gebhart/patrepeval huggingface dataset:
Microgravity diode laser spectroscopy measurements in a reacting vortex ring (2001)

The technique of Diode Laser Spectroscopy (DLS) with wavelength modulation is utilized to measure the concentration of methane in reacting vortex rings under microgravity conditions. From the measured concentration of methane, other major species such as water, carbon dioxide, nitrogen, and oxygen can be easily computed under the assumption of equilibrium chemistry with the method of Interactive Temperature with Assumed Chemistry (ITAC). The conserved scalar approach in modelling the coupling between fluid dynamics and combustion is utilized to represent the unknown variables in terms of the mixture fraction and scalar dissipation rate in conjunction with ITAC. Post-processing of the DLS measurements and the method of ITAC used in computing the species concentration are discussed. From the flame luminosity results, the increase in ring circulation appears to increase the fuel consumption rate inside the reacting vortex ring and the flame height for cases with similar fuel volumes. Preliminary results and application of ITAC show some potential capabilities of ITAC in DLS. The measured concentration of methane, and computed concentrations of water and carbon dioxide agree well with available results from numerical simulations.
Performance of energy-conserving access protocols under self-similar traffic (2003)

Since widespread commercial use of wireless technology is still many years off, there is very little data to determine what constitutes an accurate model for wireless traffic. Many studies have shown that landline network traffic does not follow a traditional Poisson model but instead exhibits self-similar behavior. Previous papers have introduced and analyzed the performance of fundamental classes of energy-conserving protocols under traditional Poisson models. In order to evaluate these protocols under a distribution which might more accurately depict future wireless network traffic, we use simulation and proven models to consider the trade-off between energy and delay under a self-similar arrival distribution.
Expectation Maximization Indoor Localization Utilizing Supporting Set for Internet of Things (2018)

With the growth of WLAN infrastructure, received signal strength (RSS) fingerprint-based WiFi indoor positioning systems have received considerable attention recently. Some existing RSS fingerprint-based localization methods estimate locations by directly matching an online testing sample with an offline database, and thus show low accuracy because RSS is known to be vulnerable to variations caused by changing environment and heterogeneous hardware. To overcome the above drawbacks, we propose an expectation maximization indoor localization approach by leveraging supporting set (EMSS). In the offline phase, we first divide a positioning area into ${G}$ grid points and index each grid by a label. All the indices of grid points form a label set $ {\Psi =\{1,2,\ldots, G\}}$ . Then, we collect the RSS fingerprints to construct an offline database for all labeled grid points. In the online phase, given an online RSS testing sample, we first construct a supporting set (SS), which is a subset of $ {\Psi }$ , selected by the similarity between the online RSS sample and offline database. So, SS is a latent space that likely includes the true label (location) of the user. Based on the SS, we then derive an expectation maximization (EM) algorithm by incorporating the fingerprint quality into the estimation of the true label. EM can intelligently estimate the location of the user by evaluating the fingerprint quality of SS. Furthermore, we propose an optimal size selection algorithm based on Bayesian information criterion to adaptively determine the size of SS. Our method can effectively mitigate the impacts of changing environment and heterogeneous hardware without fingerprint and hardware calibrations, and can thus be practically applied. Experimental results verify that EMSS performs significantly better than some existing fingerprint-based methods.
Are Short Telomeres Hallmarks of Cancer Recurrence? (2013)

Exposure to radiation and some chemotherapeutic agents is associated with an increased risk of developing second cancers. Short telomeres are almost universally associated with malignant cancer progression. An unanswered question is whether inherited short telomeres or therapy-related telomere shortening is a biomarker of the development of second malignant neoplasms.
System Level Thermal Performance Evaluation of New Inverted Exposed Pad Packages for Automotive Applications (2006)

