gebhart/patrepeval huggingface dataset:
Protective effects of Red/Near Infrared Radiation on Murine Cardiac Ischemia/Reperfusion Injury (2010)

Red/Near infrared radiation (R/NIR) has been reported to reduce myocardial infarct (MI) size in rabbits after ischemia/reperfusion (I/R) injury (Lohr N.L, JMCC 2009). The precise mechanisms responsible for the cardioprotective effects of R/NIR are incompletely understood. We sought to identify the most beneficial wavelengths in the R/NIR light spectrum for limiting murine cardiac I/R injury. Anesthetized and ventilated mice underwent left coronary artery ligation for 60 min followed by reperfusion. R/NIR was applied for three min at the beginning of reperfusion. Area at risk (AAR) and MI size were measured at 24h of reperfusion. We investigated several wavelengths at varying levels of irradiance. A 19% decrease of MI/AAR was observed in wild mice when hearts were irradiated with red light (690 nm) at 0.06 W/cm2 of irradiance for 3 min at the time of reperfusion (59 ± 9% control group, n=7, vs 47 ± 7% irradiated group, n=6, P&lt;0.05). The cardioprotective effect of light appears related to both the specific wavelength and the level of irradiance across the broad spectrum of R/NIR radiation. By defining the specific wavelengths that provide maximal cardioprotection, genetically altered mice will further provide the precise mechanisms underling the cardioprotective effect of R/NIR. This work was supported by NIH grant R01AI050875 and laboratory royalties from licensed patents.
Abstract LB-053: Next-generation sequencing of T-cell receptor-beta gene rearrangements reveals dramatic expansion of T-cell clonotypes after CART-EGFRvIII therapy for glioblastoma (2017)

Abstract We are interested in the T cell repertoire in glioblastoma (GBM) patients who have been administered peripherally infused CART-EGFRvIII adoptive T cell therapy for recurrent EGFRvIII-positive GBM. On neuropathologic evaluation following GBM tumor resection, we noticed that several subjects had a robust lymphocytic infiltrate in their tumors following CART-EGFRvIII infusion, which was out of proportion to the level of CART-EGFRvIII genomic sequences observed. We sought to quantify the T cell infiltrate in five subjects whose tumors were resected at different time points following CART infusion (days 6-104). In these five subjects, we analyzed the T cell clonotypic repertoire in the infusion product and in pre- and post-infusion brain tumor specimens by deep sequencing the T cell receptor (TCR) Vβ chain of tumor-infiltrating T cells. Data analysis was performed using ImmunoSeq and exported data were further examined using Graphpad Prism. The infusion products in these patients were highly polyclonal with no clones represented above 1%. We found that in all five of these subjects, the number and frequency of unique TCRVβ clonotypes increased by several thousand (~20-fold) in post-infusion GBM specimens, and only a small portion of these unique TCRs were shared with pre-existing tumor-infiltrating specific T cells (TILs). A consistent finding in these patients was that the clonotype compositional diversity of T cells in the tumor bed post-infusion was considerably larger than the pre-CART vs. infusion product sharing frequency. These data indicate there was a significant increase in the number and clonotypic diversity of tumor-infiltrating T cells following intravenous CART-EGFRvIII infusion, but only a small proportion appears to be derived from the infusion product. Collectively, these results show that CART infusion can trigger accumulation of TILs. Whether or not these TILs respond to GBM neoantigens remains to be investigated. Citation Format: Donald M. O'Rourke, Fang Chen, Zev A. Binder, Irina Kulikovskaya, Minnal Gupta, Jeffrey Finklestein, David E. Ambrose, MacLean P. Nasrallah, Carl H. June, Simon F. Lacey, J. Joseph Melenhorst. Next-generation sequencing of T-cell receptor-beta gene rearrangements reveals dramatic expansion of T-cell clonotypes after CART-EGFRvIII therapy for glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-053. doi:10.1158/1538-7445.AM2017-LB-053
Memory hierarchy design for stream computing (2005)

