gebhart/patrepeval huggingface dataset:
Hardware implementation of the Smith-Waterman algorithm using a systolic architecture (2014)

This paper presents the design of a systolic processor for DNA local pairwise alignment. The main building block of the processor is a 1D array of processing elements that allows pipeline processing to reduce the execution time with respect to software tools. We aligned two sequences of 4096 nucleotides from the ABO blood group gene of human and house mouse using ModelSim-Altera to verify the hardware design. The hardware simulation results were compared with software simulation results, showing the functionality of the design. The design can only be synthesized on the targeted FPGA for processing 256 nucleotides simultaneously due to hardware limitations (ALUTs and registers), but could be implemented for aligning larger sequences by using a bigger device or FPGA arrays. The design could also be used to implement other dynamic programming algorithms by modifying the processing element.
Synthesis of dl-gabaculine utilizing direct allylic amination as the key step (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of dl-gabaculine utilizing direct allylic amination as the key stepStephen P. Singer and K. Barry SharplessCite this: J. Org. Chem. 1978, 43, 7, 1448–1455Publication Date (Print):March 1, 1978Publication History Published online1 May 2002Published inissue 1 March 1978https://doi.org/10.1021/jo00401a034RIGHTS & PERMISSIONSArticle Views262Altmetric-Citations40LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Cyclic amidines. Part IV. 5: 6: 11: 12-Tetrahydro-5: 11-endomethylenephenhomazine and Tröger's base (1955)

F. C. Cooper and M. W. Partridge, J. Chem. Soc., 1955, 991 DOI: 10.1039/JR9550000991
Functional heterogeneity of culture-grown bone marrow-derived macrophages. I. Antigen presenting function. (1980)

Abstract Pure murine macrophage (mph) populations with functional properties similar to those of normal mph in various stages of development in vitro were grown from small numbers of bone marrow precursors in cultures containing L cell-conditioned medium (CM) or lung CM as the source of colony-stimulating factor (CSF). The mph were characterized for antigen-presenting function in inducing antigen-specific proliferation of primed T cells as well as for accessory cell activity in the allospecific cytotoxic T cell response. During exponential growth in L cell CM, mph developed la-dependent antigen-presenting activity for a number of antigens (tuberculin purified protein derivative, keyhole limpet hemocyanin, and polymeric and monomelic bacterial flagellin) to a level lower than that of normal mph from the spleen or the peritoneal cavity. The activity declined at the onset of stationary phase. Mph raised in lung CM developed higher antigen-presenting activity that did not decline after stationary phase. This functional difference was reflected in the content of la-bearing cells. Furthermore, cultured mph appeared to be somewhat deficient in the processing of small antigens since they presented large antigens more effectively than small ones with the same or different antigenic determinants, when compared with normal mph. In other functional characteristics such as antigen uptake, phagocytosis, accessory cell activity in the cytotoxic response, or stimulation of T cell proliferation in the presence of free antigen, cultured mph, irrespective of CSF and growth phase, were indistinguishable from normal mph and from each other, suggesting that la-dependent antigen presentation may not be involved in these activities. Cell size fractionation of exponential phase BM mph showed that the Ia+ antigen-presenting cell was a small mph.
Activation of human monocyte cytotoxicity by natural and recombinant immune interferon. (1983)

Human T cell hybridomas were established by fusion of SH9 cells, the 6-thioguanine-resistant mutant line of human T lymphoma Hut 102-B2, with concanavalin A-stimulated human peripheral blood lymphocytes. Hybridoma line L38 produced a macrophage activating factor (MAF) with the ability to activate human peripheral blood monocytes to show enhanced cytotoxicity against human colon adenocarcinoma HT-29 cells in a 72-hr 125iododeoxyuridine-release assay. The L38 line was then cloned by the limiting dilution technique and two sublines, L38B and L38D, were found to produce high levels of MAF constitutively. Interferon activity was also detected in L38B and L38D supernatants. When interferon activity was neutralized with specific antiserum to purified human immune interferon (IFN-gamma), MAF activity was abrogated. To confirm that the MAF activity is indeed due to IFN-gamma, IFN-gamma was purified from the culture supernatant of another human T cell hybridoma, L265K2, a cell line known to produce high levels of IFN-gamma. Two highly purified IFN-gamma fractions with m.w. of 20,000 and 25,000, respectively, were obtained by NaDodSO4/polyacrylamide gel electrophoresis (SDS-PAGE). Similar fractions were obtained from IFN-gamma derived from human peripheral blood lymphocyte (PBL) cultures induced with 12-0-tetradecanoylphorbol-13-acetate (TPA) and phytohemagglutinin (PHA). In comparison, Escherichia coli-derived recombinant human IFN-gamma separated by SDS-PAGE yielded two major active fractions with m.w. of 17,000 and 34,000. With all three types of preparations, a close correlation was found between the presence of IFN-gamma activity demonstrable in an antiviral assay and MAF activity in individual fractions. Substantial quantitative differences were observed in the ability of various human IFN to activate monocytes. Although no MAF activity was detected with IFN-alpha and IFN-beta at concentrations up to 200 U/ml, both natural and recombinant IFN-gamma showed marked MAF activity at concentrations as low as 0.3 to 1 U/ml.
Halogen-acetylureas (1939)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHalogen-acetylureasIrwin A. Pearl and William M. DehnCite this: J. Am. Chem. Soc. 1939, 61, 6, 1377–1378Publication Date (Print):June 1, 1939Publication History Published online1 May 2002Published inissue 1 June 1939https://pubs.acs.org/doi/10.1021/ja01875a016https://doi.org/10.1021/ja01875a016research-articleACS PublicationsRequest reuse permissionsArticle Views62Altmetric-Citations1LEARN 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
WESBES: A wireless embedded sensor for improving human comfort metrics using temporospatially correlated data (2012)

