gebhart/patrepeval huggingface dataset:
The case for elastic operating system services in fos (2012)

Given exponential scaling, it will not be long before chips with hundreds of cores are standard. For OS designers, this new trend in architectures provides a new opportunity to explore different research directions in scaling operating systems. The primary question facing OS designers over the next ten years will be: What is the correct design of OS services that will scale up to hundreds or thousands of cores, and adapt to the unprecedented variability in demand of the system resources? A fundamental research challenge addressed in this paper is to identify some characteristics of such a scalable OS service for next multicore and cloud computing chips.
A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching (2016)

We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore s direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art any-time solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each.
Multi-objective variable subset selection using heterogeneous surrogate modeling and sequential design (2016)

Constructing surrogate models of high-dimensional complex black-box systems from simulation-based data requires an appropriate choice of surrogate model type, as well as identification of the most influential input parameters. As including irrelevant input parameters results in a longer surrogate model training process and potentially increases the risk of overfitting, it is important to identify a small set of relevant parameters during the adaptive modeling phase of the surrogate modeling process. A multi-objective optimization step is proposed to identify both the appropriate model type as well as a parameters subset. The obtained model can be used for evaluation intensive applications such as exploration, sensitivity analysis or optimization.
Processes = protocols + policies (2004)

Business process modeling and enactment are notoriously complex, especially in open settings where the participants are autonomous, requirements must be continually finessed, and exceptions frequently arise because of real-world or organizational problems.Traditional approaches, which attempt to capture processes as monolithic flows, have proved inadequate in addressing these challenges.This paper describes a novel approach centered around the concepts of protocols and policies.A (business) protocol is a modular, public specification of an interaction among different roles that achieves a desired goal.A policy is a typically private description of a participant's business logic that controls how it participates in a protocol.We conceptualize a business process be conceptualized as a cohesive set of protocols, to be enacted by agents playing the specified roles in the protocols.This approach presupposes a semantics for protocols that supports reasoning about them and, especially, about enacting them in a flexible, context-sensitive manner.We develop such a semantics based on commitments, which capture the essence of the relationships among roles without unnecessarily constraining their behaviors.This paper develops OWL-P, a language for specifying protocols, and associated tools.OWL-P specifications of protocols compile into skeletons for each role.Each skeleton corresponds to a set of rules with place-holders for policies.Developing an agent involves composing the skeletons for its intended roles and supplying the necessary policies to flesh them out.The key benefits of this approach are (1) a separation of concerns between protocols and policies in contrast to traditional monolithic approaches; (2) reusability of protocol specifications based on design abstractions such as specialization and aggregation; and (3) flexibility of enactment of processes in a manner that respects local policies while adapting continually.
Caspase-8 deficiency in mouse embryos triggers chronic RIPK1-dependent activation of inflammatory genes, independently of RIPK3 (2018)

Deletion of the Casp8 gene in epithelial tissues of mice results in severe inflammatory pathologies. Its ubiquitous deletion, or its specific deletion in endothelial cells, results in intrauterine death associated with capillary damage. These pathologies are all preventable by co-deletion of Casp8 and the genes encoding either the RIPK1 or the RIPK3 protein kinase. Since activation of RIPK3 in Caspase-8-deficient cells can trigger necroptotic cell death, and since RIPK1 can activate RIPK3, it is widely assumed that the inflammatory states resulting from Caspase-8 deficiency occur as a consequence of RIPK3-induced necroptosis. Here, we report that although on a Ripk3-null background Casp8 deletion in mice does not result in outright pathological changes, it triggers enhanced expression of a variety of inflammatory genes in utero, which gradually subsides after birth. Deletion of Ripk1, or even of only one of its two alleles, obliterates this activation. Resembling the embryonic pathology observed in RIPK3-expressing cells, the activation of inflammatory genes observed on a Ripk3-null background seems to be initiated in endothelial cells. Analysis of endothelial cells isolated from livers of Caspase-8-deficient embryos revealed neither an increase in the amount of RIPK1 in these cells after Casp8 deletion, nor triggering of RIPK1 phosphorylation. These findings indicate that the triggering of inflammation by Casp8 deletion in mice occurs, in part, independently of necroptosis or other functions of RIPK3, and rather reflects enhanced RIPK1-dependent signaling for activation of inflammatory genes.
Room temperature continuous wave operation of single-mode, edge-emitting photonic crystal Bragg lasers (2008)

