gebhart/patrepeval huggingface dataset:
Phospholipid-porphyrin conjugates: deciphering the driving forces behind their supramolecular assemblies (2022)

Phospholipid-porphyrin conjugates (Pl-Por) are nowadays considered as a unique class of building blocks that can self-assemble into supramolecular structures that possess multifunctional properties and enhanced optoelectronics characteristics compared to their monomeric counterparts. However, despite their versatile properties, little is known about the assembling mechanism of Pl-Por conjugates and their molecular organization inside these assemblies. To gain a better understanding on their assembling properties, we synthesized two new series of Pl-Por conjugates with different alkyl sn2-chain lengths linked via an amide bond to either pheophorbide-a (PhxLPC) or pyropheophorbide-a (PyrxLPC). By combining a variety of experimental techniques with molecular dynamics simulations, we investigated both the assembling and optical properties of the Pl-Por either self-assembled or when incorporated into lipid bilayers. We demonstrated that Pl-Por conjugates can form assemblies that mimic lipid bilayer structures. Moreover, our results highlight that the non-covalent interactions between porphyrin cores play a central role in controlling both the structure of the lipid bilayer membranes and their subsequent optical properties. The fluidity of the phospholipid bilayer in which the Pl-Por conjugates were incorporated, was shown to play an important role in driving their interaction within the lipid matrix. Altogether, this work could be used as guidelines for the design of new Pl-Por conjugates that self-assemble into bilayer-like supramolecular structures with tunable morphology and optical properties.
Digital control of dual actuator hard disk drive systems (2003)

In this dissertation, we investigate the design of digital controllers for dual actuator hard disk drive systems. The dual actuator disk drive system consists of a coarse actuator (voice coil motor, VCM) and a fine actuator (piezoelectric transducer, PZT). Three aspects of dual actuator disk servo are studied: track following control, track settling and seeking control, and multi-rate control for computational saving. 
First, the track following problem is addressed for dual actuator disk drive systems. We present the design of digital controllers for dual actuator servo systems and the analysis of their robust stability and performance. The design is divided into two steps. In the first step, the stability of the coarse actuator loop is an important consideration. In the second step, the fine actuator loop is designed by loop shaping for superior performance of the overall system. Robustness is studied by μ-analysis after the closed loop system is augmented with various weightings. Simulation and experimental results demonstrate the effectiveness of the proposed design. 
Next, the track settling and seeking control is presented for the dual actuator hard disk drive system. The control design method is called the dual actuator reference trajectory re-design (RTRD). In RTRD, the original minimum jerk reference trajectory for VCM and another “redesigned” minimum jerk reference trajectory are combined to determine the reference trajectory for PZT for faster settling of the recording head on the target track. The RTRD is divided into three steps. In the first step, the coarse actuator controller is designed to be stable and achieve the basic performance. In the second step, the fine actuator controller is designed for superior performance of the overall system. Finally the reference signals are generated for both VCM and PZT actuators. Simulations and experimental results demonstrate the effectiveness of the proposed scheme. 
Finally, multi-rate control is studied for computation saving. The dual actuator disk drive system involves two actuators, i.e. VCM and PZT, with different bandwidths, and the two feedback loops are closed at different rates: a fast rate for a high bandwidth PZT loop and a slow rate for a low bandwidth VCM loop. The slow rate VCM controller is further decomposed and interlaced so that computational saving by multi-rate control may be distributed uniformly at all fast rate sampling instances. The experimental results show that the multi-rate implementations achieve regulation performance of the position error signal at about the same level as the single-rate implementation while realizing significant computational saving.
Alternate Parallel Processing Approach for FEM (2012)

In this work we present a new alternate way to formulate the finite element method (FEM) for parallel processing based on the solution of single mesh elements called FEM-SES. The key idea is to decouple the solution of a single element from that of the whole mesh, thus exposing parallelism at the element level. Individual element solutions are then superimposed node-wise using a weighted sum over concurrent nodes. A classic 2-D electrostatic problem is used to validate the proposed method obtaining accurate results. Results show that the number of iterations of the proposed FEM-SES method scale sublinearly with the number of unknowns. Two generations of CUDA enabled NVIDIA GPUs were used to implement the FEM-SES method and the execution times were compared to the classic FEM showing important performance benefits.
PEVD-Based Speech Enhancement in Reverberant Environments (2020)

