lateral position of the scanning pattern is registered simultaneously for image reconstruction. Dynamical characteristics of the fiber cantilever are experimentally studied with special consideration on factors determining the resolution of the scanning pattern, including frequency and amplitude ratios between two components of the driving signal and fetching duration used for an en face image. With the developed probe implemented in our established OCT system, en face OCT images of typical samples are obtained with satisfying resolution and contrast, demonstrating the feasibility of such fiber cantilever with asymmetry structure for realizing two dimensional scanning by single actuator, potentially applicable to endoscopic OCT imaging.
Bundle Methods for Regularized Risk Minimization (2010)

A wide variety of machine learning problems can be described as minimizing a regularized risk functional, with different algorithms using different notions of risk and different regularizers. Examples include linear Support Vector Machines (SVMs), Gaussian Processes, Logistic Regression, Conditional Random Fields (CRFs), and Lasso amongst others. This paper describes the theory and implementation of a scalable and modular convex solver which solves all these estimation problems. It can be parallelized on a cluster of workstations, allows for data-locality, and can deal with regularizers such as L1 and L2 penalties. In addition to the unified framework we present tight convergence bounds, which show that our algorithm converges in O(1/e) steps to e precision for general convex problems and in O(log (1/e)) steps for continuously differentiable problems. We demonstrate the performance of our general purpose solver on a variety of publicly available data sets.
On efficiently processing nearest neighbor queries in a loosely coupled set of data sources (2004)

We propose a family of algorithms for processing nearest neighbor (NN) queries in an integration middleware that provides federated access to numerous loosely coupled, autonomous data sources connected through the internet. Previous approaches for parallel and distributed NN queries considered all data sources as relevant, or determined the relevant ones in a single step by exploiting additional knowledge on object counts per data source. We propose a different approach that does not require such detailed statistics about the distribution of the data. It iteratively enlarges and shrinks the set of relevant data sources. Our experiments show that this yields considerable performance benefits with regard to both response time and effort. Additionally, we propose to use only moderate parallelism instead of querying all relevant data sources at the same time. This allows us to trade a slightly increased response time for a lot less effort, hence maximizing the cost profit ratio, as we show in our experiments. Thus, the proposed algorithms clearly extend the set of NN algorithms known so far.
Expression of bacterial Rubisco genes in <i>Escherichia coli</i> (1986)

Abstract The structural genes for three forms of Rubisco have been isolated from bacteria and introduced into various plasmids. Apart from details of the sequences which have been obtained from these constructs, they are now being exploited for mutagenesis to determine the identity and specific function of the individual amino acid residues that compose the active site. These methods have been applied to a plasmid that contains the structural gene for the simplest form of Rubisco from Rhodospirillum rubrum to obtain mutant enzymes with altered activity. The construct pRR2119 is also expressed to very high levels in Escherichia coli and enough recombinant protein of both the wild-type and m utant enzymes can be obtained for detailed physico-chemical studies. Other vectors have now been constructed, containing the genes of prokaryotic Rubisco that assemble into an active form I enzyme. The levels of expression are acceptable and the product is similar to the authentic enzyme. These constructs are now being used for mutagenesis in vitro to attempt to alter the relative rates of the oxygenase and carboxylase activities.
Out of the cold: libraries in the Baltic States after communism (1998)

Points to the unique cultural, ethnic and linguistic identities of the three Baltic States: Estonia, Latvia and Lithuania; despite being for many years under the political and economic sway of one large neighbour or another. For over 500 years, the state of libraries and librarianship has been a reliable measure of varying degrees of freedom and subjugation in these countries. Traces the influences of religion, academic and private collections, Russian rule and the emergence of nationalism, the development of professional librarianship, independence following World War 1, and domination by the Soviet Union. Shows not only the effects of politics on libraries but also their counterbalancing role. Documents past preoccupations with Soviet propaganda and censorship with a view to assessing the current state of libraries as they enter a new era of political freedom, information technology and co-operation. Notes specific projects aimed at establishing Web sites and online public access catalogues (OPACs) in individual countries. Concludes that the fundamental steps to developing Baltic library networks and to decentralize the library system have been firmly established. Attributes these advancements to the unity of the people in their single minded determination to regain and promote the strong national identity that they feel has been denied them for so long.
Mapping mRNA and Protein Expression with High Signal-to-Background in Diverse Organisms (2016)

