gebhart/patrepeval huggingface dataset:
Quantitative Characterization of Memory Contention (2012)

On multicore processors, co-executing applications compete for shared resources, such as cache capacity and memory bandwidth. This leads to suboptimal resource allocation and can cause substantial performance loss, which makes it im-portant to effectively manage these shared resources. This, however, requires insights into how the applications are im-pacted by such resource sharing. While there are several methods to analyze the perfor-mance impact of cache contention, less attention has been paid to general, quantitative methods for analyzing the im-pact of contention for memory bandwidth. To this end we introduce the Bandwidth Bandit, a general, quantitative, profiling method for analyzing the performance impact of contention for memory bandwidth on multicore machines. The profiling data captured by the Bandwidth Bandit is presented in a bandwidth graph. This graph accurately cap-tures the measured application’s performance as a function of its available memory bandwidth, and enables us to deter-mine how much the application suffers when its available bandwidth is reduced. To demonstrate the value of this data, we present a case study in which we use the bandwidth graph to analyze the performance impact of memory contention when co-running multiple instances of single threaded ap-plication. 1.
The role of ultrasound in enhancing mesenchymal stromal cell-based therapies (2020)

Mesenchymal stromal cells (MSCs) have been a popular platform for cell-based therapy in regenerative medicine due to their propensity to home to damaged tissue and act as a repository of regenerative molecules that can promote tissue repair and exert immunomodulatory effects. Accordingly, a great deal of research has gone into optimizing MSC homing and increasing their secretion of therapeutic molecules. A variety of methods have been used to these ends, but one emerging technique gaining significant interest is the use of ultrasound. Sound waves exert mechanical pressure on cells, activating mechano-transduction pathways and altering gene expression. Ultrasound has been applied both to cultured MSCs to modulate self-renewal and differentiation, and to tissues-of-interest to make them a more attractive target for MSC homing. Here, we review the various applications of ultrasound to MSC-based therapies, including low-intensity pulsed ultrasound, pulsed focused ultrasound, and extracorporeal shockwave therapy, as well as the use of adjunctive therapies such as microbubbles. At a molecular level, it seems that ultrasound transiently generates a local gradient of cytokines, growth factors, and adhesion molecules that facilitate MSC homing. However, the molecular mechanisms underlying these methods are far from fully elucidated and may differ depending on the ultrasound parameters. We thus put forth minimal criteria for ultrasound parameter reporting, in order to ensure reproducibility of studies in the field. A deeper understanding of these mechanisms will enhance our ability to optimize this promising therapy to assist MSC-based approaches in regenerative medicine.
Machine Learning-based Methods for Reconfigurable Antenna Mode Selection in MIMO Systems (2022)

MIMO technology has enabled spatial multiple access and has provided a higher system spectral efficiency (SE). However, this technology has some drawbacks, such as the high number of RF chains that increases complexity in the system. One of the solutions to this problem can be to employ reconfigurable antennas (RAs) that can support different radiation patterns during transmission to provide similar performance with fewer RF chains. In this regard, the system aims to maximize the SE with respect to optimum beamforming design and RA mode selection. Due to the non-convexity of this problem, we propose machine learning-based methods for RA antenna mode selection in both dynamic and static scenarios. In the static scenario, we present how to solve the RA mode selection problem, an integer optimization problem in nature, via deep convolutional neural networks (DCNN). A Multi-Armed-bandit (MAB) consisting of offline and online training is employed for the dynamic RA state selection. For the proposed MAB, the computational complexity of the optimization problem is reduced. Finally, the proposed methods in both dynamic and static scenarios are compared with exhaustive search and random selection methods.
Context-Aware Crowd Counting (2018)