We report the first room temperature CW operation of two dimensional single-mode edge-emitting photonic crystal Bragg lasers. Single-mode lasing with single-lobed, diffraction limited far-fields is obtained for 100microm wide and 550microm long on-chip devices. We also demonstrate the tuning of the lasing wavelength by changing the transverse lattice constant of the photonic crystal. This enables a fine wavelength tuning sensitivity (change of the lasing wavelength/change of the lattice constant) of 0.072. This dependence proves that the lasing mode is selected by the photonic crystal lattice.
Manipulating the Charging Energy of Nanocrystal Arrays (2005)

The electronic properties of metal nanocrystal quantum dot solids in the insulating state have been measured as a function of nanocrystal diameter under conditions of controlled inter-nanocrystal separation. Such properties of these weakly coupled nanocrystal arrays (see image), in particular the array charging energy, can be manipulated through experimental control of the nanocrystal diameter and mean inter-nanocrystal separation.
Improved high‐speed de‐excitation system for brushless synchronous machines tested on a 20 MVA hydro‐generator (2015)

Synchronous machines with brushless excitation have the disadvantage that the field winding is not accessible for the de‐excitation of the machine. This means that, despite the proper operation of the protection system, the slow de‐excitation time constant may produce severe damage in the event of an internal short circuit. A high‐speed de‐excitation system for these machines was developed, and this study presents the continuation of a previously published study. This study presents the design by computer simulation and the results of the first commissioning of this de‐excitation system in a commercial 20 MVA hydro‐generator. The de‐excitation is achieved by inserting resistance in the field circuit, obtaining a dynamic response similar to that achieved in machines with static excitation. In this case, a non‐linear discharge resistor was used, making the dynamic response even better.
Electrostatic interactions in the cellular dynamics of the interferon‐receptor complex (1988)

Using membrane preparations of the interferon receptor, prepared from cells of the Burkitt line, Daudi, we have examined the binding of three human recombinant alpha-interferons. 1. We discovered a binding titration of the interferons IFN-alpha A and IFN-alpha D in the pH range 6-9. Receptor binding, negligible at pH 6, rises to a maximum close to pH 9. We have shown that binding of IFN-alpha A at basic pH is to the same receptors as at neutrality and that IFN-receptor complexes extracted with digitonin are more stable at basic pH than they are at neutrality. 2. The recombinant interferon, IFN-alpha B, shows little change of binding in the pH range 6-9. At its basic optimum the binding of IFN-alpha A approaches that of IFN-alpha B, while at neutral pH the binding of IFN-alpha A is 3-4 times less. This difference at neutral pH is seen on intact cells as well as on membrane preparations. The specific activity of IFN-alpha B is close to that of IFN-alpha A, both of which are 10-20 times more active than IFN-alpha D; and the binding titration is, therefore, independent of the initial binding affinities. 3. Using hybrid IFNs constructed from the DNA sequences of alpha D and alpha B, we have isolated the sequence responsible for the binding titration to the segment comprising amino acids 61-92. Examination of these sequences reveals that Lys-84 is present in all the IFN-alpha except IFN-alpha B where it is replaced by Glu; and Tyr-90, present in most of the common IFN-alpha including alpha A and alpha D, is replaced by Asp in IFN-alpha B. Lys and Tyr would normally titrate in the pH range 6-9. We conclude that the binding titration is due to an electrostatic interaction and we propose that the interaction is between IFN-receptor complexes. The role of the interaction in the binding losses that accompany the antiproliferative effects of IFN is discussed.
Optimization of long range potential interaction parameters in ion mobility spectrometry (2018)