In situ hybridization (ISH) techniques allow for the study of the nucleic acid expression within whole biological samples. The quality of probes for ISH dictates how accurate and bright the signal is for the experiment; however, there is currently not a systematic way to determine what the best probe set would be. In response to this, we have developed a framework to optimize an ISH probe set to achieve the greatest signal-to-background ratio. As methods like ISH help obtain more information about biological processes, there is a growing desire to simultaneously analyze various targets within the same sample to examine these complex genetic interactions. To facilitate this, a novel amplification technique called hybridization chain reaction (HCR) has allowed for the in situ detection of multiple target mRNAs concurrently in zebrafish embryos. We have now expanded this technology further by adapting HCR amplification for ISH to other model organisms, particularly, whole mount Drosophila melanogaster embryos and formalin-fixed parafin-embedded human tissue sections. Beyond looking at mRNA, immunohistochemistry (IHC) provides another tool to understand biological systems by analyzing protein expression patterns. The ability to easily look at both mRNAs and proteins in the same sample offers significant advantages as each provides unique information, but current methods are technically difficult and labor intensive. In response, we have engineered a scheme to use HCR to amplify signal for IHC. We then used this advancement to develop a straightforward protocol using HCR amplification for simultaneous detection of multiple proteins and mRNAs with a high signal-to-background ratio.
Accurate and fast 3D colon segmentation in CT colonography (2009)

This paper introduces an adaptive level set method for 3D segmentation of colon tissue in CT colonography filled with air and opacified fluid. First, most of the opacified liquid is removed by a threshold value. The closed contours are propagated toward the desired 3D region boundaries through the iterative evolution of the adaptive level sets function. The proposed method has been tested on 22 real CT colonography datasets with various pathologies, and the segmentation accuracy has achieved 98.40%.
Immunopathology of cardiac transplant rejection (1995)

Transplant rejection represents a diverse series of complex immunological events beginning with allorecognition and lymphocyte activation and differentiation, followed by interactions of antibodies and activated lymphocytes with the vascular endothelium and subsequent cellular infiltration into the allograft, and, finally, the inflammatory process leading to tissue injury. This paper reviews how these events contribute to the different types of cardiac transplant rejection, including cardiac allograft vasculopathy.
Quantitation and Distribution of Simple and Acylated Anthocyanins and Other Phenolics in Blueberries (1994)

ABSTRACT Simple and acylated anthocyanins and other phenolics in ten cultivars and hybrids of lowbush and one cultivar of highbush blueberries were extracted, isolated and quantified by reversed phase HPLC and capillary gas liquid chromatography. All cultivars contained nonacylated glucosides and galactosides of delphinidin, cyanidin, petunidin, peonidin, and malvidin. Each anthocyanin also occurred in the acetylated form in eight of eleven cultivars. Total anthocyanins in blueberries ranged from 110 to 260 mg/100g of fresh berries. ‘Blomidon’ berries contained the lowest and ‘Chignecto’ berries the highest level. Acetylated anthocyanins made up to 35% of the total anthocyanins in ‘Chignecto’. Chlorogenic acid was the major colorless phenolic of lowbush and highbush blueberries, at 50–100 mg/100 g fresh fruit.
Coupling of ATP synthesis and methane formation from methanol and molecular hydrogen in <i>Methanosarcina barkeri</i> (1984)

The addition of methanol to a cell suspension of Methanosarcina barkeri resulted in an increase of the intracellular ATP concentration from 1 nmol/mg to 10 nmol/mg protein and in the formation of a proton-motive force delta p of -130 mV. delta p consisted of more than 90% of the membrane potential delta psi. These values were similar under N2 and under H2. The addition of the uncoupler tetrachlorosalicylanilide to the above system under N2 led to a drastic decrease of both, the ATP concentration and the delta p and to a stop of methanogenesis. With methanol and H2, however, methane formation continued, although the effect of the uncoupler on the ATP pool and on delta p was a under N2. The proton-translocating ATPase inhibitor N,N'-dicyclohexylcarbodiimide caused a rapid exhaustion of the ATP pool and a discontinuation of methane synthesis, whereas delta p was unaffected. Inhibition of methane formation under these conditions could be relieved by the addition of the uncoupler tetrachlorosalicylanilide. These results demonstrate that methane formation according to the equation CH3OH + H2----H2----CH4 + H2O was coupled to ATP synthesis by a chemiosmotic mechanism and was under the control of delta psi: Methane formation only proceeded if the delta psi generated was used for ATP synthesis or if an uncoupler was present. Under N2, methane formation according to the equation 4CH3OH ----CO2 + 3CH4 + 2H2O was abolished by an uncoupler, because one step in the oxidation of methanol to 1 CO2 apparently depended on an energized state of the membrane.
Quantitative investigation of alveolar structures with OCT using total liquid ventilation during mechanical ventilation (2012)

