gebhart/patrepeval huggingface dataset:
CD137 Identifies a Population of Regulatory T Cells That Inhibit Anti-Tumor Immune Responses In Adoptive Immunotherapy (2010)

Abstract Abstract 2093 Background: Adoptive immunotherapy is a promising novel approach to the treatment of cancer. However, clinical translation of adoptively transferred CD4 T cells is limited by cotransfer of an inhibitory population of regulatory CD4 T cells (Tregs). We identified a method of isolating viable antitumor CD4 T cells while excluding Tregs based on two surface markers—CD44 and CD137. Methods: We have developed a model for adoptive cell therapy of lymphoma whereby anti-tumor T cells are generated in vivo through vaccination with a CpG-loaded whole cell vaccine (CpG/H11). These vaccine-induced cells can protect from lethal tumor challenge when isolated and transferred into lethally irradiated, syngeneic recipient mice. We investigated the subsets of T cells involved in the anti-tumor response through a combination of in vitro and in vivo assays. Results: Adoptive transfer of CD137negCD44hi CD4 T cells, but not other sub-populations, provided protection from B cell lymphoma. We demonstrate that the population of CD137posCD44hi CD4 T cells consists primarily of activated Tregs. In vitro, these CD137pos cells suppressed the proliferation of effector cells in a contact-dependent manner. We observed that this CD137pos Treg population persisted following adoptive transfer and maintained expression of FoxP3 as well as CD137. Moreover, the addition of CD137posCD44hi CD4 cells to CD137negCD44hi CD4 cells suppressed the antitumor immune response. In the presence of CD137posCD44hi CD4 T cells, homing of other T cell populations to tumor sites was disrupted. These results suggest that CD137 expression on CD4 T cells defines a population of activated Tregs that prevent antitumor immune responses. Conclusions: Our findings identify two surface markers that can be used to facilitate the enrichment of anti-tumor CD4 T cells while depleting an inhibitory Treg population. This approach has direct applicability to clinical trials for patients with lymphoma. Disclosures: No relevant conflicts of interest to declare.
Broadening and shifting of the Raman Q branch in pure D2 and D2–He mixtures, I: experimental results and comparison with theory (1994)

We report the broadening and shifting of the Raman Q-branch lines in D 2 and D 2 –He mixtures, all at 305.2 K. The width and shift of each line were extracted by fitting a simple Lorentzian profile to the experimental data. From a linear fit of the widths and shifts as a function of density we have determined broadening and shifting coefficients with an uncertainty of ±0.5%. None of the existing semiclassical or quantal calculations agree with the measurements at this level of accuracy. It is pointed out that the removal of certain approximations in the calculations should bring theory and experiment into closer agreement.
New methods for exploiting program structure and behavior in computer architecture (2005)

Micro-architectural techniques of the next decade will have to be more efficient and scalable in order to handle growing workloads and longer communication and memory latencies. We believe that information about program structure, the data and control relationships between instructions, can be used as a powelful framework for new techniques. We argue that program structure information has several inherent advantages over frameworks that associate information either with instructions in isolation or with data. We present summaries of four novel methods that apply program structure information to memory system problems from disambiguation and data cache bandwdith to. prefetching and coherence optimization.
PRISM: Improving the Performance of Inverse-Multiplexed TCP in Wireless Networks (2007)

Multi-homed mobile hosts in physical proximity may spontaneously team up to form a community and run high-bandwidth applications by pooling their low wireless widearea network (WWAN) bandwidths together for communication with a remote application server. Utilizing their high-bandwidth wireless local-area network (WLAN), the thus-teamed mobile hosts can aggregate and distribute the application content among themselves. This paper first justifies the need for such a mobile collaborative community (MC2), or a community, to improve user-perceived network bandwidth and utilization. Then, existing one-to-one communication protocols like TCP are shown to suffer significant performance degradation due to frequent out-of-order packet deliveries. To address this TCP problem, we propose a proxy-based inverse multiplexer, called PRISM, that enables TCP to efficiently utilize the community members' WWAN connections while avoiding the performance degradation. PRISM runs at the proxy's network layer as a routing component and stripes each TCP flow over multiple WWAN links by exploiting the transport-layer feedback information. Moreover, it masks a variety of adverse effects specific to each WWAN link via an intelligent ACK-control mechanism. Finally, PRISM enables TCP to respond correctly to dynamically-changing network states through a sender-side enhancement of congestion control. PRISM has been evaluated with experimentation on a testbed as well ns-2-based simulation. Our experimental evaluation has shown PRISM to improve TCP's performance by up to 310% even with two collaborative mobile hosts. Our in-depth simulation study has also shown that PRISM delivers a near-optimal aggregated bandwidth in the community, and improves network utilization significantly
Applications-specific microcoded architectures for efficient fixed-rate FFT (2003)

