gebhart/patrepeval huggingface dataset:
Adaptive Robust Traffic Engineering in Software Defined Networks (2018)

One of the key advantages of Software-Defined Networks (SDN) is the opportunity to integrate traffic engineering modules able to optimize network configuration according to traffic. Ideally, the network should be dynamically reconfigured as traffic evolves, so as to achieve remarkable gains in the efficient use of resources with respect to traditional static approaches. Unfortunately, reconfigurations cannot be too frequent due to a number of reasons related to route stability, forwarding rules instantiation, individual flows dynamics, traffic monitoring overhead, etc.In this paper, we focus on the fundamental problem of deciding whether, when and how to reconfigure the network during traffic evolution. We propose a new approach to cluster relevant points in the multi-dimensional traffic space taking into account similarities in optimal routing and not only in traffic values. Moreover, to provide more flexibility to the decisions on when to apply a reconfiguration, we allow some overlap between clusters that can guarantee a good-quality routing regardless of the transition instant.We compare our algorithm with state-of-the-art approaches in realistic network scenarios. Results show that our method significantly reduces the number of reconfigurations with a negligible deviation of the network performance with respect to the continuous update of the network configuration.
Novel electrochemical biosensors for investigating the interactions between atezolizumab and PD-1/PD-L1 and screening their small-molecular inhibitors (2022)

PD-1/PD-L1 pathway plays an important role in tumor immunotherapy. A novel immobilized overexpression cell electrochemical sensor was constructed using N-doped graphene-chitosan-Pt nanoparticles (NGR–CS–PtNPs) and polyaniline (PANI) to investigate the interaction between atezolizumab and HEK293 cells overexpressing PD-1 or PD-L1 proteins. The binding constant between atezolizumab and PD-L1-HEK293 cells was calculated to be 2.4 × 107 M−1. Using this method to screen 18 main components from Aidi injection (ADI), it was found that the binding constant between ginsenoside Rg1 and PD-1-HEK293 cells was 9.9 × 104 M−1. Then, a new electrochemical immunosensor was constructed using Au nanoparticles and 11-mercaptoundecanoic acid (11-MUA). The calculated binding constant between atezolizumab and purified PD-L1 protein was 6.11 × 109 M−1, and IC50 value was 2.73 ng/mL. Meanwhile, with the concentration of ginsenosides Rg1 increasing to 20 μM, the inhibition rate reached a maximum, which was about 50%. Electrochemical sensing technology was originally used to investigate the interactions between atezolizumab and PD-1/PD-L1. And using the above novel sensors, small molecule inhibitors targeting PD-1/PD-L1 could be screened and evaluated at different levels, leading to more accurate outcomes. Additionally, electrochemical sensors require simple equipment, low material costs, accompanying with the advantages of rapidity, sensitivity and high selectivity.
Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus (2015)

The 2013-2015 West African epidemic of Ebola virus disease (EVD) reminds us of how little is known about biosafety level 4 viruses. Like Ebola virus, Lassa virus (LASV) can cause hemorrhagic fever with high case fatality rates. We generated a genomic catalog of almost 200 LASV sequences from clinical and rodent reservoir samples. We show that whereas the 2013-2015 EVD epidemic is fueled by human-to-human transmissions, LASV infections mainly result from reservoir-to-human infections. We elucidated the spread of LASV across West Africa and show that this migration was accompanied by changes in LASV genome abundance, fatality rates, codon adaptation, and translational efficiency. By investigating intrahost evolution, we found that mutations accumulate in epitopes of viral surface proteins, suggesting selection for immune escape. This catalog will serve as a foundation for the development of vaccines and diagnostics. VIDEO ABSTRACT.
A study on zeta potential and dielectric constant of liposomes (1994)

Zeta potential and dielectric constant of the liposomes were measured to study the effect of some of the formulation factors and in vitro ageing. Sonication affects zeta potential and dielectric constant of the liposomes. The ageing study showed an increase in the dielectric constant and zeta potential of liposomes at different storage temperatures. These two electrical parameters could be useful in studying structural alterations in liposomal vesicles and system as a function of different conditions. Particle size distribution and optical density were also measured, for comparison.
Deep learning to predict the lab-of-origin of engineered DNA (2018)

