gebhart/patrepeval huggingface dataset:
Building Your Own Big Data Analysis Infrastructure for Biodiversity Science (2017)

The size of biodiversity data sets, and the size of people’s questions around them, are outgrowing the capabilities of desktop applications, single computers, and single developers. Numerous articles in the corporate sector (Delgado 2016) have been written on how much time professionals spend manipulating and formatting large data sets compared to the time they spend on the important work of doing analysis and modeling. To efficiently move large research questions forward, the biodiversity domain needs to transition towards shared infrastructure with the goal of providing a mise en place for researchers to do research with large data. The GUODA (Global Unified Open Data Access) collaboration was formed to explore tools and use cases for this type of collaborative work on entire biodiversity data sets. Three key parts of that exploration have been: the software and hardware infrastructure needed to be able to work with hundreds of millions of records and terabytes of data quickly, removing the impediment of data formatting and preparation, and workflows centered around GitHub for interacting with peers in an open and collaborative manner. We will describe our experiences building an infrastructure based on Apache Mesos, Apache Spark, HDFS, Jupyter Notebooks, Jenkins, and Github. We will also enumerate what resources are needed to do things like join millions of records, visualize patterns in whole data sets like iDigBio and the Biodiversity Heritage Library, build graph structures of billions of nodes, analyze terabytes of images, and use natural language processing to explore gigabytes of text. In addition to the hardware and software, we will describe the kinds of skills needed by staff to design, build, and use this sort of infrastructure and highlight some experiences we have with training students. Our infrastructure is one of many that are possible. We hope that by showing the amount and type of work we have done to the wider community, other organizations can understand what they would need to speed up their research programs by developing their own collaborative computation and development environments.
Magnetic Field Measurement using Scanning Magnetoresistance Microscope with Spin-Valve Sensor (2006)

We developed a new microfabricated cantilever with a spin-valve sensor (MR cantilever) for a scanning magnetoresistance microscope (SMRM). Since the spin-valve sensor has a self-biasing mechanism, it allows the SMRM to respond to the observed magnetic field linearly without any external bias magnetic field, hence making the SMRM more sensitive to magnetic fields. We successfully obtained SMRM images of a magnetic garnet thin film using the new MR cantilever.
Expression Profiles of Antimicrobial Peptides in the Genital Tract of Women Using Progesterone Intrauterine Devices Versus Combined Oral Contraceptives (2014)

The use of hormonal contraceptives influences AMP expression differently in genital secretions compared to ectocervical tissue. This suggests that the impact of sex hormones on local immune defenses varies in different compartments of the FGM, and likely in different locations across the FGT.
<i>Coxiella burnetii</i>, the agent of Q fever, stimulates an atypical M2 activation program in human macrophages (2008)

Coxiella burnetii is an obligate intracellular bacterium, responsible for Q fever, which survives in macrophages by interfering with their microbicidal competence. As functional polarization of macrophages is critical for their microbicidal activity, we studied the activation program of monocyte-derived macrophages (MDM) stimulated with C. burnetii. This program was markedly distinct from that induced by lipopolysaccharides (LPS), a canonical inducer of M1 polarization. Indeed, C. burnetii up-regulated the expression of genes associated with M2 polarization, including TGF-beta1, IL-1 receptor antagonist (IL-1ra), CCL18, the mannose receptor and arginase-1, and only up-regulated the expression of two genes associated with M1 polarization, namely IL-6 and CXCL8. In contrast, C. burnetii down-regulated the expression of genes associated with M1 polarization such as TNF, CD80, CCR7 and TLR-2. Functional analyses showed that C. burnetii-stimulated MDM produced high levels of TGF-beta1 and CCL18, and expressed the mannose receptor and arginase-1, the latter being associated with the prevention of nitric oxide production by MDM. Finally, C. burnetii induced the release of IL-6 and CXCL8 at a lower level than LPS-stimulated MDM. Our results suggest that C. burnetii stimulated an atypical M2 activation program that may account for the persistence of C. burnetii in macrophages.
Tailoring of the porous structure of soft emulsion-templated polymer materials (2016)

This paper discusses the formation of soft porous materials obtained by the polymerization of inverse water-in-silicone (polydimethylsiloxane, PDMS) emulsions. We show that the initial state of the emulsion has a strong impact on the porous structure and properties of the final material. We show that using a surfactant with different solubilities in the emulsion continuous phase (PDMS), it is possible to tune the interaction between emulsion droplets, which leads to materials with either interconnected or isolated pores. These two systems present completely different behavior upon drying, which results in macroporous air-filled materials in the interconnected case and in a collapsed material with low porosity in the second case. Finally, we compare the mechanical and acoustical properties of these two types of bulk polymer monoliths. We also describe the formation of micrometric polymer particles (beads) in these two cases. We show that materials with an interconnected macroporous structure have low mechanical moduli and low sound speed, and are suitable for acoustic applications. The mechanical and acoustical properties of the materials with a collapsed porous structure are similar to those of non-porous silicone, which makes them acoustically inactive.
SRAM supply voltage scaling: A reliability perspective (2009)