The enhancement of noisy speech is important for applications involving human-to-human interactions, such as telecommunications and hearing aids, as well as human-to-machine interactions, such as voice-controlled systems and robot audition. In this work, we focus on reverberant environments. It is shown that, by exploiting the lack of correlation between speech and the late reflections, further noise reduction can be achieved. This is verified using simulations involving actual acoustic impulse responses and noise from the ACE corpus. The simulations show that even without using a noise estimator, our proposed method simultaneously achieves noise reduction, and enhancement of speech quality and intelligibility, in reverberant environments over a wide range of SNRs. Furthermore, informal listening examples highlight that our approach does not introduce any significant processing artefacts such as musical noise.
Bayesian Convolutional Neural Networks with Many Channels are Gaussian Processes. (2018)

There is a previously identified equivalence between wide fully connected neural networks (FCNs) and Gaussian processes (GPs). This equivalence enables, for instance, test set predictions that would have resulted from a fully Bayesian, infinitely wide trained FCN to be computed without ever instantiating the FCN, but by instead evaluating the corresponding GP. In this work, we derive an analogous equivalence for multi-layer convolutional neural networks (CNNs) both with and without pooling layers, and achieve state of the art results on CIFAR10 for GPs without trainable kernels. We also introduce a Monte Carlo method to estimate the GP corresponding to a given neural network architecture, even in cases where the analytic form has too many terms to be computationally feasible. Surprisingly, in the absence of pooling layers, the GPs corresponding to CNNs with and without weight sharing are identical. As a consequence, translation equivariance, beneficial in finite channel CNNs trained with stochastic gradient descent (SGD), is guaranteed to play no role in the Bayesian treatment of the infinite channel limit - a qualitative difference between the two regimes that is not present in the FCN case. We confirm experimentally, that while in some scenarios the performance of SGD-trained finite CNNs approaches that of the corresponding GPs as the channel count increases, with careful tuning SGD-trained CNNs can significantly outperform their corresponding GPs, suggesting advantages from SGD training compared to fully Bayesian parameter estimation.
Large Scale Production of Photonic Crystals on Scintillators (2016)

Heavy inorganic scintillator based detectors are used in various applications. You can find them in high energy physics as well as in nuclear medical imaging systems but also in homeland security radiation monitoring devices. In all these different detectors, light is produced in the scintillator and has to be transported towards a photodetector. The standard optical coupling of such a detector suffers from an inefficient light extraction towards the photodetector due to the high index of refraction of the scintillator and the accompanying total internal reflections. With the means of photonic nanostructuring of the different surfaces of the scintillator, the light transport can be optimized, which has a direct impact on the timing and light yield performance of the detector. Previous work from our group has already shown that photonic crystals (PhCs) can be used as diffraction gratings to improve the light coupling between a photodetector and a scintillator. Moreover, nanoscale surface structuring techniques could also be extended to the sidewalls, the wrapping, or the detector itself, which would open up a number of new possibilities for optimization of the light transport of scintillation based detectors. To show that PhCs can also be produced on a large industrial scale, we started to investigate different methods for cheap and large area PhC structuring. In this work, the current results on our efforts on PhC scintillator production will be described. The different projects include nanoimprint technologies, interference lithography and colloidal lithography. To conclude, we will summarize the different efforts of our group and collaborators and show up-to-date results of PhC improved scintillators.
Antiangiogenesis immunotherapy induces epitope spreading to Her-2/neu resulting in breast tumor immunoediting (2009)

Matthew M Seavey, Yvonne PatersonDepartment of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USAAbstract: Targeting tumors using cancer vaccine therapeutics has several advantages including the induction of long-term immunity, prime boost strategies for additional treatments and reduced side effects compared to conventional chemotherapeutics. However, one problem in targeting tumor antigens directly is that this can lead to antigen loss or immunoediting. We hypothesized that directing the immune response to a normal cell type required for tumor growth and survival could provide a more stable immunotherapeutic target. We thus examined the ability of an antiangiogenesis, Listeria monocytogenes (Lm)-based vector to deliver extracellular and intracellular fragments of the mouse vascular endothelial growth factor receptor-2/Flk-1 molecule, Lm-LLO-Flk-E1, and Lm-LLO-Flk-11 respectively, in an autochthonous model for Her-2/neu+ breast cancer. We found that these vaccines could cause epitope spreading to the endogenous tumor protein Her-2/neu and significantly delay tumor onset. However, tumors that grew out overtime accumulated mutations in the Her-2/neu molecule near or within cytotoxic T lymphocytes epitopes. We show here for the first time how an antiangiogenesis immunotherapy can be used to delay the onset of a spontaneous tumor through epitope spreading and determine a possible mechanism of how immunoediting of an endogenous tumor protein can allow for tumor escape and outgrowth in an autochthonous mouse model for Her-2/neu+ breast cancer.Keywords: Listeria, Her-2/neu, immunotherapy, antiangiogenesis, immunoediting
Cell-to-cell movement of plastids in plants (2012)

