gebhart/patrepeval huggingface dataset:
DNAsomes: Multifunctional DNA‐Based Nanocarriers (2010)

Multifunctional DNAsomes: DNA–lipid amphiphiles self-assemble into novel “DNAsomes”—liposome-like core–shell structures with subunits composed of branched DNA–lipid hybrid molecules. These DNAsomes can be precisely tuned over a wide range in terms of both size and surface charge. More importantly, DNAsome is a natural carrier of small interfering RNA (siRNA) due to DNA–RNA base-pairing, enabling efficient co-delivery of drugs and siRNA. The DNAsome represents a universal multifunctional drug vector for simultaneous delivery of drugs, tracer dyes, or antibodies, along with genes, siRNA, or antisense nucleic acids. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Understanding Selective Delay as a Method for Efficient Secure Speculative Execution (2020)

Since the introduction of Meltdown and Spectre, the research community has been tirelessly working on speculative side-channel attacks and on how to shield computer systems from them. To ensure that a system is protected not only from all the currently known attacks but also from future, yet to be discovered, attacks, the solutions developed need to be general in nature, covering a wide array of system components, while at the same time keeping the performance, energy, area, and implementation complexity costs at a minimum. One such solution is our own delay-on-miss, which efficiently protects the memory hierarchy by i) selectively delaying speculative load instructions and ii) utilizing value prediction as an invisible form of speculation. In this article we dive deeper into delay-on-miss, offering insights into why and how it affects the performance of the system. We also reevaluate value prediction as an invisible form of speculation. Specifically, we focus on the implications that delaying memory loads has in the memory level parallelism of the system and how this affects the value predictor and the overall performance of the system. We present new, updated results but more importantly, we also offer deeper insight into why delay-on-miss works so well and what this means for the future of secure speculative execution.
A Novel Control-flow based Intrusion Detection Technique for Big Data Systems (2016)

Security and distributed infrastructure are two of the most common requirements for big data software. But the security features of the big data platforms are still premature. It is critical to identify, modify, test and execute some of the existing security mechanisms before using them in the big data world. In this paper, we propose a novel intrusion detection technique that understands and works according to the needs of big data systems. Our proposed technique identifies program level anomalies using two methods - a profiling method that models application behavior by creating process signatures from control-flow graphs; and a matching method that checks for coherence among the replica nodes of a big data system by matching the process signatures. The profiling method creates a process signature by reducing the control-flow graph of a process to a set of minimum spanning trees and then creates a hash of that set. The matching method first checks for similarity in process behavior by matching the received process signature with the local signature and then shares the result with all replica datanodes for consensus. Experimental results show only 0.8% overhead due to the proposed technique when tested on the hadoop map-reduce examples in real-time.
Evaluation of a whole cell, p57- vaccine against Renibacterium salmoninarum (1999)

A whole cell Renibacterium salmoninarum vaccine was developed using 37 degrees C heat treated cells that were subsequently formalin fixed; this treatment reduced bacterial hydrophobicity and cell associated p57. Coho salmon Oncorhynchus kisutch were immunized with the p57- vaccine by either a combination of intraperitoneal (i.p.) and intramuscular (i.m.) injections or per os. In the first experiment, i.p./i.m. vaccination of coho salmon with p57- cells in Freund's Incomplete Adjuvant (FIA) conferred a statistically significant increase in mean time to death after the salmon were i.p. challenged with 4.1 x 10(6) colony forming units (cfu) of R. salmoninarum. There was no significant difference in response between fish immunized with R. salmoninarum cell surface extract in FIA and those immunized with extracellular protein (ECP) concentrated from culture supernatant in FIA. The i.p. challenge dose resulted in complete mortality of all fish by Day 43. In a second experiment, fish were orally vaccinated with p57- R. salmoninarum cells encased in a pH protected, enteric-coated antigen microsphere (ECAM). Fish were bath challenged with 4.2 x 10(6) cfu ml-1 on Day 0 and sampled at time points of 0 (pre-challenge), 50, 90, or 150 d immersion challenge. Vaccine efficacy was determined by monitoring the elaboration of p57 in the kidneys of vaccinated and control fish. Fish vaccinated orally demonstrated a significantly lower concentration of p57 (p < 0.01) at Day 150 post challenge compared to fish receiving ECAMs alone. Fish receiving p57 cells without ECAM coating also showed a significantly lower p57 level (p < 0.03) versus control. In contrast, fish injected intraperitoneally with the p57- cells or fish fed p57+ R. salmoninarum cells in ECAMs demonstrated no significant difference (p > 0.05) versus controls. In summary, these studies suggest the preliminary efficacy of 37 degrees C treatment of R. salmoninarum cells as an oral bacterial kidney disease vaccine.
MIMO communication system with user scheduling based on reduced channel state information (publication date 09-10-2008) (2008)