SRAM leakage power is a significan fraction of the total power consumption on a chip. Various system level techniques have been proposed to reduce this leakage-power by reducing (scaling) the supply voltage. SRAM supply voltage scaling reduces the leakage-power, but it increases stored-data failure rate due to commonly known failure mechanisms, for example, soft-errors. This work studies SRAM leakage-power reduction using system level design techniques, with a data-reliability constraint. A statistical or probabilistic setup is used to model failure mechanisms like soft-errors or process-variations, and error-probability is used as a metric for reliability. Error models which combine various SRAM cell failure mechanisms are developed. In a probabilistic setup, the bit-error probability increases due to supply voltage reduction, but it can be compensated by suitable choices of error-correction code and data-refresh (scrubbing) rate. The trade-offs between leakage-power, supply voltage reduction, data-refresh rate, error-correction code, and decoding error probability are studied. The leakage-power - including redundancy overhead, coding power, and data-refresh power - is set as the cost-function and an error-probability target is set as the constraint. The cost-function is minimized subject to the constraint, over the choices of data-refresh rate, error-correction code, and supply voltage. Using this optimization procedure, simulation results and circuit-level leakage-power reduction estimates are presented.
Effect of Herpes Simplex Virus Type 2 Infection on Mitochondrial Gene Expression (1988)

Summary A cDNA clone derived from the mitochondrial cytochrome oxidase I gene has been used to show that the level of mitochondrially encoded RNA species declines during herpes simplex virus type 2 infection in a manner similar to that for RNA species derived from nuclear genes. In contrast to the situation for nuclear genes, however, no change in the transcription rate of the mitochondrial genome during infection was detected, indicating that post-transcriptional processes alone are responsible for the decline in the levels of mitochondrial RNA species during infection. Two stages in this post-transcriptional degradation have been defined, only one of which is dependent upon viral protein synthesis in the infected cell.
Optical Implementations In Boltzmann Machines (1987)

Boltzmann machines can be used to obtain solutions to problems for which direct mathematical calculation of a solution is not possible or would take too long. The range of problems for which such a machine might be useful is very broad, and inversion of a linear equation is described as one example. A method is described that allows time-intensive operations on a computer to be replaced with a highly parallel optical system that can be incorporated in such a way as to let the computer take full advantage of the speed of the optics without sacrificing the precision possible in the computer. A tie is made between Boltzmann machines and neural networks, and it is shown how a Boltzmann machine may perform functions demonstrated by other neural network architectures.
Thin-layer chromatographic and high resolution mass spectrometric determination of .beta.-hydroxyphenylethylamines in tissues as dansyl-acetyl derivatives (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThin-layer chromatographic and high resolution mass spectrometric determination of .beta.-hydroxyphenylethylamines in tissues as dansyl-acetyl derivativesDavid A. Durden, Augusto V. Juorio, and Bruce A. DavisCite this: Anal. Chem. 1980, 52, 12, 1815–1820Publication Date (Print):October 1, 1980Publication History Published online1 May 2002Published inissue 1 October 1980https://pubs.acs.org/doi/10.1021/ac50062a009https://doi.org/10.1021/ac50062a009research-articleACS PublicationsRequest reuse permissionsArticle Views494Altmetric-Citations28LEARN 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
Axial bond length contraction in CuX5 complexes. Structures of hexaamminechromium(III) pentabromocuprate(II) and hexaamminechromium(III) tribomodichlorocuprate(II) (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAxial bond length contraction in CuX5 complexes. Structures of hexaamminechromium(III) pentabromocuprate(II) and hexaamminechromium(III) tribomodichlorocuprate(II)Steven A. Goldfield and Kenneth N. RaymondCite this: Inorg. Chem. 1971, 10, 11, 2604–2607Publication Date (Print):November 1, 1971Publication History Published online1 May 2002Published inissue 1 November 1971https://pubs.acs.org/doi/10.1021/ic50105a047https://doi.org/10.1021/ic50105a047research-articleACS PublicationsRequest reuse permissionsArticle Views51Altmetric-Citations24LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Enhanced Light Extraction from Organic Light‐Emitting Diodes with 2D SiO<sub>2</sub>/SiN<i><sub>x</sub></i> Photonic Crystals (2003)

