gebhart/patrepeval huggingface dataset:
PORTFILER: Port-Level Network Profiling for Self-Propagating Malware Detection (2021)

Recent self-propagating malware (SPM) campaigns compromised hundred of thousands of victim machines on the Internet. It is challenging to detect these attacks in their early stages, as adversaries utilize common network services, use novel techniques, and can evade existing detection mechanisms. We propose PORTFILER (PORT-Level Network Traffic ProFILER), a new machine learning system applied to network traffic for detecting SPM attacks. PORTFILER extracts port-level features from the Zeek connection logs collected at a border of a monitored network, applies anomaly detection techniques to identify suspicious events, and ranks the alerts across ports for investigation by the Security Operations Center (SOC). We propose a novel ensemble methodology for aggregating individual models in PORTFILER that increases resilience against several evasion strategies compared to standard ML baselines. We extensively evaluate PORTFILER on traffic collected from two university networks, and show that it can detect SPM attacks with different patterns, such as WannaCry and Mirai, and performs well under evasion. Ranking across ports achieves precision over 0.94 with low false positive rates in the top ranked alerts. When deployed on the university networks, PORTFILER detected anomalous SPM-like activity on one of the campus networks, confirmed by the university SOC as malicious. PORTFILER also detected a Mirai attack recreated on the two university networks with higher precision and recall than deep-learning-based autoencoder methods.
Stereocontrolled Synthesis of 2′-α-C-Branched Nucleoside Analogues and their Incorporation into Oligodeoxyribonucleotides (1993)

The stereoselective synthesis of 2′-α-C-branched nucleosides by a radical addition reaction is described. These new nucleosides were incorporated into oligodeoxyribonucleotides. Measurement of melting temperatures (Tm) of DNA/RNA duplexes and the nuclease resistance of these oligoribodeoxynucleotides are presented.
Fabrication and Characterization of 3D Multi-Electrode Array on Flexible Substrate for In Vivo EMG Recording from Expiratory Muscle of Songbird (2018)

This work presents fabrication and characterization of flexible three-dimensional (3D) multi-electrode arrays (MEAs) capable of high signal-to-noise (SNR) electromyogram (EMG) recordings from the expiratory muscle of a songbird. The fabrication utilizes a photoresist reflow process to obtain 3D structures to serve as the electrodes. A polyimide base with a PDMS top insulation was utilized to ensure flexibility and biocompatibility of the fabricated 3D MEA devices. SNR measurements from the fabricated 3D electrode show up to a 7x improvement as compared to the 2D MEAs.
Solid surface tension measured by a liquid drop under a solid film (2013)

We show that a drop of liquid a few hundred microns in diameter placed under a solid, elastic, thin film (∼10 μm thick) causes it to bulge by tens of microns. The deformed shape is governed by equilibrium of tensions exerted by the various interfaces and the solid film, a form of Neumann's triangle. Unlike Young's equation, which specifies the contact angles at the junction of two fluids and a (rigid) solid, and is fundamentally underdetermined, both tensions in the solid film can be determined here if the liquid-vapor surface tension is known independently. Tensions in the solid film have a contribution from elastic stretch and a constant residual component. The residual component, extracted by extrapolation to films of vanishing thickness and supported by analysis of the elastic deformation, is interpreted as the solid-fluid surface tension, demonstrating that compliant thin-film structures can be used to measure solid surface tensions.
QRS Detection by Rules Based Multiple Channel Combinatorial Optimization (2023)

Abstract A multiple channel QRS detector is described. Separately for each channel, the detector generates sequences of peaks and statistically scores them according to: 1) peak prominence; 2) temporal regularity; 3) peak shape similarity; and 4) number of skipped beats. In the case of unstructured rhythms, the temporal regularity score is null and does not contribute to sequence quality. If at least one winning score from any channel exceeds a quality threshold, multi-channel sequences are generated from the winning sequences’ peaks and scored according to the above measures and peak time coherence across channels. The winning multi-channel sequence is then selected. The algorithm was applied to both channels of the MIT-BIH Arrhythmia Database. Over the entire database, the sensitivity (SE) and positive predictive value (PPV) were 99.93% and 99.96% respectively. For record 203, generally considered the most difficult one in the database, the SE and PPV were 99.80% and 99.76% respectively. The present algorithm fits within the framework of a previously described algorithm that can detect sinus rhythm in high noise conditions (e.g. waist based textile electrode recordings of a jogging subject).
High power enhancement cavities for generation of XUV and X-ray radiation of high brilliance (2011)