State-of-the-art methods for counting people in crowded scenes rely on deep networks to estimate crowd density. They typically use the same filters over the whole image or over large image patches. Only then do they estimate local scale to compensate for perspective distortion. This is typically achieved by training an auxiliary classifier to select, for predefined image patches, the best kernel size among a limited set of choices. As such, these methods are not end-to-end trainable and restricted in the scope of context they can leverage. In this paper, we introduce an end-to-end trainable deep architecture that combines features obtained using multiple receptive field sizes and learns the importance of each such feature at each image location. In other words, our approach adaptively encodes the scale of the contextual information required to accurately predict crowd density. This yields an algorithm that outperforms state-of-the-art crowd counting methods, especially when perspective effects are strong.
Subrenal capsule assay in choosing cytostatics for gynaecological tumours. (1985)

The subrenal capsule assay (SRCA) was used to test the sensitivity of gynaecological tumours to chemotherapy. The total number of the assays was 95, ovarian cancer being the most often tested. Of the SRCAs 92% were evaluable. Of the 59 evaluable assays for ovarian cancer, 52% showed sensitivity, 41% intermediate sensitivity, and 7% resistance to chemotherapy. The previously treated tumours were less sensitive than the untreated ones (p less than 0.01). To the most often tested drug combinations, DOX (doxorubicin) + C (cyclophosphamide) + DDP (cisplatin), DOX + C + Tegafur, and C + V (vincristine), resistance was observed in 10-20% of the assays. However, there was marked interindividual variation. Twenty-five assays of the squamous cell carcinomas were evaluable. Of the tumours 28% were sensitive, 48% intermediately sensitive, and 24% were resistant. Five of 7 sensitive tumours were previously untreated. The combination of DDP and VP-16 (etoposide) was tested most often, followed by Bleo (bleomycin) as a single agent. DDP + VP-16 was significantly superior to Bleo (p less than 0.01). The results of the SRCA and the clinical outcome of the patients could be compared in 31 cases. An overall predictive accuracy rate of 81% was achieved. It was concluded that the SRCA has predictive value in determining chemotherapy responsiveness of gynaecological tumours.
Cryoablation for clinically localized prostate cancer using an argon‐based system: complication rates and biochemical recurrence (2000)

A PSA level before cryotherapy of < 10 ng/mL and an undetectable PSA nadir after cryotherapy were associated with the highest BRFS. Cryoablation of the prostate, with low morbidity, seems to be a viable option in managing patients by salvage therapy after radiation therapy and for the primary treatment of clinically localized prostate cancer.
Fluorogen-activating proteins (2011)

Using phage display technology, antibody V L or V H domains have been selected for their binding to non-fluorescent dye molecules. The dye molecules (fluorogens) then become fluorescent [1] while bound within a dimer of the antibody fragments. These fluorogenactivating proteins (FAPs) are being developed for use as tags for the fluorescent imaging of proteins. Antibody-based FAPs can utilize different arrangements of immunoglobulin variable light and heavy domains
The Current Landscape in Biostatistics of Real-World Data and Evidence: Causal Inference Frameworks for Study Design and Analysis (2021)

As real-world data (RWD) become more readily available, the regulatory agencies, medical product developers, and other key stakeholders have increasing interests in exploring the use of real-world evidence (RWE) to support regulatory decisions alternative to traditional clinical trials. To facilitate and promote statistical research in design, analysis, and interpretation of RWE studies for regulatory decision making, the ASA Biopharmaceutical Section established the RWE Scientific Working Group to address challenges and identify opportunities in the statistical research of this area. This article provides a landscape assessment of relevant causal inference frameworks for study design and analysis that generates RWE. Two companion articles of the Working group review statistical landscape on the use of RWE for medical product label expansion and the other on using RWE to inform clinical trial design and analysis.
A Layout Methodology For The Synthesis Of High Speed Global Clock Nets (1992)

