gebhart/patrepeval huggingface dataset:
Visualization of Individual DNA Molecules in Solution by Light Microscopy: DAPI Staining Method1 (1981)

A method was developed to visualize individual DNA molecules in solution under a fluorescent microscope connected to a highly sensitive video camera. DNA stained with a fluorescent dye, DAPI, revealed thin extended filaments, thicker filaments and rapidly transforming folded structures dependent upon the solution conditions. Structural transitions were observed and recorded as video images. Our observations indicated the possibility that DNA has the ability of supercoiling itself. This DAPI staining method will have wide possible application in the study of DNA and chromatin.
Top management perception of strategic information processing in a turbulent environment (1995)

Extant strategic management literature provides only partial answers to the important question: what variables affect top managers′ ability to process complicated, novel, ambiguous, or dynamic strategic information in a turbulent environment? Drawing on cognitive psychology, personality theory, management theory, organizational theory, and management information systems literature, proposes that nine personal attributes and four contextual attributes affect top managers′ information‐processing capability. The nine personal attributes are: cognitive complexity, knowledge, mental model of success, openmindedness, time orientation, personal values, tolerance for ambiguity, locus of control, and time devoted to environmental scanning. The four contextual attributes are: rewards and incentives, culture, structure of strategic planning process, and executive support systems. Thirteen propositions are postulated regarding the types of attributes that are conducive for top managers′ ability in processing complicated, novel, ambiguous, or dynamic information.
Effect of varying bilayer spacing distribution on reaction heat and velocity in reactive Al/Ni multilayers (2009)

Self-propagating reactions in Al/Ni nanostructured multilayer foils are examined both experimentally and computationally to determine the impact of variations in reactant spacing on reaction properties. Heats of reaction and reaction velocities have been characterized as a function of average bilayer spacing for sputter-deposited, single-bilayer foils (having a uniform bilayer spacing) and for dual-bilayer foils (having two different bilayer spacings that are labeled thick and thin). In the latter case, the spatial distribution of the thick and thin bilayers is found to have a significant effect on reaction velocity, with coarse distributions leading to much higher reaction velocities than fine distributions. Numerical simulations of reaction velocity match experimental data well for most spatial distributions, with the exception of very coarse distributions or distributions containing very small bilayer spacings. A simple model based on thermal diffusivities and reaction velocities is proposed to predict when the spatial distribution of thick and thin bilayers becomes coarse enough to affect reaction velocity. This combination of experiment and simulation will allow for more effective design and prediction of reaction velocities in both sputter-deposited and mechanically processed reactive materials with variable reactant spacings.
Silicon MOS amplifier operation in the integrate and dump mode for gigahertz band lightwave communication systems (1990)

The operation of a MOS amplifier in the integrate and dump mode is discussed. This mode of operation results in the suppression of the input load resistor noise while retaining the advantages of a large dynamic range and no equalization requirement. The technique is useful in improving the receiver sensitivity in circuit topologies such as the nonintegrating front. Several aspects of its MOS implementation are presented, along with test results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Elicitation of anti-viral cytotoxic T lymphocytes with purified viral and H-2 antigens. (1980)

The minimal molecular requirements for elicitation of secondary anti-Sendai virus CTL were investigated. The hemagglutinin-neuraminidase (HN) glycoprotein of Sendai virus and the H-2Kk glycoprotein of YAC tumor cells were purified and incorporated into phospholipid vesicles. These unilamellar liposomes were then tested for the ability to elicit H-2 restricted secondary anti-Sendai virus CTL. The results indicate that these well-defined vesicles were capable of eliciting secondary anti-Sendai virus CTL which lysed only target cells possessing the H-2Kk haplotype and modified with inactivated Sendai virus.
The Current State of Hormonal Therapy for Prostate Cancer (2002)

Androgen deprivation therapy remains a mainstay of treatment for men with prostate cancer. New uses for hormonal therapy, including use in the adjuvant and neoadjuvant setting, are being evaluated. Prevention of the side effects of therapy has led to the development of alternative schedules and therapeutics.
Communicating, Interpreting, and Executing High-Level Instructions for Human-Robot Interaction (2011)

In this paper, we address the problem of communicating, instructions to a robot team member. This requires specifying the tasks in an unambiguous manner, translating them into operational procedures, and carrying out those procedures in a persistent yet reactive manner. We report our response to these issues, after which we demonstrate their combined use in controlling a mobile robot in a multi-room office setting on tasks similar to those in search-and-rescue operations. We conclude by discussing related research and suggesting directions for future work.
Using GPUs for machine learning algorithms (2005)