An extensive 3-D conjugate numerical study is conducted to assess the thermal performance of the novel 54 lead SOIC (with inverted exposed Cu pad) packages for automotive applications. The thermal performance of the modified designs with exposed pad are investigated, ranging from smaller die/flag size to larger ones, with single or multiple heat sources operating under various powering conditions. The thermal performance is compared to other existing packages with typical application to the automotive industry. The impact of the lead frame geometrical structure and die attach material on the overall thermal behavior is evaluated. Under one steady state (4W) operating scenario, the package reaches a peak temperature of 117.1°C, corresponding to a junction-to-heatsink thermal resistance Rjhs of 4.27°C/W. For the design with a slightly smaller Cu alloy exposed pad (Cu Alloy), the peak temperature reached by the FETs is 117.8°C, slightly higher than for the design with the intermediate size flag. In this case, the junction-to-heatsink thermal resistance Rj-hs is 4.45°C/W. The worst case powering scenario is identified, with 1.312W/FET and total power of 10.5W, barely satisfying the overall thermal budget. The variation of the peak (junction) temperature is also evaluated for several powering scenarios. Finally, a comparison with a different exposed pad package is made. The impact of the higher thermal conductivity (solder) die attach is evaluated and compared to the epoxy die attach in the 54 lead SOIC package. Several cases are evaluated in the paper, with an emphasis on the superior thermal performance of new packages for automotive applications.
USP13 Genetics and Expression in a Family With Thyroid Cancer (2022)

Abstract Purpose: Papillary thyroid carcinoma (PTC) is the most common type of thyroid carcinoma and its incidence has greatly increased in the last 30 years. Ubiquitin-specific protease 13 (USP13) is a class of deubiquitinating enzymes (DUBs) and plays an important role in cellular functions such as cell cycle regulation, DNA damage repair and is implicated in different cell signaling pathways. Studies regarding the role of USP13 in cancer development and progression are divergent and there are no previous data regarding the role of USP13 gene in PTCs. In this study, we investigated the genetic cause of PTC diagnosed in multiple members of a Brazilian family. Methods: Whole exome sequencing identified a heterozygous missense variant c.1483G&gt;A (p.V495M) in the USP13 gene that fully segregates with the disease. We investigated whether the USP13 c.1483G&gt;A variant found in our PTC patients impacts USP13 protein stability and function in thyroid cancer cells, MDA-T32, by clycloheximide chase assay.Results: The specific variant (c.1483G&gt;A) preserves protein stability for longer hours compared to the non-mutated USP13 protein. Moreover, USP13 overexpression increased the potential of a single cell to form colony and the USP1 3 c.1483G&gt;A variant enhanced the effects seen in USP13 overexpression. Conclusion: Our study suggests that USP13 may enhance tumorigenesis in PTC; in addition, the p.V495M (c.1483G&gt;A) variant may contribute to PTC formation.
Differentiated BGP Update Processing for Improved Routing Convergence (2006)

Internet routers today can be overwhelmed by a large number of BGP updates triggered by events such as session resets, link failures, and policy changes. Such excessive updates can delay routing convergence, which, in turn, degrades the performance of delay- and jitter-sensitive applications. This paper proposes a simple and novel idea of differentiated processing of BGP updates to reduce routers' load and improve routing convergence without changing the protocol semantics. Based on a set of criteria, BGP updates are grouped into different priority classes. Higher-priority updates are processed and propagated sooner, while lower-priority ones, not affecting routing decisions, can be delayed to both reduce routers' load and improve routing convergence. We first present a general methodology for update classification, update processing, and priority-state inference. By analyzing real BGP data obtained from Route Views, we show that our update classification is feasible and beneficial. We further propose two differentiated update processing (DUP) algorithms and evaluate them using the SSFNet BGP simulator on several realistic network topologies. The algorithms are shown to be very effective for large networks, yielding 30% fewer updates and reducing convergence time by 80%. Our scheme is simple and light-weight with little added processing overhead. It can be deployed incrementally, since BGP messages are not modified and every BGP router makes routing decisions independently.
Microscope-Integrated Intraoperative Ultrahigh-Speed Swept-Source Optical Coherence Tomography for Widefield Retinal and Anterior Segment Imaging (2018)

