gebhart/patrepeval huggingface dataset:
Neuronal Spike Shapes (NSS): A Straightforward Approach to Investigate Heterogeneity in Neuronal Excitability States (2023)

ABSTRACT The mammalian brain exhibits a remarkable diversity of neurons, contributing to its intricate architecture and functional complexity. The analysis of multimodal single-cell datasets enables the investigation of cell types and states heterogeneity. In this study, we introduce the Neuronal Spike Shapes (NSS), a straightforward approach for the exploration of excitability states of neurons based on their Action Potential (AP) waveforms. The NSS method describes the AP waveform based on a triangular representation complemented by a set of derived electrophysiological (EP) features. To support this hypothesis, we validate the proposed approach on two datasets of murine cortical neurons, focusing it on GABAergic neurons. The validation process involves a combination of NSS-based clustering analysis, features exploration, Differential Expression (DE), and Gene Ontology (GO) enrichment analysis. Results show that the NSS-based analysis captures neuronal excitability states that possess biological relevance independently of cell subtype. In particular, Neuronal Spike Shapes (NSS) captures, among others, a well-characterized fast-spiking excitability state, supported by both electrophysiological and transcriptomic validation. Gene Ontology Enrichment Analysis reveals voltage-gated potassium ( K + ) channels as specific markers of the identified NSS partitions. This finding strongly corroborates the biological relevance of NSS partitions as excitability states, as the expression of voltage-gated K + channels regulates the hyperpolarization phase of the AP, being directly implicated in the regulation of neuronal excitability.
Secure in-VM monitoring using hardware virtualization (2009)

Kernel-level attacks or rootkits can compromise the security of an operating system by executing with the privilege of the kernel. Current approaches use virtualization to gain higher privilege over these attacks, and isolate security tools from the untrusted guest VM by moving them out and placing them in a separate trusted VM. Although out-of-VM isolation can help ensure security, the added overhead of world-switches between the guest VMs for each invocation of the monitor makes this approach unsuitable for many applications, especially fine-grained monitoring. In this paper, we present Secure In-VM Monitoring (SIM), a general-purpose framework that enables security monitoring applications to be placed back in the untrusted guest VM for efficiency without sacrificing the security guarantees provided by running them outside of the VM. We utilize contemporary hardware memory protection and hardware virtualization features available in recent processors to create a hypervisor protected address space where a monitor can execute and access data in native speeds and to which execution is transferred in a controlled manner that does not require hypervisor involvement. We have developed a prototype into KVM utilizing Intel VT hardware virtualization technology. We have also developed two representative applications for the Windows OS that monitor system calls and process creations. Our microbenchmarks show at least 10 times performance improvement in invocation of a monitor inside SIM over a monitor residing in another trusted VM. With a systematic security analysis of SIM against a number of possible threats, we show that SIM provides at least the same security guarantees as what can be achieved by out-of-VM monitors.
Raman spectroscopy of template grown single wall carbon nanotubes in zeolite crystals (2003)

Single wall carbon nanotubes with diameter 0.4 nm grown in the channels of AlPO4-5 crystals were studied by Raman spectroscopy and ab initio density functional calculations. In the experiment up to 19 different laser lines were used to characterize vibrational properties. Spectra depend strongly on the energy of the laser line used for excitation. Even though the observed Raman spectra were very rich on lines only two types of nanotubes with different chiralities, (5,0) and (4,2), were found to be responsible for the observed response. The frequencies of the radial breathing modes were reliably assigned. Even though the (5,0) is metallic, the A1g mode does not couple to the electronic continuum and the Peierls-type mechanism does not shift the mode toward lower frequencies. A strong response was also observed for frequencies around 1250 cm−1. The positions of two peaks assigned to the (5,0) do not depend on the laser energy whereas only one peak was observed for the (4,2) nanotube. Its frequency shifts with the laser energy like the D line of large diameter nanotubes, but the rate of the shift is only one half of the value known for the latter. These unexpected results could be traced back to the phonon dispersion of the narrow tubes.
Comparing LabPQR and the Spectral Gamut Mapping Framework (2010)

In this paper, two strategies of spectral printing were implemented and compared: using the Interim Connection Space LabPQR and the Spectral Gamut Mapping Framework (SGMF). The LabPQR approach involved at first, converting spectral information to a lower-dimensional Interim Connection Space and then interpolation using a multi-dimensional lookup table. The SGMF approach involved at first, converting spectral information into CIELAB values for multiple illuminants and then performing direct searches of multiple histogram tables to find matches to these CIELAB values. Additionally, an optimization that used a CIEDE2000-based uniform color space was applied to both approaches. These approaches were tested and compared. The differences between these two methods involved the tradeoffs between interpolation (LabPQR) and indexing/searching of quantized predetermined tables (SGMF). LabP resulted in better colorimetric accuracy under a single illuminant with better spatial image quality. The SGMF approach resulted in slightly better spectral accuracy with a reduction in colorimetric accuracy and noticeable spatial artifacts in low frequency image areas.
Parthenocissus tricuspiduta Activity Directed against Human Red Blood Cells Coated with C3b (1981)