Many Fourier transform applications have to operate at fixed sample rates in the low to medium range, especially in signal processing systems. Hence, in order to arrive at efficient implementations, hardware sharing is required as in microcoded architectures. Very efficient application-specific realizations spanning a wide throughput range are proposed for FFT algorithms. Novel single-cycle address computations are presented to obtain these results. Tradeoffs between the architectural alternatives are provided. The designs have been used as test vehicles for the architectural strategy in an automated synthesis tool box geared toward digital signal processing applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comprehensive analysis of photonic-crystal surface-emitting lasers via time-dependent three-dimensional coupled-wave theory (2019)

We develop a time-dependent three-dimensional coupled-wave theory (3D-CWT) for the transient analysis of photonic-crystal surface-emitting lasers (PCSELs). Our model takes into account the temporal evolution of both the photon and carrier distribution inside PCSELs, which enable the analysis of various above-threshold lasing characteristics including the relaxation oscillation, spatial hole burning, and multimode lasing. With the developed time-dependent 3D-CWT, we perform transient analysis of the high-power, high-beam-quality PCSELs with double-lattice photonic crystals and reproduce the experimental results of near-field patterns and lasing spectra under high current injection. Our theory enables the comprehensive understanding of the device physics of PCSELs toward the realization of higher-power continuous-wave lasing and short-pulse lasing.
Digital sampling of acoustic impulse noise: Implications for exposure measurement and damage risk criteria (2022)

Current standards for the measurement of impulse noise (e.g., MIL-STD-1474E) recommend using a sampling rate of at least 200 kHz in order to accurately estimate the risk of hearing damage. The given motivation for this high sampling rate is to ensure a temporal resolution in the impulse waveform fine enough to accurately capture the peak pressure. However, the Nyquist-Shannon sampling theorem specifies that a sampled signal can accurately reconstruct both the amplitude and phase information of a signal given the sampling rate is at least twice the highest frequency present in the original signal. Thus, it is possible to reconstruct a band limited signal with the same temporal resolution as one captured at a higher sampling rate if the contributions of energy above the Nyquist rate can be ignored. In this study, resampling techniques are applied to a signal sampled at 48 kHz to extract A-weighted sound pressure energy estimates within 0.1 dB of those obtained at a higher sampling rate. Our results suggest sampling rates for impulsive noise should be based on the range of frequencies expected to make a contribution to injury risk rather than on concerns about temporal resolution.
Detection of Postcolonoscopy Colorectal Neoplasia by Multi-target Stool DNA (2021)

The high PPV of mt-sDNA 0-9 years after a negative screening colonoscopy suggests that lesions were likely missed on previous examination or may have arisen de novo. mt-sDNA as an interval test after negative screening colonoscopy warrants further study.
A Computational Workflow Translates a 58-Gene Signature to a Formalin-Fixed, Paraffin-Embedded Sample-Based Companion Diagnostic for Personalized Treatment of the BRAF-Mutation-Like Subtype of Colorectal Cancers (2017)