Ultrahigh-speed SS-OCT enables widefield intraoperative viewing in the posterior and anterior eye. Widefield imaging visualizes ocular structures and pathology without requiring OCT realignment. [Ophthalmic Surg Lasers Imaging Retina. 2018;49:94-102.].
Time-dependent plasmonic response of gold nanoparticles embedded in doped strontium titanate films for high-temperature gas sensing (2020)

Conducting oxide films on optical fibers offer significant advantages as sensing layers in high temperature, harsh environments (e.g., solid oxide fuel cells or power plant boiler systems), where many traditional sensors degrade rapidly. In particular, oxides exhibiting the perovskite crystal structure are highly stable under substitution of the constituent atoms as well as under high concentrations of cation and oxygen vacancies. Strontium titanate (STO), for example, maintains the perovskite crystal structure under high dopant concentrations both on the “A-site” (Sr substitution) and “Bsite” (Ti substitution). As a result, STO and other perovskite oxides form a rich family of materials whose unique electrical, magnetic, and optical properties can be continuously tuned based upon the concentrations of the constituent atoms. Structural stability, in conjunction with an interconnected vacancy defect chemistry and optical as well as electrical properties, suggests great promise for this material system in the realm of harsh environment sensing. In this work, donor-doped strontium titanate films containing gold nanoparticles are investigated for gas sensing characteristics at high temperature (up to 680&deg;C) under oxidizing and reducing conditions. Using time resolved, in-situ optical transmission measurements in conjunction with room-temperature ex-situ measurements of planar films, the relationship between the Au localized surface plasmon resonance (LSPR) response in the visible and oxide free-carrier based response in NIR is investigated.
microRNA-29b prevents liver fibrosis by attenuating hepatic stellate cell activation and inducing apoptosis through targeting PI3K/AKT pathway (2014)

microRNA-29b (miR-29b) is known to be associated with TGF-β-mediated fibrosis, but the mechanistic action of miR-29b in liver fibrosis remains unclear and is warranted for investigation. We found that miR-29b was significantly downregulated in human and mice fibrotic liver tissues and in primary activated HSCs. miR-29b downregulation was directly mediated by Smad3 through binding to the promoter of miR-29b in hepatic stellate cell (HSC) line LX1, whilst miR-29b could in turn suppress Smad3 expression. miR-29b transduction in the liver of mice prevented CCl4 induced-fibrogenesis, concomitant with decreased expression of α-SMA, collagen I and TIMP-1. Ectopic expression of miR-29b in activated HSCs (LX-1, HSC-T6) inhibited cell viability and colony formation, and caused cell cycle arrest in G1 phase by downregulating cyclin D1 and p21cip1. Further, miR-29b induced apoptosis in HSCs mediated by caspase-9 and PARP. miR-29b inhibited its downstream effectors of PIK3R1 and AKT3 through direct targeting their 3'UTR regions. Moreover, knockdown of PIK3R1 or AKT3 suppressed α-SMA and collagen I and induced apoptosis in both HSCs and in mice. In conclusion, miR-29b prevents liver fibrogenesis by inhibiting HSC activation and inducing HSC apoptosis through inhibiting PI3K/AKT pathway. These results provide novel mechanistic insights for the anti-fibrotic effect of miR-29b.
[A phase I study of combination-therapy with gemcitabine and epitope peptides derived from human vascular endothelial growth factor receptor for unresectable or recurrent pancreas cancer]. (2008)