Abstract Genetic engineering projects are rapidly growing in scale and complexity, driven by new tools to design and construct DNA. There is increasing concern that widened access to these technologies could lead to attempts to construct cells for malicious intent, illegal drug production, or to steal intellectual property. Determining the origin of a DNA sequence is difficult and time-consuming. Here deep learning is applied to predict the lab-of-origin of a DNA sequence. A convolutional neural network was trained on the Addgene plasmid dataset that contained 42, 364 engineered DNA sequences from 2230 labs as of February 2016. The network correctly identifies the source lab 48% of the time and 70% it appears in the top 10 predicted labs. Often, there is not a single “smoking gun” that affiliates a DNA sequence with a lab. Rather, it is a combination of design choices that are individually common but collectively reveal the designer.
Fatty acid uptake by isolated rat heart myocytes represents a carrier-mediated transport process. (1988)

The mechanism by which fatty acids enter cardiomyocytes is unclear. Therefore, the influx kinetics of [3H]oleate into isolated rat heart myocytes were examined. Cells were incubated at 37 degrees C with [3H]oleate bound to albumin in various molar ratios and the initial rate of uptake (V0) was determined as a function of the unbound oleate concentration in the medium. V0 was saturable with increasing oleate concentrations incubated (Km 78 nM; Vmax 1.9 nmol X min-1 per 10(6) cells) and temperature dependent with an optimum at 37 degrees C. Furthermore, binding of [3H]oleate to isolated plasma membranes of cardiomyocytes was saturable, revealing a KD of 42 nM, and was inhibited by heat denaturation or trypsin pretreatment of the membranes. From these membranes a single 40-kD protein with high affinity for a variety of long chain fatty acids was isolated. With a monospecific antibody to this membrane protein, binding as well as cellular influx of [3H]oleate was selectively inhibited. These data indicate that at least a portion of myocardial fatty acid uptake is mediated by a specific membrane protein.
Keratinocyte growth factor-2 (2000)

Growth factors are a group of hormone-like polypeptides playing a central role in the complex processes of tissue repair. In the case of repair of cutaneous wounds specific growth factors stimulate keratinocyte migration into the wounds and are present in wound fluid [1]. Growth factors such as platelet-derived growth factor (PDGF), fibroblast growth factor-2 (FGF-2) and transforming growth factor-β (TGF-β3) are currently in clinical trials of chronic skin wounds while epidermal growth factor (EGF) is being used in clinical trials of ocular wound healing. EGF and PDGFs have demostrated acceleration of epidermal regeneration in cutaneous wounds in man [2-5].
A Rapid and Economical Method of Preparing Radioiodinated Cyclic Nucleotide Derivatives for use in Radioimmunoassays (1990)

2'-O-succinyladenosine 3':5'-cyclic monophosphate tyrosyl methyl ester (ScAMP-TME) and 2'-O-succinylguanosine 3':5'-cyclic monophosphate tyrosyl methyl ester (ScGMP-TME) were radioiodinated using chloramine T and Na125I. The resulting radiolabeled cyclic nucleotide derivatives, ScAMP-125I-TME and ScGMP-125I-TME, were subsequently purified by reverse-phase chromatography on Sep-Pak C18 cartridges (Waters Associates, Milford, MA) and tested as tracers in sensitive radioimmunoassays for cAMP and cGMP, respectively. Purified ScAMP-125I-TME and ScGMP-125I-TME functioned in the respective radioimmunoassays for up to 12 weeks when suspended in a 1:1 (v:v) mixture of n-propanol and 20 mM sodium acetate, pH 6.0. Thus, this purification method enables rapid and economical preparation of tracers for cyclic nucleotide radioimmunoassays. Furthermore, our findings suggest that reverse-phase chromatography may be applicable to the purification of other small polar molecules to which tyrosyl groups have been added for the purpose of radioiodination.
Imaging of activated microglia with PET and [11C]PK 11195 in corticobasal degeneration (2004)