The problem of optimizing Lennard-Jones (L-J) potential parameters to perform collision cross section (CCS) calculations in ion mobility spectrometry has been undertaken. The experimental CCS of 16 small organic molecules containing carbon, hydrogen, oxygen, nitrogen, and fluoride in N<sub>2</sub> was compared to numerical calculations using Density Functional Theory (DFT). CCS calculations were performed using the momentum transfer algorithm IMoS and a 4-6-12 potential without incorporating the ion-quadrupole potential. A ceteris paribus optimization method was used to optimize the intercept σ and potential well-depth ϵ for the given atoms. This method yields important information that otherwise would remain concealed. Results show that the optimized L-J parameters are not necessarily unique with intercept and well-depth following an exponential relation at an existing line of minimums. Similarly, the method shows that some molecules containing atoms of interest may be ill-conditioned candidates to perform optimizations of the L-J parameters. The final calculated CCSs for the chosen parameters differ 1% on average from their experimental counterparts. This result conveys the notion that DFT calculations can indeed be used as potential candidates for CCS calculations and that effects, such as the ion-quadrupole potential or diffuse scattering, can be embedded into the L-J parameters without loss of accuracy but with a large increase in computational efficiency.
Digital holographic microscopy applied to life sciences (2007)

Digital holographic microscopy (DHM) is applied to life sciences applications and demonstrate its capability of real-time imaging and quantitative measurements of physiological parameters such as cell volume or mean cell hemoglobin concentration (MCHC) of erythrocyte cells. DHM has the advantage to be non-invasive (no phototoxicity, no contrast agents) and allows a high throughput measurements.
1019 Collaborative Surgical Team Training in Virtual Reality Is Superior to Individual Learning: A Randomised Controlled Trial (2022)

Abstract Aim This study aimed to assess if multiplayer virtual reality training was superior to single player training for acquisition of both technical and non-technical skills in learning complex open surgery. Method 40 participants (20 novice surgeons and 20 novice scrub nurses) were enrolled in this study and randomised to solo or team virtual reality training learning anterior approach total hip arthroplasty. Solo participants trained with virtual avatar counterparts, whilst teams trained in pairs (surgeon and scrub nurse). Both groups underwent 5 VR training sessions over 6 weeks. Subsequently, they underwent a real-life assessment in which they performed AA-THA on a high-fidelity model with real equipment in a simulated operating theatre. Teams performed together and solo participants were randomly paired up with a solo player of the opposite role. Videos of the assessment were marked by two blinded expert assessors. The primary outcome was team performance as graded by the NOTECHs II score. Secondary outcomes were procedure time, technical errors from an expert pre-defined protocol and acetabular component positioning. Results Teams outperformed solo trained participants in non-technical skills in the real-world assessment (NOTECHS-II score 50.3 ± 6.04 vs 43.90 ± 5.90, p=0.0275). They completed the assessment 28.11% faster than solos (31.22 minutes ±2.02 vs 43.43 ±2.71, p=0.01), and made close to half the number of technical errors when compared to the solo group (12.9 ± 8.3 vs 25.6 ± 6.1, p=0.001). Conclusions Multiplayer training appears to lead to faster surgery with fewer technical errors and the development of superior non-technical skills.
Analysis of Long-Term Sustainability Challenges & Optimization of Solar Thermal Lemongrass Essential Oil Extraction Systems (2022)