In this contribution we present an enhancement cavity designed such that the spot sizes on all mirrors are increased significantly with respect to a standard bow-tie resonator. This is achieved by operating an all-curved mirror resonator (ACR) close to the border of its stability range. In Fig. 1, a standard design resonator (SR) in the stability range center, consisting of 4 mirrors with equal radii of curvature (300 mm). For comparison, the repetition rate of both resonator designs was set to 250 MHz, with two pulses circulating inside the cavity, and the focus radius to 30 μm. Fig. 1c shows the spot sizes on the mirrors. In the ACR the spot area is increased by more than 14 times with respect to the SR, suggesting that at the same intensity on the mirrors an average power higher by more than an order of magnitude can be achieved. In conjunction with a modified version of the CPA system described, which is planned to seed our ACR, Mega-Watt circulating average powers for ultrashort MHz-repetition-rate pulses come into reach for the first time.
Plume Expansion and Ionization in a Microlaser Plasma Thruster (2008)

Abstract : Ion density measurements have been performed on the plasma generated by an ablative diode laser thruster using a negatively biased flat plate probe. The biased probe data was coupled with measurement of the ablation crater through use of a scanning electron microscope (SEM). The SEM was used to analyze the post-pulse ablation spots to determine the volume of fuel ablated. The micro-laser plasma thruster (micro-LPT) discussed here ablates a target material through the back surface by focusing the laser through a transparent substrate in a process typically referred to as Transmissive mode (T-mode) ablation. The target materials investigated were polyvinyl chloride (PVC) and glycidyl azide polymer (GAP), while the substrates used were cellulose acetate and Kapton(Tradename). Peak ion densities for a GAP (target)/acetate (substrate) were found to be 1.6x10(exp 7)/cu cm, while for GAP/kapton and PVC/acetate the peak ion densities were 4.5x10(exp 7)/cu cm and 7.9x10(exp 9)/cu cm respectively. Although these corresponded to low ionization fractions calculated from the observed mass loss, the results indicate there are ways to improve the ionization fraction and in turn increase the specific impulse.
FUT2 and FUT3 depending cut-off values in PSC-patients increase diagnostic accuracy of CA19–9 for detection of biliary malignancies (2012)

Introduction: Patients with primary sclerosing cholangitis (PSC) are at increased risk of developing biliary malignancies as cholangiocellular carcinoma (CCA) or gall bladder carcinoma (GBCA). Ultrasound and CA19–9 are the most commonly use screening parameters. FUT2- and FUT3-gene status influences CA19–9 levels.
Data from AMG 757, a Half-Life Extended, DLL3-Targeted Bispecific T-Cell Engager, Shows High Potency and Sensitivity in Preclinical Models of Small-Cell Lung Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Small-cell lung cancer (SCLC) is an aggressive neuroendocrine tumor with a high relapse rate, limited therapeutic options, and poor prognosis. We investigated the antitumor activity of AMG 757, a half-life extended bispecific T-cell engager molecule targeting delta-like ligand 3 (DLL3)—a target that is selectively expressed in SCLC tumors, but with minimal normal tissue expression.&lt;/p&gt;Experimental Design:&lt;p&gt;AMG 757 efficacy was evaluated in SCLC cell lines and in orthotopic and patient-derived xenograft (PDX) mouse SCLC models. Following AMG 757 administration, changes in tumor volume, pharmacodynamic changes in tumor-infiltrating T cells (TILs), and the spatial relationship between the appearance of TILs and tumor histology were examined. Tolerability was assessed in nonhuman primates (NHPs).&lt;/p&gt;Results:&lt;p&gt;AMG 757 showed potent and specific killing of even those SCLC cell lines with very low DLL3 expression (&lt;1,000 molecules per cell). AMG 757 effectively engaged systemically administered human T cells, induced T-cell activation, and redirected T cells to lyse tumor cells to promote significant tumor regression and complete responses in PDX models of SCLC and in orthotopic models of established primary lung SCLC and metastatic liver lesions. AMG 757 was well tolerated with no AMG 757-related adverse findings up to the highest tested dose (4.5 mg/kg weekly) in NHP. AMG 757 exhibits an extended half-life in NHP, which is projected to enable intermittent administration in patients.&lt;/p&gt;Conclusions:&lt;p&gt;AMG 757 has a compelling safety and efficacy profile in preclinical studies making it a viable option for targeting DLL3-expressing SCLC tumors in the clinical setting.&lt;/p&gt;&lt;/div&gt;
Bridging the gap between cellulose chemistry and heterogeneous catalysis (2011)

Although cellulosic biomass offers a promising alternative as an abundant renewable resource in the production of biofuels and platform chemicals, so far only a few studies have reported its aqueous-phase conversion into glucose or sugar alcohols using solid chemocatalysts. The principal reason is that these polymeric biomolecules with semi-crystalline structure cannot penetrate the pores of conventional heterogeneous chemocatalysts. New advances in the conversion of cellulose thus require the design of efficient multifunctional catalytic systems with sterically accessible acid and metal sites.
Laser Fluorimetry: Detection of Aflatoxin B1 in Contaminated Corn (1978)

A high sensitivity laser fluorimeter designed specifically for use with high pressure liquid chromatography (HPLC) is described. An amplitude modulated He-Cd ion laser at 325 nm irradiates a flowing droplet of eluent from an HPLC column, and fluorescence is detected in phase with the modulation by a lockin amplifier. The fluorimeter is capable of detecting 750 fg of each of the four commonly occurring aflatoxins, and has a linear range of over three orders of magnitude. Using a two-step chromatography procedure, this device is capable of quantitating aflatoxin B1 to 100 ppt in corn. Following extraction of the aflatoxin from corn, the extract is given a preliminary cleanup on a normal phase thin layer chromatography (TLC) plate. The aflatoxin B1 is recovered, and injected onto a reverse phase HPLC column. Experiments with aflatoxin B1 standards show a constant ratio for conversion of aflatoxin B1 to aflatoxin B2A over roughly three orders of magnitude. The recovery of aflatoxin B1 from the TLC plates, although slightly nonlinear above 10 ppb permits linear quantitation of aflatoxin B1 in white and yellow corn in the range from 0.1 to 10 ppb with an average root mean square (rms) error of 26%.
Tracking Stem Cell Differentiation in the Setting of Automated Optogenetic Stimulation (2010)

Membrane depolarization has been shown to play an important role in the neural differentiation of stem cells and in the survival and function of mature neurons. Here, we introduce a microbial opsin into ESCs and develop optogenetic technology for stem cell engineering applications, with an automated system for noninvasive modulation of ESC differentiation employing fast optogenetic control of ion flux. Mouse ESCs were stably transduced with channelrhodopsin-2 (ChR2)-yellow fluorescent protein and purified by fluorescence activated cell sorting (FACS). Illumination of resulting ChR2-ESCs with pulses of blue light triggered inward currents. These labeled ESCs retained the capability to differentiate into functional mature neurons, assessed by the presence of voltage-gated sodium currents, action potentials, fast excitatory synaptic transmission, and expression of mature neuronal proteins and neuronal morphology. We designed and tested an apparatus for optically stimulating ChR2-ESCs during chronic neuronal differentiation, with high-speed optical switching on a custom robotic stage with environmental chamber for automated stimulation and imaging over days, with tracking for increased expression of neural and neuronal markers. These data point to potential uses of ChR2 technology for chronic and temporally precise noninvasive optical control of ESCs both in vitro and in vivo, ranging from noninvasive control of stem cell differentiation to causal assessment of the specific contribution of transplanted cells to tissue and network function.
Oxide-based platform for reconfigurable superconducting nanoelectronics (2013)

We report quasi-1D superconductivity at the interface of LaAlO3 and SrTiO3. The material system and nanostructure fabrication method supply a new platform for superconducting nanoelectronics. Nanostructures having line widths w ~ 10 nm are formed from the parent two-dimensional electron liquid using conductive atomic force microscope lithography. Nanowire cross-sections are small compared to the superconducting coherence length in LaAlO3/SrTiO3, placing them in the quasi-1D regime. Broad superconducting transitions versus temperature and finite resistances in the superconducting state well below Tc ≈ 200 mK are observed, suggesting the presence of fluctuation- and heating-induced resistance. The superconducting resistances and V-I characteristics are tunable through the use of a back gate. Four-terminal resistances in the superconducting state show an unusual dependence on the current path, varying by as much as an order of magnitude. This new technology, i.e., the ability to 'write' gate-tunable superconducting nanostructures on an insulating LaAlO3/SrTiO3 'canvas', opens possibilities for the development of new families of reconfigurable superconducting nanoelectronics.
Multi-sensory integration using sparse spatio-temporal encoding (2013)

The external world consists of objects that stimulate multiple sensory pathways simultaneously, such as auditory, visual and touch. Our brains receive and process these sensory streams to arrive at a coherent internal representation of the world. Though much attention has been paid to these streams individually, their integration is comparatively less well understood. In this paper we propose the principle of sparse spatio-temporal encoding as a foundation to build a framework for multi-sensory integration. We derive the dynamics that govern a network of oscillatory units that achieves phase synchronization, and is capable of binding related attributes of objects. We simulate objects that produce simultaneous visual and auditory input activations. We demonstrate that our system can bind features in both these sensory modalities. We examine the effect of varying a tuning function that governs the ability of the units to synchronize, and show that by broadening this function we reduce the ability of the network to disambiguate mixtures of objects. Thus, our model offers the potential to study brain disorders such as autism, which may arise from a disruption of synchronization.
Modified Probabilistic Data Association algorithms (2014)

Probabilistic Data Association (PDA) algorithm has shown promising performance in symbol detection and interference cancellation in different communication schemes. This paper proposes new algorithms that build on PDA and introduce modifications in the way the symbol being detected is treated. While PDA models this symbol as a discrete sample from a constellation, PDA with symbol uncertainty (SU-PDA) views it as a sum of a deterministic symbol and random noise, while the Gaussian PDA (G-PDA) models it as a random variable with either a single Gaussian or Gaussian mixture distribution. The proposed algorithms are tested via computer simulations on both simulated and experimentally measured channels. The performance study reveals that the SU-PDA and G-PDA outperform the conventional PDA with the performance gain ranging from few dBs on measured channel with block fading up to and exceeding 10 dB on the simulated channel with fast fading.
Single-Domain Antibodies Targeting Neuraminidase Protect against an H5N1 Influenza Virus Challenge (2014)

Highly pathogenic H5N1 viruses are a zoonotic threat. Outbreaks of avian influenza caused by these viruses occur in many parts of the world and are associated with tremendous economic loss, and these viruses can cause very severe disease in humans. In such cases, small-molecule inhibitors of the viral NA are among the few treatment options for patients. However, treatment with such drugs often results in the emergence of resistant viruses. Here we show that single-domain antibody fragments that are specific for NA can bind and inhibit H5N1 viruses in vitro and can protect laboratory mice against a challenge with an H5N1 virus, including an oseltamivir-resistant virus. In addition, plant-produced VHH fused to a conventional Fc domain can protect in vivo even in the absence of NA-inhibitory activity. Thus, NA of influenza virus can be effectively targeted by single-domain antibody fragments, which are amenable to further engineering.
Multiple Quantum Well Retromodulators for Spacecraft-to-Spacecraft Laser Interrogation, Communication, and Navigation (2001)

This paper describes a novel concept for laser-based interrogation, communication, and navigation between multiple spacecraft platforms using a gimbaled laser source on a pursuer spacecraft and a target board populated with retromodulators (modulating retroreflectors) integrated on a host spacecraft. The combined laser source and retroreflectors can provide centimeter-level relative positioning between each vehicle, as well as spacecraft-tospacecraft laser communication via semiconductor-based Multiple Quantum Well retromodulators. Additionally, strategies are developed for utilizing the target board retromodulator array to provide relative attitude between each vehicle. In this scenario, each reflector has its own unique modulating code sequence, allowing the returned signals to be discriminated and processed by the pursuer spacecraft to determine the relative orientation. Based on additional attitude sensing capability, three classes of host spacecraft are considered: fully-cooperative, partiallycooperative, and non-cooperative. Numerical simulations using a five-sensor target board demonstrate the potential of the concept, and preliminary test results demonstrate reflector discrimination capability.
Improvement of the weighted essentially nonoscillatory scheme based on the interaction of smoothness indicators (2017)