Several classes of applications with abundant fine-grain parallelism, such as media and signal processing, graphics, and scientific computing, have become increasingly dominant consumers of computing resources. Prior research has shown that stream processors provide an energy-efficient, programmable approach to achieving high performance for these applications. However, given the strong compute capabilities of these processors, efficient utilization of bandwidth, particularly when accessing off-chip memory, is crucial to sustaining high performance. 
This thesis explores tradeoffs in, and techniques for, improving the efficiency of memory and bandwidth hierarchy utilization in stream processors. We first evaluate the appropriate granularity for expressing data-level parallelism—entire records or individual words—and show that record-granularity expression of parallelism leads to reduced intermediate state storage requirements and higher sustained bandwidths in modern memory systems. We also explore the effectiveness of software- and hardware-managed memories, and identify the relative merits of each type of memory within the context of stream computing. Software-managed memories are shown to efficiently support coarse-grain and producer-consumer data reuse, while hardware-managed memories are shown to effectively capture fine-grain and irregular temporal reuse. 
We introduce three new techniques for improving the efficiency of off-chip memory bandwidth utilization. First, we propose a stream register file architecture that enables indexed, arbitrary access patterns, allowing a wider range of data reuse to be captured in on-chip, software-managed memory compared to current stream processors. We then introduce epoch-based cache invalidation—a technique that actively identifies and invalidates dead data—to improve the performance of hardware-managed caches for stream computing. Finally, we propose a hybrid bandwidth hierarchy that incorporates both hardware- and software-managed memory, and allows dynamic reallocation of capacity between these two types of memories to better cater to application requirements. Our analyses and evaluations show that these techniques not only provide performance improvements for existing streaming applications but also broaden the capabilities of stream processors, enabling new classes of applications to be executed efficiently.
Ancient Venom Systems: A Review on Cnidaria Toxins (2015)

Cnidarians are the oldest extant lineage of venomous animals. Despite their simple anatomy, they are capable of subduing or repelling prey and predator species that are far more complex and recently evolved. Utilizing specialized penetrating nematocysts, cnidarians inject the nematocyst content or “venom” that initiates toxic and immunological reactions in the envenomated organism. These venoms contain enzymes, potent pore forming toxins, and neurotoxins. Enzymes include lipolytic and proteolytic proteins that catabolize prey tissues. Cnidarian pore forming toxins self-assemble to form robust membrane pores that can cause cell death via osmotic lysis. Neurotoxins exhibit rapid ion channel specific activities. In addition, certain cnidarian venoms contain or induce the release of host vasodilatory biogenic amines such as serotonin, histamine, bunodosine and caissarone accelerating the pathogenic effects of other venom enzymes and porins. The cnidarian attacking/defending mechanism is fast and efficient, and massive envenomation of humans may result in death, in some cases within a few minutes to an hour after sting. The complexity of venom components represents a unique therapeutic challenge and probably reflects the ancient evolutionary history of the cnidarian venom system. Thus, they are invaluable as a therapeutic target for sting treatment or as lead compounds for drug design.
Osteochondral Autograft: Proceedings of the International Consensus Meeting on Cartilage Repair of the Ankle (2018)

This international consensus derived from leaders in the field will assist clinicians with osteochondral autograft as a treatment strategy for osteochondral lesions of the talus.
Optical Characterization of Gate Oxide Charging Damage by Photoreflectance Spectroscopy (2000)

Thin gate oxide charging damage induced by plasma exposure in the metal-oxide-semiconductor (MOS) structure has been studied by photoreflectance (PR) spectroscopy. The PR signal intensity around the photon energy of 3.4 eV is found to decrease as the plasma exposure time increases. The capacitance–voltage ( C – V ) characteristic shows the generation of SiO 2 /Si interface states as well as that of electron trap sites in the oxides induced by the DC mode Ar plasma exposure. The SiO 2 /Si interface state plays the role of a recombination center for the photo generated carriers, resulting in the decrease in the surface potential change. On the other hand, the electron trapped in the oxide increases the surface potential. Therefore, the decrement in the PR signal intensity is considered to correspond primarily to the SiO 2 /Si interface state generation induced by the plasma-process, because the signal intensity decreases with the decrease of the surface potential.
Speechforms: from web to speech and back (2011)