Clock distribution in chips is important. Its importance becomes harder to overlook as the system being designed uses higher clock frequencies and larger number of flip-fiops, and requires careful system partitioning into several chips and fabrication in Multi-Chip Module. In this scenario where several chips are treated as synchronous islands, we will be concerned not only with reducing intra-chip skew but also with minimizing interchip delay. Related topics of this paper are system partitioning, high performance system, clocking schemes, clock distribution structures, clock synthesis and layout, buffer design, boundary scan test, intra-chip skew minimization, and inter-chip synchronization.
A study of [Os(bipy)2(PVP)3.3(PS)6.7Cl]+ polymer film modified electrodes using neutron reflectivity (1999)

Neutron reflectivity was used to obtain spatial distributions within [Os(bipy)2(PVP)3.3(PS)6.7Cl]+ modified Au electrodes (where PVP represents poly(4-vinylpyridine) and PS represents polystyrene) in contact with increasing concentrations of two types of electrolyte, perchlorate and p-toluenesulfonate. Film swelling and corresponding solvent ingress were observed to be more pronounced in p-toluenesulfonate media than in perchlorate media, yet the effects were found to be of lesser magnitude than for the corresponding homopolymer system, [Os(bipy)2(PVP)10Cl]+. Film structural changes upon immersion in solvent and redox cycling in electrolyte were determined. A comparison with the film maintained in OsII and OsIII oxidation states revealed further film swelling in the oxidized state.
Conservative-Bayesian Mechanism Design (2010)

Classical Bayesian mechanism design is “centralized”, that is, the designer is assumed to know the distribution D from which the players ’ type profile has been drawn. We instead investigate a very “de-centralized ” Bayesian model, where the designer has no knowledge at all, and each player only has some probabilistic information about D. For this decentralized model and many contexts of interest, where the goal is to maximize revenue, we show that, for arbitrary type distributions D (in particular, correlated ones), it is possible to design mechanisms matching to a significant extent the performance of the optimal centralized mechanisms. Our results are “existential ” for a broad class of contexts (including combinatorial auctions) and “con-structive ” for auctions of a single good. ∗This work has been partially funded by the Office of Naval Research under award number N00014091059. (Any opinions, findings, and conclusions or recommendations expressed in this email are those of the author (s) and do not necessarily reflect the views of the Office of Naval Research.) 1
A Modular Synthesis of Conformationally Preorganised Extended β‐Strand Peptidomimetics (2015)

Invited for the cover of this issue is the group of Andrew D. Hamilton and Sam Thompson at the University of Oxford (UK). The image depicts a new class of conformationally constrained β-strand mimetics mediating the interaction between two subunits of a protein that controls transcription. Read the full text of the article at 10.1002/chem.201501366.
Review of the systems analysis of interactions between the thermal, lubricant, and combustion processes of diesel engines (2010)

A review of technologies surrounding the thermal management system of the modern diesel engine with increased attention on fuel consumption is presented. A system-based approach has been adopted, looking at the interaction with other key systems. Previous innovation has aimed at reducing the power consumption of the cooling system or incorporating different cooling strategies and improving the engine warm-up rate for improved fuel consumption by higher operating temperatures. Electrical pumps can operate independently of the engine speed, and precision cooling and nucleate boiling have improved the heat transfer within the engine, reducing coolant flow requirements by 90 per cent. Improved warm-up rates have been demonstrated by using reduced thermal inertia or energy recovery systems either simulated on the test rig or through heat exchangers with exhaust gases. The resultant reduction in the fuel consumption is a result of various effects of the temperature on both the lubricating system and the combustion process. Despite difficulties in accurately measuring the engine friction, studies suggest that an increase in the engine temperature from 50°C to 80°C reduces the engine friction by 44 per cent because of 67 per cent lower oil viscosity. Simultaneous reduction in the emissions of nitogen oxides (NO x ) and the fuel consumption of 13.5 per cent and 0.7 per cent respectively have been achieved by including the engine thermal system in the calibration procedure. However, in-cylinder data needs to be studied to understand fully the mechanisms involved. Hotter engine temperatures reduce ignition delay, making combustion occur earlier in the cycle, which has a positive effect on the fuel consumption but a negative effect on the NO x emissions. Engine thermal management requires a system-based approach if the effects are to be fully understood but offers potential as an additional parameter in engine calibration.
A subset of diffuse-type gastric cancer is susceptible to mTOR inhibitors and checkpoint inhibitors (2019)

mTOR inhibitors and checkpoint inhibitors might be useful for the treatment of a subset of diffuse-type GCs which may develop from intestinal-type GCs.
Postoperative outcomes in oesophagectomy with trainee involvement (2021)