When utilized properly, energy management systems (EMS) can offer significant energy savings by optimizing the efficiency of heating, ventilation, and air-conditioning (HVAC) systems. However, difficulty often arises due to the constraints imposed by the need to maintain an acceptable level of comfort for a building's occupants. This challenge is compounded by the fact that human comfort is difficult to define in a measurable way. One way to address this problem is to provide a building manager with direct feedback from the building's users. Still, this data is relative in nature, making it difficult to determine the actions that need to be taken, and while some useful comfort correlations have been devised, such as ASHRAE's Predicted Mean Vote index, they are rules of thumb that do not connect individual feedback with direct, diverse feedback sensing. As they are a correlation, quantifying effects of climate, age of buildings and associated defects such as draftiness, are outside the realm of this correlation. Therefore, the contribution of this paper is the Wireless Embedded Smart Block for Environment Sensing (WESBES); an affordable wireless sensor platform that allows subjective human comfort data to be directly paired with temporospatially correlated objective sensor measurements for use in EMS. The described device offers a flexible research platform for analyzing the relationship between objective and subjective occupant feedback in order to formulate more meaningful measures of human comfort. It could also offer an affordable and expandable option for real world deployment in existing EMS.
Lack of evidence of stimulatory autoantibodies to platelet‐derived growth factor receptor in patients with systemic sclerosis (2009)

The present results raise questions regarding the existence of agonistic autoantibodies to PDGFR in SSc.
Towards 100G packet processing: Challenges and technologies (2009)

Driven by media-rich and bandwidth-intensive Internet applications, 100 Gigabit Ethernet embodies the next logical and necessary line speed following 10G/40G, although enormous challenges exist. Can today's device technologies scale, or will new, disruptive approaches be required to overcome throughput and power density limitations? The evolution of field programmable gate array (FPGA) and application-specific integrated circuit (ASIC) technology was analyzed concerning speed, density, power, and pin interfacing. While clock frequencies cannot keep up with the higher interface speeds, massive parallelism and deep pipelining are needed to scale the throughput. The state-of-the-art architectures and algorithms for every aspect of packet processing are described. In addition, we look at alternative memory concepts and cover some emerging technologies: asynchronous FPGAs as a means for boosting the system clock and serial interfaces reducing the pin count between devices. Thereby, economic considerations limit the choice between the options. We conclude that although significant effort is necessary in terms of device and board technology, economic 100G networking is viable.
Multiple Absorption Components in the Post-Periastron He I P Cygni Absorption Troughs of Eta Carinae (2015)

We have obtained more than 100 high spectral resolution (R approx. 90,000) spectra of the massive binary star eta Carinae since 2012 in an effort to continue our orbital and long-term echelle monitoring of this extreme binary (Richardson et al. 2010, AJ, 139, 1534) with the CHIRON spectrograph on the CTIO 1.5 m telescope (Tokovinin et al. 2013, PASP, 125, 1336) in the 4550-7500A region. We increased our monitoring efforts and observation frequency as the periastron event of 2014 has approached, and resumed observations in October. We note that since mid-October, we have observed unusual multiple absorption components in the P Cygni troughs of the He I lines (4714, 5876, 6678, and 7065; 4921 and 5015 are blended with Fe II). In particular, we note that these components extend to -700 km/s, well beyond the terminal wind speed of the primary. These absorptions are likely related to clumps and turbulence in the wind-wind collision region and bow shock, as suggested by the high-velocity absorption observed by Groh et al. (2010, A&A, 519, 9) in the He I 10830A transition and our pre-periastron observations (Richardson et al. 2014, ATel #6336). In these cases, we suspect that we look along an arm of the shock cone and that we see a fast absorption change from the other collision region shortly after periastron. Further, high spectral resolution data are highly encouraged, especially for resolving powers greater than 50,000. These observations were obtained with the CTIO 1.5 m telescope, operated by the SMARTS Consortium, and were obtained through both SMARTS and NOAO programs 2012A-0216, 2012B-0194, and 2013b-0328. We thank Emily MacPherson (Yale) for her efforts in scheduling the observations that we have and will obtain in the coming weeks and months.
Exploring the use of automated vehicles as last mile connection of train trips through an agent-based simulation model: An application to Delft, Netherlands (2017)

The last mile in a public transport trip is known to bring a large disutility for passengers, because the conventional transport modes for this stage of the trip can, in many cases, be rather slow, inflexible and not provide a seamless experience to passengers. Fully automated vehicles (AVs), that is, those which do not need a driver, could act as a first mile/last mile connection to mass public transport modes. In this paper, we study a system that we call Automated Last-Mile Transport (ALMT), which consists of a fleet of small, fully automated, electric vehicles to improve the last mile performance of a trip done in a train. An agent-based simulation model was proposed for the ALMT whereby a dispatching algorithm distributes travel requests amongst the available vehicles using a FIFO sequence and selects a vehicle based on a set of specified control conditions (e.g. travel time to reach a requesting passenger). The model was applied to the case-study of the connection between the train station Delft Zuid and the Technological Innovation Campus (Delft, The Netherlands) in order to test the methodology and understand the performance of the system in function of several operational parameters and demand scenarios. The most important conclusion from the baseline scenario was that the ALMT system was only able to compete with the walking mode and that additional measures were needed to increase the performance of the ALMT system in order to be competitive with cycling. Relocating empty vehicles or allowing pre-booking of vehicles led to a significant reduction in average waiting time, whilst allowing passengers to drive at a higher speed led to a large reduction in average travel time, whilst simultaneously reducing system capacity as energy use is increased.
A low cost uncooled infrared microbolometer focal plane array using the CMOS n-well layer (2002)

This paper reports a low-cost, 256-pixel uncooled infrared microbolometer focal plane array (FPA) implemented using a 0.8 /spl mu/m CMOS process where the n-well layer is used as the active microbolometer material. The suspended n-well structure is obtained by simple front-end bulk etching of the fabricated CMOS dies, while the n-well region is protected from etching by electrochemical etch-stop technique within a TMAH solution. Electrical connections to the suspended n-well are obtained with polysilicon interconnect layer instead of aluminum to increase the thermal isolation of the pixel by an order of magnitude. Since polysilicon has very low TCR and high resistance, the effective TCR of the pixel is reduced to 0.34%/K, even though the n-well TCR is measured to be 0.58%/K. A 16/spl times/16 pixel array prototype with 80 /spl mu/m/spl times/80 /spl mu/m pixel sizes has successfully been implemented. The pixel resistance measurements show that pixels are very uniform with a nonuniformity of 1.23%. Measurements and calculations show that the detector and the array provide a responsivity of 1200 V/W, a detectivity of 2.2/spl times/10/sup 8/ cm/Hz/sup 1/2//W, and a noise equivalent temperature difference (NETD) of 200 mK at 0.5 Hz frame rate with fully serial readout scheme. This performance can be further increased by using other advanced readout techniques, therefore, the CMOS n-well microbolometer approach seems to be a very cost-effective method to produce large focal plane arrays for low-cost infrared imaging applications.
Power Devices and ICs (2013)

Power Devices and ICs control the energy flow between a power source and one or more electrical loads, regulating voltage and current, driving motors, charging batteries and facilitating safety functions in applications ranging from kilovolt power distribution and high speed trains to automotive electronics, computer servers, notebooks, tablets and smartphones. High Power and Two-Carrier Devices such as thyristors and IGBTs rely in part on minority-carrier conduction typically operating from line frequencies up to tens of kilohertz. Power MOSFETs comprising majority carrier conduction in highly paralleled double-diffused (DMOS) transistors offer low on-resistance at megahertz switching speeds varying in construction from dense vertical trench gate DMOS and low-gate-charge lateral devices below 100V, to lateral RESURF and vertical superjunction DMOS at higher voltages. High Voltage and Power ICscombine isolated power devices with control circuitry using BCD process technology to realize complex functions and power system integration monolithically. Wide Bandgap Power Devices (WBG) such as SiC and GaN promise to extend power device capability to current densities and operating temperatures beyond the limit of silicon.
A traveling wave based single-ended fault location algorithm using DWT for overhead lines combined with underground cables (2010)