A multiple-input, multiple-output (MIMO) communication system is configured to perform user scheduling with reduced channel station information. The system includes multiple terminals and at least one base station configured to communicate with the terminals. The base station is operative to obtain channel vector magnitudes for respective ones of the terminals, to identify a subset of the terminals based on the channel vector magnitudes, to obtain channel vector phase information for the identified subset of terminals, and to utilize the channel vector phase information to control transmission to the identified subset of terminals. The system may be, for example, a multi-user MIMO system in which the multiple terminals comprise autonomous single-antenna terminals.
<title>Minimisation of thermal effects on the polarisation in a polarimetric sensor using a single-mode optical fibre</title> (1998)

Optic fibre sensors and especially polarimetric ones provide high accuracy and sensitivity. They are insensitive to electromagnetic perturbations. The simulation of an angular position polarimetric sensor using telecom single-mode optic fibre as a transducer showed a thermal dependence [Mane 95], [Mane 96].
Inhibition of<i>Listeria monocytogenes</i>in cottage cheese manufactured with a lacticin 3147‐producing starter culture (1999)

The efficacy of using a lacticin 3147-producing starter as a protective culture to improve the safety of cottage cheese was investigated. This involved the manufacture of cottage cheese using Lactococcus lactis DPC4268 (control) and L. lactis DPC4275, a bacteriocin-producing transconjugant strain derived from DPC4268. A number of Listeria monocytogenes strains, including a number of industrial isolates, were assayed for their sensitivity to lacticin 3147. These strains varied considerably with respect to their sensitivity to the bacteriocin. One of the more tolerant strains, Scott A, was used in the cottage cheese study; the cheese was subsequently inoculated with approximately 10(4) L. monocytogenes Scott A g-1. The bacteriocin concentration in the curd was measured at 2560 AU ml-1, and bacteriocin activity could be detected throughout the 1 week storage period. In cottage cheese samples held at 4 degrees C, there was at least a 99.9% reduction in the numbers of L. monocytogenes Scott A in the bacteriocin-containing cheese within 5 d, whereas in the control cheeses, numbers remained essentially unchanged. At higher storage temperatures, the kill rate was more rapid. These results demonstrate the effectiveness of lacticin 3147 as an inhibitor of L. monocytogenes in a food system where post-manufacture contamination by this organism could be problematic.
Modeling the optical coupling across the anterior chamber of the eye towards polarimetric glucose sensing (2014)