Trainee involvement was not found to be associated with significantly inferior postoperative outcomes for selected patients undergoing oesophagectomy. The results support continued supervised trainee involvement in oesophageal cancer surgery.
ChemInform Abstract: Reactions of P(MeNCH2CH2)3N with Primary, Secondary, and Tertiary Alkyl Halides: Evidence for a Solvent‐Enhanced Dehydrohalogenation. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Cutting Edge: The UNC93B1 Tyrosine-Based Motif Regulates Trafficking and TLR Responses via Separate Mechanisms (2014)

Sensing of nucleic acids by TLRs is crucial in the host defense against viruses and bacteria. Unc-93 homolog B1 (UNC93B1) regulates the trafficking of nucleic acid-sensing TLRs from the endoplasmic reticulum to endolysosomes, where the TLRs encounter their respective ligands and become activated. In this article, we show that a carboxyl-terminal tyrosine-based sorting motif (YxxΦ) in UNC93B1 differentially regulates human nucleic acid-sensing TLRs in a receptor- and ligand-specific manner. Destruction of YxxΦ abolished TLR7, TLR8, and TLR9 activity toward nucleic acids in human B cells and monocytes, whereas TLR8 responses toward small molecules remained intact. YxxΦ in UNC93B1 influenced the subcellular localization of human UNC93B1 via both adapter protein complex (AP)1- and AP2-dependent trafficking pathways. However, loss of AP function was not causal for altered TLR responses, suggesting AP-independent functions of YxxΦ in UNC93B1.
One-electron reduction potential of m-AMSA+[9-(2-methoxy-4-methylsulphonylaminoanilino)acridinium] as measured by pulse radiolysis (1984)

The absorption spectrum of one-electron reduced m-AMSA+ has been measured by pulse radiolysis. The radical species formed, m-AMSA˙, is readily oxidized by oxygen, flavin mononucleotide, and triquat; m-AMSA+ itself acts as an oxidant of the one electron reduced species of nicotinamide adenine dinucleotide. The one-electron reduction potential of the m-AMSA+/m-AMSA˙ couple at pH 7, E17, has been determined to be –803 ± 10 mV (vs. NHE) by studying the equilibrium established between m-AMSA+/m-AMSA˙ and a low-potential bipyridinium compound used as a redox indicator.
Mouse 2.0 (2009)

In this paper we present novel input devices that combine the standard capabilities of a computer mouse with multi-touch sensing. Our goal is to enrich traditional pointer-based desktop interactions with touch and gestures. To chart the design space, we present five different multi-touch mouse implementations. Each explores a different touch sensing strategy, which leads to differing form-factors and hence interactive possibilities. In addition to the detailed description of hardware and software implementations of our prototypes, we discuss the relative strengths, limitations and affordances of these novel input devices as informed by the results of a preliminary user study.
Threshold improvement of low-density lattice codes via spatial coupling (2012)

Spatially-coupled low-density lattice codes (LDLC) are constructed using protographs. By using Monte Carlo density evolution with single-Gaussian messages, we observe that the threshold of the spatially-coupled LDLC is within 0.22 dB of capacity of the unconstrained power channel. This is in contrast with a 0.5 dB noise threshold for the conventional LDLC construction.
Multiepitope CD8+ T cell response to a NY-ESO-1 peptide vaccine results in imprecise tumor targeting (2002)