We are performing a phase I clinical trial of combination-therapy with gemcitabine and epitope peptide derived from human vascular endothelial growth factor receptor (VEGFR) for advanced pancreas cancer. The aim of this study was to evaluate the safety, immunological response and tumor response. Six patients have been enrolled at present. During the clinical course, no major adverse events were observed. Additionally, two out of 6 cases showed a minor shrinkage of the tumor. Immunological response has not been analyzed yet. These results indicated that a combination-therapy with gemcitabine and epitope peptides derived from VEGFR could be tolerable.
Appendix E: Speckle Contrast when a Dynamic Diffuser is Projected onto a Random Screen (2020)

Our goal in this appendix is to find expressions for speckle contrast when an object to be projected is first imaged onto a changing diffuser, and is then projected onto a screen for viewing. We consider two types of random diffuser, one for which the diffuser uniformly fills the projection lens but does not overfill it, and a second that overfills the projection lens. In the former case, for a uniformly transmitting object, a pure phase diffuser image is projected onto the screen, while for the second case, each resolution cell of the projector lens produces a fully developed speckle amplitude. A third case, a deterministic diffuser with certain orthogonality properties, is considered in the main text but not in this appendix. In both cases considered here, the optically rough viewing screen introduces speckle within each resolution element of the eye. The symbols and geometry assumed here are discussed in Section 7.4.
Intragraft Findings During Costimulation Blockade in Non-human Primate Renal Allotransplantation (1998)

24 We have analyzed biopsies taken from normally functioning renal allografts of rhesus monkeys following transplantation with anti-CD154 (hu5C8) induction (n=4), and compared them to biopsies from rejecting rhesus allografts (n=2) and normal non-transplanted rhesus kidneys (n=4). Graft histology has been evaluated by hematoxylin/eosin staining. Intragraft transcription for the T cell receptor (TCR) β-chain, CD80, L-selectin, IL-1β, IL-2, 3, 4, 5, 6, 8, 10, 15, IFN-γ and TNF-α genes has been studied by semi-quantitative RT-PCR. PCR products have been quantified by high performance liquid chromatography and standardized to actin from the same biopsy. One month after transplantation all hu5C8 allografts were characterized by significant mononuclear cell infiltrates despite normal function (creatinine < 0.8 mg/dl) that has persisted for > 30 days post biopsy. These infiltrates were confined to the interstitium and were not associated with endothelial or tubular changes. This was in stark contrast to the rejecting grafts in which infiltrates were accompanied by tubulitis, endotheliitis, necrosis and interstitial hemorrhage. Normal kidneys were free of infiltrates or pathological changes. Hu5C8 biopsies were found to have increased expression of TCRβ-chain, CD80, L-selectin, IFN-γ, IL-1β and IL-15 when compared with normal or rejecting allografts. TNF-α was also a prominent transcript in all hu5C8 biopsies. Rejecting biopsies were unique in their expression of the inflammatory transcripts IL-6 and IL-8. No biopsies were found to have transcripts for the IL-2, 3 or 5. Low level IL-4 was detected in one hu5C8 biopsy as was IL-10. These data demonstrate that significant lymphocytic activity including pro-inflammatory TH1 cytokine expression occurs during costimulation blockade with hu5C8. Despite this, there is no apparent injury to the allograft. L-selectin expression and lymphoid aggregation also suggests that active homing to the allograft is taking place. The prominence of TNF-α is consistent with regulatory induction of apoptosis within the graft. Study of subsequent biopsies from long surviving hu5C8 animals is underway to further characterize these infiltrates and determine their role in graft survival following costimulation blockade.
AQUA: Scalable Rowhammer Mitigation by Quarantining Aggressor Rows at Runtime (2022)