The introduction of a 2D photonic crystal layer is demonstrated to be an effective way to solve light trapping problems in organic light emitting diodes (OLEDs). The overall effect of the photonic crystal structure on the performance of the OLED is investigated by means of current–voltage–luminance measurements and lifetime tests. A schematic of the structure of the OLED device is shown in the Figure.
Set-at-a-time access to XML through DOM (2003)

To support the rapid growth of the web and e-commerce, W3C developed DOM as an application programming interface that provides the abstract, logical tree structure of an XML document. In this paper, we propose ordered-set-at-a-time extensions for DOM while maintaining its tightly managed navigational nature. In particular, we define the NodeSequence interface with functions that filter, navigate, and transform sequences of nodes simultaneously. The extended DOM greatly simplifies writing some application code, and it can reduce the communications overhead and response time between a client application and the DOM server to provide applications with more efficient processing. As validation of our proposals, we present application examples that compare the convenience and efficiency of DOM with and without extensions.
The use of mesenchymal stromal cells in acute and chronic heart disease (2016)

This chapter examines the therapeutic use of Mesenchymal stromal cells (MSCs) for acute and chronic ischemic heart disease in the preclinical and clinical setting as well as the possible mechanisms involved in their reversal of cardiac remodeling. MSCs are a particularly attractive candidate due to their ease of isolation, immune privilege, ability to stimulate endogenous cardiac stem cells (CSCs), and the release of beneficial paracrine factors. MSCs are particularly effective in preventing abnormal cardiac remodeling in the setting of acute MI (AMI) owing to their potent immunomodulatory properties, which are particularly important for the use of allogeneic MSCs. The antifibrotic effects of MSCs are accompanied by both cardiomyogenesis and neovascularization. Possible mechanisms leading to vasculogenesis include the differentiation of MSCs into vascular smooth muscle cells and endothelial cells, the release of pro-angiogenic and pro-arteriogenic paracrine factors, as well as the recruitment of endothelial progenitor cells (EPCs).
A multi-dimensional evaluation of the nanomanipulator, a scientific sollaboration system (1999)

The nanoManipulator system provides a natural scientist with the ability to interact directly with materials ranging in size from DNA to cells (Finch, Chi, Taylor II, Falvo, Washburn, &amp; Superfine, 1995). By providing a virtual environment interface to an atomic force microscope (AFM), the nanoManipulator allows users to see, feel, and modify individual biological samples or groups of samples in a fluid or dry environment. A distributed version of the nanoManipulator is under development. This will allow scientists to conduct experiments and collaborate across distances during the scientific process (Brooks, Jr., et al., 1998).We are evaluating the distributed nanoManipulator and its impact on scientific collaboration using a multi-dimensional framework (see Fig. 1).This framework highlights the importance of examining process and outcome in research, scientific experimentation, and collaboration technology. Each of these dimensions suggests important questions whose answers will help determine if collaboration technology will fit into and support and/or change the process of research and scientific experimentation. Each of these dimensions is discussed below.
Properties of Nanomodified Fiber-Reinforced Cementitious Composites (2017)

This paper presents the development of nanomodified fiber-reinforced cementitious composite (FRCC) mixtures. A total of seven mixtures were prepared using general use cement and a constant dosage of slag (40% replacement by mass of the base binder). Also, nanosilica was incorporated in six mixtures at a dosage of 6% by mass of the base binder, whereas one mixture was without nanosilica as a reference. Basalt fiber (BF) pellets (made of basalt fibers encapsulated by polyamide resin) were used to produce BFRCC. Three mixtures had BF pellets with different lengths (25 mm, 36 mm, or both), whereas two mixtures incorporated BF pellets and polypropylene fibers. The performance of the cementitious composites was evaluated in terms of compressive and flexural strengths and toughness. In addition, the bond strength of glass fiber-reinforced polymer (GFRP) bars embedded in either the cementitious composites or normal-strength concrete was determined. Test results revealed that adding 2.5% by volume of 36-mm-long BF pellets to the mixture achieved the best performance. This BFRCC favorably showed high residual flexural strength and ductility compared to those of other mixtures. Furthermore, it achieved better bond strength to GFRP bars compared to both the nanomodified mixture without fibers and normal strength concrete.
Tumour necrosis factor a during human pregnancy and labour: maternal plasma and amniotic fluid concentrations and release from intrauterine tissues (1994)

