gebhart/patrepeval huggingface dataset:
Identification of Fur, Aconitase, and Other Proteins Expressed by <i>Mycobacterium tuberculosis</i> under Conditions of Low and High Concentrations of Iron by Combined Two-Dimensional Gel Electrophoresis and Mass Spectrometry (1999)

Iron plays a critical role in the pathophysiology of Mycobacterium tuberculosis. To gain a better understanding of iron regulation by this organism, we have used two-dimensional (2-D) gel electrophoresis, mass spectrometry, and database searching to study protein expression in M. tuberculosis under conditions of high and low iron concentration. Proteins in cellular extracts from M. tuberculosis Erdman strain grown under low-iron (1 microM) and high-iron (70 microM) conditions were separated by 2-D polyacrylamide gel electrophoresis, which allowed high-resolution separation of several hundred proteins, as visualized by Coomassie staining. The expression of at least 15 proteins was induced, and the expression of at least 12 proteins was decreased under low-iron conditions. In-gel trypsin digestion was performed on these differentially expressed proteins, and the digestion mixtures were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry to determine the molecular masses of the resulting tryptic peptides. Partial sequence data on some of the peptides were obtained by using after source decay and/or collision-induced dissociation. The fragmentation data were used to search computerized peptide mass and protein sequence databases for known proteins. Ten iron-regulated proteins were identified, including Fur and aconitase proteins, both of which are known to be regulated by iron in other bacterial systems. Our study shows that, where large protein sequence databases are available from genomic studies, the combined use of 2-D gel electrophoresis, mass spectrometry, and database searching to analyze proteins expressed under defined environmental conditions is a powerful tool for identifying expressed proteins and their physiologic relevance.
Probing <i>N</i><sup>6</sup>-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA (2013)

N(6)-methyladenosine (m(6)A) is the most abundant modification in mammalian mRNA and long noncoding RNA (lncRNA). Recent discoveries of two m(6)A demethylases and cell-type and cell-state-dependent m(6)A patterns indicate that m(6)A modifications are highly dynamic and likely play important biological roles for RNA akin to DNA methylation or histone modification. Proposed functions for m(6)A modification include mRNA splicing, export, stability, and immune tolerance; but m(6)A studies have been hindered by the lack of methods for its identification at single nucleotide resolution. Here, we develop a method that accurately determines m(6)A status at any site in mRNA/lncRNA, termed site-specific cleavage and radioactive-labeling followed by ligation-assisted extraction and thin-layer chromatography (SCARLET). The method determines the precise location of the m(6)A residue and its modification fraction, which are crucial parameters in probing the cellular dynamics of m(6)A modification. We applied the method to determine the m(6)A status at several sites in two human lncRNAs and three human mRNAs and found that m(6)A fraction varies between 6% and 80% among these sites. We also found that many m(6)A candidate sites in these RNAs are however not modified. The precise determination of m(6)A status in a long noncoding RNA also enables the identification of an m(6)A-containing RNA structural motif.
Specification-based testing of reactive software: tools and experiments (1997)

Testing commercial software is expensive and time consuming. Automated testing methods promise to save a great deal of time and money throughout the software industry. One approach that is well-suited for the reactive systems found in telephone switching systems is specification-based testing. We have built a set of tools to automatically test software applications for violations of safety properties expressed in temporal logic. Our testing system automatically constructs finite state machine oracles corresponding to safety properties, builds test harnesses, and integrates them with the application. The test harness then generates inputs automatically to test the application. We describe a study examining the feasibility of this approach for testing industrial applications. To conduct this study we formally modeled an Automatic Protection Switching system (APS), which is an application common to many telephony systems. We then asked a number of computer science graduate students to d...
Extrathymic development of V alpha 14-positive T cells. (1993)

It is known that rearrangement of the T cell antigen receptor (TCR) gene occurs in the thymus during T cell development and consequently results both in the deletion of DNA between the variable (V) and diversity/joining segments and in the formation of a circular DNA with recombination signal sequences. Here, we provide evidence that V alpha 14+ TCR gene rearrangements take place in extrathymic sites, such as bone marrow, liver, and intestine, but not in spleen, because we were able to detect frequent productive and nonproductive V alpha 14+ coding and signal sequences as a result of TCR rearrangements in extrathymic sites. Similar findings were also detected in athymic mice. Quantitative analysis shows that the relative amounts of V alpha 14 gene-mediated signal sequences in extrathymic tissues are higher than those in thymus. On the contrary, TCR rearrangements of V alpha 1.1 T cells, which are known to develop in the thymus, were mainly detected in the thymus, Peyer's patch, and spleen, but not in other extrathymic tissues, showing patterns distinct from V alpha 14 TCR rearrangements. These findings are evidence of extrathymic development of V alpha 14+ T cells. Differential characteristic TCR rearrangement patterns also indicate that distinct TCR repertoires are generated in different lymphoid tissues.
Role of media transformation in multimedia messaging (2005)