Colorectal cancer patients with the <i>BRAF</i>(p.V600E) mutation have poor prognosis in metastatic setting. Personalized treatment options and companion diagnostics are needed to better treat these patients. Previously, we developed a 58-gene signature to characterize the distinct gene expression pattern of <i>BRAF</i>-mutation-like subtype (accuracy 91.1%). Further experiments repurposed drug Vinorelbine as specifically lethal to this <i>BRAF</i>-mutation-like subtype. The aim of this study is to translate this 58-gene signature from a research setting to a robust companion diagnostic that can use formalin-fixed, paraffin-embedded (FFPE) samples to select patients with the <i>BRAF</i>-mutation-like subtype. <i>BRAF</i> mutation and gene expression data of 302 FFPE samples were measured (mutants = 57, wild-type = 245). The performance of the 58-gene signature in FFPE samples showed a high sensitivity of 89.5%. In the identified <i>BRAF</i>-mutation-like subtype group, 50% of tumours were known <i>BRAF</i> mutants, and 50% were <i>BRAF</i> wild-type. The stability of the 58-gene signature in FFPE samples was evaluated by two control samples over 40 independent experiments. The standard deviations (SD) were within the predefined criteria (control 1: SD = 0.091, SD/Range = 3.0%; control 2: SD = 0.169, SD/Range = 5.5%). The fresh frozen version and translated FFPE version of this 58-gene signature were compared using 170 paired fresh frozen and FFPE samples and the result showed high consistency (agreement = 99.3%). In conclusion, we translated this 58-gene signature to a robust companion diagnostic that can use FFPE samples.
Dynamic Security Orchestration for CDN Edge-Servers (2018)

Content Delivery Networks (CDNs) aim to provide high Quality of Service (QoS) in serving digital content. To achieve high QoS, CDNs employ edge-servers that cache content in the vicinity of end-users. Edge-servers are vulnerable to attacks that degrade the QoS of end-users. Protecting edge-servers against these threats is vital and complex. The attack mitigation must be immediate, and its overhead should have the least impact on the QoS of legitimate end-users. In this paper, we demonstrate a software-based security system that can be programmed to automatically react to threats by deploying and managing security function chains. Using high-level security policies, a network operator can program a desired system behavior. We demonstrate how our system automatically deploys security function chains to handle real-world threats.
Specific Substitutions at Amino Acid 256 of the Sarcoplasmic/Endoplasmic Reticulum Ca2+ Transport ATPase Mediate Resistance to Thapsigargin in Thapsigargin-resistant Hamster Cells (1998)

High levels of resistance to thapsigargin (TG), a specific inhibitor of intracellular Ca2+ transport ATPases (SERCAs), can be developed in culture by stepwise exposure of mammalian cells to increasing concentrations of TG. We have identified, in two independently selected TG-resistant hamster cell lines of different lineages, mutant forms of SERCA. In the TG-resistant Chinese hamster lung fibroblast cell line DC-3F/TG, a T --> C change at nucleotide 766 introduces a Phe256 --> Leu alteration within the first cytosolic loop of the SERCA. In contrast, in the TG-resistant Syrian hamster smooth muscle cell line DDT/TG 4 microM, a T --> C change at nucleotide 767 introduces a Phe256 --> Ser mutation at that position. When these specific mutations are introduced into a wild-type full-length avian SERCA1 cDNA, transfection experiments reveal that Ca2+ transport function and ATP hydrolytic activity are not altered by such mutations. However, a 4-5-fold resistance to TG inhibition of Ca2+ transport function occurs upon the introduction of either the Phe256 --> Leu or the Phe256 --> Ser mutation into wild-type SERCA1. These specific mutations also render the hydrolytic activity of the ATPase resistant to inhibition by TG. Our results not only implicate amino acid 256 in TG-SERCA interactions, but also demonstrate that specific mutations within SERCA can mediate resistance to TG.
Thermocatalytic CO2-Free Production of Hydrogen and Carbon from Hydrocarbon Fuels (2003)

This invention relates to a novel process for sustainable CO.sub.2 -free production of hydrogen and carbon by thermocatalytic decomposition (or dissociation, pyrolysis, cracking) of hydrocarbon fuels over carbon-based catalysts in the absence of air and/or water. The process is applicable to any hydrocarbon fuel, including sulfurous fuels. Combination of a catalytic reactor with a gas separation unit allows to produce high purity hydrogen (at least, 99.0 v %) completely free of carbon oxides. In a preferred embodiment, sustainable continuous production of hydrogen and carbon is achieved by both internal and external activation of carbon catalysts. Internal activation of carbon catalyst is accomplished by recycling of hydrogen-depleted gas containing unsaturated and aromatic hydrocarbons back to the reactor. External activation can be achieved via surface gasification of carbon catalysts by hot combustion gases during catalyst heating. The process can conveniently be integrated with any
Optimization of capillary zone electrophoresis/electrospray ionization parameters for the mass spectrometry and tandem mass spectrometry analysis of peptides (1992)

