gebhart/patrepeval huggingface dataset:
Test Problems for Large-Scale Multiobjective and Many-Objective Optimization (2016)

The interests in multiobjective and many-objective optimization have been rapidly increasing in the evolutionary computation community. However, most studies on multiobjective and many-objective optimization are limited to small-scale problems, despite the fact that many real-world multiobjective and many-objective optimization problems may involve a large number of decision variables. As has been evident in the history of evolutionary optimization, the development of evolutionary algorithms (EAs) for solving a particular type of optimization problems has undergone a co-evolution with the development of test problems. To promote the research on large-scale multiobjective and many-objective optimization, we propose a set of generic test problems based on design principles widely used in the literature of multiobjective and many-objective optimization. In order for the test problems to be able to reflect challenges in real-world applications, we consider mixed separability between decision variables and nonuniform correlation between decision variables and objective functions. To assess the proposed test problems, six representative evolutionary multiobjective and many-objective EAs are tested on the proposed test problems. Our empirical results indicate that although the compared algorithms exhibit slightly different capabilities in dealing with the challenges in the test problems, none of them are able to efficiently solve these optimization problems, calling for the need for developing new EAs dedicated to large-scale multiobjective and many-objective optimization.
Quasi-ballistic thermal transport from nanoscale interfaces observed using ultrafast coherent soft x-ray beams (2011)

Heat dissipation from a nanoscale hot-spot is expected to be non-diffusive when a hot-spot is smaller than the phonon mean free path of the substrate. Our technique of observing diffraction of coherent soft x-ray pulses allows for very high resolution (~pm) of thermally-induced surface distortion, as well as femtosecond time resolution of dynamics. We successfully model our experimental results with a diffusive transport model that is modified to include an additional boundary resistance. These results confirm the importance of considering ballistic transport away from a nanoscale heat source, and identify a means of correctly accounting for this ballistic transport.
Observation of x-ray magnetic circular dichroism at the Rh M2,3 edge in Co-Rh alloys (1994)

The M2,3 edge of Rh in Co-Rh alloys shows measurable x-ray magnetic circular dichroism. Such dichroism is not present, however, for analogous alloys of Co-Ru. The induced Ru magnetic moment, if any, is thus demonstrated to be significantly smaller than the induced Rh moment in otherwise similar Co alloys.
COMMON FIXED POINT THEOREM IN CONE METRIC SPACE UNDER CONTRACTIVE MAPPINGS (2016)

In this paper we prove a common fixed point theorem for two Banach pairs of mappings which satisfy the contraction conditions in cone metric spaces without the assumption of normality condition.
<title>Closed equation to incorporate quality of service criteria in network planning</title> (2002)

We have developed a closed equation that allows calculation of the optimal bandwidth based on estimates of volume and quality of service criteria of user traffic. The basic assumption underlying the equation is that traffic to be dropped at a bottleneck link should not be sent to that link in the first place. Instead, such traffic should be dropped as early as possible. The equation was validated with simulations using a topology and a traffic mix typical for 3G radio access networks. The quality of service of user traffic to the routers on either side of the backup link was considerably better compared to standard methods. The equation uses only a few parameters based on the traffic demand matrix and is easily incorporated in a network-planning tool to calculate backup links or bandwidth requirements for logical pipes. It can also be used as basis for complete network planning.
Xylene Selectivity at the External Surface of Hierarchical Zeolites: Experiment and Molecular Modeling (2022)

Hierarchical faujasite zeolites made up of nanoparticle aggregates (NAs) and layer-like structures (LL) are evaluated for xylene adsorption in both gas and liquid phases. For NA zeolites, several samples with varying external surfaces and meso/macropore volumes are considered. Compared to conventional faujasite, xylene adsorption isotherms as measured by means of thermogravimetric experiments display higher adsorption capacities for the NA faujasites. This adsorption capacity increase is found to be linked to the zeolite external surface area. However, in the case of the LL zeolite, despite its large external surface, the xylene adsorption capacity is found to be comparable to that of the conventional zeolite. For all hierarchical samples, the paraxylene selectivities assessed through batch adsorption experiments in the liquid phase are smaller than that for the conventional zeolite. The observed selectivity decrease seems to be associated with the decrease in functional window adsorptive sites when enhancing the external surface. To shed light on the observed phenomenon, Monte Carlo simulations in the Grand Canonical ensemble are performed to investigate xylene adsorption for a bulk infinite zeolite and a zeolite sample exhibiting an external surface. For the latter sample, the external surface chosen is made up of incomplete cavities and, therefore, defective window sites. In agreement with our experiments, the results from molecular simulation indicate a selectivity loss associated with the sample large external surface.
Tensegrity and the Emergence of Complex Mechanical Behavior in Living Cells (2000)