Millions of people worldwide are affected by diabetes. While glucose sensing technology has come a long way over the past several decades, the current commercially available techniques are still invasive, often leading to poor patient compliance. To minimize invasiveness, focus has been placed on optical techniques to ascertain blood glucose concentrations. Optical polarimetry has shown promise and progress as a viable technique for glucose sensing. Recent developments in polarimetric glucose sensing have been focused on overcoming time varying corneal birefringence due to motion artifacts. Beyond corneal birefringence, the next hurdle toward making this approach viable is the ability to couple polarized light across the eye’s anterior chamber. The eye is ideally suited to couple light to the retina. The index mismatch between the air and cornea is partially responsible for the beam bending toward the retina and, while good for vision, it complicates our ability to couple light across the anterior chamber without using an index matching device when performing polarimetric glucose monitoring. In this report, we have designed and modeled a non-index matched coupling scheme constructed with commercially available optics. The optical ray tracing model was performed using CODE V to verify the feasibility of a reflective based non-index matched coupling scheme with respect to index of refraction and anatomical restraints. The ray tracing model was developed for a dual-wavelength system and the effect of refraction and reflection at each optical interface within the setup was evaluated. The modeling results indicate a reflective based optical coupling design could be added to existing polarimetric glucose systems thus removing the need for placing an index matched eye-coupling mechanism over the eye prior to data collection.
The regulation of flowering time by daylength in Arabidopsis. (1998)

We are studying several Arabidopsis mutants that show altered regulation of flowering time in response to daylength. One of the mutations we are studying, constans, delays flowering under long days but has no effect under short days. Analysis of the expression of the CONSTANS gene, and modification of its expression in transgenic plants, suggests that this gene promotes flowering in response to long days and that the delay in flowering that occurs in wild-type plants under short days is at least in part due to regulation of CONSTANS gene transcription. We describe genetic approaches that we are taking to identify genes that act in the same genetic pathway as CONSTANS, and in particular the relationship between CONSTANS and two other genes that we are studying. These are LATE ELONGATED HYPOCOTYL, for which we have a dominant mutant allele that causes late flowering, and EARLY SHORT DAYS 4, whose inactivation causes early flowering. In addition to their effects on flowering time, the over-expression of CONSTANS and the inactivation of EARLY SHORT DAYS 4 cause the Arabidopsis shoot to become determinate and therefore to terminate development prematurely. This phenotype is discussed in light of other genes that have previously been shown to be required to maintain indeterminate development of the shoot.
Random Variation of Detector Efficiency: A Countermeasure Against Detector Blinding Attacks for Quantum Key Distribution (2015)

In the recent decade, it has been discovered that QKD systems are extremely vulnerable to side-channel attacks. In particular, by exploiting the internal working knowledge of practical detectors, it is possible to bring them to an operating region whereby only certain target detectors are sensitive to detections. Crucially, the adversary can use this loophole to learn everything about the secret key without introducing any error to the quantum channel. In this paper, as a step toward overcoming detector blinding attacks, we focus on an experimentally convenient countermeasure, where the efficiency of the detectors is randomly varied.
Measurement of <i>in Vivo</i> Drug Load Distribution of Cysteine-Linked Antibody–Drug Conjugates Using Microscale Liquid Chromatography Mass Spectrometry (2014)

Analysis of samples containing intact antibody-drug conjugates (ADC) using mass spectrometry provides a direct measurement of the drug-load distribution. Once dosed, the drug load distribution changes due to a combination of biological and chemical factors. Liquid chromatography-mass spectrometry (LC-MS) methods to measure the in vivo drug load distribution have been established for ADCs containing native disulfide bonds (lysine-linked or cysteine-linked). However, because of an IgG reduction step in conjugation processes, using LC-MS to analyze intact cysteine-linked ADCs requires native conditions, thus limiting sensitivity. While this limitation has been overcome at the analytical scale, to date, these methods have not been translated to a smaller scale that is required for animal or clinical doses/sampling. In this manuscript, we describe the development of ADC specific affinity capture reagents for processing in vivo samples and optimization of native LC-MS methods at a microscale. These methods are then used to detect the changing drug load distribution over time from a set of in vivo samples, representing to our knowledge the first native mass spectra of cysteine-linked ADCs from an in vivo source.
miR-125b and miR-100 Are Predictive Biomarkers of Response to Induction Chemotherapy in Osteosarcoma (2016)