Abstract An extract of seeds from Parthenocissus tricuspidata strongly agglutinated red blood cells (RBC) coated with C3b. RBC coated with C3d, C4b or C4d and noncomplement‐coated RBC were very weakly agglutinated. There was no correlation of reactivity with RBC groups.
ARMA/FDTD technique for reflection properties of periodic structures at oblique incidence and developing wide angle EBG application (2015)

Metamaterials including Meta-surface are widely researched to enhance antenna applications. Electromagnetic Band Gap (EBG) structure and Frequency Selective surface (FSS) are one of the meta-surface. In order to enhance the antenna properties, the meta-surfaces are used near the antenna. In this situation, reflection characteristics at oblique incidence are important properties. On the other hand, the meta-surface are composed by periodic structures. In this paper, the reflection properties of meta-surface at oblique incidence case are researched by using ARMA/FDTD technique. Furthermore, we will indicate wide angle EM absorber which based on EMG.
Author response: WDR90 is a centriolar microtubule wall protein important for centriole architecture integrity (2020)

Cells are made up of compartments called organelles that perform specific roles. A cylindrical organelle called the centriole is important for a number of cellular processes, ranging from cell division to movement and signaling. Each centriole contains nine blades made up of protein filaments called microtubules, which link together to form a cylinder. This well-known structure can be found in a variety of different species. Yet, it is unclear how centrioles are able to maintain this stable architecture whilst carrying out their various different cell roles. In early 2020, a group of researchers discovered a scaffold protein at the center of centrioles that helps keep the microtubule blades stable. Further investigation suggested that another protein called WDR90 may also help centrioles sustain their cylindrical shape. However, the exact role of this protein was poorly understood. To determine the role of WDR90, Steib et al. – including many of the researchers involved in the 2020 study – used a method called Ultrastructure Expansion Microscopy to precisely locate the WDR90 protein in centrioles. This revealed that WDR90 is located on the microtubule wall of centrioles in green algae and human cells grown in the lab. Further experiments showed that the protein binds directly to microtubules and that removing WDR90 from human cells causes centrioles to lose their scaffold proteins and develop structural defects. This investigation provides fundamental insights into the structure and stability of centrioles. It shows that single proteins are key components in supporting the structural integrity of organelles and shaping their overall architecture. Furthermore, these findings demonstrate how ultrastructure expansion microscopy can be used to determine the role of individual proteins within a complex structure.
Mask-Pix2Pix Network for Overexposure Region Recovery of Solar Image (2019)

Overexposure may happen for imaging of solar observation as extremely violet solar bursts occur, which means that signal intensity goes beyond the dynamic range of imaging system of a telescope, resulting in loss of signal. For example, during solar flare, Atmospheric Imaging Assembly (AIA) of Solar Dynamics Observatory (SDO) often records overexposed images/videos, resulting loss of fine structures of solar flare. This paper makes effort to retrieve/recover missing information of overexposure by exploiting deep learning for its powerful nonlinear representation which makes it widely used in image reconstruction/restoration. First, a new model, namely, mask-Pix2Pix network, is proposed for overexposure recovery. It is built on a well-known Pix2Pix network of conditional generative adversarial network (cGAN). In addition, a hybrid loss function, including an adversarial loss, a masked L1 loss and a edge mass loss/smoothness, are integrated together for addressing challenges of overexposure relative to conventional image restoration. Moreover, a new database of overexposure is established for training the proposed model. Extensive experimental results demonstrate that the proposed mask-Pix2Pix network can well recover missing information of overexposure and outperforms the state of the arts originally designed for image reconstruction tasks.
Voltammetric Discrimination of DNA Single Base‐Pair Mismatches via Taq DNA Ligase‐Based Mismatch Recognition (2011)

