gebhart/patrepeval huggingface dataset:
Performance Modeling and Empirical Measurements in a System Designed for Batch and Time-Sharing Users (1899)

If any design goal is common to all computer system organization schemes, it is that of providing both externally to the user of the computational facility and internally with respect to utilization of system resources. Thus, generally speaking, there are at least two dimensions to this design objective. On the one hand, effective service is the external satisfaction of a broad spectrum of user demands. For example, the ideal system might be visualized as one which economically provides a large number of programming languages; machine compatibility with other computers of widely diverse hardware; and rapid computation. On the other hand, effective service is the internal utilization of all system components so as to increase computational efficiency. In this respect, system structures are implemented which strive to maximize sub-system simultaneity and system throughput. For example, a degree of macro-parallelism is attained in many present day systems by allowing a central processing unit (CPU) and input/output controller to share the use of a main memory register, thereby enabling processing and input/output (I/O) to proceed concurrently (for one or several independent programs, depending upon the system software).
An efficient synthetic route to (.+-.)-nanaomycin A (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn efficient synthetic route to (.+-.)-nanaomycin ATadashi Kometani, Yoshio Takeuchi, and Eiichi YoshiiCite this: J. Org. Chem. 1983, 48, 15, 2630–2632Publication Date (Print):July 1, 1983Publication History Published online1 May 2002Published inissue 1 July 1983https://pubs.acs.org/doi/10.1021/jo00163a051https://doi.org/10.1021/jo00163a051research-articleACS PublicationsRequest reuse permissionsArticle Views252Altmetric-Citations29LEARN 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
High-index overlay for high reflectance DBR gratings in LiNbO/sub 3/ channel waveguides (1997)

A thin overlay of high refractive index material is used to obtain high reflectance DBR waveguides in lithium niobate. Silicon, deposited by e-beam evaporation, is found to be a suitable material for this purpose because of its high refractive index, transparency to 1.3- and 1.5-μm wavelengths, opacity to the visible spectrum, and ease of etching. Experimental results match the theory extremely well and, to the best of our knowledge, exhibit the highest reflection per unit length from a lithium niobate corrugated waveguide reported to date on on insulator technology, waveguide filters.
Suzaku observation of TeV blazar the 1ES 1218+304: clues on particle acceleration in an extreme TeV blazar (2008)

We observed the TeV blazar 1ES 1218+304 with the X-ray astronomy satellite Suzaku in May 2006. At the beginning of the two-day continuous observation, we detected a large flare in which the 5-10 keV flux changed by a factor of ~2 on a timescale of 5x10^4 s. During the flare, the increase in the hard X-ray flux clearly lagged behind that observed in the soft X-rays, with the maximum lag of 2.3x10^4 s observed between the 0.3-1 keV and 5-10 keV bands. Furthermore we discovered that the temporal profile of the flare clearly changes with energy, being more symmetric at higher energies. From the spectral fitting of multi-wavelength data assuming a one-zone, homogeneous synchrotron self-Compton model, we obtain B~0.047 G, emission region size R = 3.0x10^16 cm for an appropriate beaming with a Doppler factor of delta = 20. This value of B is in good agreement with an independent estimate through the model fit to the observed time lag ascribing the energy-dependent variability to differential acceleration timescale of relativistic electrons provided that the gyro-factor ξis 10^5.
Expression of CD14 by Hepatocytes: Upregulation by Cytokines during Endotoxemia (1998)

Studies were undertaken to examine hepatocyte CD14 expression during endotoxemia. Our results show that lipopolysaccharide (LPS) treatment in vivo caused a marked upregulation in CD14 mRNA and protein levels in rat hepatocytes. Detectable increases in mRNA were seen as early as 1.5 h after LPS treatment; these increases peaked at 20-fold by 3 h and returned to baseline levels by 24 h. In situ hybridization localized the CD14 mRNA expression to hepatocytes both in vitro and in vivo. Increases in hepatic CD14 protein levels were detectable by 3 h and peaked at 12 h. Hepatocytes from LPS-treated animals expressed greater amounts of cell-associated CD14 protein, and more of the soluble CD14 was released by hepatocytes from LPS-treated rats in vitro. The increases in hepatocyte CD14 expression during endotoxemia occurred in parallel to increases of CD14 levels in plasma. To provide molecular identification of the hepatocyte CD14, we cloned the rat liver CD14 cDNA. The longest clone consists of a 1,591-bp insert containing a 1,116-bp open reading frame. The deduced amino acid sequence is 372 amino acids long, has 81.8 and 62.8% homology to the amino acid sequences of mouse and human CD14, respectively, and is identical to the rat macrophage CD14. The expressed CD14 protein from this clone was functional, as indicated by NF-kappaB activation in response to LPS and fluorescein isothiocyanate-LPS binding in CHO cells stably transfected with rat CD14. A nuclear run-on assay showed that CD14 transcription rates were significantly increased in hepatocytes from LPS-treated animals, indicating that the upregulation in CD14 mRNA levels observed in rat hepatocytes after LPS treatment is dependent, in part, on increased transcription. In vitro and in vivo experiments indicated that interleukin-1beta and/or tumor necrosis factor alpha participate in the upregulation of CD14 mRNA levels in hepatocytes. Our data indicate that hepatocytes express CD14 and that hepatocyte CD14 mRNA and protein levels increase rapidly during endotoxemia. Our observations also support the idea that soluble CD14 is an acute-phase protein and that hepatocytes could be a source for soluble CD14 production.
Nuclei segmentation of fluorescence microscopy images using convolutional neural networks (2017)

Fluorescence microscopy has emerged as a powerful tool for studying cell biology because it enables the acquisition of 3D image volumes deeper into tissue and the imaging of complex subcellular structures. Quantitative analysis of these structures, which is needed to characterize the structure and constitution of tissue volumes, is facilitated by nuclei segmentation. However, manual segmentation is a laborious and intractable process due to the size and complexity of the data. In this paper, we describe a nuclei segmentation method using a deep convolutional neural network, data augmentation to generate training images of different shapes and contrasts, a refinement process combining segmentation results of horizontal, frontal, and sagittal planes in a volume, and a watershed technique to count the number of nuclei. Our results indicate that compared to 3D ground truth data, our method is able to successfully segment and count 3D nuclei.
Production and partial characterization of cellulase free xylanase by Bacillus subtilis C 01 using agriresidues and its application in biobleaching of nonwoody plant pulps (2007)

This is the first report on biobleaching of banana fibres, silk cotton and cotton pulps using xylanase. The biobleaching results of secondary fibres are promising and can be transferred to paper mills, which utilize nonwoody plant fibres as a raw material for paper production.
Automated Radioanalytical System Incorporating Microwave-Assisted Sample Preparation, Chemical Separation, and Online Radiometric Detection for the Monitoring of Total <sup>99</sup>Tc in Nuclear Waste Processing Streams (2012)

An automated fluidic instrument is described that rapidly determines the total (99)Tc content of aged nuclear waste samples, where the matrix is chemically and radiologically complex and the existing speciation of the (99)Tc is variable. The monitor links microwave-assisted sample preparation with an automated anion exchange column separation and detection using a flow-through solid scintillator detector. The sample preparation steps acidify the sample, decompose organics, and convert all Tc species to the pertechnetate anion. The column-based anion exchange procedure separates the pertechnetate from the complex sample matrix, so that radiometric detection can provide accurate measurement of (99)Tc. We developed a preprogrammed spike addition procedure to automatically determine matrix-matched calibration. The overall measurement efficiency that is determined simultaneously provides a self-diagnostic parameter for the radiochemical separation and overall instrument function. Continuous, automated operation was demonstrated over the course of 54 h, which resulted in the analysis of 215 samples plus 54 hly spike-addition samples, with consistent overall measurement efficiency for the operation of the monitor. A sample can be processed and measured automatically in just 12.5 min with a detection limit of 23.5 Bq/mL of (99)Tc in low activity waste (0.495 mL sample volume), with better than 10% RSD precision at concentrations above the quantification limit. This rapid automated analysis method was developed to support nuclear waste processing operations planned for the Hanford nuclear site.
A comparison study of automatic speech quality assessors sensitive to packet loss burstiness (2011)

The paper delves the behavior rating of new emerging automatic quality assessors of VoIP calls subject to bursty packet loss process. The examined speech quality assessment (SQA) algorithms are able to estimate speech quality of live VoIP calls at run-time using control information extracted from header content of received packets. They are especially designed to be sensitive to packet loss burstiness. The performance evaluation study is performed using a dedicated set-up software-based SQA framework. It offers a personalized packet killer and includes implementation of four SQA algorithms. A speech quality database, which covers a wide range of bursty packet loss conditions, has been created then thoroughly analyzed. Our important findings are the following: (1) all examined automatic bursty-loss aware speech quality assessors achieve a satisfactory correlation under upper (>;20%) and lower (<;10%) ranges of packet loss process (2) They exhibit a clear weakness to assess speech quality under a moderated packet loss process (3) The accuracy of sequence-by-sequence basis of examined SQA algorithms should be addressed in details for further precision.
In Situ Bioremediation of Perchlorate in Vadose Zone Soil Using Gaseous Electron Donors (2009)

Abstract : Perchlorate is a human health concern because of its ability to inhibit iodide uptake by the thyroid. Perchlorate is present in soil, groundwater, and many potable water supplies. Costs for mitigating these perchlorate impacts can be significant; thus demonstration and validation of cost-effective treatment technologies is critical to the Department of Defense (DoD). While extensive research and technology development on the treatment of perchlorate in water has been conducted, limited research and technology development has been focused on perchlorate in soil. Perchlorate contamination in soil is important because of it can be a source of groundwater contamination. Currently, available technologies for the treatment of perchlorate in soil require excavation and are not always cost-effective or practical, particularly as the depth of contamination increases. When applicable, excavation followed by anaerobic biodegradation has proven to be effective. In situ remediation of perchlorate in soil is an alternative, potentially more cost-effective solution. Gaseous electron donor injection technology or GEDIT (U.S. Patent No. 7,282,149 and patent pending) involves injection of gaseous electron donors into the soil with the purpose of promoting anaerobic biodegradation of perchlorate to water and chloride ion. This technology can be viewed as bioventing in reverse. Bioventing, a proven bioremediation technology for petroleum hydrocarbons, involves the injection of a gaseous electron acceptor (e.g., oxygen) into the vadose zone resulting in the biodegradation of an electron donor (e.g., hydrocarbons). In the present application, the electron acceptor and donor are reversed with the gaseous electron donor being injected in order to biodegrade the electron acceptor (i.e., perchlorate or nitrate).
Load-balance of intra/inter-MANET traffic over multiple internet gateways (2008)

The paper first gives an overview of the required functions for providing Internet connectivity and mobility management for mobile ad-hoc networks (MANETs). Internet gateway selection is one of these functions. Since multiple Internet gateways might exist on the same MANET domain, a hybrid metric for Internet gateway selection is proposed as a replacement of the shortest hop-count metric. The hybrid metric provides load-balancing of intra/inter-MANET traffic. Simulation results show that ad-hoc routing protocols, using our proposed metric get better performance in terms of packet delivery ratio and transmission delay, at the cost of slightly increased signalling overhead.
le-git-imate (2018)

Web-based Git hosting services such as GitHub and GitLab are popular choices to manage and interact with Git repositories. However, they lack an important security feature - the ability to sign Git commits. Users instruct the server to perform repository operations on their behalf and have to trust that the server will execute their requests faithfully. Such trust may be unwarranted though because a malicious or a compromised server may execute the requested actions in an incorrect manner, leading to a different state of the repository than what the user intended.
Phage‐displayed peptides as biosensor reagents (2000)

This study investigated the potential to utilize phage-displayed peptides as reagents in sensor applications. A library of random 12-mers displayed on phage was panned against staphylococcal enterotoxin B (SEB), a causative agent of food poisoning. Nine SEB binding phage clones were isolated, all of which share the consensus sequence Trp His Lys at their amino terminus. Binding of several of these phage was shown to be inhibited when they were assayed in a competitive enzyme-linked immunosorbent assay (ELISA) format with synthesized peptide corresponding to the peptide-encoding region of one of the clones. Whole phage were labeled with the dye Cy5, and incorporated into fluoroimmunoassays. Labeled phage were able to detect SEB down to a concentration of 1.4 ng/well in a fluorescence-based immunoassay. When incorporated into an automated fluorescence-based sensing assay, Cy5-labeled phage bound to probes coated with SEB generated a robust signal of about 10,000 pA, vs a signal of 1000 pA using a control fiber coated with streptavidin. These results demonstrate the potential for development of phage-based sensor reagents. Copyright © 2000 John Wiley & Sons, Ltd. Abbreviations used: SEB staphylococcal enterotoxin B SEB SEA staphylococcal enterotoxin A SEC 1 staphylococcal enterotoxin C1 SED staphylococcal enterotoxin D.
Regional and systemic distribution of anti-tumor x anti-CD3 heteroaggregate antibodies and cultured human peripheral blood lymphocytes in a human colon cancer xenograft. (1990)

Anti-tumor antibody (317G5) covalently coupled to an anti-CD3 antibody (OKT3) produces a heteroaggregate (HA) antibody that can target PBL to lyse tumor cells expressing the appropriate tumor Ag. The i.v. and i.p. distribution of radiolabeled HA antibody 317G5 x OKT3 and of radiolabeled cultured human PBL were studied in athymic nude mice bearing solid intraperitoneal tumor established from the human colon tumor line, LS174T. Mice were injected with 125I-labeled HA antibody, 125I-labeled anti-tumor mAb, or 111In-labeled PBL, and at designated timepoints tissues were harvested and measured for radioactivity. 125I-317G5 x OKT3 localized specifically to tumor sites. Tumor radioactivity levels (percent injected dose/gram) were lower with 125I-317G5 x OKT3 HA antibody than with 125I-317G5 anti-tumor mAb, but were similar to levels reported for other anti-tumor mAb. The major difference in radioactivity levels observed between i.v. and i.p. administration of 125I-317G5 x OKT3 was an increase in hepatic radioactivity after i.v. HA antibody administration. HA antibodies produced from F(ab')2 fragments, which exhibit decreased m. w. and decreased Fc receptor-mediated binding, demonstrated improved tumor:tissue ratios as compared to intact antibody HA. 125I-317G5 F(ab')2 x OKT3 F(ab')2 antibody levels were equivalent to intact HA antibody levels in tumor, but were lower than intact HA antibody levels in the blood, bowel, and liver. Tumor:bowel ratios (20:1 at 48 h) were highest when 317G5 F(ab')2 x OKT3 F(ab')2 was injected i.p. Autoradiography confirmed that anti-tumor x anti-CD3 HA antibodies localized specifically to intraperitoneal tumor; that i.p. administered HA antibodies penetrated tumor directly; and that i.v. administered HA antibodies distributed along tumor vasculature. Cultured human PBL distributed in moderate concentrations to intraperitoneal tumor when administered i.p., but not when administered i.v. The poor localization of i.v. injected PBL to tumor may reflect species disparity in homing receptors and/or endothelial ligands, a problem which may be overcome with a syngeneic model. These results suggest that regional therapy with HA antibodies and PBL may offer advantages over systemic therapy for initial clinical trials.
Down-modulation of interleukin-6 gene expression by 17 beta-estradiol in the absence of high affinity DNA binding by the estrogen receptor. (1994)