Abstract Existing engineering models of cell mechanics fail to incorporate current knowledge of the molecular intricacy of living cells. An alternative model of cell structure based on tensegrity architecture suggests that complex mechanical behaviors emerge in cells from collective interactions among different cytoskeletal filaments which are organized within hierarchical networks that are tensionally prestressed to ensure shape stability. This discrete network model has been controversial because it goes against prevailing views. In this article, I will review the concept behind cellular tensegrity, explain how it has become translated into mathematical terms over time, and provide reference to recent studies which provide experimental verification of predictions that have arisen from this theoretical model. Taken together, these findings suggest that tensegrity represents a robust and unified model of cell mechanics which, in contrast to alternative approaches, may facilitate future understanding of the link between mechanics and biochemistry.
Financial Monte Carlo simulation on architecturally diverse systems (2008)

Computational finance relies heavily on the use of Monte Carlo simulation techniques. However, Monte Carlo simulation is computationally very demanding. We demonstrate the use of architecturally diverse systems to accelerate the performance of these simulations, exploiting both graphics processing units and field-programmable gate arrays. Performance results include a speedup of 74times relative to an 8 core multiprocessor system (180times relative to a single processor core).
Controlled Injection of a Singular Point along a Linear Magnetic Structure (1994)

International audience
Towards Understanding the Risks of Gradient Inversion in Federated Learning (2021)

Abstract Federated learning (FL) allows the collaborative training of AI models without needing to share raw data. This capability makes it especially interesting for healthcare applications where patient and data privacy is of utmost concern. However, recent works on the inversion of deep neural networks from model gradients raised concerns about the security of FL in preventing the leakage of training data. In this work, we show that these attacks presented in the literature are impractical in real FL use-cases and provide a new baseline attack that works for more realistic scenarios where the clients’ training involves updating the Batch Normalization (BN) statistics. Furthermore, we present new ways to measure and visualize potential data leakage in FL. Our work is a step towards establishing reproducible methods of measuring data leakage in FL and could help determine the optimal tradeoffs between privacy-preserving techniques, such as differential privacy, and model accuracy based on quantifiable metrics.
In Silico and In Vivo Studies of a Tumor-Penetrating and Interfering Peptide with Antitumoral Effect on Xenograft Models of Breast Cancer (2023)

The combination of a tumor-penetrating peptide (TPP) with a peptide able to interfere with a given protein-protein interaction (IP) is a promising strategy with potential clinical application. Little is known about the impact of fusing a TPP with an IP, both in terms of internalization and functional effect. Here, we analyze these aspects in the context of breast cancer, targeting PP2A/SET interaction, using both in silico and in vivo approaches. Our results support the fact that state-of-the-art deep learning approaches developed for protein-peptide interaction modeling can reliably identify good candidate poses for the IP-TPP in interaction with the Neuropilin-1 receptor. The association of the IP with the TPP does not seem to affect the ability of the TPP to bind to Neuropilin-1. Molecular simulation results suggest that peptide IP-GG-LinTT1 in a cleaved form interacts with Neuropilin-1 in a more stable manner and has a more helical secondary structure than the cleaved IP-GG-iRGD. Surprisingly, in silico investigations also suggest that the non-cleaved TPPs can bind the Neuropilin-1 in a stable manner. The in vivo results using xenografts models show that both bifunctional peptides resulting from the combination of the IP and either LinTT1 or iRGD are effective against tumoral growth. The peptide iRGD-IP shows the highest stability to serum proteases degradation while having the same antitumoral effect as Lin TT1-IP, which is more sensitive to proteases degradation. Our results support the development of the TPP-IP strategy as therapeutic peptides against cancer.
Remodeling of left circumflex coronary arterial tree in pacing-induced heart failure (2015)

