gebhart/patrepeval huggingface dataset:
Adhesion energy characterization of monolayer graphene by vibrational spectroscopy (2013)

As at nano/micro-scale van der Waals forces often dominate various other types of forces, the accurate adhesion characterization of graphene (Gr) is essential to its processing, manipulation, and possible integration into integrated circuits and other nano/micro-scale devices. Since 2010, the reported (experimental) adhesion energy of monolayer Gr with silicon dioxide (SiO2) has increased from 151 ± 28 mJ/m2 to 450 ± 20 mJ/m2. Here, we report a set of adhesion energy values for Gr monolayers on a SiO2 substrate by adopting a unique vibrational spectroscopy approach based on the motion of adhesive microparticles on a vibrating substrate. The reported results indicate that the work-of-adhesion measurements of monolayer Gr on SiO2 could be highly scattered and its mean value is determined as WSiO2−Gr = 1160.26 mJ/m2, which is the highest value reported to date. Unlike the reported existing methods, the current non-contact and non-destructive spectral technique requires no knowledge of the mechanical properties of Gr. Based on the reported data, with the current approach, it is also demonstrated that the weak adhesive interactions between a polystyrene latex microparticle and SiO2 substrate across the monolayer Gr can be detected as well.
ExPLoit: Extracting Private Labels in Split Learning (2021)

Split learning is a popular technique used for vertical federated learning (VFL), where the goal is to jointly train a model on the private input and label data held by two parties. This technique uses a split-model, trained end-to-end, by exchanging the intermediate representations (IR) of the inputs and gradients of the IR between the two parties. We propose ExPLoit - a label-leakage attack that allows an adversarial input-owner to extract the private labels of the label-owner during split-learning. ExPLoit frames the attack as a supervised learning problem by using a novel loss function that combines gradient-matching and several regularization terms developed using key properties of the dataset and models. Our evaluations show that ExPLoit can uncover the private labels with near-perfect accuracy of up to 99.96%. Our findings underscore the need for better training techniques for VFL.
Abstract 97: Ablation of Calpain-Targeted Site in Cardiac Myosin Binding Protein C Is Cardioprotective (2012)

Rationale: Cardiac myosin binding protein-C (cMyBP-C) phosphorylation is essential for normal heart function. We recently demonstrated a direct correlation between cMyBP-C dephosphorylation and its degradation during ischemia-reperfusion (I-R) injury. Strikingly, cMyBP-C phosphorylation protects the heart from I-R injury. However, the mechanism of cMyBP-C-mediated cardioprotection is unknown. Objective: To determine if preventing cMyBP-C proteolysis and cleavage confers cardioprotection during I-R injury. Methods and Results: cMyBP-C is a substrate for calpains and dephosphorylation makes cMyBP-C more susceptible to proteolysis. In patients with heart failure, such proteolysis leads to the cleavage and release of the predominant N'-fragment (40 kDa) in association with increased calpain activity. MS/MS analysis identified a cardiac-specific phosphorylation motif responsible for the release of the 40 kDa fragment, 272-TSLAGAGRR-280, which we term the calpain-targeted site (CTS). Next, we utilized cardiac-specific transgenic mice expressing cMyBP-C[[Unable to Display Character: △]]CTS in which CTS motif was ablated and bred into cMyBP-C null (t/t) mice. We hypothesized that ablation of the CTS motif would confer resistance to calpain-mediated proteolysis and thus protect the heart from I-R injury. An animal that transgenically expressed the normal cardiac isoform, cMyBP-CWT, served as a control. Histological, electron microscopic and immunofluorescence analyses confirm that cMyBP-C[[Unable to Display Character: &amp;#8710;]]CTS incorporates normally into the cardiac sarcomere and results in complete rescue of the cMyBP-Ct/t phenotype, compared control groups. Moreover, echocardiography and in vivo hemodynamic studies revealed that cMyBP-C[[Unable to Display Character: &amp;#8710;]]CTS:t/t mice have normal cardiac function, similar to control mice. Altogether, these data suggest that cMyBP-C[[Unable to Display Character: &amp;#8710;]]CTS is benign. Compared to cMyBP-CWT, cMyBP-C[[Unable to Display Character: &amp;#8710;]]CTS protein is protected from calpain-mediated degradation. Finally, we determined that ablation of the CTS reduced infarct size and preserved cMyBP-C stability and cardiac function during I-R injury. Conclusion: Our data suggest that preserving cMyBP-C stability by thwarting calpain-mediated proteolysis protects cardiac structure and function from I-R injury, as a supportive therapy.
Characterization of the effects of the novel non-steroidal antiestrogen EM-800 on basal and estrogen-induced proliferation of T-47D, ZR-75-1 and MCF-7 human breast cancer cellsin vitro (1997)