The aims of this study were: to quantify immunoreactive tumour necrosis factor alpha (TNF-alpha) concentrations in maternal plasma and amniotic fluid obtained from women during pregnancy and labour, both at term and preterm; and to establish the effects of bacterial endotoxin and cytokines on the in vitro release of TNF-alpha from intrauterine tissues. Maternal plasma TNF-alpha concentrations did not change during pregnancy (457.2 +/- 102.9 ng/l, mean +/- SEM, N = 52) or at the time of labour (543.5 +/- 138.6 ng/l, N = 43). In contrast, amniotic fluid TNF-alpha concentrations increased significantly (p < 0.05) during pregnancy (early pregnancy, EP, 93.0 +/- 24.8 ng/l, N = 7; preterm not-in-labour, PNIL, 186.8 +/- 42.9 ng/l, N = 16; term not-in-labour. TNIL, 499.7 +/- 150.9 ng/l, N = 13) and in association with preterm labour (preterm in-labour, PIL, 958.7 +/- 575.6 ng/l, N = 5 vs PNIL, 186.8 +/- 42.9 ng/l, N = 16). Choriodecidual and placental explants (N = 3) maintained in in vitro culture released TNF-alpha. Furthermore, the release of TNF-alpha was increased significantly (p < 0.05) by bacterial endotoxin (lipopolysaccharide, 10 ng/l-10 mg/l) but was not affected by the following cytokines at the indicated doses: interleukin-1 alpha (0.28 nmol/l), interleukin-6 (12.5 nmol/l), granulocyte colony-stimulating factor (2.5 nmol/l), granulocyte-macrophage colony-stimulating factor (35 nmol/l), macrophage colony-stimulating factor (1.2 nmol/l), leukaemia inhibitory factor (0.45 nmol/l) and transforming growth factor-beta (0.4 nmol/l).(ABSTRACT TRUNCATED AT 250 WORDS)
Inhibitory Effects of <i>Coptidis rhizoma</i> and Berberine on Cocaine‐Induced Sensitization (2007)

Substantial evidence suggests that the behavioral and reinforcing effects of cocaine can be mediated by the central dopaminergic systems. Repeated injections of cocaine produce an increase in locomotor activity and the expression of tyrosine hydroxylase (TH) in the main dopaminergic areas. Protoberberine alkaloids affect neuronal functions. Coptidis rhizoma (CR) and its main compound, berberine (BER) reduced the dopamine content in the central nervous system. In order to investigate the effects of CR or BER on the repeated cocaine-induced neuronal and behavioral alterations, we examined the influence of CR or BER on the repeated cocaine-induced locomotor activity and the expression of TH in the brain by using immunohistochemistry. Male SD rats were given repeated injections of saline or cocaine hydrochloride (15 mg/kg, i.p. for 10 consecutive days) followed by one challenge injection on the 4th day after the last daily injection. Cocaine challenge (15 mg/kg, i.p) produced a larger increase in locomotor activity and expression of TH in the central dopaminergic areas. Pretreatment with CR (50, 100, 200 and 400 mg/kg, p.o.) and BER (200 mg/kg, p.o.) 30 min before the daily injections of cocaine significantly inhibited the cocaine-induced locomotor activity as well as TH expression in the central dopaminergic areas. Our data demonstrate that the inhibitory effects of CR and BER on the repeated cocaine-induced locomotor activity were closely associated with the reduction of dopamine biosynthesis and post-synaptic neuronal activity. These results suggest that CR and BER may be effective for inhibiting the behavioral effects of cocaine by possibly modulating the central dopaminergic system.
Reactivation of Latent Tuberculosis Infection in TNF-Deficient Mice (2003)

TNF-deficient mice are highly susceptible to Mycobacterium tuberculosis H37Rv infection. Here we asked whether TNF is required for postinfectious immunity in aerosol-infected mice. Chemotherapy for 4 wk commencing 2 wk postinfection reduced CFU to undetectable levels. While wild-type mice had a slight rise in CFU, but controlled infection upon cessation of chemotherapy, TNF-deficient mice developed reactivation of infection with high bacterial loads in lungs, spleen, and liver, which was fatal within 13-18 wk. The increased susceptibility of TNF-deficient mice was accompanied by diminished recruitment and activation of T cells and macrophages into the lung, with defective granuloma formation and reduced inducible NO synthase expression. Reduced chemokine production in the lung might explain suboptimal recruitment and activation of T cells and uncontrolled infection. Therefore, despite a massive reduction of the mycobacterial load by chemotherapy, TNF-deficient mice were unable to compensate and mount a protective immune response. In conclusion, endogenous TNF is critical to maintain latent tuberculosis infection, and in its absence no specific immunity is generated.
Simvastatin inhibits cytokine‐stimulated Cyr61 expression in osteoblastic cells: A therapeutic benefit for arthritis (2010)

Simvastatin inhibited cytokine-stimulated Cyr61 expression in osteoblastic cells and suppressed disease progression and osteoblastic expression of Cyr61 in inflammatory arthritis. This finding indicates that simvastatin may have potential as a therapeutic agent for inflammatory arthritis.