gebhart/patrepeval huggingface dataset:
Dataset for "Towards dual frequency comb VECSELs with DMD laser-ablated spatial mode masks" (2019)

This dataset supports the publication: Jonathan Woods, Daniel Heath, Jake Daykin, Theo Chen Sverre, Ben Mills, Arnaud Garnache, Anne Tropper, and Vasilis Apostolopoulos 'Towards dual frequency comb VECSELs with DMD laser-ablated spatial mode masks' Proceedings Volume 10901, Vertical External Cavity Surface Emitting Lasers (VECSELs) IX; 109010I (2019) https://doi.org/10.1117/12.2508680
A novel approach for estimating muscle fiber conduction velocity by spatial and temporal filtering of surface emg signals (2003)

We describe a new method for the estimation of muscle fiber conduction velocity (CV) from surface electromyography (EMG) signals. The method is based on the detection of two surface EMG signals with different spatial filters and on the compensation of the spatial filtering operations by two temporal filters (with CV as unknown parameter) applied to the signals. The transfer functions of the two spatial filters may have different magnitudes and phases, thus the detected signals have not necessarily the same shape. The two signals are first spatially and then temporally filtered and are ideally equal when the CV value selected as a parameter in the temporal filters corresponds to the velocity of propagation of the detected action potentials. This approach is the generalization of the classic spectral matching technique. A theoretical derivation of the method is provided together with its fast implementation by an iterative method based on the Newton's method. Moreover, the lowest CV estimate among those obtained by a number of filter pairs is selected to reduce the CV bias due to nonpropagating signal components. Simulation results indicate that the method described is less sensitive than the classic spectral matching approach to the presence of nonpropagating signals and that the two methods have similar standard deviation of estimation in the presence of additive, white, Gaussian noise. Finally, experimental signals have been collected from the biceps brachii muscle of ten healthy male subjects with an adhesive linear array of eight electrodes. The CV estimates depended on the electrode location with positive bias for the estimates from electrodes close to the innervation or tendon regions, as expected. The proposed method led to significantly lower bias than the spectral matching method in the experimental conditions, confirming the simulation results.
Effects of cyclic AMP response element binding protein–Zhangfei (CREBZF) on the unfolded protein response and cell growth are exerted through the tumor suppressor p53 (2013)

Zhangfei/CREBZF, a basic region-leucine zipper (bLZip) transcription factor, is a potent suppressor of growth and the unfolded protein response (UPR) in some cancer cell lines, including the canine osteosarcoma cell line, D-17. However, the effects of Zhangfei are not universal, and it has no obvious effects on untransformed cells and some cancer cell lines, suggesting that Zhangfei may act through an intermediary that is either not induced or is defective in cells that it does not affect. Here we identify the tumor suppressor protein p53 as this intermediary. We show the following: in cells ectopically expressing Zhangfei, the protein stabilizes p53 and co-localizes with it in cellular nuclei; the bLZip domain of Zhangfei is required for its profound effects on cell growth and interaction with p53. Suppression of p53 by siRNA at least partially inhibits the effects of Zhangfei on the UPR and cell growth. The effects of Zhangfei on D-17 cells is mirrored by its effects on the p53-expressing human osteosarcoma cell line U2OS, while Zhangfei has no effect on the p53-null osteosarcoma cell line MG63. In U2OS cells, Zhangfei displaces the E3 ubiquitin ligase mouse double minute homolog 2 (Mdm2) from its association with p53, suggesting a mechanism for the effects of Zhangfei on p53.
A Multilayered Thin Film Insulator for Harsh Environments (2002)

Abstract The status of work to develop a reliable high temperature dielectric thin film for use with thin film sensors is presented. The use of thin films to electrically insulate thin film sensors on engine components minimizes the intrusiveness of the sensor and allows a more accurate measurement of the environment. A variety of insulating films were investigated for preventing electrical shorting caused by insulator failure between the sensor and the component. By alternating layers of sputtered high temperature ceramics, a sequence of insulating layers was devised that prevents pinholes from forming completely through the insulator and maintains high electrical resistivity at high temperatures. The major technical challenge remaining is to optimise the fabrication of the insulator with respect to composition to achieve a reliable high temperature insulating film. Data from the testing of various potentially insulating thin film systems is presented and their application to thin film sensors is also discussed.
Monitoring high-intensity focused ultrasound (HIFU) therapy using radio frequency ultrasound backscatter to quantify heating (2005)