The solution chemistry conditions necessary for optimum analysis of peptides by capillary zone electrophoresis (CZE)/electrospray ionization mass spectrometry and CZE electrospray ionization tandem mass spectrometry have been studied. To maximize the signal-to-noise ratio of the spectra it was found necessary to use acidic CZE buffers of low ionic strength. This not only increases the total ion current, but it also serves to fully protonate the peptides, minimizing the distribution of ion current across the ensemble of possible charge states.The use of acidic buffers protonates the peptides, which is advantageous for mass spectrometry and tandem mass spectrometry analysis, but is problematic with CZE when bare fused silica CZE columns are used. These conditions produce positively charged peptides, and negatively charged silanol moieties on the column wall, inducing adsorption of the positively charged peptides, thus causing zone broadening and a loss in separation efficiency. This problem was circumvented by the preparation of chemically modified CZE columns, which, when used with acidic CZE buffers, will have a positively charged inner column wall. The electrostatic repulsion between the positively charged peptides and the positively charged CZE column wall minimizes adsorption problems and facilitates high efficiency separations. Full-scan mass spectra were acquired from injections of as little as 160 fmols of test peptides, with CZE separation efficiencies of up to 250,000 theoretical plates.
Repair of DNA Alkylation Damage by the Escherichia coli Adaptive Response Protein AlkB as Studied by ESI‐TOF Mass Spectrometry (2010)

DNA alkylation can cause mutations, epigenetic changes, and even cell death. All living organisms have evolved enzymatic and non-enzymatic strategies for repairing such alkylation damage. AlkB, one of the Escherichia coli adaptive response proteins, uses an α-ketoglutarate/Fe(II)-dependent mechanism that, by chemical oxidation, removes a variety of alkyl lesions from DNA, thus affording protection of the genome against alkylation. In an effort to understand the range of acceptable substrates for AlkB, the enzyme was incubated with chemically synthesized oligonucleotides containing alkyl lesions, and the reaction products were analyzed by electrospray ionization time-of-flight (ESI-TOF) mass spectrometry. Consistent with the literature, but studied comparatively here for the first time, it was found that 1-methyladenine, 1,N (6)-ethenoadenine, 3-methylcytosine, and 3-ethylcytosine were completely transformed by AlkB, while 1-methylguanine and 3-methylthymine were partially repaired. The repair intermediates (epoxide and possibly glycol) of 3,N (4)-ethenocytosine are reported for the first time. It is also demonstrated that O (6)-methylguanine and 5-methylcytosine are refractory to AlkB, lending support to the hypothesis that AlkB repairs only alkyl lesions attached to the nitrogen atoms of the nucleobase. ESI-TOF mass spectrometry is shown to be a sensitive and efficient tool for probing the comparative substrate specificities of DNA repair proteins in vitro.
Adaptive Clustering for Energy Efficient Wireless Sensor Networks Based on Ant Colony Optimization (2009)

Summary form only given: Energy supply in wireless sensor networks (WSNs) is limited and non-replenishable, and energy efficiency is the most important feature in designing these networks. One way to reduce the energy consumption of WSNs and hence prolong the lifespan of these networks is to use adaptive clustering algorithms. In this paper, we use Ant Colony Optimization for Clustering (ACO-C) to propose a new energy aware clustering protocol for WSNs. By using appropriate cost functions, implemented at the base station, our algorithm minimizes and distributes the cost of long distance transmissions and data aggregating among all sensor nodes evenly. Simulation results show the effectiveness of our protocol over other well known clustering algorithms in terms of both network lifetime and data delivery to the base station.
Assessment of TRAM Aesthetics: The Importance of Subunit Integration (2006)

From these assessments, the authors derived a set of aesthetic rules for TRAM flap reconstruction. They believe that methodical application of these rules on a consistent basis can lead to the production of maximal aesthetic outcomes in TRAM breast reconstruction.
Method to determine the transverse shear modulus (GRT) of softwoods using full field strain measurements in off-axis compression (2008)