Congestive heart failure (CHF) is a very serious heart disease that manifests an imbalance between left ventricle supply and demand. Although the mechanical demand of the failing heart has been well characterized, the systematic remodeling of the entire coronary arterial tree that constitutes the supply of the myocardium is lacking. We hypothesize that the well-known increase in ventricle wall stress during CHF causes coronary vascular rarefaction to increase the vascular flow resistance, which in turn compromises the perfusion of the heart. Morphometric (diameters, length, and numbers) data of the swine left circumflex (LCx) arterial tree were measured in both CHF (n = 6) and control (n = 6) groups, from which a computer reconstruction of the entire LCx tree was implemented down to the capillary level to enable a hemodynamic analysis of coronary circulation. The vascular flow resistance was increased by ∼75% due to a significant decrease of vessel numbers (∼45%) and diameters in the first capillary segments (∼10%) of the LCx arterial tree after 3-4 wk of pacing. The structural remodeling significantly changed the wall shear stress in vessel segments of the entire LCx arterial tree of CHF animals. This study enhances our knowledge of coronary arterial tree remodeling in heart failure, which provides a deeper understanding of the deterioration of supply-demand relation in left ventricle.
Saddle-like deformation in a dielectric elastomer actuator embedded with liquid-phase gallium-indium electrodes (2014)

We introduce a dielectric elastomer actuator (DEA) composed of liquid-phase Gallium-Indium (GaIn) alloy electrodes embedded between layers of poly(dimethylsiloxane) (PDMS) and examine its mechanics using a specialized elastic shell theory. Residual stresses in the dielectric and sealing layers of PDMS cause the DEA to deform into a saddle-like geometry (Gaussian curvature K < 0). Applying voltage U to the liquid metal electrodes induces electrostatic pressure (Maxwell stress) on the dielectric and relieves some of the residual stress. This reduces the longitudinal bending curvature and corresponding angle of deflection #. Treating the elastomer as an incompressible, isotropic, NeoHookean solid, we develop a theory based on the principle of minimum potential energy to predict the principal curvatures as a function of U. Based on this theory, we predict a dependency of # on U that is in strong agreement with experimental measurements performed on a GaIn-PDMS composite. By accurately modeling electromechanical coupling in a soft-matter DEA, this theory can inform improvements in design and fabrication.
Catalyst functionalized buffer sorbent pebbles for rapid separation of carbon dioxide from gas mixtures (2023)

A method for separating CO.sub.2 from gas mixtures uses a slurried media impregnated with buffer compounds and coating the solid media with a catalyst or enzyme that promotes the transformation of CO.sub.2 to carbonic acid. Buffer sorbent pebbles with a catalyst or enzyme coating are provided for rapid separation of CO.sub.2 from gas mixtures.
Factors Controlling the Trafficking and Processing of a Leader-Derived Peptide Presented by Qa-1 (2000)

Many leader-derived peptides require TAP for presentation by class I molecules. This TAP dependence can either be ascribed to the inability of proteases resident in the endoplasmic reticulum (ER) to trim leader peptide precursors into the appropriate epitope or the failure of a portion of the leader segment to gain access to the lumen of the ER. Using the Qa-1 binding epitope, Qdm derived from a class Ia leader as a model, we show that many cell types lack ER protease activity to trim this peptide at its C terminus. However, both T1 and T2 cells contain appropriate protease activity to process the full length D(d) leader (DL) when introduced into the ER lumen. Nevertheless, both T1 cells treated with the TAP inhibitor ICP47 and TAP(-) T2 cells fail to present this epitope from either the intact D(d) molecule or a minigene encoding the DL. This indicates that the portion of the leader containing Qdm does not gain access to the ER. However, changing the Arg at P7 of the DL to a Cys can alter its trafficking and allows for TAP-independent presentation of the Qdm epitope.
SARS-CoV-2 Virion Infectivity and Cytokine Production in Primary Human Airway Epithelial Cells (2022)