Our objective was to test whether or not plastids and mitochondria, the two DNA-containing organelles, move between cells in plants. As our experimental approach, we grafted two different species of tobacco, Nicotiana tabacum and Nicotiana sylvestris. Grafting triggers formation of new cell-to-cell contacts, creating an opportunity to detect cell-to-cell organelle movement between the genetically distinct plants. We initiated tissue culture from sliced graft junctions and selected for clonal lines in which gentamycin resistance encoded in the N. tabacum nucleus was combined with spectinomycin resistance encoded in N. sylvestris plastids. Here, we present evidence for cell-to-cell movement of the entire 161-kb plastid genome in these plants, most likely in intact plastids. We also found that the related mitochondria were absent, suggesting independent movement of the two DNA-containing organelles. Acquisition of plastids from neighboring cells provides a mechanism by which cells may be repopulated with functioning organelles. Our finding supports the universality of intercellular organelle trafficking and may enable development of future biotechnological applications.
Individually addressed large-scale patterning of conducting polymers by localized electric fields (2004)

A scaleable and site-specific patterning approach with individual addressability is demonstrated via an electropolymerization process within the gap of electrodes. The method can pattern conducting polymer structures by applying a bias between desired electrodes in a monomer vapor. The reaction is proposed to happen in a thin water film condensed inside the electrode gap at ambient environment. It is possible to pattern different conducting polymers on the same substrate by exposing to different monomers. Proof-of-concept experiments on pyrrole and thiophene have shown the generality of this simple and robust method, which enables the real-time monitoring of the resistance and deposition of the conducting polymers. Finally, chemical sensing of the patterned polypyrrole structures to ethanol vapor and ammonia gas are presented.
Synthesis of α‐cobalt(ii) hydroxide using ultrasound radiation (2000)

Cobalt hydroxide with an interlayer spacing of 7.53 Å and needle-like morphology has been synthesized with the aid of ultrasound radiation. Characterization by powder X-ray diffraction, transmission electron microscopy, thermogravimetric analysis, FT-IR spectroscopy, as well as elemental analysis, indicates the formation of α-cobalt hydroxide. Thermal decomposition of the hydroxide at 300 °C under air or argon yields nanometer-sized oxide particles of Co3O4 (ca. 9 nm) and CoO (ca. 6 nm), respectively.
1236: Virtual “V”-Poster: Novel Concept in Scientific Conferencing (2007)

You have accessJournal of UrologyPodium 37, Monday, May 21, 2007, 3:30 - 5:30 pm1 Apr 20071236: Virtual “V”-Poster: Novel Concept in Scientific Conferencing Georges-Pascal Haber, Yi-Chia Lin, Mihir M. Desai, Ralph V. Clayman, and Inderbir S. Gill Georges-Pascal HaberGeorges-Pascal Haber More articles by this author , Yi-Chia LinYi-Chia Lin More articles by this author , Mihir M. DesaiMihir M. Desai More articles by this author , Ralph V. ClaymanRalph V. Clayman More articles by this author , and Inderbir S. GillInderbir S. Gill More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)31450-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1236: Virtual “V”-Poster: Novel Concept in Scientific Conferencing." The Journal of Urology, 177(4S), p. 407 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 407 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Georges-Pascal Haber More articles by this author Yi-Chia Lin More articles by this author Mihir M. Desai More articles by this author Ralph V. Clayman More articles by this author Inderbir S. Gill More articles by this author Expand All Advertisement PDF DownloadLoading ...
Supplementary Figures: Supplementary Figure 1.; Supplementary Figure 2.; Supplementary Tables: Supplementary Table 1.; Supplementary Table 2.; Supplementary Table 3.; Supplementary Table 4. from Circulating Biomarkers and Resistance to Endocrine Therapy in Metastatic Breast Cancers: Correlative Results from AZD9496 Oral SERD Phase I Trial (2023)

&lt;p&gt;Supplementary Figures: Supplementary Figure 1. Summary of duration on AZD9496 therapy, previous therapies, and circulating biomarkers status at baseline for each patient ranked by ascending dose; Supplementary Figure 2. Tumor pharmacodynamics. Supplementary Tables: Supplementary Table 1. Study Plan showing time-points of collection of biosamples for exploratory research; Supplementary Table 2. ddPCR primers and probes;Supplementary Table 3. Antibodies and conditions for IHC analysis Antibodies for IHC analysis; Supplementary Table 4. Patients with {greater than or equal to}1 CTC/7.5 mL WB within 120 days of fulvestrant wash-out period prior C1D1.&lt;/p&gt;
Extended Functionality Attacks on IoT Devices: The Case of Smart Lights (2016)