Rowhammer allows an attacker to induce bit flips in a row by rapidly accessing neighboring rows. Rowhammer is a severe security threat as it can be used to escalate privilege or break confidentiality. Moreover, the threshold of activations needed to induce Rowhammer continues to reduce and new attacks like Half-Double break existing solutions that refresh victim rows. The recently proposed Randomized Row-Swap (RRS) scheme is resilient to Half-Double as it provides mitigation by swapping an aggressor row with a random row. However, to ensure security, the threshold for triggering a row-swap must be set much lower than the Rowhammer threshold, leading to a significant performance loss of 20% on average, at a Rowhammer threshold of 1K. Furthermore, the SRAM overhead for storing the indirection table of RRS becomes prohibitively large – 2.4MB per rank at a Rowhammer threshold of 1K. Our goal is to develop a scalable Rowhammer mitigation that incurs negligible performance and storage overheads.To this end, we propose AQUA, a Rowhammer mitigation that breaks the spatial correlation between aggressor and victim rows by dynamically quarantining the aggressor row in a dedicated region of memory. AQUA allows for an effective row migration threshold much higher than in RRS, leading to an order of magnitude less slowdown and SRAM. As the security of AQUA is not reliant on keeping the destination row a secret, we further reduce the SRAM overheads of the indirection table by storing it in DRAM, and accessing it on-demand. We derive the size of the quarantine region required to ensure security for AQUA and show that reserving about 1% of DRAM is sufficient to mitigate Rowhammer at a threshold of 1K. Our evaluations show that AQUA incurs an average slowdown of 2% and an SRAM overhead (for mapping and migration) of only 41KB per rank at a Rowhammer threshold of 1K.
Peptide‐Functionalized Polyurethane Coatings Prepared via Grafting‐To Strategy to Selectively Promote Endothelialization (2017)

Endothelialization, formation of endothelial cells (ECs) layer on cardiovascular implant surface, is considered an ideal approach to prevent restenosis (renarrowing of blood vessel mainly due to the accumulation of proliferated vascular smooth muscle cells, SMCs) and thrombosis. In this study, the possibility of using polyurethane (PU) as a coating platform for functionalization with peptide to enhance endothelialization on implants is explored. PUs are synthesized through metal-free organocatalytic polymerization followed by chemical conjugation with an EC-specific REDV peptide through thiol-ene reaction. Meanwhile, the free isocyanate groups of PU allow for covalent grafting of REDV-functionalized PU (PU/REDV) to silanize implant materials (nitinol and PET). PU/REDV coating with peptide grafting density of ≈2 nmol cm<sup>-2</sup> selectively accommodates primary human umbilical vein ECs (HUVECs) and retards spreading of primary human umbilical artery SMCs (HUASMCs). In addition, a layer of HUVECs is formed within 3 d on PU/REDV-coated surfaces, while proliferation of HUASMCs is inhibited. The selectivity is further confirmed by coculture of HUVECs and HUASMCs. Moreover, the PU/REDV-coated surfaces are less thrombogenic as evidenced by reduced number and activity of adhered platelets. Therefore, PU/REDV can be potentially used as a coating of cardiovascular implants to prevent restenosis and thrombosis by promoting endothelialization.
High-temperature thermal stability driven by magnetization dilution in CoFeB free layers for spin-transfer-torque magnetic random access memory (2018)

Spin-transfer-torque magnetic random access memory (STT-MRAM) is the most promising emerging non-volatile embedded memory. For most applications, a wide range of operating temperatures is required, for example -40 °C to +150 °C for automotive applications. This presents a challenge for STT-MRAM, because the magnetic anisotropy responsible for data retention decreases rapidly with temperature. In order to compensate for the loss of thermal stability at high temperature, the anisotropy of the devices must be increased. This in turn leads to larger write currents at lower temperatures, thus reducing the efficiency of the memory. Despite the importance of high-temperature performance of STT-MRAM for energy efficient design, thorough physical understanding of the key parameters driving its behavior is still lacking. Here we report on CoFeB free layers diluted with state-of-the-art non-magnetic metallic impurities. By varying the impurity material and concentration to modulate the magnetization, we demonstrate that the magnetization is the primary factor driving the temperature dependence of the anisotropy and thermal stability. We use this understanding to develop a simple model allowing for the prediction of thermal stability of STT-MRAM devices from blanket film properties, and find good agreement with direct measurements of patterned devices.