The spatial distribution and temporal history of tissue temperature is an essential indicator of thermal therapy progress, and treatment safety and efficacy. Magnetic resonance methods provide the gold standard noninvasive measurement of temperature but are costly and cumbersome compared to the therapy itself. We have been developing the use of ultrasound backscattering for real-time temperature estimation; ultrasonic methods have been limited to relatively low temperature rise, primarily due to lack of sensitivity at protein denaturation temperatures (50−70&amp;lt;th&amp;gt;°C). Through validation experiments on gel phantoms and ex vivo tissue we show that temperature rise can be accurately mapped throughout the therapeutic temperature range using a new BioHeat Transfer Equation (BHTE) model-constrained inverse approach. Speckle-free temperature and thermal dose maps are generated using the ultrasound calibrated model over the imaged region throughout therapy delivery and post-treatment cooling periods. Results of turkey breast tissue experiments are presented for static HIFU exposures, in which the ultrasound calibrated BHTE temperature maps are shown to be very accurate (within a degree) using independent thermocouple measurements. This new temperature monitoring method may speed clinical adoption of ultrasound-guided HIFU therapy. [Work supported by Army MRMC.]
Neutralization of factor X activity by factor X-specific monoclonal antibodies (1992)

Factor X, a vitamin K-dependent protein, is the plasma zymogen for the active serine protease factor Xa. Factor Xa is the proteolytic enzyme for prothrombinase, the multi-protein membrane complex that catalyses the cleavage of prothrombin to thrombin. A panel of 10 monoclonal antibodies (identified by their corresponding clone numbers: 1, 2, 3, 5, 7, 26, 27, 54, 73, and 79) to factor X were produced by immunizing mice with purified factor X. All of the antibodies bound both human factor X and factor Xa in a solid-phase ELISA and binding of the antibodies was not affected by removal of Ca2+ with EDTA. In immunoblot analysis, antibody alpha HFX-54 bound to the light chain and antibodies alpha HFX-1, -5, -7, and -26 bound to the heavy chain of reduced factor X. Antibodies alpha BFX-2b, alpha HFX-27, -54, and -73 prolonged both the factor X-dependent clotting time and activated partial thromboplastin time (APTT) of normal plasma while antibody alpha HFX-1 only prolonged the APTT. None of the antibodies significantly inhibited factor X activation by purified Russell's viper venom factor X activator. In prothrombin activation assays using purified factor Xa, factor Va, prothrombin, Ca2+ and phospholipid vesicles, seven of the antibodies (alpha HFX-1, -3, -26, -27, -54, -73 and alpha BFX2b) showed some inhibition of thrombin generation ranging from 18 to 60% of the control. The decrease in factor X plasma clotting activity was most likely due to inhibition of factor Xa activity in prothrombinase, although some antibody-dependent inhibition of factor X activation may contribute to the observed inhibition of plasma clotting. Prothrombinase activity on platelets was inhibited in an identical manner by the monoclonal antibodies. When prothrombin was activated in the absence of factor Va, only antibody alpha BFX-2b inhibited activation. Calcium-independent determinants on both the heavy chain (determinants 1 and 26) and light chain (determinant 54) of factor X may play a role in prothrombin activation by prothrombinase. Other epitopes (antibodies alpha HFX-3, -27, -73) appeared to be influenced by association of factor Xa with factor Va. Topographic regions on factor X important for factor X activation and factor Xa function may be identified by the use of these monoclonal antibodies.
A Cortical Extracellular Simulation Model to Create Synthetic Neural Recordings (2021)