Using dedicated hardware to do machine learning typically ends up in disaster because of cost, obsolescence, and poor software. The popularization of graphic processing units (GPUs), which are now available on every PC, provides an attractive alternative. We propose a generic 2-layer fully connected neural network GPU implementation which yields over 3/spl times/ speedup for both training and testing with respect to a 3 GHz P4 CPU.
5′-Phosphate and 5′-Phosphonate Ester Derivatives of (N)-Methanocarba Adenosine with in Vivo Cardioprotective Activity (2013)

Activation of a cardiac myocyte P2X4 receptor protects against heart failure. 5'-Phosphonate and 5'-phosphate analogues of AMP containing a (N)-methanocarba (bicyclo[3.1.0]hexane) system could protect from heart failure by potentially activating this cardioprotective channel. Phosphoesters and phosphonodiesters were synthesized and administered in vivo via a miniosmotic pump in a mouse ischemic heart failure model and most significantly increased intact heart contractile function (echocardiography) compared to vehicle infusion. Several new thio and deuterated phosphate derivatives were protective in a calsequestrin (CSQ) overexpressing heart failure model. Diethyl (7, MRS4084) and diisopropyl (8, MRS4074) phosphotriesters were highly protective in the ischemic model. Substitution of 2-Cl with iodo reduced protection in the CSQ model. Diisopropyl ester 16 (MRS2978) of (1'S,2'R,3'S,4'R,5'S)-4'-(6-amino-2-chloropurin-9-yl)-2',3'-(dihydroxy)-1'-(phosphonoethylene)bicyclo[3.1.0]hexane was highly efficacious (CSQ), while lower homologue 1'-phosphonomethylene derivative 14 was inactive. Thus, we identified uncharged carbocyclic nucleotide analogues that represent potential candidates for the treatment of heart failure, suggesting this as a viable and structurally broad approach.
The Warfighter Associate: Decision-Support and Metrics for Mission Command (2013)

Abstract : This report describes a unique and promising intelligent agent plug-in technology for Mission Command Systems the Warfighter Associate (WA) that enables individuals and teams to respond more effectively to the cognitive challenges of Mission Command. The WA uses a doctrinally based knowledge representation to model role-specific workflows and continuously monitors the state of the operational environment to enable decision-support, delivering the right information to the right person at the right time. Capabilities include: (1) monitoring communications in chat rooms and other sources, (2) automatically plotting tactical graphics in a common operating picture, (3) reporting the current tactical situation, and (4) recommending courses of action (COAs) with respect to the necessary staff collaborations, re-tasking of assets, and required reporting. Specifically, two interrelated, hierarchical knowledge graphs based on the Observe, Orient, Decide, and Act (OODA) Loop model workflows and the state of the operational environment, facilitating doctrinally based recommendations for COAs based on available assets and asset capabilities. The knowledge graphs are state traces, measuring the staff cognitive demands across scenario runtimes as dynamic events unfold on the battlefield. Mission Command performance metrics can be automatically derived from the traces. Last, we discuss the potential of this technological approach to support Control and Command agility.
Blautia stercoris sp. nov., isolated from human faeces (2011)

Strain GAM6-1T is a novel, strictly anaerobic, non-spore-forming, Gram-stain-positive bacterium that was isolated from the faeces of a healthy individual. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GAM6-1T was most closely related to Blautia producta ATCC 27340T (95.7 % sequence similarity), in the family Lachnospiraceae. Strain GAM6-1T did not exhibit catalase or oxidase activity. The strain's cellular fatty acids were of the straight-chain saturated and mono-unsaturated types, with C14:0 (24.10 %), C16:0 (19.09 %) and C16:0 dimethylacetal (14.35 %) predominant. Strain GAM6-1T was able to produce acid from various carbohydrates. Glucose fermentation produced acetic acid as the major short-chain fatty acid. The genomic DNA G+C content of strain GAM6-1T was 35.6 mol%. Based on phenotypic, genotypic and phylogenetic evidence, strain GAM6-1T (=KCTC 5981T=JCM 17204T) is considered to represent a novel species, for which the name Blautia stercoris sp. nov. is proposed.
I. Selective Protection of α- or Side-chain Carboxyl Groups of Aspartic and Glutamic Acid. A Facile Synthesis of β-Aspartyl and γ-Glutamyl Peptides (1969)

(S)-3-Benzyloxycarbonyl-5-oxo-4-oxazolidineacetic acid (IIa) and (S)-3-benzyloxycarbonyl-5-oxo-4-oxazolidinepropionic acid (IIb) were utilized for the selective protection of side-chain carboxyl group of corresponding α-aminodicarboxylic acids and the synthesis of β-aspartyl and γ-glutamyl peptides as an α-carboxyl protected intermediates. It was found that 5-oxazolidinone ring, the α-carboxyl protecting group, was easily removed under not only the condition of alkaline hydrolysis but also catalytic hydrogenolysis. Thus a facile synthesis of β-aspartyl and γ-glutamyl peptides was achieved by the coupling of IIa and IIb with benzyl ester of amino acids and peptides followed by hydrogenolytic removal of all the protecting groups.
Fourier interpolation stochastic optical fluctuation imaging (2015)