This paper presents a single-ended traveling wave based fault location method for power transmission systems where overhead lines are combined with underground cables. Bewley diagrams are used to determine the traveling wave patterns. The proposed method utilizes Discrete Wavelet Transform (DWT) to extract the transient information from the recorded voltage signals. The squares of the wavelet transform coefficients (WTC <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) are calculated in order to determine the energy of the signal which is used to identify the faulted section (underground cable or overhead line) and subsequently to locate the fault. The transient voltages for different types of faults and locations along the overhead section as well as the underground cable section are obtained through EMTP simulations. MATLAB Wavelet Toolbox is used to process the simulated transients and apply the proposed method. The performance of the method is tested on various scenarios.
Recombinant human erythropoietin (rHuEPO): more than just the correction of uremic anemia. (2003)

Hematopoiesis is controlled by numerous interdependent humoral and endocrine factors. Erythropoietin (EPO), a hydrophobic sialoglycoproteic hormone, plays a crucial role in the regulation of hematopoiesis, and induces proliferation, maturation and differentiation of the erythroid cell line precursors. Thanks to recombinant DNA techniques, different recombinant hormones can now be produced at low cost and in large amounts. This has led to greater understanding of the pathophysiological factors regulating hematopoiesis. This in turn, hasprompted the search for new therapeutic approaches. EPO might also be used to treat patients with different types of anemia: uremics, newborns, patients with anemia from cancer or myeloproliferative disease, thalassemia, bone marrow transplants, chronic infectious diseases. Besides erythroid cells, EPO affects other blood cell lines, such as myeloid cells, lymphocytes and megakaryocytes. It can also enhance polymorphonuclear cell phagocytosis and reduce macrophage activation, thus modulating the inflammatory process. Hematopoietic and endothelial cells probably have the same origin, and the discovery of eyrthropoietin receptors also on mesangial, myocardial and smooth muscle cells has prompted research into the non-erythropoietic function of the hormone. EPO has an important, direct, hemodynamic and vasoactive effect, which does not depend only on an increase in hematocrit and viscosity. Moreover, EPO and its receptors have been found in the brain, suggesting a role in preventing neuronal death. Finally, the recently discovered interaction between EPO and vascular endothelial growth factor (VEGF), and the ability of EPO to stimulate endothelial cell mitosis and motility may be of importance in neovascularization and wound healing.
Crystal structure at 3 Å of mistletoe lectin I, a dimeric type‐II ribosome‐inactivating protein, complexed with galactose (2003)

The X-ray structure of mistletoe lectin I (MLI), a type-II ribosome-inactivating protein (RIP), cocrystallized with galactose is described. The model was refined at 3.0 A resolution to an R-factor of 19.9% using 21 899 reflections, with Rfree 24.0%. MLI forms a homodimer (A-B)2 in the crystal, as it does in solution at high concentration. The dimer is formed through contacts between the N-terminal domains of two B-chains involving weak polar and non-polar interactions. Consequently, the overall arrangement of sugar-binding sites in MLI differs from those in monomeric type-II RIPs: two N-terminal sugar-binding sites are 15 A apart on one side of the dimer, and two C-terminal sugar-binding sites are 87 A apart on the other side. Galactose binding is achieved by common hydrogen bonds for the two binding sites via hydroxy groups 3-OH and 4-OH and hydrophobic contact by an aromatic ring. In addition, at the N-terminal site 2-OH forms hydrogen bonds with Asp27 and Lys41, and at the C-terminal site 3-OH and 6-OH undergo water-mediated interactions and C5 has a hydrophobic contact. MLI is a galactose-specific lectin and shows little affinity for N-acetylgalactosamine. The reason for this is discussed. Structural differences among the RIPs investigated in this study (their quaternary structures, location of sugar-binding sites, and fine sugar specificities of their B-chains, which could have diverged through evolution from a two-domain protein) may affect the binding sites, and consequently the cellular transport processes and biological responses of these toxins.
REVIEW OF SOME PROCESSES FOR CERAMIC‐TO‐METAL JOINING (1993)

Abstract Various methods are discussed for the joining of ceramics to metals and vice versa. State‐of‐the‐art techniques including refractory metallizations and active metal brazing are detailed from both a processing and applications standpoint. Various approaches to forming ceramic/metal joints or thin film coatings have been developed over the years to address the need to combine the properties of both types of materials for both electrical and structural applications. These methods address not only physical and chemical compatibility concerns but also the need for bonds between dissimilar materials to survive the rigors of use generated by such inevitable mismatches as can be found in expansion, elastic, reactive and thermal cycling behavior.