Synthetic extracellular neural recordings allow precise knowledge of when and which neuron spikes in a recording, and therefore are important to assess and refine spike detection and sorting algorithms. Such algorithms are strongly dependent on the spike waveform shapes. Therefore, it is critical for a model that generates synthetic recordings to incorporate the factors changing the waveform shape in the neural environment. In this paper, we present a simulation tool that models frequency-filtering and layer-inhomogeneity of cortical layers, where most actual extracellular recordings are performed. The tool uses simulated transmembrane currents of neurons from NEURON, and implements line-source-approximation, method-of-images, and low-pass filtering to calculate the potentials on MATLAB.
The furrows of Rhinolophidae revisited (2012)

Rhinolophidae, a family of echolocating bats, feature very baroque noseleaves that are assumed to shape their emission beam. Zhuang & Muller (Zhuang & Muller 2006 Phys. Rev. Lett. 97, 218701 (doi:10.1103/PhysRevLett.97.218701); Zhuang & Muller 2007 Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 76(Pt. 1), 051902 (doi:10.1103/PhysRevE.76.051902)) have proposed, based on finite element simulations, that the furrows present in the noseleaves of these bats act as resonance cavities. Using Rhinolophus rouxi as a model species, they reported that a resonance phenomenon causes the main beam to be elongated at a particular narrow frequency range. Virtually filling the furrows reduced the extent of the main lobe. However, the results of Zhuang & Muller are difficult to reconcile with the ecological background of R. rouxi. In this report, we replicate the study of Zhuang & Muller, and extend it in important ways: (i) we take the filtering of the moving pinnae into account, (ii) we use a model of the echolocation task faced by Rhinolophidae to estimate the effect of any alterations to the emission beam on the echolocation performance of the bat, and (iii) we validate our simulations using a physical mock-up of the morphology of R. rouxi. In contrast to Zhuang & Muller, we find the furrows to focus the emitted energy across the whole range of frequencies contained in the calls of R. rouxi (both in simulations and in measurements). Depending on the frequency, the focusing effect of the furrows has different consequences for the estimated echolocation performance. We argue that the furrows act to focus the beam in order to reduce the influence of clutter echoes.
A Novel and Autonomic Model to Enhance Performance and Security of a Relational Database Management System (2011)

IJAR - Indian Journal of Applied Research (IJAR) IJAR is a double reviewed monthly print journal that accepts research works from scholars, academicians, professors, doctorates, lecturers, and corporate in their respective expertise of studies.
Predicting Cellular Growth from Gene Expression Signatures (2009)

Maintaining balanced growth in a changing environment is a fundamental systems-level challenge for cellular physiology, particularly in microorganisms. While the complete set of regulatory and functional pathways supporting growth and cellular proliferation are not yet known, portions of them are well understood. In particular, cellular proliferation is governed by mechanisms that are highly conserved from unicellular to multicellular organisms, and the disruption of these processes in metazoans is a major factor in the development of cancer. In this paper, we develop statistical methodology to identify quantitative aspects of the regulatory mechanisms underlying cellular proliferation in Saccharomyces cerevisiae. We find that the expression levels of a small set of genes can be exploited to predict the instantaneous growth rate of any cellular culture with high accuracy. The predictions obtained in this fashion are robust to changing biological conditions, experimental methods, and technological platforms. The proposed model is also effective in predicting growth rates for the related yeast Saccharomyces bayanus and the highly diverged yeast Schizosaccharomyces pombe, suggesting that the underlying regulatory signature is conserved across a wide range of unicellular evolution. We investigate the biological significance of the gene expression signature that the predictions are based upon from multiple perspectives: by perturbing the regulatory network through the Ras/PKA pathway, observing strong upregulation of growth rate even in the absence of appropriate nutrients, and discovering putative transcription factor binding sites, observing enrichment in growth-correlated genes. More broadly, the proposed methodology enables biological insights about growth at an instantaneous time scale, inaccessible by direct experimental methods. Data and tools enabling others to apply our methods are available at http://function.princeton.edu/growthrate.
Gene Expression Profiling in Chronic Myeloid Leukemia Patients Treated with Hydroxyurea (2002)