Since estrogens play a predominant role in the development and growth of human breast cancer, antiestrogens represent a logical approach to the treatment of this disease. The present study compares the effects of the novel nonsteroidal anti-estrogen EM-800 and related compounds with those of a series of anti-estrogens on basal and 17 beta-estradiol (E2)-induced cell proliferation in human breast cancer cell lines. In the absence of added E2, EM-800 and related compounds failed to change basal cell proliferation, thus showing the absence of intrinsic estrogenic activity in the ER-positive T-47D, ZR-75-1 and MCF-7 cell lines. The stimulation of T-47D cell proliferation induced by 0.1 nM E2 was competitively blocked by a simultaneous incubation with EM-652, EM-800, OH-tamoxifen, OH-toremifene, ICI 182780, ICI 164384, droloxifene, tamoxifen and toremifene at apparent Ki values of 0.015, 0.011-0.017, 0.040-0.054, 0.043, 0.044, 0.243 and 0.735 nM, approx. 10 nM and > 10 nM, respectively. Similar data were obtained in ZR-75-1 and/or MCF-7 cells. Moreover, EM-652 was 6-fold more potent than OH-Tamoxifen in inhibiting the proportion of cycling MCF-7 cells. Our data show that EM-800 and EM-652 are the most potent known antiestrogens in human breast cancer cells in vitro and that they are devoid of the estrogenic activity of OH-tamoxifen and droloxifene suggested by stimulation of cell growth in the absence of estrogens in ZR-75-1 and MCF-7 cells.
Reducing outage maintenance costs by performance based maintenance (2005)

The limitation of funding for traditional maintenance has resulted in some electrical distribution equipment having maintenance cycles extended well beyond historical levels. In addition, more maintenance funds are directed to rotating apparatus, such as electrical generators, process drives, compressors and supporting motors. This is necessary due to the added wear associated with rotating machinery versus stationary electrical distribution equipment. The need for maintenance on electrical distribution equipment, such as air and liquid-filled power distribution transformers, low and medium voltage circuit breakers, starters and motor-control centers still exists, but is subject to greater cost constraints within all facilities. A new approach, termed performance based maintenance, can utilize past and ongoing equipment maintenance records to prioritize electrical distribution equipment with greater detail. This allows for applying maintenance dollars to the electrical distribution equipment with the greatest need for maintenance, and also redirecting limited funds to more effective predictive practices or capital improvements
SBES/FGM Simulation of Film-Cooled Surface Heat Transfer and Near-Wall Reaction (2020)

Abstract Accurate numerical prediction of surface heat transfer in the presence of film cooling within aero-engine sub-components, such as blade effusion holes and combustor liners, has long been a goal of the aero-engine industry. It requires accurate simulation of the turbulent mixing and reaction processes between freestream and the cooling flow. In this study, the Stress Blended Eddy Simulation (SBES) turbulence model is used together with the Flamelet Generated Manifold (FGM) combustion model to calculate the surface heat flux upstream and downstream of an effusion cooling hole. The SBES model employs a blending function to automatically switch between RANS and LES based on the local flow features, and thus significantly reduces the computational cost compared to a full LES simulation. All simulations are run using ANSYS Fluent®, a commercial finite-volume CFD solver. The test case corresponds to an experimental rig run at MIT, which is essentially a flat plate brushed by a uniform freestream of argon with ethylene seeded inside, and is cooled by either a reacting air or non-reacting nitrogen jet inclined at 35 degrees to the freestream. Calculations are performed for both reacting and non-reacting jet cooling cases across a range of jet-to-stream blowing ratios, and compared with the experimental data. The effects of mesh resolution are also investigated. Calculations are also performed across a range of Damköhler number (i.e. flow to chemical time ratio) from zero to 30, with unity blowing ratio, and the differences in the maximum surface heat flux magnitude in the reacting and non-reacting cases at a specific location downstream of the hole are investigated. Results from these analyses show good correlation with the experimental heat flux data upstream and downstream of the cooling hole, including the heat flux augmentation due to local reaction. Results from the Damköhler number sweep also show a good match with the experimental data across the range investigated.
Inducible nitric oxide synthase: Regulation, structure, and inhibition (2019)