Solar thermal lemongrass (Cymbopogon flexuosus) essential oil extraction is a potential sustainable livelihood for the Indian rural population. In this work, an extensive review of existing extraction techniques, their performances, fitness to the context, as well as sustainability and efficiency factors has been elaborated. While microwave assisted methods can reduce the extraction time and increase the yield, it is at the cost of added complexity and dependency on electric energy, which can be unfit for communities that experience scarce supply. It is required to measure the performance of the microwave hydrodiffusion and gravity (MHG), and microwave steam diffusion (MSDf) methods with the lemongrass genus to verify their advantage over steam distillation, which in the study’s context remains the favorite. The study has unveiled that four key factors need to be considered for ensuring the sustainability of the livelihood: (a) implementation price, (b) operational price, (c) energy consumption, and (d) extraction time. Essential oil extraction can be optimized by six different categories of efficiency factors: (a) post-harvesting drying, (b) plant rehydration, (c) plant chopping size, (d) water to grass ratio, solid loading or plant packing, (e) temperature, steam heat, pressure and airflow, and (f) microwave power.
Identification of the Druggable Concavity in Homology Models Using the PLB Index (2007)

Identification of the druggable concavity, in which drug-like molecules are highly inclined to bind, is an important step in structure-based drug design. We previously proposed an index named PLB (propensity for ligand binding), which is based on the amino acid composition characteristically observed at the small molecule binding sites in the X-ray structures of the complexes between proteins and drug-like small molecules. The PLB index was proven to be useful in identifying the druggable concavities in the quality X-ray structures of proteins. Here, we apply the PLB to predicting the druggable concavity in target proteins using the structures of homologous proteins constructed by homology modeling. In this study, we assembled a set of reference proteins that were accurately determined by X-ray analysis in forms of complexes with drug-like small molecules. Homology models for the reference protein were constructed using multiple homologous proteins as templates. The PLB index was then used to predict the druggable concavity. If the template protein in a complex with a drug-like small molecule was used, the druggable concavity was predicted well, with a prediction rate of 78%. When only the apo protein was available as the template, the practical prediction rate was 71%. Interestingly, even when the percent sequence identity between the reference and template proteins was lower than 30, the PLB index could successfully identify the druggable concavity in some cases. This study demonstrates the practical value of applying the PLB index to identifying the drugabble concavity in the homology model.
OFDM and FBMC transmission techniques: a compatible high performance proposal for broadband power line communications (2010)

A filter bank multicarrier (FBMC) system having a high level of compatibility with the IEEE P1901 OFDM scheme is proposed. In order to reach the level of robustness, selectivity and performance required by the broadband power line, the approach is based on near perfect reconstruction (NPR) filters combined with OQAM modulation. A key feature of the approach is the fractionally-spaced sub-channel equalizer, which is able to compensate the channel distortions and cope with residual timing offsets. The system initialization procedure and the results of OFDM are exploited by FBMC and an efficient and accurate technique is described for the derivation of the sub-channel equalizer coefficients from the OFDM frequency domain equalizer coefficients. Then, the impact of the filter impulse response on the efficiency in packet transmission is minimized. Finally, the impact of the sub-channel spacing is investigated and, in a comparison on similar basis, it appears that the proposed FBMC system can reach 228 Mbit/s in maximum bit rate, versus 197 Mbit/s for OFDM, while providing a higher level of tone protection and robustness to jammers.
Suppl. Fig. 4: Influence of imaging sequence. from Combined PET Imaging of the Inflammatory Tumor Microenvironment Identifies Margins of Unique Radiotracer Uptake (2023)

&lt;p&gt;(A) T/B ratios, (B-D) tracer volumes, (E-J) areas of unique tracer uptake and overlapping regions. No significant effect on volumetric data was observed based on the order of imaging experiments.&lt;/p&gt;
Auto-FuzzyJoin: Auto-Program Fuzzy Similarity Joins Without Labeled Examples (2021)