Positron emission tomography (PET) using [(11)C]PK 11195, a ligand for peripheral benzodiazepine receptor binding sites, offers the opportunity to image activated microglia in vivo. This tool may therefore be used to display the occurrence of microglial activation in the course of neurodegeneration. A patient with the clinical diagnosis of corticobasal degeneration (CBD) and left-sided symptoms was studied using fluorodeoxyglucose (FDG) and [(11)C]PK 11195 PET. We found a marked right hemispheric hypometabolism and asymmetric microglial activation in corresponding areas of the basal ganglia and right temporal and parietal cortex. [(11)C]PK 11195 PET suggests involvement of microglial activation in the pathogenesis of CBD.
DSB Task Force on Cyber Supply Chain (2017)

Abstract : At the request of the Secretary of Defense, this study assessed the organization, missions, and authorities that encompass the use of microelectronics and components in Department of Defense (DoD) weapons systems. The task force found that the capital cost of maintaining a DoD-owned Trusted Foundry is not a feasible expense. The task force recommends that the Department develop a long-term strategy for access to state-of-the-art commercial foundry capabilities that does not rely exclusively on trust; and continue research and development (R and D) investments of DoD agencies for a technology-enabled strategy that fosters new tools to better defend against cyber supply chain attacks.
Supramolecular Electrostatic Nanoassemblies for Bacterial Forensics (2011)

Electrostatic nanoassemblies were employed to identify bacterial growth conditions. They comprise a cationic conjugated oligoelectrolyte and fluorescein-tagged ssDNA and were optimized with a hybrid, computational neural network model. The photoluminescence spectra contained the oligomer and sensitized fluorescein emission. The spectra changed depending on the growth history of the bacteria introduced (see figure).
ON OPERATION-PREOPEN SETS IN TOPOLOGICAL SPACES ∗ (2008)

In this paper, we present concepts of pre p-open sets and pre p- closures of a subset in a topological space, where p is an operation on the family of all preopen sets of the topological space, and study some topological properties on them. As its application, we introduce the concept of pre p-Ti spaces (i = 0,1/2,1,2) and study some properties of these spaces. 1 Introduction Throughout this paper, (X,�) represents a nonempty topological space on which no separation axioms are assumed, unless otherwise mentioned. The closure and interior of A ⊂ X are denoted by Cl(A) and Int(A) respectively. The power set of X will be denoted by P(X). An operation onis a function frominto P(X) such that U ⊂ U for every set U ∈ �, where U denotes the value (U) of at U. In 1979, Kasahara (11) firstly defined and investigated the concept of operations on �. He used the following symbol as the operation on �, i.e., a function � : � → P(X) is called an operation onif U ⊂ �(U) holds for any U ∈ �. He generalized the notion of
ISDN and ISO/MPEG Layer III Audio Coding: Powerful New Tools for Broadcast and Audio Production (1993)

The combination of two new technologies is about to transform an important aspect of the broadcast industry. The first, ISDN, or Integrated Services Digital Network, is poised to alter the delivery of telephone services worldwide by converting connection from the lumbering analog voice format invented at the turn of the century to a digital infoproduct approprate to the 21st century. The second, ISO/MPEG Layer III audio compression represents the latest in the development of methods for the coding of digital audio using high bit-rate reduction factors. Together, these technologies make it possible to convey broadcast-quality audio with the convenience, ubiquity, and low cost of the dial-up telco network.
Inhibition of Thrombin-Induced Platelet Aggregation Using Human Single Chain Fv Antibodies Specific for TREM-Like Transcript-1. (2006)

Abstract Platelets play a duel role in our cardiovascular system. They are important in maintaining our vascular integrity. They also facilitate the progression of cardiovascular diseases (CVD) such as arteriosclerosis. In more severe cases, displaced platelet aggregates can lead to myocardial infarction or stroke. Because of their prominent role, anti-platelet therapies are used to reduce mortality associated with CVD. However, the use of these therapies is sometimes associated with bleeding complications, thrombocytopenia or non-responsiveness and the search for new therapeutic targets continues. Some of the recent treatment strategies include molecules that target platelet membrane receptors. The success shown by this class of therapeutics has prompted us to evaluate the recently characterized murine platelet receptor, TREM like transcript 1 (TLT-1), as a therapeutic target. Murine studies suggest that TLT-1 is a platelet specific protein found in α-granules of platelets and megakaryocytes. Here we asked if human TLT-1 was also linage specific and if platelet aggregation could be modulated through interaction with TLT-1 specific antibodies. We evaluated human TLT-1 (hTLT-1) for pattern of expression in the peripheral blood and we found that hTLT-1, like its mouse counterpart, is platelet specific. To address TLT-1 function we panned a naïve human library of single chain fragments (scFvs) with a TLT-1 extracellular domain/human fc fusion protein to produce monoclonal antibodies specific for hTLT-1. We isolated six scFv clones using ELISA to detect reactivity to the fusion protein and confirmed their specificity by flow cytometry on cells transfected with TLT-1 and purified human platelets. These scFvs were then tested to see if they would disrupt or enhance platelet aggregation. Here we demonstrate, for the first time, inhibition of thrombin induced platelet activation using scFv that are specific for TLT-1. Taken together these results suggest TLT-1 is a potential target for therapeutic intervention of cardiovascular disease.
Generalized eigenvalue passivity assessment of descriptor systems with applications to symmetric and singular systems (2012)

SUMMARY This paper proposes general eigenvalue‐based passivity tests for descriptor state space systems, extending the already available tests for standard state space systems. Generalized eigenvalue tests are proposed to identify passivity violations in the positive‐real and bounded‐real cases. The important practical case of singular descriptor state space systems is also treated. The proposed passivity tests for descriptor systems can be used in the important case of symmetric (reciprocal) systems, as symmetric systems can always be cast in an explicitly reciprocal descriptor state space format. Also, passivity violation assessment methods are developed in the important case of strictly proper symmetric systems, as in that case the classical test matrices for passivity assessment are undefined. Finally, some pertinent numerical examples are given to demonstrate the usefulness and scope of the different passivity violation assessment tests. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Directed Sequencing of Plant Specific DNA Identifies the Dietary History of Four Species of Auchenorrhyncha (Hemiptera) (2021)

Abstract Auchenorrhyncha (Hemiptera) includes several families of sap-feeding insects that tend to feed on a wide-range of host plants. Some species within Auchenorrhyncha are major agricultural pests that transmit plant pathogens or cause direct feeding damage. Nearly all pest Auchenorrhyncha are highly polyphagous, have mobile nymphs, and colonize crops from noncrop habitats. We examined whether methods for gut content analysis developed for more specialized Hemiptera identify dietary history of polyphagous Auchenorrhyncha. We used high-throughput sequencing of the plant genes trnF and ITS to examine the dietary history of Circulifer tenellus (Baker) (Cicadellidae), Colladonus geminatus (Van Duzee) (Cicadellidae), Colladonus montanus reductus (Van Duzee) (Cicadellidae), and Lycorma delicatula (White) (Fulgoridae). C. tenellus is a vector of the vegetable pathogens Candidatus Phytoplasma trifolii and beat curly top virus. Both Colladonus species are vectors of Ca. Phytoplasma pruni, the pathogen associated with X-disease of stone fruits. Lycorma delicatula is an invasive pest of grape and ornamentals in the eastern United States. Results showed spring hosts for C. tenellus included Brassicaceae, especially Sisymbrium sp. (tumble mustard), and spring hosts for both Colladonus species included Taraxacum sp. (dandelion). Gut content analysis also detected a decrease in host-breadth by L. delicatula from early to late instars. Results demonstrate that directed sequencing of plant DNA identified the dietary history of leafhopper and planthopper pests. Expanded use of gut content analysis will help identify the noncrop sources of phytoplasma-infected C. tenellus and Colladonus, and to examine seasonal changes in host shifts by L. delicatula.
Assessing Perceived Image Quality Using Steady-State Visual Evoked Potentials and Spatio-Spectral Decomposition (2017)

Steady-state visual evoked potentials (SSVEPs) are neural responses, measurable using electroencephalography (EEG), that are directly linked to sensory processing of visual stimuli. In this paper, SSVEP is used to assess the perceived quality of texture images. The EEG-based assessment method is compared with conventional methods, and recorded EEG data are correlated to obtained mean opinion scores (MOSs). A dimensionality reduction technique for EEG data called spatio-spectral decomposition (SSD) is adapted for the SSVEP framework and used to extract physiologically meaningful and plausible neural components from the EEG recordings. It is shown that the use of SSD not only increases the correlation between neural features and MOS to r = -0.93, but also solves the problem of channel selection in an EEG-based image-quality assessment.
Supplementary Figures 1-7 from A PSMA-Targeting CD3 Bispecific Antibody Induces Antitumor Responses that Are Enhanced by 4-1BB Costimulation (2023)

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Distance-based indexing and its applications in bioinformatics (2007)

Distance-based indexing is a general solution to the problem of searching based on similarity of complex data types. Distances between pairs of data objects are specified by a metric function, which is positive definite, symmetric and satisfies the triangle inequality. Distance-based indexing is exploited in many data intensive applications, such as multimedia and biological databases. This dissertation concerns distance-based indexing in the context of the MoBIoS (Molecular Biology Information System) project, a next generation DBMS aimed at bioinformatics applications. 
The three primary contributions of this dissertation include evaluation and improvement of existing distance-based index structures, a pivot space model for the pivot selection problem of distance-based indexing and the MoBIoS Index software package. 
For the first part, we designed a bi-directional construction algorithm for Metric Tree (M-tree). It increased the construction speed and improved the query performance. Then, we conducted a comparative analysis of the performance of M-tree, General Hyper-plane Tree (GHT) and Vantage Point Tree (VPT) on biological work loads, and VPT turned out to be the optimal choice. Further, we designed better heuristics for pivot selection and partition of VPT. 
Superior to multi-dimensional indexing in its generality, distance-based indexing is difficult by virtue that no coordinate structure is available and thus many mathematical tools in Rn cannot be applied. A common method used is to map the metric space into Rn and then apply geometric methods. Summarizing this method, we propose the pivot space model, which demonstrates the validity of tackling distance-based problems in Rn. Further, we study distance-based indexing from the perspective of dimension reduction. We prove that the only form of dimension reduction leading to performance gain for distance-based indexing is pivot selection, which does not create new dimensions. To adapt general dimension reduction techniques to distance-based problems, we propose a heuristic that approximates the dimensions created by dimension reduction. As a demonstration, a dimension reduction algorithm and a method to estimate the intrinsic dimension of data are proposed based on Principal Component Analysis (PCA). These ideas are evaluated on a test suite consisting of synthetic and real workloads. 
The MoBIoS Index was released in 2006. It supports similarity queries for user defined data types and distance functions. It has been used to build several biological application.
Laser-produced plasma source development for EUV lithography (2009)

We are developing a CO<sub>2</sub> laser driven Tin plasma EUV source for HVM EUVL. This approach enables cost-effective EUV power scaling by high-conversion efficiency and full recovery of Tin fuel. The RF-excited, multi 10 kW average power pulsed CO<sub>2</sub> laser system is a MOPA (master oscillator power amplifier) configuration and operates at 100 kHz with 20 ns pulse width. The EUV light source is scalable to in-band 200 W IF power with a single 20-kW CO<sub>2</sub> laser beam. EUV chamber is kept uncontaminated by using a small size droplet target and effective Tin exhaust by magnetic plasma guiding. Characterization of the plasma flow in uniform magnetic field was studied by monitoring the motion of Tin plasma stream in a large vacuum chamber, depending on the magnetic flux up to 2 T. Topics relevant for HVM source is reported on continuous operation and Tin vapor evacuation.
Measured linear–quadratic–Gaussian controlled damping (2005)

This paper investigates experimentally the characteristics of LQG control for controlled vibration mitigation. The control algorithm is implemented in LabVIEW RT. The controller performance is measured at a test set-up consisting of a vibrating taut cable with MR damper. Measurements of the closed-loop system clearly point out that LQG control enables damping vibrations with respect to their intensity and frequency. When the cable is excited at constant frequency, the desired control force is dissipative and proportional to the vibration velocity at the damper position. Thus, for the system under consideration, LQG control ends up in the desired viscosity. With increasing frequency of the cable excitation, the desired viscosity decreases. The desired viscosities for the first four cable modes depend on the pole locations of the observer and regulator. The nearer they are located, the higher are the desired viscosities. Therefore, a design parameter describing precisely the distance between observer and regulator poles is introduced. Based on this design parameter, the paper proposes a systematic method of LQG controller design for practical applications.