Summary The weighted essentially nonoscillatory scheme is improved by introducing new smoothness indicators that evaluate the interactions among the classical smoothness indicators suggested by Jiang and Shu. The effect of the key parameters in the new smoothness indicators on the scheme is systematically investigated. The improved scheme has smaller dissipation with larger weight assignment to the discontinuous stencils and higher numerical accuracy with weights closer to the ideal weights. To verify the theory, benchmark problems governed by the linear transport equation, the 1‐dimensional nonlinear Burgers equation, and the Euler equations are conducted and analyzed, respectively. Better computational performances both on numerical resolution and accuracy are shown in the comparisons with other classical weighted essentially nonoscillatory schemes.
Oxyhemoglobin‐induced suppression of KV channels by enhanced tyrosine kinase activity and channel endocytosis (2006)

Oxyhemoglobin (oxyhb) released following SAH has been implicated in cerebral vasospasm as it causes cerebral artery constriction and increases tyrosine kinase activity. Voltage-dependent, Ca2+-selective and K+-selective ion channels play an important role in the regulation of cerebral artery diameter and represent potential targets of oxyhb. Here, we demonstrate that acute exposure (10 min) of oxyhb selectively decreases 4-AP-sensitive, voltage-dependent K+ channel (KV) currents by ≈30 % in myocytes isolated from rabbit cerebral arteries, but did not directly alter the activity of voltage-dependent Ca2+ channels (VDCCs) or large conductance Ca2+-activated (BK) channels. A combination of tyrosine kinase inhibitors abolished the ability of oxyhb to decrease KV channel currents. To explore whether oxyhb altered trafficking of KV channels to the plasma membrane, we used an antibody generated against surface KV 1.5 channels. In the presence of oxyhb, staining of surface KV 1.5 was markedly reduced, while staining with the early endosomal marker, EEA-1, was enhanced. Further, oxyhb caused a loss of spatial distinction between staining with KV 1.5 and the general anti-phosphotyrosine antibody, PY-102. We propose that oxyhb-induced suppression of KV currents occurs via a mechanism involving tyrosine phosphorylation and channel endocytosis. This novel mechanism may contribute to oxyhb-induced cerebral artery constriction following SAH. Supported by the Totman Medical Research Trust Fund and the NIH (P20 RR16435 & R01 HL078983).
ERK and p38 MAPK, but not NF-κB, Are Critically Involved in Reactive Oxygen Species–Mediated Induction of IL-6 by Angiotensin II in Cardiac Fibroblasts (2001)

We recently reported that angiotensin II (Ang II) induced IL-6 mRNA expression in cardiac fibroblasts, which played an important role in Ang II-induced cardiac hypertrophy in paracrine fashion. The present study investigated the regulatory mechanism of Ang II-induced IL-6 gene expression, focusing especially on reactive oxygen species (ROS)-mediated signaling in cardiac fibroblasts. Ang II increased intracellular ROS in cardiac fibroblasts, and the increase was completely inhibited by the AT-1 blocker candesartan and the NADH/NADPH oxidase inhibitor diphenyleneiodonium (DPI). We first confirmed that antioxidant N-acetylcysteine, superoxide scavenger Tiron, and DPI suppressed Ang II-induced IL-6 expression. Because we observed that exogenous H(2)O(2) also increased IL-6 mRNA, the signaling pathways downstream of Ang II and exogenous H(2)O(2) were compared. Ang II, as well as exogenous H(2)O(2), activated ERK, p38 MAPK, and JNK, which were significantly inhibited by N-acetylcysteine and DPI. In contrast with exogenous H(2)O(2), however, Ang II did not influence phosphorylation and degradation of IkappaB-alpha/beta or nuclear translocation of p65, nor did it increase NF-kappaB promoter activity. PD98059 and SB203580 inhibited Ang II-induced IL-6 expression. Truncation and mutational analysis of the IL-6 gene promoter showed that CRE was an important cis-element in Ang II-induced IL-6 gene expression. NF-kappaB-binding site was important for the basal expression of IL-6, but was not activated by Ang II. Ang II phosphorylated CREB through the ERK and p38 MAPK pathway in a ROS-sensitive manner. Collectively, these data indicated that Ang II stimulated ROS production via the AT1 receptor and NADH/NADPH oxidase, and that these ROS mediated activation of MAPKs, which culminated in IL-6 gene expression through a CRE-dependent, but not NF-kappaB-dependent, pathway in cardiac fibroblasts.