In this paper we consider the security aspects of Internet of Things (IoT) devices, which bridge the physical and virtual worlds. We propose a new taxonomy of attacks, which classifies them into four broad categories. The most interesting category (which we call functionality extension attacks) uses the designed functionality of the IoT device to achieve a totally different effect. To demonstrate this type of attack, we consider the case of smart lights (whose original functionality is just to control the color and intensity of the lights in a particular room) and show how to use them to achieve unrelated effects. In the first attack, we use smart lights as a covert LIFI communication system to exfiltrate data from a highly secure (or even fully airgapped) office building. We implemented the attack and were able to read the leaked data from a distance of over 100 meters using only cheap and readily available equipment. In another attack, we showed that an attacker can strobe the lights at a frequency which may trigger seizures in people suffering from photosensitive epilepsy (in the same way that rapidly flashing video games can cause such seizures). In our experiments, we have tested both high-end and lower-end smart light systems, ranging from an expensive Philips HUE system to a cheap system manufactured by LimitlessLED. In addition, we consider other weaknesses of the systems we tested, and propose feasible remedies for the problems we found.
A Low-Profile Tapered Slot Antenna Array with Two-Decade (20:1) Bandwidth (2021)

Realizing an antenna for ultra-wide bandwidth operation while maintaining a low profile are two necessary steps for many space-based antenna arrays. As the desire for more bandwidth increases, so does the complexity and engineering required to make such an element viable. Traditionally, to achieve bandwidths stretching from UHF to SHF require physically large elements with a half wavelength spacing in an array setting to get the desired performance. Some antennas even sacrifice performance (mismatch, loss) to achieve a wide bandwidth. The tapered slot antenna design presented in this paper achieves a 20:1 bandwidth, and is electrically small. The design takes advantage of a multiplexed matched feed method to get a good match across each band. The element is built utilizing 3D printing to aid the producibility of the unique structures associated with the design. The array aperture is dual linear with vertical and horizontal polarizations.
ChemInform Abstract: Practical and Highly Regio‐ and Stereoselective Synthesis of 2‐Substituted Dihydropyridines and Piperidines: Application to the Synthesis of (‐)‐Coniine. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Damage to trifluoroacetamido-terminated organic self-assembled monolayers (SAMs) on aluminum, titanium, copper and gold by aluminum K.alpha. x-rays is due principally to electrons (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDamage to trifluoroacetamido-terminated organic self-assembled monolayers (SAMs) on aluminum, titanium, copper and gold by aluminum K.alpha. x-rays is due principally to electronsRobert L. Graham, Colin D. Bain, Hans A. Biebuyck, Paul E. Laibinis, and George M. WhitesidesCite this: J. Phys. Chem. 1993, 97, 37, 9456–9464Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://doi.org/10.1021/j100139a033RIGHTS & PERMISSIONSArticle Views270Altmetric-Citations81LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (4 MB) Get e-Alerts
Chronic liver inflammation modifies DNA methylation at the precancerous stage of murine hepatocarcinogenesis (2015)

Chronic liver inflammation precedes the majority of hepatocellular carcinomas (HCC). Here, we explore the connection between chronic inflammation and DNA methylation in the liver at the late precancerous stages of HCC development in Mdr2(-/-) (Mdr2/Abcb4-knockout) mice, a model of inflammation-mediated HCC. Using methylated DNA immunoprecipitation followed by hybridization with "CpG islands" (CGIs) microarrays, we found specific CGIs in 76 genes which were hypermethylated in the Mdr2(-/-) liver compared to age-matched healthy controls. The observed hypermethylation resulted mainly from an age-dependent decrease of methylation of the specific CGIs in control livers with no decrease in mutant mice. Chronic inflammation did not change global levels of DNA methylation in Mdr2(-/-) liver, but caused a 2-fold decrease of the global 5-hydroxymethylcytosine level in mutants compared to controls. Liver cell fractionation revealed, that the relative hypermethylation of specific CGIs in Mdr2(-/-) livers affected either hepatocyte, or non-hepatocyte, or both fractions without a correlation between changes of gene methylation and expression. Our findings demonstrate that chronic liver inflammation causes hypermethylation of specific CGIs, which may affect both hepatocytes and non-hepatocyte liver cells. These changes may serve as useful markers of an increased regenerative activity and of a late precancerous stage in the chronically inflamed liver.
Characterizing the CapEx and OpEx Tradeoffs in Next Generation Fiber-to-the-Home Networks (2008)

Network cost analyses based on a new modeling methodology are used to evaluate advanced GPON architectures. The relative merits of reach extension and higher splitter port counts are examined from both CapEx and OpEx perspectives.