A considerable number of human diseases have an inflammatory component, and a key mediator of immune activation and inflammation is inducible nitric oxide synthase (iNOS), which produces nitric oxide (NO) from l-arginine. Overexpressed or dysregulated iNOS has been implicated in numerous pathologies including sepsis, cancer, neurodegeneration, and various types of pain. Extensive knowledge has been accumulated about the roles iNOS plays in different tissues and organs. Additionally, X-ray crystal and cryogenic electron microscopy structures have shed new insights on the structure and regulation of this enzyme. Many potent iNOS inhibitors with high selectivity over related NOS isoforms, neuronal NOS, and endothelial NOS, have been discovered, and these drugs have shown promise in animal models of endotoxemia, inflammatory and neuropathic pain, arthritis, and other disorders. A major issue in iNOS inhibitor development is that promising results in animal studies have not translated to humans; there are no iNOS inhibitors approved for human use. In addition to assay limitations, both the dual modalities of iNOS and NO in disease states (ie, protective vs harmful effects) and the different roles and localizations of NOS isoforms create challenges for therapeutic intervention. This review summarizes the structure, function, and regulation of iNOS, with focus on the development of iNOS inhibitors (historical and recent). A better understanding of iNOS' complex functions is necessary before specific drug candidates can be identified for classical indications such as sepsis, heart failure, and pain; however, newer promising indications for iNOS inhibition, such as depression, neurodegenerative disorders, and epilepsy, have been discovered.
Tunable Frequency Selective Surfaces and Negative-Zero-Positive Index Metamaterials Based on Liquid Crystals (2008)

We utilize the properties of aligned nematic liquid crystal (LC) cells in the design of: (i) a new type of metamaterial whose index of refraction is tunable from negative, through zero, to positive values and (ii) micron-scale metallodielectric and all-dielectric tunable frequency selective surfaces (FSSs). The metamaterial is constructed by randomly doping a liquid crystal substrate with coated dielectric (non-magnetic) spheres and can be utilized over a large spectral range. FSSs with a liquid crystal superstrate are synthesized using conventional and genetic algorithm methods to exhibit broadband tunable filter characteristics at mid-infrared (mid-IR) wavelengths. These LC tunable FSS structures can be used to develop a new class of infrared/optical switches for terahertz applications.
Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations (2022)

An imbalance in the gut microbiome is linked to immune disorders, such as autoimmune, allergic, and chronic inflammatory disorders. Elucidation of disease mechanisms is a matter of urgency. It requires precise elucidation of the structure-based mechanisms of protein interactions involved in disease onset. In addition, an understanding of the protein dynamics is vital because these fluctuations affect the function and interaction of disease-associated proteins. Experimental evaluation of not only protein interactions, functions, and structures but also the dynamics are time-consuming; therefore, computational predictions are necessary to elucidate disease mechanisms. Here, we introduce recent studies on structure-based analyses of proteins using computational approaches, particularly artificial intelligence (AI) and molecular dynamics (MD) simulations.
Plasmon coupling in vertical split-ring resonator metamolecules (2015)

The past decade has seen a number of interesting designs proposed and implemented to generate artificial magnetism at optical frequencies using plasmonic metamaterials, but owing to the planar configurations of typically fabricated metamolecules that make up the metamaterials, the magnetic response is mainly driven by the electric field of the incident electromagnetic wave. We recently fabricated vertical split-ring resonators (VSRRs) which behave as magnetic metamolecules sensitive to both incident electric and magnetic fields with stronger induced magnetic dipole moment upon excitation in comparison to planar SRRs. The fabrication technique enabled us to study the plasmon coupling between VSRRs that stand up side by side where the coupling strength can be precisely controlled by varying the gap in between. The resulting wide tuning range of these resonance modes offers the possibility of developing frequency selective functional devices such as sensors and filters based on plasmon coupling with high sensitivity.
Mechanistic Study of Nucleation Enhancement in Atomic Layer Deposition by Pretreatment with Small Organometallic Molecules (2019)