Abstract An electrochemical approach for single base‐specific detection of label‐free target single‐strand DNA (ssDNA) was demonstrated. The approach was based on the high ligation selectivity of Taq DNA ligase coupled with ferrocenated gold nanoparticle/streptavidin conjugate‐based voltammetric detection method. The ferrocene (Fc) moieties of Fc‐capped gold nanoparticle/streptavidin conjugates, which were selectively bound to the biotinylated DNA layer, were found to be close enough to the underlying electrode surface for facile electron transfer. The proposed electrochemical method was evaluated with label‐free target DNA strands making all possible base pair combinations at the 3′‐OH side of capture probe, and showed significant voltammetric signals only with a perfect match target strand.
Polyvalent 2D Entry Inhibitors for Pseudorabies and African Swine Fever Virus (2017)

African swine fever virus (ASFV) is one of the most dangerous viruses for pigs and is endemic in Africa but recently also spread into the Russian Federation and the Eastern border of the EU. So far there is no vaccine or antiviral drug available to curtail the infection. Thus, control strategies based on novel inhibitors are urgently needed. Another highly relevant virus infection in pigs is Aujeszky's disease caused by the alphaherpesvirus pseudorabies virus (PrV). This article reports the synthesis and biological evaluation of novel extracellular matrix-inspired entry inhibitors based on polyglycerol sulfate-functionalized graphene sheets. The developed 2D architectures bind enveloped viruses during the adhesion process and thereby exhibit strong inhibitory effects, which are equal or better than the common standards enrofloxacin and heparin as demonstrated for ASFV and PrV. Overall, the developed polyvalent 2D entry inhibitors are nontoxic and efficient nanoarchitectures, which interact with various types of enveloped viruses. Therefore they prevent viral adhesion to the host cell and especially target viruses that rely on a heparan sulfate-dependent cell entry mechanism.
Receiver buffer requirement for video streaming over TCP (2006)

TCP is one of the most widely used transport protocols for video streaming. However, the rate variability of TCP makes it difficult to provide good video quality. To accommodate the variability, video streaming applications require receiver-side buffering. In current practice, however, there are no systematic guidelines for the provisioning of the receiver buffer, and smooth playout is insured through over-provisioning. In this work, we are interested in memory-constrained applications where it is important to determine the right size of receiver buffer in order to insure a prescribed video quality. To that end, we characterize video streaming over TCP in a systematic and quantitative manner. We first model a video streaming system analytically and derive an expression of receiver buffer requirement based on the model. Our analysis shows that the receiver buffer requirement is determined by the network characteristics and desired video quality. Experimental results validate our model and demonstrate that the receiver buffer requirement achieves desired video quality.
Inversion using Bayesian hyper‐prior formulation for sharp boundaries (2008)

Geological discontinuities commonly occur in nature. Sharp jumps such as distinct layering or formation of localized bodies in the subsurface can occur due to various geological processes. However, the bandwidth of the geophysical signals such as seismic or electromagnetics probing the Earth often produces smooth representations of the model via imaging or inversion. Introducing informative priors through regularization process has been shown to produce discontinuous model. Among the various classes of the regularization operators that preserve discontinuity are total variation norm, compactness constraints and Lp norm such as sparse spike solutions. In this paper we focus on a Bayesian hyper model formulation originally developed for image processing applications to geophysical inversion of the data. Both the locations and the magnitude of the discontinuities are considered unknowns which are commonly encountered in practical applications. Using a series of examples we compare this approach with other well known approaches such as total variation and L1 inversion in the wavelet domain.
Underwater Navigation of AUVs Using Uncorrelated Measurement Error Model of USBL (2022)

&lt;i&gt;This article presents a modeling method for the uncorrelated measurement error of the ultra-short baseline (USBL) acoustic positioning system for aiding navigation of underwater vehicles. The Mahalanobis distance (MD) and principal component analysis are applied to decorrelate the errors of USBL measurements, which are correlated in the x- and y-directions and vary according to the relative direction and distance between a reference station and the underwater vehicles. The proposed method can decouple the radial-direction error and angular direction error from each USBL measurement, where the former and latter are independent and dependent, respectively, of the distance between the reference station and the vehicle. With the decorrelation of the USBL errors along the trajectory of the vehicles in every time step, the proposed method can reduce the threshold of the outlier decision level. To demonstrate the effectiveness of the proposed method, simulation studies were performed with motion data obtained from a field experiment involving an autonomous underwater vehicle and USBL signals generated numerically by matching the specifications of a specific USBL with the data of a global positioning system. The simulations indicated that the navigation system is more robust in rejecting outliers of the USBL measurements than conventional ones. In addition, it was shown that the erroneous estimation of the navigation system after a long USBL blackout can converge to the true states using the MD of the USBL measurements. The navigation systems using the uncorrelated error model of the USBL, therefore, can effectively eliminate USBL outliers without loss of uncontaminated signals.&lt;/i&gt;
Figure S4 from The Human CD38 Monoclonal Antibody Daratumumab Shows Antitumor Activity and Hampers Leukemia–Microenvironment Interactions in Chronic Lymphocytic Leukemia (2023)