The cancer-testis antigen NY-ESO-1 is one of the most promising candidates for generic vaccination of cancer patients. Here we analyzed the CD8 + T cell response to a NY-ESO-1 peptide vaccine composed of the two previously defined peptides 157-165 and 157-167, administered with GM-CSF as a systemic adjuvant. The NY-ESO-1 peptide vaccine elicited a CD8 + T cell response directed against multiple distinct epitopes in the 157-167 region, as revealed by using A2/peptide multimers incorporating overlapping A2 binding peptides in this region. However, only a minor fraction of the elicited CD8 + T cells, namely those recognizing the peptide 157-165 with sufficiently high functional avidity, recognized the naturally processed target on NY-ESO-1 + tumor cells. In contrast, the majority of peptide 157-165-specific CD8 + T cells exhibited lower functional avidity and no tumor reactivity. In addition, vaccine-elicited CD8 + T cells specific for other overlapping epitopes in the 157-167 region failed to significantly recognize NY-ESO-1-expressing tumor targets. Thus, because of the complexity of the CD8 + T cell repertoire that can be elicited by vaccination with synthetic peptides, a precise definition of the targeted epitope, and hence, of the corresponding peptide to be used as immunogen, is required to ensure a precise tumor targeting.
Laser Coulomb-explosion imaging of small molecules (2005)

We use intense few-cycle laser pulses to ionize molecules to the point of Coulomb explosion. We use Coulomb's law or ab initio potentials to reconstruct the molecular structure of ${\mathrm{D}}_{2}\mathrm{O}$ and $\mathrm{S}{\mathrm{O}}_{2}$ from the correlated momenta of exploded fragments. For ${\mathrm{D}}_{2}\mathrm{O}$, a light and fast system, we observed about $0.3\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$ and 15\ifmmode^\circ\else\textdegree\fi{} deviation from the known bond length and bond angle. By simulating the Coulomb explosion for equilibrium geometry, we showed that this deviation is mainly caused by ion motion during ionization. Measuring three-dimensional structure with half bond length resolution is sufficient to observe large-scale rearrangements of small molecules such as isomerization processes.
BLoG (2010)

Post-silicon bug localization -- the process of identifying the location of a detected hardware bug and the cycle(s) during which the bug produces error(s) -- is a major bottleneck for complex integrated circuits. Instruction Footprint Recording and Analysis (IFRA) is a promising post-silicon bug localization technique for complex processor cores. However, applying IFRA to new processor microarchitectures can be challenging due to the manual effort required to implement special microarchitecture-dependent analysis techniques for bug localization. This paper presents the Bug Localization Graph (BLoG) framework that enables application of IFRA to new processor microarchitectures with reduced manual effort. Results obtained from an industrial microarchitectural simulator modeling a state-of-the-art complex commercial microarchitecture (Intel Nehalem, the foundation for the Intel Core™ i7 and Core™ i5 processor families) demonstrate that BLoG-assisted IFRA enables effective and efficient post-silicon bug localization for complex processors with high bug localization accuracy at low cost.
Towards a Holistic Approach to Fault Management (2011)

Systems with high dependability requirements are increasingly relying on complex on-line fault management systems. Such fault management systems involve a combination of multiple steps – monitoring, data analysis, planning, and execution – that are typically independently developed and optimized. We argue that it is inefficient and ineffective to improve any particular fault management step without taking into account its interactions and dependencies with the rest of the steps. Through six real-life examples, we demonstrate this inefficiency and how it results in systems that either under-perform or are over-budget. We propose a holistic approach to fault management that is aware of all relevant aspects, and explicitly considers the couplings between the different fault management steps. We believe it will produce systems that will better meet cost, performance, and dependability objectives.
Combination treatment with highly bioavailable curcumin and NQO1 inhibitor exhibits potent antitumor effects on esophageal squamous cell carcinoma (2019)

These findings suggest the potential usefulness of THC and its combination with NQO1 inhibitor as a therapeutic option for ESCC.