Thermal atomic layer deposition (ALD) of metals on metal oxide surfaces typically suffers from nucleation delays that result in poor-quality films. The poor nucleation may be caused by a lack of suitable chemisorption sites on the oxide surface, which are needed for metal nucleation to occur. In this work, we demonstrate that prefunctionalizing the surface with a single monolayer of small organometallic molecules from the vapor phase can lead to a significant increase in surface coverage of the metal deposited by ALD. This process is demonstrated for Pt ALD from (methylcyclopentadienyl)trimethylplatinum (MeCpPtMe3) and O2, with nucleation enhanced almost 3-fold at 100 ALD cycles after the pretreatment. We hypothesize that the high coverage of the organometallic molecule provides an alternative chemisorption mechanism for the platinum precursor and thus leads to an increase in its uptake. The proposed chemisorption mechanism is robust across several organometallic molecule pretreatments and could potentially be exploited for other organometallic-based metal ALD processes. This chemisorption mechanism was probed using in situ quadrupole mass spectrometry (QMS). The growth of the platinum deposits was investigated in depth through scanning electron microscopy (SEM) and grazing incidence small-angle X-ray scattering (GISAXS). These studies show that the pretreatment also results in the improved wettability of Pt nanoparticles (NPs). The improved wettability is likely to affect the Pt diffusion properties, further contributing to the enhancement observed on the treated substrates. In addition, GISAXS and SEM studies indicate the growth of larger, denser, and more highly ordered Pt NPs at early cycle numbers, which subsequently coalesce into continuous and pinhole-free films. Surface pretreatment by organometallic molecules therefore introduces a potential route to achieve improved nucleation and growth of ultrathin films.
Isolation of a laminin-binding protein from the protozoan parasite Leishmania donovani that may mediate cell adhesion (1999)

Extracellular matrix (ECM)-binding proteins on the surface of Leishmania are thought to play a crucial role in the onset of leishmaniasis, as these parasites invade mononuclear phagocytes in various organs after migrating through the ECM. In a previous report, we presented several lines of evidence suggesting that Leishmania has a specific receptor for laminin, a major ECM protein, with a Kd in the nanomolar range. Here we describe the identification, purification and biochemical characterization of the Leishmania laminin receptor. When the outer membrane proteins of L. donovani were blotted on to nitrocellulose paper and probed with laminin, a prominent laminin-binding protein of 67 kDa was identified. The purified protein was isolated by a three-step process involving DEAE–cellulose, Con A (concanavalin A)–Sepharose and laminin–Sepharose affinity chromatography and was used to raise a monospecific antibody. The same protein was obtained when parasite membrane extracts were adsorbed to antibody affinity matrix and eluted with glycine. The affinity-purified protein bound to laminin in a detergent-solubilized form as well as after integration into artificial bilayers, and was subsequently characterized as an integral membrane protein. Metaperiodate oxidation and metabolic inhibition of glycosylation studies indicate the binding protein to be glycoprotein in nature and that N-linked oligosaccharides play a part in the interaction of laminin with the binding protein. Surface-labelled parasites attached to microtitre wells coated with laminin and the 67 kDa protein blocked the adhesion to laminin substrate. We propose that the 67 kDa protein is an adhesin involved in the attachment of Leishmaniato host tissues.
Synergistic Effect of Mesenchymal Stem Cells Infected with Recombinant Adenovirus Expressing Human BDNF on Erectile Function in a Rat Model of Cavernous Nerve Injury (2012)

The erectile function was more preserved after injection with MSCs infected with rAd/hBDNF in rat with ED caused by cavernous nerve injury. Therefore, the use of MSC infected with rAd/hBDNF may have a better treatment effect on ED cause by cavernous nerve injury.
Exosome-Derived miR-25-3p and miR-92a-3p Stimulate Liposarcoma Progression (2017)