This paper describes SpeechForms, a system that uses novel techniques to automatically identify form element semantics and form element content, and to semi-automatically generate language models that allow users to fill out each web form element by voice. Preliminary experimental results show that simple per-element language models are faster and may be more accurate than statistical n-gram language models trained on large amounts of web text data. Index Terms: language modeling, form understanding, information retrieval
The Sodium Iodide Symporter (NIS) as an Imaging Reporter for Gene, Viral, and Cell-based Therapies (2012)

Preclinical and clinical tomographic imaging systems increasingly are being utilized for non-invasive imaging of reporter gene products to reveal the distribution of molecular therapeutics within living subjects. Reporter gene and probe combinations can be employed to monitor vectors for gene, viral, and cell-based therapies. There are several reporter systems available; however, those employing radionuclides for positron emission tomography (PET) or singlephoton emission computed tomography (SPECT) offer the highest sensitivity and the greatest promise for deep tissue imaging in humans. Within the category of radionuclide reporters, the thyroidal sodium iodide symporter (NIS) has emerged as one of the most promising for preclinical and translational research. NIS has been incorporated into a remarkable variety of viral and non-viral vectors in which its functionality is conveniently determined by in vitro iodide uptake assays prior to live animal imaging. This review on the NIS reporter will focus on 1) differences between endogenous NIS and heterologously-expressed NIS, 2) qualitative or comparative use of NIS as an imaging reporter in preclinical and translational gene therapy, oncolytic viral therapy, and cell trafficking research, and 3) use of NIS as an absolute quantitative reporter.
Deterministic Lateral Displacement: Challenges and Perspectives (2020)

The advent of microfluidics in the 1990s promised a revolution in multiple industries from healthcare to chemical processing. Deterministic lateral displacement (DLD) is a continuous-flow microfluidic particle separation method discovered in 2004 that has been applied successfully and widely to the separation of blood cells, yeast, spores, bacteria, viruses, DNA, droplets, and more. Deterministic lateral displacement is conceptually simple and can deliver consistent performance over a wide range of flow rates and particle concentrations. Despite wide use and in-depth study, DLD has not yet been fully elucidated or optimized, with different approaches to the same problem yielding varying results. We endeavor here to provide up-to-date expert opinion on the state-of-art and current fundamental, practical, and commercial challenges with DLD as well as describe experimental and modeling opportunities. Because these challenges and opportunities arise from constraints on hydrodynamics, fabrication, and operation at the micro- and nanoscale, we expect this Perspective to serve as a guide for the broader micro- and nanofluidic community to identify and to address open questions in the field.
The Wall Ahead is Made of Rubber (2008)

Silicon technology evolution over the last four decades has yielded an exponential increase in integration densities with continual improvements of performance and power consumption at each technology generation. This steady progress has created a sense of entitlement for the riches that future process generations would bring. Today, however, classical process scaling seems to be dead and living up to technology expectations requires continuous innovation at many levels, which comes at steadily progressing implementation and design costs. Solutions to problems need to cut across layers of abstractions and require coordination between software, architecture and circuit features.
The Wide Complex Tachycardia Formula: Derivation and validation data (2019)

A recent publication (May et al., 2019) introduced a novel means (i.e. WCT Formula) to automatically distinguish ventricular tachycardia and supraventricular wide complex tachycardia using modern-day computerized electrocardiogram software measurements. In this article, a summary of data components relating to the derivation and validation of the WCT Formula is presented.
ChatCache: A Hierarchical Semantic Redundancy Cache System for Conversational Services at Edge (2021)