Fuzzy similarity join is an important database operator widely used in practice. So far the research community has focused exclusively on optimizing fuzzy join \textit{scalability}. However, practitioners today also struggle to optimize fuzzy-join \textit{quality}, because they face a daunting space of parameters (e.g., distance-functions, distance-thresholds, tokenization-options, etc.), and often have to resort to a manual trial-and-error approach to program these parameters in order to optimize fuzzy-join quality. This key challenge of automatically generating high-quality fuzzy-join programs has received surprisingly little attention thus far. In this work, we study the problem of "auto-program" fuzzy-joins. Leveraging a geometric interpretation of distance-functions, we develop an unsupervised \textsc{Auto-FuzzyJoin} framework that can infer suitable fuzzy-join programs on given input tables, without requiring explicit human input such as labeled training data. Using \textsc{Auto-FuzzyJoin}, users only need to provide two input tables $L$ and $R$, and a desired precision target $τ$ (say 0.9). \textsc{Auto-FuzzyJoin} leverages the fact that one of the input is a reference table to automatically program fuzzy-joins that meet the precision target $τ$ in expectation, while maximizing fuzzy-join recall (defined as the number of correctly joined records). Experiments on both existing benchmarks and a new benchmark with 50 fuzzy-join tasks created from Wikipedia data suggest that the proposed \textsc{Auto-FuzzyJoin} significantly outperforms existing unsupervised approaches, and is surprisingly competitive even against supervised approaches (e.g., Magellan and DeepMatcher) when 50\% of ground-truth labels are used as training data.
Simulation study comparing the helmet-chin PET with a cylindrical PET of the same number of detectors (2017)

There is a growing interest in developing brain PET scanners with high sensitivity and high spatial resolution for early diagnosis of neurodegenerative diseases and studies of brain functions. Sensitivity of the PET scanner can be improved by increasing the solid angle. However, conventional PET scanners are designed based on a cylindrical geometry, which may not be the most efficient design for brain imaging in terms of the balance between sensitivity and cost. We proposed a dedicated brain PET scanner based on a hemispheric shape detector and a chin detector (referred to as the helmet-chin PET), which is designed to maximize the solid angle by increasing the number of lines-of-response in the hemisphere. The parallax error, which PET scanners with a large solid angle tend to have, can be suppressed by the use of depth-of-interaction detectors. In this study, we carry out a realistic evaluation of the helmet-chin PET using Monte Carlo simulation based on the 4-layer GSO detector which consists of a 16 × 16 × 4 array of crystals with dimensions of 2.8 × 2.8 × 7.5 mm<sup>3</sup>. The purpose of this simulation is to show the gain in imaging performance of the helmet-chin PET compared with the cylindrical PET using the same number of detectors in each configuration. The sensitivity of the helmet-chin PET evaluated with a cylindrical phantom has a significant increase, especially at the top of the (field-of-view) FOV. The peak-NECR of the helmet-chin PET is 1.4 times higher compared to the cylindrical PET. The helmet-chin PET provides relatively low noise images throughout the FOV compared to the cylindrical PET which exhibits enhanced noise at the peripheral regions. The results show the helmet-chin PET can significantly improve the sensitivity and reduce the noise in the reconstructed images.
TNF/iNOS-producing dendritic cells are the necessary evil of lethal influenza virus infection (2009)

Respiratory infection with highly pathogenic influenza A viruses is characterized by the exuberant production of cytokines and chemokines and the enhanced recruitment of innate inflammatory cells. Here, we show that challenging mice with virulent influenza A viruses, including currently circulating H5N1 strains, causes the increased selective accumulation of a particular dendritic cell subset, the tipDCs, in the pneumonic airways. These tipDCs are required for the further proliferation of influenza-specific CD8(+) T cells in the infected lung, because blocking their recruitment in CCR2(-/-) mice decreases the numbers of CD8(+) effectors and ultimately compromises virus clearance. However, diminution rather than total elimination of tipDC trafficking by treatment with the peroxisome proliferator-activated receptor-gamma agonist pioglitazone moderates the potentially lethal consequences of excessive tipDC recruitment without abrogating CD8(+) T cell expansion or compromising virus control. Targeting the tipDCs in this way thus offers possibilities for therapeutic intervention in the face of a catastrophic pandemic.