Despite the development of combined modality treatments against liposarcoma in recent years, a significant proportion of patients respond only modestly to such approaches, possibly contributing to local or distant recurrence. Early detection of recurrent or metastatic disease could improve patient prognosis by triggering earlier clinical intervention. However, useful biomarkers for such purposes are lacking. Using both patient plasma samples and cell lines, we demonstrate here that miR-25-3p and miR-92a-3p are secreted by liposarcoma cells through extracellular vesicles and may be useful as potential biomarkers of disease. Both miR-25-3p and miR-92a-3p stimulated secretion of proinflammatory cytokine IL6 from tumor-associated macrophages in a TLR7/8-dependent manner, which in turn promoted liposarcoma cell proliferation, invasion, and metastasis via this interaction with the surrounding microenvironment. Our findings provide novel and previously unreported insight into liposarcoma progression, identifying communication between liposarcoma cells and their microenvironment as a process critically involved in liposarcoma progression. This study establishes the possibility that the pattern of circulating miRNAs may identify recurrence prior to radiological detectability while providing insight into disease outcome and as a possible approach to monitor treatment efficacy. <i>Cancer Res; 77(14); 3846-56. ©2017 AACR</i>.
Therapeutic Potential of Fucoidan in Myocardial Ischemia (2011)

Fucoidan, a sulfated polysaccharide extracted from brown seaweed, is a candidate for the treatment of ischemic diseases. The aim of this study was to measure the therapeutic potential of fucoidan in a rat model of myocardial ischemia-reperfusion injury. Forty rats were submitted to myocardial ischemia-reperfusion injury by transient occlusion of the left coronary artery. Rats were then randomized into 2 groups: fucoidan (5 mg/kg, intramuscularly; n = 20) or control (saline intramuscularly; n = 20) was administered 1 hour before injury and daily thereafter for 1 month. At 1 month, plasma levels of stromal cell-derived factor-1α (SDF-1α) were assessed by enzyme-linked immunosorbent assay kit. Hearts were evaluated by histoimmunochemistry. Fucoidan induced significant antifibrotic effects, reducing the infarct scar size by almost 30% on Sirius red-stained sections (9.45% ± 4.27% vs. 13% ± 5.67% in controls; P = 0.03). Vascular density in the fucoidan group (α-actin, RECA-1, or lectin BS1 stained) was increased by 40% (2.18 ± 0.79 mm vs. 1.49 ± 0.42 mm in controls ×200; P = 0.001). Plasma SDF-1α at 1 month was not significantly different between the 2 groups. However, increased immunostaining density of SDF-1α and vascular endothelial growth factor in fibrotic ischemic tissues was observed in fucoidan-treated animals versus controls. In conclusion, fucoidan enhanced tissue repair in myocardial ischemia-reperfusion by promoting revascularization (in situ vascular endothelial growth factor and SDF-1α overexpression) and limiting fibrosis. Consequently, fucoidan may be useful for myocardial ischemic patients.
Immune Response Elicited by DNA Vaccination Using Lactococcus lactis Is Modified by the Production of Surface Exposed Pathogenic Protein (2014)

In this study, we compared immune responses elicited by DNA immunization using Lactococcus lactis or L. lactis expressing the Staphylococcus aureus invasin Fibronectin Binding Protein A (FnBPA) at its surface. Both strains carried pValac:BLG, a plasmid containing the cDNA of Beta-Lactoglobulin (BLG), and were designated LL-BLG and LL-FnBPA+ BLG respectively. A TH2 immune response characterized by the secretion of IL-4 and IL-5 in medium of BLG reactivated splenocytes was detected after either oral or intranasal administration of LL-FnBPA+ BLG. In contrast, intranasal administration of LL-BLG elicited a TH1 immune response. After BLG sensitization, mice previously intranasally administered with LL-BLG showed a significantly lower concentration of BLG-specific IgE than the mice non-administered. Altenatively administration of LL-FnBPA+ BLG didn't modify the BLG-specific IgE concentration obtained after sensitization, thus confirming the TH2 orientation of the immune response. To determine if the TH2-skewed immune response obtained with LL-FnBpA+ BLG was FnBPA-specific or not, mice received another L. lactis strain producing a mutated form of the Listeria monocytogenes invasin Internalin A intranasally, allowing thus the binding to murine E-cadherin, and containing pValac:BLG (LL-mInlA+ BLG). As with LL-FnBPA+ BLG, LL-mInlA+ BLG was not able to elicit a TH1 immune response. Furthermore, we observed that these difference were not due to the peptidoglycan composition of the cell wall as LL-FnBPA+ BLG, LL-mInlA+ BLG and LL-BLG strains shared a similar composition. DNA vaccination using LL-BLG elicited a pro-inflammatory TH1 immune response while using LL-FnBPA+ BLG or LL-mInlA+ BLG elicited an anti-inflammatory TH2 immune response.
On E. W. Dijkstra's position paper on “fairness:'' (1988)

No abstract available.