Stochastic Optical Fluctuation Imaging (SOFI) is a super-resolution fluorescence microscopy technique which allows to enhance the spatial resolution of an image by evaluating the temporal fluctuations of blinking fluorescent emitters. SOFI is not based on the identification and localization of single molecules such as in the widely used Photoactivation Localization Microsopy (PALM) or Stochastic Optical Reconstruction Microscopy (STORM), but computes a superresolved image via temporal cumulants from a recorded movie. A technical challenge hereby is that, when directly applying the SOFI algorithm to a movie of raw images, the pixel size of the final SOFI image is the same as that of the original images, which becomes problematic when the final SOFI resolution is much smaller than this value. In the past, sophisticated cross-correlation schemes have been used for tackling this problem. Here, we present an alternative, exact, straightforward, and simple solution using an interpolation scheme based on Fourier transforms. We exemplify the method on simulated and experimental data.
In search of a novel target — Phosphatidylserine exposed by non-apoptotic tumor cells and metastases of malignancies with poor treatment efficacy (2011)

This study was performed in the aim to identify potential targets for the development of novel therapy to treat cancer with poor outcome or treatment efficacy. We show that the negatively charged phospholipid phosphatidylserine (PS) is exposed in the outer leaflet of their plasma membrane not only in tumor cell lines, but also in metastases and primary cultures thereof, which contrasts with a lack of PS exposure by differentiated non-tumorigenic counterparts. Studied tumor cell lines were derived from non-tumorigenic and malignant melanomas, prostate- and renal cancer, glioblastoma and a rhabdomyosarcoma. Importantly, also metastases of melanoma expose PS and there is a correlation between malignancy of melanoma cell lines from different stages of tumor progression and PS exposure. The PS exposure we found was neither of apoptotic nor of experimental artificial origin. Finally potentially malignant and non-malignant cells could be differentiated by sorting of a primary cell culture derived from a glioblastoma based on PS exposure, which has so far not been possible within one culture due to lack of a specific marker. Our data provide clear evidence that PS could serve as uniform marker of tumor cells and metastases as well as a target for novel therapeutic approaches based on e.g. PS-specific host defense derived peptides.
THE RADAR ARCHITECTURE FOR PERSONAL COGNITIVE ASSISTANCE (2007)

Current desktop environments provide weak support for carrying out complex user-oriented tasks. Although individual applications are becoming increasingly sophisticated and feature-rich, users must map their high-level goals to the low-level operational vocabulary of applications, and deal with a myriad of routine tasks (such as keeping up with email, keeping calendars and websites up-to-date, etc.). An alternative vision is that of a personal cognitive assistant. Like a good secretary, such an assistant would help users accomplish their high-level goals, coordinating the use of multiple applications, automatically handling routine tasks, and, most importantly, adapting to the individual needs of a user over time. In this paper we describe the architecture and its implementation for a personal cognitive assistant called RADAR. Key features include. (a) extensibility through the use of a plug-in agent architecture. (b) transparent integration with legacy applications and data of today's desktop environments, and. (c) extensive use of learning so that the environment adapts to the individual user over time.
Monotherapy with mastic does not eradicate Helicobacter pylori infection from mice (2003)

Despite reported beneficial effects in ulcer patients and the good in vitro activity of mastic against H. pylori, this compound is unable to eradicate H. pylori infection from mice.
[The suitability of selected humic acid batches as culture media additives for isolating thermophilic Campylobacter species]. (1990)

Using freshly poured respectively five days under light and air stored Campylobacter media blood or lignite humic acids containing Mueller-Hinton-Agar proved to be better for isolation of a Campylobacter field strain than unsupplemented or peat humic acids containing media. The observed differences between the used media are probably caused by three different ability to prevent the accumulation of a photochemically induced toxicity by storing of media under light and air. The storage of blood respectively lignite humic acids containing media over fourteen days under dark and air leads to a time and trend dependent decrease of the colony counts of the Campylobacter field strain. By means of equations of spline functions the observed decrease in ability of media to support the growth of thermophilic Campylobacter can be described mathematically. By using the mathematical model the theoretical extend of growth of Campylobacter on the media can be determinate with respect to the applied inoculum and to the time of storage of media. The cause of decrease in the isolations rate with respect to the time of storage and the cause of different effectiveness of the used humic acids in the media are discussed.
Identification of a μ-δ opioid receptor heteromer-biased agonist with antinociceptive activity (2013)