The emergence of new SARS-CoV-2 variants and the replacement of preceding isolates have been observed through B.1.1.7, B.1.351, B.1.617.2, and B.1.1.529 lineages (corresponding to alpha, beta, delta, and omicron variants of concern (VoC), respectively). However, there is still a lack of biological evidence to which extent those VoC differ from the ancestral lineages. By exploiting human airway epithelial cell (HAEC) cultures, which closely resemble the human airway architecture and physiology, we report distinctive SARS-CoV-2 tropism in different respiratory tissues. In general, SARS-CoV-2 VoC predominantly infect and replicate in HAEC better than the progenitor USA-WA1 isolate or the BavPat1 isolate, which contains the D614G mutation, even though there is little to no difference between variants regarding their infectivity (i.e., virion-per-vRNA copy ratio). We also observe differential tissue-specific innate immunity activation between the upper and lower respiratory tissues in the presence of the virus. Our study provides better comprehension of the behavior of the different VoC in this physiologically relevant ex vivo model.
Discovery of survival factor for primitive chronic myeloid leukemia cells using induced pluripotent stem cells (2015)

A definitive cure for chronic myeloid leukemia (CML) requires identifying novel therapeutic targets to eradicate leukemia stem cells (LSCs). However, the rarity of LSCs within the primitive hematopoietic cell compartment remains a major limiting factor for their study in humans. Here we show that primitive hematopoietic cells with typical LSC features, including adhesion defect, increased long-term survival and proliferation, and innate resistance to tyrosine kinase inhibitor (TKI) imatinib, can be generated de novo from reprogrammed primary CML cells. Using CML iPSC-derived primitive leukemia cells, we discovered olfactomedin 4 (OLFM4) as a novel factor that contributes to survival and growth of somatic lin(-)CD34(+) cells from bone marrow of patients with CML in chronic phase, but not primitive hematopoietic cells from normal bone marrow. Overall, this study shows the feasibility and advantages of using reprogramming technology to develop strategies for targeting primitive leukemia cells.
Hemangiomalike Masses of the Retina (1988)

We have followed five patients, each of whom had a solitary unilateral vascular mass of the sensory retina. The lesions were white or pink and often had hemorrhage and exudate on their surface or surrounding area. They appeared to be acquired, as three of the five patients were specifically noted to have normal fundi at some time before presentation. Fluorescein angiography and angioscopy demonstrated the masses to be composed of numerous vessels supplied by the retinal circulation. Slow growth was documented in one patient. Visual loss was variable and was due to leakage-related complications, including exudative detachment, recurrent vitreous hemorrhage, and cystoid macular edema. Four patients were treated with cryopexy, and in all four, this successfully caused involution of the lesions. Two patients had improvement in vision after treatment: one had stabilization, and one had deterioration. This report provides support for the existence of a distinct entity that we have called hemangiomalike mass of the retina, since no histopathologic evidence is yet available (to our knowledge). It also supports the use of judicious cryopexy to lesions associated with visual loss.
Solid–Liquid–Vapor Etching of Semiconductor Nanowires (2015)

The vapor-liquid-solid (VLS) mechanism enables the bottom-up, or additive, growth of semiconductor nanowires. Here, we demonstrate a reverse process, whereby catalyst atoms are selectively removed from the eutectic catalyst droplet. This process, which is driven by the dicarbonyl precursor 2,3-butanedione, results in axial nanowire etching. Experiments as a function of substrate temperature, etchant flow rate, and nanowire diameter support a solid-liquid-vapor (SLV) mechanism. An etch model with reaction at the liquid-vapor interface as the rate-limiting step is consistent with our experiments. These results identify a new mechanism to in situ tune the concentration of semiconductor atoms in the catalyst droplet.
Selective synthesis of citrus flavonoids prunin and naringenin using heterogeneized biocatalyst on graphene oxide (2019)

Citrus flavonoids, prunin and naringenin, are selectively produced from hydrolysis of naringin using the enzyme naringinase supported on graphene oxide.
Nitroaromatic Amino Acids as Inhibitors of Neuronal Nitric Oxide Synthase (1998)

Nitric oxide (NO.) is an important biomodulator of many physiological processes. The inhibition of inappropriate production of NO. by the isoforms of nitric oxide synthase (NOS) has been proposed as a therapeutic approach for the treatment of stroke, inflammation, and other processes. In this study, certain 2-nitroaryl-substituted amino acid analogues were discovered to inhibit NOS. Analogues bearing a 5-methyl substituent on the aromatic ring demonstrated maximal inhibitory potency. For two selected inhibitors, investigation of the kinetics of the enzyme showed the inhibition to be competitive with l-arginine. Additionally, functional NOS inhibition in tissue preparations was demonstrated.
MICROFLUIDIC ELECTROPORATION FOR DELIVERY OF CELL- PENETRATING PEPTIDE CONJUGATES OF PEPTIDE NUCLEIC ACIDS (PNA) FOR ANTISENSE INHIBITION OF INTRACELLULAR BACTERIA (2014)

Cell penetrating peptides (CPPs) have been used for a myriad of cellular delivery applications and were recently explored for delivery of antisense agents such as peptide nucleic acids (PNAs) for bacterial inhibition. In this report, we show that microfluidic electroporation delivery dramatically increases the bioavailability of CPP-PNAs to kill Salmonella macrophages which is typical in animals and humans. Electroporation delivers the molecules without involving endocytosis and greatly increases the antisense effect. The decrease in the average number of Salmonella per macrophage under a 1200 V/cm and 5 ms pulse was a factor of 9 higher than that without electroporation.
Multi‐layer modeling of diffusion of water in acrylamide‐grafted aliphatic polyesters (1998)

Abstract A new mass transfer model for layered structures, based on an implicit multi‐step integration algorithm including concentration dependent diffusivities, has been developed and applied to systems of water diffusing in electron beam pre‐irradiated, acrylamide‐grafted aliphatic polyesters (poly(ϵ‐caprolactone) and poly(1, 5‐dioxepan‐2‐one)). The much higher water solubility and water diffusivity in the amorphous crosslinked poly(1, 5‐dioxepan‐2‐one) than in the semicrystalline poly(ϵ‐caprolactone) is explained as being due to the fact that crystals are more effective crosslinks than the chemical crosslinks. Water solubility in the grafted layer is a function of the concentration of polyacrylamide, but it is believed to be limited by compressive swelling‐induced stresses. The zero concentration water diffusivity in the graft layer passes through a maximum, whereas the graft‐layer density passes through a minimum with increasing acrylamide concentration. It is suggested that this is because the accessible free volume for the penetrating water molecule is increased in the initial stages of grafting because the matrix polymer chains are separated by growing acrylamide graft chains. At later stages, the accessible free volume decreases because additional polyacrylamide chains are growing adjacent to the already existing ones and thus fill up empty spaces.
Focal physiological uncoupling of cerebral blood flow and oxidative metabolism during somatosensory stimulation in human subjects. (1986)

Coupling between cerebral blood flow (CBF) and cerebral metabolic rate of oxygen (CMRO2) was studied using multiple sequential administrations of 15O-labeled radiotracers (half-life, 123 sec) and positron emission tomography. In the resting state an excellent correlation (mean r, 0.87) between CBF and CMRO2 was found when paired measurements of CBF and CMRO2 from multiple (30-48) brain regions were tested in each of 33 normal subjects. Regional uncoupling of CBF and CMRO2 was found, however, during neuronal activation induced by somatosensory stimulation. Stimulus-induced focal augmentation of cerebral blood flow (29% mean) far exceeded the concomitant local increase in tissue metabolic rate (mean, 5%), when resting-state and stimulated-state measurements were obtained in each of 9 subjects. Stimulus duration had no significant effect on response magnitude or on the degree of CBF-CMRO2 uncoupling observed. Dynamic, physiological regulation of CBF by a mechanism (neuronal or biochemical) dependent on neuronal firing per se, but independent of the cerebral metabolic rate of oxygen, is hypothesized.