To develop new treatment possibilities for patients with severe lung diseases it is crucial to understand the lung function on an alveolar level. Optical coherence tomography (OCT) in combination with intravital microscopy (IVM) are used for imaging subpleural alveoli in animal models to gain information about dynamic and morphological changes of lung tissue during mechanical ventilation. The image content suitable for further analysis is influenced by image artifacts caused by scattering, refraction, reflection, and absorbance. Because the refractive index varies with each air-tissue interface in lung tissue, these effects decrease OCT image quality exceedingly. The quality of OCT images can be increased when the refractive index inside the alveoli is matched to the one of tissue via liquid-filling. Thereby, scattering loss can be decreased and higher penetration depth and tissue contrast can be achieved. To use the advantages of liquid-filling for in vivo imaging of small rodent lungs, a suitable breathing fluid (perfluorodecalin) and a special liquid respirator are necessary. Here we show the effect of liquid-filling on OCT and IVM image quality of subpleural alveoli in a mouse model.
A Sperm Membrane Protein That Binds in a Species-specific Manner to the Egg Extracellular Matrix Is Homologous to von Willebrand Factor (1995)

We have purified a sperm membrane protein, designated zonadhesin, that binds in a species-specific manner to the extracellular matrix (zona pellucida) of the egg, and cloned its cDNA. The cDNA encodes a novel protein with a single transmembrane segment separating a 36 amino acid, highly basic intracellular C terminus from a 2418-amino acid extracellular region. The extracellular sequence specifies a mosaic protein comprising a unique N-terminal domain, a mucin-like domain, and five tandem domains proximal to the membrane that are homologous to prepro von Willebrand factor. The N-terminal and mucin-like domains were absent from zonadhesin that bound to the egg extracellular matrix, suggesting that processing occurs during sperm maturation and/or capacitation. By Northern blotting and in situ hybridization, zonadhesin mRNA was detected only within the testis, where it was expressed primarily in haploid spermatids. The unique domain structure of zonadhesin suggests multiple functions, one of which is to mediate sperm adhesion to the zona pellucida.
Synthesis of Analogs of D-Ala--D-Ala as Potential Inhibitors of Bacterial Cell Wall Biosynthesis. (1984)

The syntheses of the L,L- and D,D-stereoisomers of N- phenoxyacetyl -X-alanine in which X = Ser, Ala( beta Cl ) or Arg, are described. The antibacterial activity of these peptides and some of their synthetic intermediates has been examined. Four of the intermediates in which X = Ala( beta Cl ) and Arg(NO2), which possess C-terminal benzyl ester groups, were active against viridans streptococci and Streptococcus agalactiae. The D,D-enantiomers were more active than the corresponding L,L-isomers. None of the compounds were active against beta-lactamase producing bacteria or acted as beta-lactamase inhibitors.
Adsorption of polyadenylate and other polynucleotides to unmodified cellulose (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdsorption of polyadenylate and other polynucleotides to unmodified cellulosePaul A. Kitos and Harold AmosCite this: Biochemistry 1973, 12, 25, 5086–5091Publication Date (Print):December 1, 1973Publication History Published online1 May 2002Published inissue 1 December 1973https://pubs.acs.org/doi/10.1021/bi00749a010https://doi.org/10.1021/bi00749a010research-articleACS PublicationsRequest reuse permissionsArticle Views43Altmetric-Citations7LEARN 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
Strength‐Toughness Relations in Sintered and Isostatically Hot‐Pressed ZrO <sub>2</sub> ‐Toughened Al <sub>2</sub> O <sub>3</sub> (1986)

The fracture toughness of fine‐grained undoped ZrO 2 ‐toughened Al 2 O 3 (ZTA) was essentially unchanged by postsintering hot isostatic pressing and increased monotonically with ZrO 2 additions up to 25 wt%. The strength of ZTA with 5 to 15 wt% tetragonal ZrO 2 , which depended monotonically on the amount of ZrO 2 present before hot isostatic pressing, was increased by pressing but became almost constant between 5 and 15 wt% ZrO 2 addition. The strength appeared to be controlled by pores before pressing and by surface flaws after pressing; the size of flaws after pressing increased with ZrO 2 content. The strength of ZTA containing mostly monoclinic ZrO 2 (20 to 25 wt%) remained almost constant despite the noticeable density increase upon hot isostatic pressing because the strength was controlled by preexisting microcracks whose extent did not change on postsintering pressing. These strength‐toughness relations in sintered and isostatically hot‐pressed ZTA are explained on the basis of R ‐curve behavior. The importance of the contribution of microcracks to the toughness of ZTA is emphasized.
Treatment of ocular melanoma metastatic to the liver by hepatic arterial chemotherapy. (1997)

The results of hepatic arterial chemotherapy with fotemustine produced a high response rate and survival similar to chemoembolization therapy. It involves no major toxicity and preserves the quality of life. To assess further its effectiveness, a randomized study to compare hepatic intraarterial versus intravenous chemotherapy is being planned.
The Role of Oral Administration of Oatmeal Fermented by<i>Lactobacillus reuteri</i>R2LC on Bacterial Translocation after Acute Liver Failure Induced by Subtotal Liver Resection in the Rat (1995)

The occurrence of bacterial translocation from the gut in 90% hepatectomy-induced ALF could be prevented by fermented oatmeal, which implies possibilities for biologically balancing the enteric bacterial ecology.