The multimedia messaging service (MMS) is a popular wireless application that allows mobile subscribers to send and receive messages comprising a variety of media types to and from mobile handsets. As a result of the increasing popularity of MMS across all wireless networks, a variety of mobile handsets are available with MMS capabilities. Handset vendors add extra features to their handsets to make them more appealing to subscribers, so that handsets from different vendors differ in their capabilities. As a result of this diversity, a multimedia message sent from one handset may render improperly or may not render at all on a different model. However, mobile subscribers expect to experience the richness of the content, irrespective of the type of content or the capability of their handset. This implies that media component(s) in a multimedia message have to be adapted to suit the characteristics of a particular handset. Media transformation is the process of conversion and adaptation of various media objects in accordance with the target handset characteristics. It is done in real time while the target handset is retrieving the multimedia message. The paper focuses on the importance and beneficial role of media transformation in an MMS environment. The techniques currently deployed by the available services are presented. The need for enhanced intelligence at the transformation server is discussed. Schemes for implementing some of the techniques and their effectiveness are presented.
Isotopic effects on the electronic properties of H2O and D2O in the vacuum uv (1977)

Optical and dielectric functions of liquid H2O and D2O at 25 °C were obtained in the 2–9.2 eV region of photon energy. The reflectance was measured for several angles of incidence at a liquid–semicylindrical-window interface. The refractive index n and absorption coefficient k were obtained by a least-squares fit of calculated to experimental reflectance. The principle difference observed was the contraction of the D2O spectra due to the mass effect of the heavier isotope.
Biological Briefs (1939)

Other| October 01 1939 Biological Briefs Ruth Sherman Ruth Sherman Search for other works by this author on: This Site PubMed Google Scholar The American Biology Teacher (1939) 2 (1): 15. https://doi.org/10.2307/4436946 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Ruth Sherman; Biological Briefs. The American Biology Teacher 1 October 1939; 2 (1): 15. doi: https://doi.org/10.2307/4436946 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe American Biology Teacher Search This content is only available via PDF. Article PDF first page preview Close Modal You do not currently have access to this content.
A COMPUTER-BASED AUTOMATIC METHOD FOR DETERMINING VISUAL ACUITY* (1970)

A computer-based automatic method for clinical visual acuity determinations is described. The procedure employs the staircase method of threshold determination using Landolt C's, and has been tested on 14 subjects representative of normal optometry clinic patients. Though more precise due to small step size, the results show fair agreement with manual determinations performed at the same time using the Snellen chart. The automatic method required more time because (1) subjects used 4 instead of 26 response alternatives, and (2) a mean step size of 1.15:1 instead of 1.5 or 2:1 was used. While most series of repeated automatic determinations were stable, a few subjects showed improvement or deterioration apparently due to practice or fatigue, respectively. Economic aspects of computer assistance for optometric examinations are briefly discussed and attention is drawn to the potential value of time-sharing and remote operation.
<title>High Energy Glass Lasers</title> (1975)

A number of laboratories throughout the world are actively pursuing the development of pulsed high power Nd:glass lasers for use in their laser fusion and laser plasma interaction studies programs. Perhaps the most ambitious programs in this field have been undertaken by the Lawrence Livermore Laboratory where several irradiation facilities are in operation and where the 4-arm ARGUS and 20-arm SHIVA lasers are currently under construction. These systems are designed to provide the energy, power and wavefront uniformity required to spherically implode nuclear fuel targets such as the deuterjw-tritium (DT) solid sphere, in an effort to achieve thermonuclear fusion through inertial confinement.(1)
The use of data in outlet locational planning: a preliminary ex amination across retail and service sectors (2005)

A key pre‐requisite of locational decision‐making in retailing is appropriate sources of data. These have become increasingly available from a number of internal and external sources in recent years. Coupled with concomitant decreases in the cost of technology, locational decision‐making can now, more than ever, be based on more than subjective practices alone. This paper aims to assess how the use of data varies across four named retail and service sectors, an area of research that has hitherto been neglected. A postal questionnaire was distributed to approximately 300 locational planning managers to ascertain the use of data in decision‐making. Analysis of variance (ANOVA) was used to examine how the use of 21 named datasets varied by sector. A number of significant differences in data usage and sharing emerged and are reported here. It is concluded that data use is by no means uniform across different retail and service types, and that future research that addresses inter‐sectoral differences in locational planning practices would be appropriate.
Activation of intraislet lymphoid cells causes destruction of islet cells. (1991)