Method to determine the transverse shear modulus (GRT) of softwoods using full field strain measurements in off-axis compression
Extreme Heat Shielding of Clay/Chitosan Nanobrick Wall on Flexible Foam (2018)

Flexible polyurethane foam (PUF) is widely used in bedding, transportation, and furniture, despite being highly flammable. In an effort to decrease the flammability of the polymer, an environmentally friendly flame retardant coating was deposited on polyurethane foam (PUF) via layer-by-layer assembly. Treated foam was subjected to three different fire scenarios, 10 s torch test, cone calorimetry, and a 900 s burn-through test, to evaluate the thermal shielding behavior of an eight bilayer chitosan/vermiculite clay nanocoating. In each fire scenario, the nanocoating acts as a thermal shield from the flames by successfully protecting the backside of the PUF, whereas the side directly exposed to the flame results in a hollowed nanocoating that maintains the complex three-dimensional porous structure of the foam. Cone calorimetry reveals that the coating reduces the peak heat release rate and total smoke release by 53 and 63%, respectively, whereas a temperature gradient greater than 200 °C is observed across a 2.5 cm thick coated foam sample during the rigorous burn-through fire test. The thermal shielding behavior of this polymer/clay nanocoating makes this system very attractive in improving the fire safety of polyurethane foam used for insulating applications.
Temperature sensors for use in muscle microcalorimetry (2011)

In order to measure the heat production of small samples of heart muscle, very sensitive temperature sensors are required. In this paper, we survey a range of candidate temperature sensors for use in a microcalorimeter for studying cardiac muscle tissue. The key metrics (noise-equivalent temperature, thermal mass and noise-equivalent heat) of eight different temperature and heat sensors are compared. The sensor that would potentially allow the greatest heat resolution utilises the phenomenon of vapour pressure. An initial prototype of this thermometer has been constructed, and the design of a new sensor is outlined.
A label-free size-based micro coulter counter system for circulating rare tumor cells (2013)

In clinical and biological fields, circulating tumor cells (CTCs) have been becoming an important topic because of their critical role in cancer metastasis. Many researchers reported that the number of CTCs is highly-related with the survival rates of cancer patients. Hence, we described a label-free size-based micro coulter counter system to count CTCs in human blood. We examined OVCAR-3 cells spiked blood samples and obtained decent results with 88% efficiency. Furthermore, we tested breast cancer patient samples and detected CTCs in 24 patient samples. Therefore, the developed system shows a facile way to count CTCs regardless of biomarkers.
Message routing latency-minimizing method in an ASIC design for distributed cooperative communication protocol processing (1998)

In the field of distributed systems, research proceeds on reducing communication overhead by using a ring-type high-speed network to interconnect nodes and to reduce the number of transmissions, and by migrating cooperative functions such as load distribution and fault tolerance from conventional applications to lower-layer communication protocols. To raise the overall performance of such distributed systems, message routing latency at each node must be reduced, and to this end, we have incorporated communication protocol processing in an LSI chip. This LSI uses the received message and system-status data stored on the LSI to perform input-message path control (decide whether to transfer the message to the host or relay it) and to update specific fields in the message to be relayed. In the conventional method, processing of necessary message fields began after they had all been received and placed into a buffer. In this LSI, however, a set of modules are activated in sequence as fields that require various types of processing are received. This scheme is achieved by adopting a data-driven-type distributed control system and implementing all functions through wired logic control. As a result, message updating and relay latency has been minimized to 2.55 μs. The LSI has been achieved by a gate array of about 400 K gates using a 0.35-μm CMOS process. © 1998 Scripta Technica. Syst Comp Jpn, 29(3): 39–58, 1998
Experimental Demonstration of Coherent MAP Detection for Nonlinearity Mitigation in Long-Haul Transmissions (2010)

We implemented a maximum a posteriori probability (MAP) detection scheme for mitigating nonlinear phase distortion. We demonstrated 1 dB improvement in system performance and ~2dB higher nonlinearity tolerance after 6,000 km transmission.