The mechanism of repression of the interleukin-6 (IL-6) promoter by 17 beta-estradiol (E2) was investigated in cells transfected with wild-type (wt) or mutant estrogen receptor (ER) expression vectors. In transient transfection experiments, IL-1-induced activation of the IL-6 promoter was efficiently inhibited by wt ER. However, estrogen receptors carrying mutations within or over-lapping with the DNA binding domain did not repress IL-6 promoter activity. A mutant receptor lacking the N-terminal transactivator function-1 but retaining the C-terminal transactivator function-2 also repressed activation of the IL-6 promoter. Our recent experiments indicate the requirement for both the nuclear factor (NF)-IL6 and the NF-kappa B sites in the IL-6 promoter for activation by IL-1. We now show that activation of the IL-6 promoter, elicited by a combination of NF-IL6 and the p65 subunit of NF-kappa B, can be inhibited by the wt receptor but not by a receptor containing a mutation in its DNA binding domain. Although a deletion within the DNA binding domain of ER abolished the repressor function of the receptor, a chimeric receptor ER-GR CAS1, in which the DNA binding domain of ER was swapped with the complementary region from the glucocorticoid receptor, retained the inhibitory effects on the IL-6 promoter. This was in contrast to the absolute dependence of ER on its own DNA binding domain for activation of typical estrogen response element-containing promoters, as reported previously by other investigators. Furthermore, the repression of the IL-6 promoter by a combination of ER and E2, unlike activation of estrogen response elements by the same combination, did not appear to be mediated via high affinity binding of the receptor to the promoter. In functional experiments, the transactivator function of ER was totally inhibited by overexpression of p65 and to a lesser extent by that of NF-IL6. These results indicate that ER may repress gene expression in the absence of high affinity DNA binding.
Recent advances in hair cell regeneration research (2008)

Much has been accomplished since the discovery of postembryonic hair cell production and hair cell regeneration in nonmammals decades ago. No therapies for hair cell regeneration are under clinical trials, but research is yielding potentially important discoveries that are likely to lead to the development of therapeutic methods for inducing hair cell regeneration in the mammalian inner ear.
A method of producing strong magnetic fields (1924)

Abstract There are only two methods of producing a strong magnetic field. The first is by a solenoid, and the second by a solenoid with an iron core in it. The iron is introduced for the purpose of diminishing the magnetic resistance of the magnetic flux, and makes possible the production of much stronger fields than can be obtained without it. This is the principle on which modern electro-magnets are constructed, and by means of them it is possible to obtain field up to 60 kilogauss in a volume of a few cubic millimetres. The saturation of iron, however, makes it impossible to go further than this. According to the present theory of ferro-magnetism we can hardly hope to obtain any ferro-magnetic material which will give a much higher saturation-value than the iron used in modern electro-magnets; and without such a material it is impossible to increase the field obtainable by this means.
Application of Machine Learning to Proteomics Data: Classification and Biomarker Identification in Postgenomics Biology (2013)

Mass spectrometry is an analytical technique for the characterization of biological samples and is increasingly used in omics studies because of its targeted, nontargeted, and high throughput abilities. However, due to the large datasets generated, it requires informatics approaches such as machine learning techniques to analyze and interpret relevant data. Machine learning can be applied to MS-derived proteomics data in two ways. First, directly to mass spectral peaks and second, to proteins identified by sequence database searching, although relative protein quantification is required for the latter. Machine learning has been applied to mass spectrometry data from different biological disciplines, particularly for various cancers. The aims of such investigations have been to identify biomarkers and to aid in diagnosis, prognosis, and treatment of specific diseases. This review describes how machine learning has been applied to proteomics tandem mass spectrometry data. This includes how it can be used to identify proteins suitable for use as biomarkers of disease and for classification of samples into disease or treatment groups, which may be applicable for diagnostics. It also includes the challenges faced by such investigations, such as prediction of proteins present, protein quantification, planning for the use of machine learning, and small sample sizes.