The spatial-temporal locality has been observed in various scenarios for conversational services with either voice or text requests. Given the current cloud-based processing mechanism, integrating such a service with caching is a promising way to improve responsiveness, reduce in-network transmission, and avoid computational redundancy. Goes beyond precise redundancy and fuzzy redundancy, semantic redundancy adapts to the diversity in command expression, and is considered as a practical solution for conversational services. In this paper, we introduce a hierarchical cache design inspired by semantic redundancy for conversational services. We propose a scalable edge system ChatCache to incorporate the hierarchical cache design and serve single or multiple users. We discussed the cache efficiency with different similarity match policies, and evaluate the responsiveness and scalability of ChatCache on heterogeneous edge platforms. On most of the evaluated platforms, ChatCache reduces user-perceived latency by more than 91.7% for voice requests, more than 81.6% for text requests. The throughput of ChatCache reaches 42.6 throughput tps for voice requests, and 64.4 tps for text requests, which is comparable with mainstream cloud cognitive services. The promising evaluation results show the capability of ChatCache in reducing the user-perceived latency and computation redundancy with high response accuracy for conversational services.
System-level data-format exploration for dynamically allocated data structures (2001)

System-level exploration of memory organizations is a key issue in successful implementation of data dominated applications based on dynamically allocated data structures involving records and access keys. This paper presents a formalized technique for exploring different memory data-format alternatives when only the system level functional behavior of the application has been defined. Our data-format exploration approach allows to substantially minimize the number of accessed bits by rearranging the format of the data records. The technique exploits parallelism in the data transfer by analyzing the dependencies between data-record accesses. As a result, significant reduction in memory size, bandwidth, and power are obtained. We have validated our techniques using several real-life asynchronous transfer mode cell processing applications, where we have obtained reductions in memory size (up to 20%), power (up to a 60%), and bandwidth.
Preparation and Evaluation of Benzyl Methacrylate Monoliths for Capillary Chromatography (2013)

This paper describes the comprehensive fabrication of monolithic materials for use as stationary phases in capillary liquid chromatography. Several columns were synthesized in the confines of 320 µm i.d. fused-silica capillaries by single-step in situ copolymerization of benzyl methacrylate and ethylene dimethacrylate (EDMA). The polymerization procedure was optimized by varying the reaction time within the range of 0.5-20 h, and by changing the composition contents of the polymeric mixture. The EDMA content showed a predominant influence on the characteristics of the columns and hence, on their chromatographic properties. The optimum value of the thermal initiator corresponded to 5 mg/mL. Changes of the porous, hydrodynamic properties and morphology of the prepared columns were thoroughly investigated and characterized. Different solvents were used as the mobile phase to demonstrate that the resulting monoliths exhibited good permeability and mechanical stability, whereas swelling and shrinking behaviors were observed and discussed. The efficiency and performance toward different sets of analytes were obtained; mixtures of aromatic hydrocarbons and phenolic compounds were successfully separated and evaluated, and adding tetrahydrofuran to the mobile phase showed improvement in both resolution and peak shapes. The characteristics of the columns were also checked in terms of repeatability and reproducibility.
Measurements of low-pT electrons from semileptonic heavy-flavour hadron decays at mid-rapidity in pp and Pb-Pb collisions at $$ \sqrt{s_{\mathrm{NN}}}=2.76 $$ TeV (2018)

A bstract Transverse-momentum ( p T ) differential yields of electrons from semileptonic heavy-flavour hadron decays have been measured in the most central (0–10%) and in semi-central (20–40%) Pb–Pb collisions at $$ \sqrt{s_{\mathrm{NN}}}=2.76 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:msub> <mml:mi>s</mml:mi> <mml:mrow> <mml:mi>N</mml:mi> <mml:mi>N</mml:mi> </mml:mrow> </mml:msub> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>2.76</mml:mn> </mml:math> TeV. The corresponding production cross section in pp collisions has been measured at the same energy with substantially reduced systematic uncertainties with respect to previously published results. The modification of the yield in Pb–Pb collisions with respect to the expectation from an incoherent superposition of nucleon-nucleon collisions is quantified at mid-rapidity (| y | &lt; 0.8) in the p T interval 0.5–3 GeV/ c via the nuclear modification factor, R AA . This paper extends the p T reach of the R AA measurement towards significantly lower values with respect to a previous publication. In Pb–Pb collisions the p T -differential measurements of yields at low p T are essential to investigate the scaling of heavy-flavour production with the number of binary nucleon-nucleon collisions. Heavy-quark hadronization, a collective expansion and even initial-state effects, such as the nuclear modification of the Parton Distribution Function, are also expected to have a significant effect on the measured distribution.
Measuring Surgical Outcomes in Cervical Spondylotic Myelopathy Patients Undergoing Anterior Cervical Discectomy and Fusion: Assessment of Minimum Clinically Important Difference (2013)