G protein-coupled receptors play a pivotal role in many physiological signaling pathways. Mounting evidence suggests that G protein-coupled receptors, including opioid receptors, form dimers, and dimerization is necessary for receptor maturation, signaling, and trafficking. However, the physiological role of dimerization in vivo has not been well-explored because of the lack of tools to study these dimers in endogenous systems. To address this problem, we previously generated antibodies to μ-δ opioid receptor (μOR-δOR) dimers and used them to study the pharmacology and signaling by this heteromer. We also showed that the heteromer exhibits restricted distribution in the brain and that its abundance is increased in response to chronic morphine administration. Thus, the μOR-δOR heteromer represents a potentially unique target for the development of therapeutics to treat pain. Here, we report the identification of compounds targeting μOR-δOR heteromers through high-throughput screening of a small-molecule library. These compounds exhibit activity in μOR-δOR cells but not μOR or δOR cells alone. Among them, CYM51010 was found to be a μOR-δOR-biased ligand, because its activity is blocked by the μOR-δOR heteromer antibody. Notably, systemic administration of CYM51010 induced antinociceptive activity similar to morphine, and chronic administration of CYM51010 resulted in lesser antinociceptive tolerance compared with morphine. Taken together, these results suggest that CYM51010, a μOR-δOR-biased ligand, could serve as a scaffold for the development of a unique type (heteromer-biased) of drug that is more potent and without the severe side effects associated with conventional clinical opioids.
Towards optimizing hadoop provisioning in the cloud (2009)

Data analytics is becoming increasingly prominent in a variety of application areas ranging from extracting business intelligence to processing data from scientific studies. MapReduce programming paradigm lends itself well to these data-intensive analytics jobs, given its ability to scale-out and leverage several machines to parallely process data. In this work we argue that such MapReduce-based analytics are particularly synergistic with the pay-as-you-go model of a cloud platform. However, a key challenge facing end-users in this environment is the ability to provision MapReduce applications to minimize the incurred cost, while obtaining the best performance. This paper first motivates the importance of optimally provisioning a MapReduce job, and demonstrates that existing approaches can result in far from optimal provisioning. We then present a preliminary approach that improves MapReduce provisioning by analyzing and comparing resource consumption of the application at hand with a database of similar resource consumption signatures of other applications. 1
Development of a stable dual cell‐line GFP expression system to study estrogenic endocrine disruptors (2008)

Environmental estrogenic endocrine disruptors are a health concern. Here we constructed a dual cell-line green fluorescence protein (GFP) expression system to identify and study endocrine disrupting compounds with activities of estrogen receptor agonists or antagonists. Human breast cancer MCF-7 cells and endometrial carcinoma Ishikawa cells were infected with a two tandem estrogen response elements--E4 promoter-GFP reporter gene construct. The use of GFP reporter enabled direct and simple evaluations of cell responses. GFP intensity in stably transfected MCF7-GFP and Ishikawa-GFP cells was dose-responsive to 17-beta-estradiol, diethylstilbestrol, 2-hydroxyestradiol, and environmental toxins bisphenol A, genistein and o-p'-DDT. Raloxifene and tamoxifen were effective antiestrogens in MCF7-GFP cells, but acted as partial estrogen receptor agonists in Ishikawa-GFP cells at concentrations of 0.1 nM and above. No synergistic effect was observed in chemical combinations between organochlorine pesticides methoxychlor, o-p'-DDT, p-p'-DDT, nor between estradiol and estrone. In summary, for the first time the effects of estrogen receptor agonists or antagonists were compared between mammary and endometrial cancer cells both stably expressing identical plasmids with GFP reporter genes under the control of tandem estrogen response elements. This dual cell-line system provides a rapid method and sensitive assay to identify environmental estrogens, antiestrogens, selective estrogen receptor modulators and to study their tissue specific effects and chemical interactions. Such a system is especially useful for direct and parallel toxicity assessments with a microfluidic cell culture device.
Identification of two isoforms of the Cak receptor kinase that are coexpressed in breast tumor cell lines. (1996)

The Cak receptor kinase is a member of a novel family of receptors that are characterized by the unique structure of the ectodomains. We have identified a new isoform of Cak that differs from the original isolate by the deletion of 37 amino acids in the cytoplasmic juxtamembrane sequence. Analysis of the genomic sequence suggests that the two isoforms arise by exon skipping. The isoform-specific insert contains the motif NPXY, which was previously shown to be involved in diverse signaling function in a number of receptors. By RNase protection analyses, we found that the long isoform, Cak I is expressed at three- to sevenfold the abundance of the short isoform (Cak II). By Western blotting, Cak I receptor was found to be expressed in mouse embryos and in adult brain. Cak II protein was not detected in mouse embryos or adult tissues, but is abundantly expressed in some breast tumor cell lines. The expression profile of Cak suggests that its primary function is likely to be in developmental regulation. The coexpression of the Cak isoforms in some epithelial cell lines suggests that heterodimer formation may be a key feature in the function of the receptor.