In vitro culture of rat islets at 24 degrees C for 7 days in tissue culture medium CMRL 1066 almost completely eliminated lymphoid cells from the islets. Immunostaining of the islets with monoclonal antibody OX4 for demonstration of class II major histocompatibility complex (MHC)-expressing cells revealed a decrease from 13.1 +/- 0.6 positive cells per islet on day 0 to 0.7 +/- 0.1 cells per islet on day 7. A comparable decrease was found using OX1 for demonstration of all leukocytes. In contrast, culture of rat islets at 24 degrees C for 7 days with tissue culture Roswell Park Memorial Institute (RPMI) 1640 medium was not as effective in eliminating lymphoid cells as in medium CMRL 1066 (3.0 +/- 0.2 class II MHC positive cells per islet at 7 days). Effective elimination of intraislet lymphoid cells apparently is due to the combined effect of low temperature culture and the tissue culture medium CMRL-1066. The second goal of the study was to determine whether the destructive effect of interferon gamma (IFN-gamma) on rat islets in culture was due to intraislet lymphoid cells. In vitro culture of rat islets with IFN-gamma (1000 units/ml) at 37 degrees C caused almost complete destruction of the islets at 7 days. If intraislet lymphoid cells were eliminated from the islets by in vitro culture at 24 degrees C followed by exposure to IFN-gamma (1000 units/ml) for 7 days at 37 degrees C, then IFN-gamma did not cause destruction of the islets and transplants of the treated islets produced normoglycemia in diabetic recipient mice. These findings indicate that intraislet lymphoid cells are responsible for destruction of islet cells when these cells (presumably macrophages) are activated by IFN-gamma. Intraislet lymphoid cells may play a significant role in destroying islet cells in autoimmune diabetes.
Diagnostic Markers and Prognostic Factors in Thyroid Cancer (2009)

There has been considerable progress identifying biomarkers in thyroid tumors that improve the accuracy of fine-needle aspiration biopsy and also help predict tumor aggressiveness or behavior. In this review we address both the clinical potential of molecular biomarkers and their usefulness, based on the most recent literature. We describe the current best clinical staging systems and the common somatic mutations in thyroid cancer. The BRAF mutation is the most common mutation in papillary thyroid cancer and has recently been reported to be associated with disease aggressiveness; it is also an independent predictor of tumor behavior. Combined testing of RET/PTC, NTRK, RAS and PAX8-PPARgamma, which are mutually exclusive mutations, helps improve the accuracy of fine-needle aspiration biopsy. Gene-expression profiling studies have identified a variety of potential molecular markers to help distinguish benign from malignant thyroid neoplasms. Expression analysis of differentially expressed microRNAs also appears to be a promising diagnostic approach for distinguishing benign from malignant thyroid neoplasm. It is especially useful for indeterminate nodules by fine-needle aspiration biopsy.
3′-Biotin-tagged microRNA-27 does not associate with Argonaute proteins in cells (2014)

Synthetic 3'-biotin-tagged microRNAs (miRNAs) have often been used to select interacting messenger RNA (mRNA) and noncoding RNA (ncRNA) targets. Here, we examined the extent of association of 3'-end biotinylated miR-27 with Argonaute (Ago) proteins in transfected human cells using a coimmunoprecipitation assay followed by Northern blot analysis. We report that biotinylated miR-27 does not efficiently associate with Ago compared to unmodified miR-27. These results suggest that 3'-end biotin-modified miRNAs are questionable monitors of miRNA function in cells.
A study of novel wafer level LED package based on TSV technology (2012)

LED (light-emitting diode) has many advantages over traditional lighting source such as higher electrical efficiency, faster response, and free of hazardous, which has been attracting more and more interesting from all of world. LED technology has achieved remarkable progress during latest years already. However, high price is still the main block for its wide application. WLP (wafer level package) is an as-know low cost packaging method, which has been demonstrated in IC (integrated circuit) industry already. Wafer level package for LED is expected as a promising solution for reduction of total LED price. Aimed at low package cost, as well as good thermal and electrical performance, a novel wafer level LED package with TSV (through silicon via) interconnection and remote phosphor was studied. And structure of the packaged LED was characterized, and light performance was tested according to standard LED testing method.
Software obfuscation from crackers' viewpoint (2006)

Various kinds of software obfuscation methods have been proposed to protect security-sensitive information involved in software implementations. This paper proposes a cracker-centric approach to give a guideline for employing existing obfuscation methods to disrupt crackers' actions.
Preparation of acid‐cleavable branched polymers for argon fluoride photoresists via reversible addition–fragmentation chain‐transfer polymerization (2011)