&lt;p&gt;Figure S4. Dynamics of human IgG concentration in daratumumab treated mice.&lt;/p&gt;
Inhibition of platelet‐derived growth factor‐induced mesangial cell proliferation by cyclooxygenase‐2 overexpression is abolished through reactive oxygen species (2006)

Proliferation of mesangial cells (MC) is an early event in many forms of glomerulonephritis. We have previously shown that platelet-derived growth factor (PDGF)-induced proliferation of MC was inhibited by the overexpression of cyclooxygenase-2 (COX-2). Since reactive oxygen species (ROS) are important mediators of mitogenic signaling, we evaluated the role of ROS in the COX-2 induced growth arrest in MC. We demonstrate that ROS are reduced in COX-2 overexpressing MC. Intracellular elevation of ROS restored PDGF-induced proliferation, while the expression of the cyclin-dependent kinase inhibitors p21(cip1) and p27(kip1) were decreased in these cells. The data suggest that COX-2 decreases ROS formation which consequently leads to the PDGF-induced inhibition of MC proliferation.
Reverse-bias emission sheds light on the failure mechanism of degraded vertical-cavity surface-emitting lasers (2006)

The phenomenon of reverse-bias electroluminescence (EL) has been exploited extensively to elucidate the physics of failure of Si-based semiconductor devices. In this article, we study the reverse-bias emission of vertical-cavity surface-emitting lasers (VCSELs) that have been stressed under accelerated temperature, humidity, and bias. Using quantitative emission microscopy in conjunction with other electrical and optical measurements, we show that the dark line defect dislocation network responsible for VCSEL degradation can be imaged directly as reverse-bias EL and that the spectra of the reverse-bias EL provide further insight into the failure mechanism.
Trapped atoms in cavity QED: coupling quantized light and matter (2005)

On the occasion of the hundredth anniversary of Albert Einstein's annus mirabilis, we reflect on the development and current state of research in cavity quantum electrodynamics in the optical domain. Cavity QED is a field which undeniably traces its origins to Einstein's seminal work on the statistical theory of light and the nature of its quantized interaction with matter. In this paper, we emphasize the development of techniques for the confinement of atoms strongly coupled to high-finesse resonators and the experiments which these techniques enable.
Photonic integrated alumina waveguide gratings for far-field structured illumination at UV wavelengths (2021)

We demonstrate far-field UV structured illumination implemented with in-tegrated aluminum oxide ( AlOx ) waveguide gratings. Based on simulation and experi-mental results, we discuss the performances of two AlO x waveguide gratings operating at λ = 360 nm.
Asymptotically Efficient Distributed Estimation With Exponential Family\n Statistics (2013)

The paper studies the problem of distributed parameter estimation in\nmulti-agent networks with exponential family observation statistics. A\ncertainty-equivalence type distributed estimator of the consensus + innovations\nform is proposed in which, at each each observation sampling epoch agents\nupdate their local parameter estimates by appropriately combining the data\nreceived from their neighbors and the locally sensed new information\n(innovation). Under global observability of the networked sensing model, i.e.,\nthe ability to distinguish between different instances of the parameter value\nbased on the joint observation statistics, and mean connectivity of the\ninter-agent communication network, the proposed estimator is shown to yield\nconsistent parameter estimates at each network agent. Further, it is shown that\nthe distributed estimator is asymptotically efficient, in that, the asymptotic\ncovariances of the agent estimates coincide with that of the optimal\ncentralized estimator, i.e., the inverse of the centralized Fisher information\nrate. From a technical viewpoint, the proposed distributed estimator leads to\nnon-Markovian mixed timescale stochastic recursions and the analytical methods\ndeveloped in the paper contribute to the general theory of distributed\nstochastic approximation.\n
Collision energy dependence of proton-bound dimer dissociation: entropy effects, proton affinities, and intramolecular hydrogen-bonding in protonated peptides (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCollision energy dependence of proton-bound dimer dissociation: entropy effects, proton affinities, and intramolecular hydrogen-bonding in protonated peptidesXueheng Cheng, Zhuchun Wu, and Catherine FenselauCite this: J. Am. Chem. Soc. 1993, 115, 11, 4844–4848Publication Date (Print):June 1, 1993Publication History Published online1 May 2002Published inissue 1 June 1993https://pubs.acs.org/doi/10.1021/ja00064a052https://doi.org/10.1021/ja00064a052research-articleACS PublicationsRequest reuse permissionsArticle Views481Altmetric-Citations176LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts