gebhart/patrepeval huggingface dataset:
Design of High-Radix Clos Network-on-Chip (2010)

Many high-radix Network-on-Chip (NOC) topologies have been proposed to improve network performance with an ever-growing number of processing elements (PEs) on a chip. We believe Clos Network-on-Chip (CNOC) is the most promising with its low average hop counts and good load-balancing characteristics. In this paper, we propose (1) a high-radix router architecture with Virtual Output Queue (VOQ) buffer structure and Packet Mode Dual Round-Robin Matching (PDRRM) scheduling algorithm to achieve high speed and high throughput in CNOC, (2) a heuristic floor-planning algorithm to minimize the power consumption caused by the long wires. Experimental results show that the throughput of a 64-node 3-stage CNOC under uniform traffic increases from 62% to 78% by replacing the baseline routers with PDRRM VOQ routers. We also compared CNOC with other NOC topologies, and found that using the new design techniques, CNOC has the highest throughput, lowest zero-load latency, and best power efficiency.
The effects of antenna gains and polarization on multipath delay spread and path loss at 918 MHz on cross-campus radio links (2003)

Results of delay spread and path loss measurements across a large college campus are presented. Two line-of-sight links were used with three different types of antennas to determine best polarizations and pointing angles. Measurements show multipath is most severe when antennas of different polarizations are used on each end of the link. Minimum delay spreads are encountered when antennas of the same polarization are used and pointed directly toward each other. As long as polarizations are matched on each side of the link, polarization does not have significant impact on delay spread or path loss. However, circularly polarized helical antennas offer multipath reduction over a wide range of pointing angles. This suggests that on point-to-point cross-campus links where a single antenna is desired to serve a broad coverage area, circular polarization could be used in lieu of channel equalization to improve bit error rates in high-speed data networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Figure 3C from Molecular Triage of Premalignant Lesions in Liquid-Based Cervical Cytology and Circulating Cell-Free DNA from Urine, Using a Panel of Methylated Human Papilloma Virus and Host Genes (2023)

&lt;p&gt;Amplification curves for the HPV TrDNA-qPCR assay on TrDNA from women with Cervical Intraepithelial Neoplasia 1 (CIN1), Cervical Intraepithelial Neoplasia 2-3 (CIN2-3) and women with no Intraepithelial Lesions or Neoplasia (NILM). TrDNA samples were analyzed for high risk HPV DNA using our HPV TrDNA SYBR green qPCR assay. HeLa genomic DNA was included as a positive control. Ct ranges are variable, but are in a similar range as the genomic control. NILM samples did not amplify.&lt;/p&gt;
Dynamic Scheduling for Delay-Critical Packets in a Networked Control System Using WirelessHART (2020)

In future industrial scenarios, Wireless Sensor Networks (WSN) are envisioned to support the traffic of Networked Control Systems (NCS). WirelessHART is a prevalent WSN protocol that uses the Time Slotted Channel Hopping (TSCH) medium access to cope with the delay and reliability requirements of NCS in the harsh industrial environment. In TSCH, time slots and frequencies can be scheduled by a network coordinator to provide Quality of Service (QoS). In contrast to previous works that consider the end-to-end delay requirement of a flow of packets, we focus on a finite sequence of time-critical packets. These packets may belong to a time-critical message whose latency could significantly impact the NCS. Given an end-to-end delay deadline, our objective is to minimize the Delay Violation Probability (DVP) for a finite sequence of packets by dynamically scheduling the time slots in each frame. This is a challenging task as DVP depends on the instantaneous state of the network and requires its transient analysis. In this work, we model the wireless NCS as a two-queue lossy wireless network and propose the first transient analysis of DVP for a finite sequence of time-critical packets. Noting that DVP cannot be directly used for dynamic resource allocation, we propose a heuristic algorithm by relating DVP with the network's throughput. The proposed heuristic maximizes the expected throughput, is computed by solving a finite-horizon Markov Decision Process (MDP), and can be implemented at the network coordinator. Using simulation we demonstrate that the MDP-based heuristic achieves lower DVP compared to the classical MaxWeight and Weighted-Fair Queuing.
Using dynamical uncertainty models for estimation of uncertainty bounds on power plant performance prediction (2007)

Predicting the performance of large scale plants can be difficult due to model uncertainties etc, meaning that one can be almost certain that the prediction will diverge from the plant performance with time. In this paper output multiplicative uncertainty models are used as dynamical models of the prediction error. These proposed dynamical uncertainty models result in an upper and lower bound on the predicted performance of the plant. The dynamical uncertainty models are used to estimate the uncertainty of the predicted performance of a coal-fired power plant. The proposed scheme, which uses dynamical models, is applied to two different sets of measured plant data. The computed uncertainty bounds cover the measured plant output, while the nominal prediction is outside these uncertainty bounds for some samples in these examples.
I-Motif-Programmed Functionalization of DNA Nanocircles (2013)

The folding of various intra- and intermolecular i-motif DNAs is systematically studied to expand the toolbox for the control of mechanical operations in DNA nanoarchitectures. We analyzed i-motif DNAs with two C-tracts under acidic conditions by gel electrophoresis, circular dichroism, and thermal denaturation and show that their intra- versus intermolecular folding primarily depends on the length of the C-tracts. Two stretches of six or fewer C-residues favor the intermolecular folding of i-motifs, whereas longer C-tracts promote the formation of intramolecular i-motif structures with unusually high thermal stability. We then introduced intra- and intermolecular i-motifs formed by DNAs containing two C-tracts into single-stranded regions within otherwise double-stranded DNA nanocircles. By adjusting the length of C-tracts we can control the intra- and intermolecular folding of i-motif DNAs and achieve programmable functionalization of dsDNA nanocircles. Single-stranded gaps in the nanocircle that are functionalized with an intramolecular i-motif enable the reversible contraction and extension of the DNA circle, as monitored by fluorescence quenching. Thereby, the nanocircle behaves as a proton-fueled DNA prototype machine. In contrast, nanorings containing intermolecular i-motifs induce the assembly of defined multicomponent DNA architectures in response to proton-triggered predicted structural changes, such as dimerization, "kiss", and cyclization. The resulting DNA nanostructures are verified by gel electrophoresis and visualized by atomic force microscopy, including different folding topologies of an intermolecular i-motif. The i-motif-functionalized DNA nanocircles may serve as a versatile tool for the formation of larger interlocked dsDNA nanostructures, like rotaxanes and catenanes, to achieve diverse mechanical operations.
Association of mitochondrial function and feed efficiency in poultry and livestock species1 (2008)

As grain prices have increased dramatically in the past year, understanding the fundamental genetic, cellular, and biochemical mechanisms responsible for feed efficiency (FE; g of gain/g of feed) or residual feed intake (RFI; an alternative feed efficiency trait that quantifies interanimal variation in DMI that is unexplained by differences in BW and growth rate) in livestock and poultry is extremely important with respect to maintaining viable meat production practices in the United States. Although breed and diet have long been known to affect mitochondrial function, few studies have investigated differences in mitochondrial function and biochemistry due to interanimal phenotypic differences in FE or RFI (i.e., variation among animals of the same breed and fed the same diet). This paper reviews existing literature on relationships of mitochondrial function and biochemistry with FE and RFI in poultry and livestock. The overall goal of all of this paper is to assist the development of tools (e.g., genetic markers or biomarkers) to aid commercial breeding companies in genetic selection that, in turn, will help maintain viable livestock and poultry industries in the United States and around the world.
Systemic HIV-1 Infection Produces a Unique Glial Footprint in Humanized Mouse Brains (2017)

Abstract Studies of innate glial cell responses for progressive human immunodeficiency virus type one (HIV-1) infection are hindered by the availability of relevant small-animal models. To overcome this hindrance, a mouse model reconstituted with humanized brain and immune systems was created. Newborn NOD/SCID/IL2Rγc -/- mice of both sexes were transplanted with human neuroglial progenitors (NPC) and hematopoietic stem cells. Intraventricular injection of NPC yielded an anatomical symmetrical glia (human astrocyte and oligodendrocyte) repopulation of the mouse brain. The human glia were observed in periventricular areas, white matter tracts, the olfactory bulb and brain stem. HIV-1 infection of these dual humanized mice led to meningeal and perivascular human leukocyte infiltration into brain. The species-specific viral-neuroimmune interactions in the infected animals were identified by deep RNA sequencing. In the corpus callosum and hippocampus overlapping human-specific transcriptional alterations were seen for interferon type 1 and 2 signaling pathways ( STAT1, 2, IRF9, ISG15, IFI6 ) and a range of host antiviral responses ( MX1, OAS1, RSAD2, BST2, SAMHD1) in infected animals. Glial cytoskeleton reorganization, oligodendrocyte differentiation and myelin ensheathment ( MBP, MOBP, PLP1, MAG and ZNF488 ) were downregulated. The data sets were confirmed by real-time PCR. The viral defense signaling patterns observed in these mice parallels the neuroimmune communication networks present in the HIV-1 infected human brain. In this manner, the new mouse model can facilitate discovery of therapeutics, viral eradication targets for virus induced nervous system diseases, and simplify HIVCure research approaches. Summary Statement We created mice with both a humanized brain and an immune system. The animals were used to investigate glial responses to HIV-1 infection. At a transcriptional level we defined the interactions between human glia and immune cells in the presence of the systemic HIV-1 infection. Noticeably, altered transcriptional changes were human specific. At five weeks after viral infection humanized mouse brain displayed potent interferon-mediated antiviral innate immune responses and alteration of neuronal progenitors differentiation and myelination. This model can be used to tests both diagnostic and therapeutic interventions for cure HIV-associated brain impairment.
Comment on “Nonreciprocal Light Propagation in a Silicon Photonic Circuit” (2012)

We show that the structure demonstrated by Feng et al. (Reports, 5 August 2011, p. 729) cannot enable optical isolation because it possesses a symmetric scattering matrix. Moreover, one cannot construct an optical isolator by incorporating this structure into any system as long as the system is linear and time-independent and is described by materials with a scalar dielectric function.
Transportation of cold plasma jet in multiple-mirror magnetic field (2017)

New experimental results on magnetic compression and transport of low-temperature arc plasma are presented. In the experiments, the transport efficiency of the plasma stream in a multiple-mirror configuration was compared with the same in a uniform solenoidal field. The magnetic compression ratio of the plasma stream varied from 5 to 60 at the initial diameter of 5 cm. As the result, the plasma with (1 – 4)×1020 m-3 density at the axis was obtained at ∼3 m distance from the plasma source. Theory predicted that a multiple-mirror magnetic field should not significantly decelerate and weaken collisional plasma. The experiment confirmed this prediction. In the presented work, we simulated the baseline scenario of GOL-NB filling by cold start plasma.
Numerical Analysis of Unsteady Exhaust Gas Flow and Its Application for Lambda Control Improvement (2003)

A multidimensional computational fluid dynamics (CFD) tool has been applied to analyze the exhaust system of a gasoline engine. Since gas flow in the exhaust manifold is affected by exhaust pulsations, prediction methods based on steady flow are not able to predict gas flow precisely enough. Therefore, a new multidimensional calculation method, called pulsation flow calculation, has been developed. A one-dimensional gas exchange simulation and a three-dimensional exhaust gas flow calculation are combined to simulate gas flow pulsations caused by the gas exchange process. Predicted gas flow in the exhaust manifold agreed with the experimental data. With the aim of reducing emissions, the pulsation flow calculation method has been applied to improve lambda feedback control using an oxygen sensor. The factors governing sensor sensitivity to the exhaust gas from each cylinder were clarified. The possibility of selecting the oxygen sensor location in the exhaust manifold on the basis of calculations was proved. The effect of an exhaust manifold with equal-length cylinder runners on achieving uniform sensor sensitivities was made clear. In addition, a new lambda feedback control method for an exhaust manifold with different-length cylinder runners is proposed.
Does Abalone Nacre Form by Heteroepitaxial Nucleation or by Growth through Mineral Bridges? (1998)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionDoes Abalone Nacre Form by Heteroepitaxial Nucleation or by Growth through Mineral Bridges?Tilman E. Schäffer, Cristian Ionescu-Zanetti, Roger Proksch, Monika Fritz, Deron A. Walters, Nils Almqvist, Charlotte M. Zaremba, Angela M. Belcher, Bettye L. Smith, Galen D. Stucky, Daniel E. Morse, and Paul K. HansmaCite this: Chem. Mater. 1998, 10, 3, 946Publication Date (Web):January 14, 1998Publication History Published online14 January 1998Published inissue 1 March 1998https://doi.org/10.1021/cm9709986Copyright © 1998 American Chemical SocietyRequest reuse permissions This publication is free to access through this site. Learn MoreArticle Views415Altmetric-Citations7LEARN 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 (12 KB) Get e-Alertsclose Get e-Alerts
A proposed helmet-PET with a jaw detector enabling high-sensitivity brain imaging (2013)

The advanced depth-of-interaction positron emission tomography (PET) detectors have been improved to provide three-dimensionally uniform detector resolution. These detectors allow a geometry that places the detectors very close to imaging subjects, because they can maintain high spatial resolution even in the peripheral region in the field-of-view (FOV) without loss of sensitivity. In this study, we are proposing a helmet-PET geometry consisting of a hemispheric-shaped detector and a jaw detector. The key points of the geometry are the closely positioned detectors and the detector covering the jaw. For each point in the FOV, we calculated the geometrical sensitivity as the relative coverage of the solid angle where the coincidence measurement was possible. We found that the hemispheric-shaped geometry had high sensitivity for the cerebrum region. In addition, the jaw detector significantly improved the sensitivity at the center region of the hemisphere, where the cerebellum is positioned during PET measurement. High sensitivity and quantitative accuracy for the cerebellum region are important especially for functional brain imaging because this region may be used as a reference value in kinetic analysis. Geometrical analysis showed that the proposed geometry has good potential for highly sensitive and accurate measurement of brain functions. In addition, numerical simulations showed the proposed geometry increases image quality especially for the central region.
Elastic modulus of low-density lipoprotein as potential indicator of its oxidation (2015)

The elastic modulus of low-density lipoprotein particles ranged between 0.1 and 2 MPa. The oxidation of low-density lipoprotein increased the number of low-density lipoprotein particles with smaller elastic moduli, indicating the decrease in low-density lipoprotein stiffness. The elastic modulus of low-density lipoprotein might be potentially useful to evaluate low-density lipoprotein oxidation.
Curative intravenous adoptive immunotherapy of Meth A murine sarcoma. A histologic and immunohistochemical assessment. (1985)

Intravenous administration of 1.5 X 10(8) syngeneic spleen cells from immune animals resulted in the complete eradication of established Meth A soft tissue sarcomas in (C57BL/6 X BALB/c) F1 mice. In mice receiving a single injection of immune spleen cells 4 days after tumor implantation in the abdominal wall, the tumors continued to grow for approximately 1 week before undergoing regression. This delay before adoptive immunity is expressed is thought to represent the time needed for the passively transferred cells to give rise to a host response of sufficient magnitude to destroy the tumor. None of the mice receiving a similar number of control spleen cells were cured of their sarcomas. Successful therapy was dependent upon the transfer of viable, immune T lymphocytes and required prior irradiation of the tumor-bearing host in order to remove suppressor T cells. Utilizing sequential histologic and immunohistochemical techniques, we attempted to characterize the cellular events of tumor regression. The earliest histologic difference between animals treated with immune and nonimmune lymphocytes was in the number of lymphocytes detected at the perimeter of the tumor in specifically immunized mice on day 6. There was also a striking difference between animals treated with immune versus nonimmune lymphocytes in the intensity and timing of the acute inflammatory response beginning on day 8. The "front" of immunologically mediated tumor destruction appeared at the lateral and deep borders of the implanted sarcomas and progressed inward. During the period of active tumor regression T lymphocytes reactive with a biotinylated mouse anti-Thy 1.2 monoclonal antibody were increased in frozen sections of tumors in mice receiving immune cells relative to the controls. During the first 3 weeks following adoptive transfer of lymphocytes, T cells reactive with Lyt-1 biotinylated mouse monoclonal antibody (helper/inducer phenotype) outnumbered their Lyt-2 (suppressor/cytotoxic) counterparts in frozen sections of tumor from both specifically immunized and control mice. By the end of the 4th week of the experiment, the sarcomas were completely eradicated in all mice receiving immune cells. The previous tumor beds were occupied by collections of lipid-laden macrophages, lymphocytes, plasma cells, and fibroblasts. Despite vigorous but delayed acute and chronic inflammatory responses at the tumor perimeters in the control mice, these tumors all progressed.(ABSTRACT TRUNCATED AT 400 WORDS)
Digital pacer detection in diagnostic grade ECG (2011)