SF-36 PCS was the most representative PRO measure. MDC appears to be the most appropriate MCID method. When MDC was applied together with HTI anchor, the MCID thresholds were: 13.39 for NDI, 3.11 for VAS, 5.56 for PCS and 5.73 for MCS.
SMART CARDS: DISTRIBUTED COMPUTING WITH $5 DEVICES (2001)

Smart cards are highly successful thanks to their unique combination of mobility and security. Based upon a single-chip microcontroller with volatile and non-volatile memories, a smart card implementes a small computer system that is very portable (credit card size), easy to use, and extremely resistant against external attacks. However, today's smart cards use proprietary protocols, application schemes, and development tools. This is due to the limitations of current technology, and it leads to situation of "splendid isolation" where smart cards are not being regarded as an integral part of the overall IT architecture. In this paper, we describe recent research towards "next generation" smart cards. It combines an advanced programming language (Java), novel hardware architectures that provide the required "MIPS budget" (RISC 32 bit), as well as an implementation of key Internet protocols (IP, HTTP) on smart cards. As a result, we show how smart cards can be seamlessly integrated within a distributed computing environment.
Anticancer Activity Driven by Drug Linker Modification in a Polyglutamic Acid‐Based Combination‐Drug Conjugate (2018)

Abstract Combination nanotherapies for the treatment of breast cancer permits synergistic drug targeting of multiple pathways. However, poor carrier degradability, poor synergism of the combined drugs, low drug release regulation, and a lack of control on final macromolecule solution conformation (which drives the biological fate) limit the application of this strategy. The present study describes the development of a family of drug delivery systems composed of chemotherapeutic (doxorubicin) and endocrine therapy (aromatase inhibitor aminoglutethimide) agents conjugated to a biodegradable poly‐ l ‐glutamic acid backbone via various linking moieties. Data from in vitro cytotoxicity and drug release assessments and animal model validation select a conjugate family member with optimal biological performance. Exhaustive physicochemical characterization in relevant media (including the study of secondary structure, size measurements, and detailed small‐angle neutron scattering analysis) correlates biological data with the intrinsic supramolecular characteristics of the conjugate. Overall, this study demonstrates how a small flexible Gly linker can modify the spatial conformation of the entire polymer–drug conjugate, promote the synergistic release of both drugs, and significantly improve biological activity. These findings highlight the need for a deeper understanding of polymer–drug conjugates at supramolecular level to allow the design of more effective polymer–drug conjugates.
Dynamics of Transition Regime in Bistable Vibration Energy Harvesters (2017)

Vibration energy harvesting can be an effective method for scavenging wasted mechanical energy for use by wireless sensors that have limited battery life. Two major goals in designing energy harvesters are enhancing the power scavenged at low frequency and improving efficiency by increasing the frequency bandwidth. To achieve these goals, we derived a magnetoelastic beam operated at the transition between mono- and bi-stable regions. By improving the mathematical model of the interaction of magnetic force and beam dynamics, we obtained a precise prediction of natural frequencies as the distance of magnets varies. Using the shooting technique for the improved model, we present a fundamental understanding of interesting combined softening and hardening responses that happen at the transition between the two regimes. The transition regime is proposed as the optimal region for energy conversion in terms of frequency bandwidth and output voltage. Using this technique, low-frequency vibration energy harvesting at around 17 Hz was possible. The theoretical results were in good agreement with the experimental results. The target application is to power wildlife biologging devices from bird flights that have consistent high power density around 16 Hz (Shafer et al., 2015, “The Case for Energy Harvesting on Wildlife in Flight,” Smart Mater. Struct., 24(2), p. 025031).