Using array technology that allows the simultaneous detection of gene expression of hundreds of genes, four patients with chronic myeloid leukemia (CML) were investigated at diagnosis and after starting administration of hydroxyurea. To detect the gene expression of peripheral blood mononuclears and granulocytes Human Cancer cDNA Array (CLONTECH) with 588 gene probes was used. Gene expression mononuclear and granulocyte profiles of patients at diagnosis were compared with the control profiles. The significant expression changes observed in most patients seemed to be important. Increased expression of c-jun N-terminal kinase 2 (JNK2), integrin alpha E, MMP-8, MMP-9 was detected in both fractions of most patients. In some samples PCNA, HDGF, MAPK p38, CD59 increased expressions were found. Significant down-regulation of expression in patients was detected in genes CDK4 inhibitor A, PURA, notch1 in mononuclears; STAT2, STAT5, RAR-alpha, MCL-1, junB, caspase 4 in granulocytes; CDK6, GADD153, ERBB-3, cadherin 5 in both fractions. Expression profiles detected in patients at diagnosis did not differ markedly from those after one-week treatment with hydroxyurea. Only in a few genes were significant changes after hydroxyurea administration observed and inter-individual expression differences were rather common.
Electric Vehicle Charging Hub Power Forecasting: A Statistical and Machine Learning Based Approach (2023)

Electric vehicles (EVs) penetration growth is essential to reduce transportation-related local pollutants. Most countries are witnessing a rapid development of the necessary charging infrastructure and a consequent increase in EV energy demand. In this context, power demand forecasting is an essential tool for planning and integrating EV charging as much as possible with the electric grid, renewable sources, storage systems, and their management systems. However, this forecasting is still challenging due to several reasons: the still not statistically significant number of circulating EVs, the different users’ behavior based on the car parking scenario, the strong heterogeneity of both charging infrastructure and EV population, and the uncertainty about the initial state of charge (SOC) distribution at the beginning of the charge. This paper aims to provide a forecasting method that considers all the main factors that may affect each charging event. The users’ behavior in different urban scenarios is predicted through their statistical pattern. A similar approach is used to forecast the EV’s initial SOC. A machine learning approach is adopted to develop a battery-charging behavioral model that takes into account the different EV model charging profiles. The final algorithm combines the different approaches providing a forecasting of the power absorbed by each single charging session and the total power absorbed by charging hubs. The algorithm is applied to different parking scenarios and the results highlight the strong difference in power demand among the different analyzed cases.
Functional Data Analysis Applied to Modeling of Severe Acute Mucositis and Dysphagia Resulting From Head and Neck Radiation Therapy (2016)

FPLS and functional principal component analysis marginally improved predictive performance compared with PLR and provided robust dose-response associations. FDA is recommended for use in normal tissue complication probability modeling.
Ephrin-B1 Reverse Signaling Activates JNK through a Novel Mechanism That Is Independent of Tyrosine Phosphorylation (2003)

Eph receptors and their cognate ligand ephrins play important roles in various biological processes such as cell migration, axon guidance, and synaptic plasticity. One characteristic feature of the Eph-ephrin signal transduction is that, upon interaction with the receptor, the transmembrane B-class ephrins become tyrosine-phosphorylated and transduce intracellular signals that lead to reorganization of the cytoskeleton. Although in vitro and genetic studies have demonstrated unequivocally the significance of this reverse signaling, the underlying mechanism remains unclear. We report here that transfection of ephrin-B1 into 293 cells resulted in robust increase in JNK activity, whereas expression of truncated ephrin-B1 lacking the cytoplasmic domain had a negligible effect, indicating that the induction of JNK activity was attributed mainly to the reverse signaling. The ephrin-B1-mediated JNK activation was reduced significantly by dominant-negative TAK1, MKK4, or MKK7. Ephrin-B1 over-expressing 293 cells became rounded in morphology. Surprisingly, ephrin-B1 that lacked all six intracellular tyrosine residues still triggered JNK activation and rounding morphology of the transfected cells. Consistent with these observations, activation of JNK and the resulting morphological changes mediated by ephrin-B1 could be abolished by the JNK inhibitor SP600125 but not the Src inhibitor PP2. Taken together, our findings have identified a novel reverse signaling pathway transduced by ephrin-B1, which is independent of tyrosine phosphorylation but involves the activation of JNK through TAK1 and MKK4/MKK7 and leads to changes in cell morphology.
Differential gene expression by RNA-Seq in Sigma-2 Receptor/TMEM97 knockout cells reveals its role in complement activation and SARS-CoV-2 viral uptake (2021)