Abstract A series of branched polymers for chemically amplified resists (CARs) were prepared through the reversible addition–fragmentation chain‐transfer (RAFT) copolymerization of three monomers with lithographic functionalities and an acid‐cleavable dimethacrylate monomer. The three monomers with lithographic functionalities were 2‐ethyl‐2‐adamantyl methacrylate, α‐γ‐butyrolactone methacrylate, and 3‐hydroxy‐1‐adamantyl methacrylate. The acid‐cleavable monomer was 2,5‐dimethyl‐2,5‐hexanediol dimethacrylate (DMHDMA), and 2‐cyanoprop‐2‐yl‐1‐dithionaphthalate was used as a chain‐transfer agent. Because DMHDMA contains two methacrylate groups, it induced the branched structures of the polymers. The degree of branching could be controlled by the molar fraction of DMHDMA in the monomer mixtures. The size and structure of the polymers obtained after hydrolysis were very close to those of linear polymers prepared by RAFT copolymerization with the same amount of reagents, only without the acid‐cleavable monomer. A preliminary lithography test using an argon fluoride source demonstrated that the acid‐cleavable branched polymers could be promising candidates for CAR materials. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Maternal mortality. (1996)

A new approach to measuring maternal mortality indicates that there are some 585,000 maternal deaths, 99% of them in developing countries. This is around 80,000 deaths more than earlier estimates have suggested and indicates a substantial underestimation of maternal mortality in the past. There is a greater disparity in levels of maternal mortality between industrialized and developing countries than in any other public health indicator. While significant progress has been made in reducing infant mortality, the same is not true for maternal mortality. Although the actions needed to reduce maternal mortality have long been known, 1 woman in 50 is still dying as a result of pregnancy-related complications and the figure rises to 1 in 10 in many parts of Africa. By contrast, the figure for developed countries can be as low as 1 in 8,000.
A Simple Physiologic Algorithm for Managing Hemodynamics Using Stroke Volume and Stroke Volume Variation: Physiologic Optimization Program (2009)

Intravascular volume status and volume responsiveness continue to be important questions for the management of critically ill or injured patients. Goal-directed hemodynamic therapy has been shown to be of benefit to patients with severe sepsis and septic shock, acute lung injury and adult respiratory distress syndrome, and for surgical patients in the operating room. Static measures of fluid status, central venous pressure (CVP), and pulmonary artery occlusion pressure (PAOP) are not useful in predicting volume responsiveness. Stroke volume variation and pulse pressure variation related to changes in stroke volume during positive pressure ventilation predict fluid responsiveness and represent an evolving practice for volume management in the intensive care unit (ICU) or operating room. Adoption of dynamic parameters for volume management has been inconsistent. This manuscript reviews some of the basic physiology regarding the use of stroke volume variation to predict fluid responsiveness in the ICU and operating room. A management algorithm using this physiology is proposed for the critically ill or injured in various settings.
Development of data acquisition and load control system by programmable logic controller for high voltage load customer (2002)

This paper proposes a PC based data acquisition and load control system (DAALCS) to fulfil load management functions for a high voltage load customer. A programmable logic controller (PLC) associated with a digital power meter has been applied to fulfil major application functions of DAALCS. In the data acquisition subsystem, two PLCs with redundant configuration are responsible for directly collecting power measurements via star connection telephone network with real time mode. 15 digital power meters with standard RS485 protocol are installed on each building substation to record more than 20 parameters for data acquisition subsystem. In the load control subsystem, six sets of PLCs with the mixture of PLC network and RS 485 channel are constructed to execute load control schemes. The load control schemes are composed of load shedding for demand monitoring, cycling on/off load control, timer control, and direct load control. The proposed system has been successfully installed and continuously operated on an academic power system. The statistical data retrieved from the database shows that the DAALCS can effectively reduce the daytime peak load during the summer season and significantly save electric energy consumption.
Render Sequence Encoding for Document Protection (2006)

We present in this paper a novel electronic document watermarking method, render sequence encoding (RSE), and then further develop a RSE authentication method for electronic documents. RSE watermarks an electronic document by modulating the display sequences of words or characters. It features large information-carrying capacity and robustness over document format transcoding. The RSE authentication method is based on the NP-complete exact traveling salesman problem, which provides a rigorous foundation for security. The RSE authentication method is secure in the sense it is extremely difficult to forge the authentication process. RSE authentication process is also easy to operate, especially in comparison to digital signatures which requires public key infrastructure for its operation
A New Z-Source DC Circuit Breaker (2011)

A novel type of circuit breaker is introduced for operation at medium-voltage dc with future naval ship power systems as a targeted application. The breaker utilizes a z-source LC circuit in order to automatically commutate a main-path SCR during a fault. Compared to existing dc circuit breakers, the z-source breaker features fast turn-off, simple control, and the source does not experience the fault current. The operation and analysis of the new breaker is presented. Component sizing is carried out for three medium-voltage power levels. Incorporation of the new breaker within a drive system is also explored. Laboratory validation is carried out on a low-voltage prototype.