Pulses from a cardiac pacemaker appear as extremely narrow and low- amplitude spikes in an ECG. These get misinterpreted for R-peaks by QRS detectors, leading to subsequent faulty analysis of several algorithms which rely on beat-segmentation. Detection of the pacer pulses, thus, necessitates sampling the ECG signal at high data rates of 4-16 kHz. In a wireless body sensor network, transmission of this high-bandwidth data to a processing gateway, for pacer detection, is extremely power consuming. In this paper, we describe a compressed sensing approach, which enables reliable detection of AAMI/EC11 specified pacer pulses using ECG data rates of 50-100 sps, an order of magnitude smaller than those used in typical detection algorithms in the literature.
Abstract 5410: Tim-3 expression and function in natural killer cells from metastatic melanoma patients (2012)

Abstract BACKGROUND: Tim-3 (T-cell immunoglobulin domain and mucin domain 3) is a type-I glycoprotein receptor with pivotal roles in immune regulation and tolerance induction. Tim-3 has opposing roles in innate and adaptive immunity. It synergizes with TLR signaling in DCs inducing the production of inflammatory cytokines, while it acts as a negative regulator of Th1/Tc1 cell function by triggering T cell apoptosis upon interaction with its ligand, galectin-9. Tim-3 is also responsible for the functional exhaustion of T cells observed in some chronic infectious diseases and tumors, such as metastatic melanoma (MM). Natural Killer (NK) cells, innate immune cells which eliminate tumors and infected cells through cytotoxicity and IFNγ production, constitutively express Tim-3. Moreover, it has been described that some tumor cells (including melanoma cells) express and secrete galectin-9. However, little is known about the role of Tim-3 on NK cells, particularly in the presence of galectin-9, in healthy or melanoma patients. METHODS: Purified NK cells from PBMCs of 20 melanoma donors (MD) and 40 healthy donors (HD) were characterized according to the expression of Tim-3 by flow cytometry. Lamp-1 expression on NK cell surface was used to measure NK cell cytotoxicity against the following target cells: i) K562 cells which don't express Galectin-9 and ii) Gmel galectin-9+ and Gmel galectin-9- sorted melanoma cells. IFNγ production was assessed by intracellular staining after 4 hours culture in presence of IL-12. RESULTS: MD NK cells express higher levels of Tim-3 compared to HD NK cells (p&amp;lt;0.05). Moreover, MD NK cells have a defect in cytotoxicity, proliferation and IFNγ production, but it still remains unclear if Tim-3 is involved in this exhausted phenotype. So far, we found that Tim-3 expression by itself (without engagement of specific ligands) does not negatively affect NK cell cytotoxicity. However, the expression of Galectin-9 by the target cells induces a decrease in NK cell cytotoxicity (Gmel Gal-9+ vs Gmel Gal-9-). CONCLUSION: These data suggest that when engaged with Galectin-9, Tim-3 expression down-modulates NK cell cytotoxicity. Therefore, galectin-9 expression may be a possible mechanism for tumors to evade immune surveillance. Given that an increasing body of data supports an important role for Tim-3/Galectin-9 interaction in immune regulation in infectious diseases and cancer, deciphering the function of Tim-3 in different cell types will be critical for potentially targeting it therapeutically. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5410. doi:1538-7445.AM2012-5410