ABSTRACT Our lab has recently shown that the Sigma-2 Receptor/Transmembrane Protein 97 (sigma-2R/TMEM97) interacts with the low-density lipoprotein receptor (LDLR) and facilitates the enhanced uptake of various ligands including lipoproteins and intrinsically disordered proteins. TMEM97 has been recently been shown to interact with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins, highlighting its potential involvement with viral entry into the cell. We hypothesized that sigma-2R/TMEM97 may play a role in facilitating viral uptake, and with the regulation of inflammatory and thrombotic pathways that are involved with viral infection. In this study, we identified the top differentially expressed genes upon the knockout of sigma-2R/TMEM97, and analyzed the genes involved with the inflammatory and thrombotic cascades, effects that are observed in patients infected with SARS-CoV-2. We found that the ablation of sigma-2R/TMEM97 resulted in an increase in Complement Component 4 Binding Protein (C4BP) proteins, at both the translational and transcriptional levels. We also showed that sigma-2R/TMEM97 interacts with the cellular receptor for SARS-CoV-2, the human angiotensin-converting enzyme 2 (ACE2) receptor, forming a protein complex, and that disruption of this complex results in the inhibition of viral uptake. The results of this study suggest that sigma-2R/TMEM97 may be a novel therapeutic target to inhibit SARS-CoV-2 viral uptake, as well as to decrease inflammatory and thrombotic effects through the modulation of the complement cascade.
A new scheme for interconnecting LANs with label switching bridges (2005)

Ethernet, which has traditionally been the dominant technology in local area networks, is now facing new challenges due to the fact that networks have scaled and today's applications require more bandwidth and increased robustness against failures. The limitations of Ethernet are mainly imposed by the spanning tree protocol, which is necessary to prevent loops and provide redundancy in a switched network. The successful deployment of Ethernet over MPLS in the metro area have proved that Ethernet LANs can be further enriched with the services enabled by the label switching technique. In this article, we propose a new LAN interconnection technique based on label switching, which enhances network services, simplifies switch functionalities, while remaining flexible enough to be easily deployed in most LAN environments.
Erratum to: Study of the Change in the Structure and Properties of High-Entropic Alloys during Thermal and Thermomechanical Processing (2021)

An Erratum to this paper has been published: https://doi.org/10.3103/S1067821221040155
COMP‐Ang1 prevents structural and functional damage of the retina in a mouse model of central retinal artery occlusion (2013)

The retina is the most metabollicaly active tissue in the body. Central retinal artery occlusion (CRAO) is a leading cause of blindness. CRAO results in retinal edema, changes in morphology, and loss of electrical function. We hypothesize that by stabilizing retinal blood vessels, the effects of CRAO can be mitigated. Cartilage Oligomatrix Protein Angiopoietin1 (COMP‐Ang1), promotes vascular stability through the Tie‐2 receptor mediated increase in adherens junctions. We tested whether COMP‐Ang1 could prevent the pathologies of CRAO. C57 mice were treated with intravitreal injections of PBS, or viral vector expressing GFP or COMP‐Ang1. Vessel occlusion in mice was accomplished by excitation of intravenously injected rose bengal by laser (588 nm) focused on the central retinal artery. COMP‐Ang1 decreased retinal edema, as evidenced by cross‐sections taken 1 day after laser, and maintained retinal morphology when compared to mice treated with control. COMP‐Ang1 improved both electrical retinal function, as assesed by scotopic electrical retinogram (ERG) (b‐wave amplitude 120 uV compared to 25uV control) and visual acuity, as determined by optokinetic tracking response (OptoMotry) (0.134 +/− 0.08 cycles/degree compared to 0.075 +/− 0.02 cycles/degree, control). These results demonstrate that promoting vascular stability may be beneficial to patients with CRAO and other retinal ischemic diseases.