Osteosarcoma is the most common primary malignancy in bone. Patients who respond poorly to induction chemotherapy are at higher risk of adverse prognosis. The molecular basis for such poor prognosis remains unclear. We investigated miRNA expression in eight open biopsy samples to identify miRNAs predictive of response to induction chemotherapy and thus maybe used for risk stratification therapy. The samples were obtained from four patients with inferior necrosis (Huvos I/II) and four patients with superior necrosis (Huvos III/IV) following induction chemotherapy. We found six miRNAs, including miR-125b and miR-100, that were differentially expressed > 2-fold (<i>p</i> < 0.05) in patients who respond poorly to treatment. The association between poor prognosis and the abundance of miR-125b and miR-100 was confirmed by quantitative reverse transcriptase-polymerase chain reaction in 20 additional osteosarcoma patients. Accordingly, overexpression of miR-125b and miR-100 in three osteosarcoma cell lines enhanced cell proliferation, invasiveness, and resistance to chemotherapeutic drugs such as methotrexate, doxorubicin, and cisplatin. In addition, overexpression of miR-125b blocked the ability of these chemotherapy agents to induce apoptosis. As open biopsy is routinely performed to diagnose osteosarcoma, levels of miR-125b and miR-100 in these samples may be used as basis for risk stratification therapy.
Anti-tumor and repairing nerve injuries: A drug-loaded monosialoganliosides micelles delivered to brain for glioblastoma (2016)

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Readout of Superconducting Nanowire Single Photon Detectors through Forward Biased Optical Modulators (2020)

Scalable, high speed data transfer between cryogenic (0.1-4 K) and room temperature environments is instrumental in a broad range of fields including quantum computing, superconducting electronics, single photon imaging and space-based communications. A promising approach to overcome the limitations of conventional wire-based readout is the use of optical fiber communication. Optical fiber presents a 100-1,000x lower heat load than conventional electrical wiring, relaxing the requirements for thermal anchoring, and is also immune to electromagnetic interference, which allows routing of sensitive signals with improved robustness to noise and crosstalk. Most importantly, optical fibers allow for very high bandwidth densities (in the Tbps/mm$^2$ range) by carrying multiple signals through the same physical fiber (Wavelength Division Multiplexing, WDM). Here, we demonstrate for the first time optical readout of a superconducting nanowire single-photon detector (SNSPD) directly coupled to a CMOS photonic modulator, without the need for an interfacing device. By operating the modulator in the forward bias regime at a temperature of 3.6 K, we achieve very high modulation efficiency (1000-10,000 pm/V) and a low input impedance of 500 $Ω$ with a low power dissipation of 40 $μ$W. This allows us to obtain optical modulation with the low, millivolt-level signal generated by the SNSPD. Optical communication is becoming the preferred I/O solution in modern, room temperature high performance systems, and this work demonstrates its suitability for scalable cryogenic readout, which could help achieve the full potential of superconducting technologies.
Use of machine learning for classification of magnetocardiograms (2004)

We describe the use of machine learning for pattern recognition in magnetocardiography (MCG) that measures magnetic fields emitted by the electrophysiological activity of the heart. We used direct kernel methods to separate abnormal MCG heart patterns from normal ones. For unsupervised learning, we introduced Direct Kernel based Self-Organizing Maps. For supervised learning we used Direct Kernel Partial Least Squares and (Direct) Kernel Ridge Regression. These results are then compared with classical Support Vector Machines and Kernel Partial Least Squares. The hyperparameters for these methods were tuned on a validation subset of the training data before testing. We also investigated the most effective pre-processing, using local, vertical, horizontal and two-dimensional (global) Mahanalobis scaling, wavelet transforms and experimented with variable selection by filtering. The results, similar for all three methods, were encouraging, exceeding the quality of classification achieved by the trained experts.
Design of a thermally balanced membrane reformer for hydrogen production (2008)

Abstract Hydrogen production by autothermal methane steam reforming in a catalytic fixed bed membrane reactor has been analyzed and simulated. The two‐compartment reactor indirectly couples the endothermic steam reforming with methane oxidation, while hydrogen is separated by a permselective Pd membrane. Simulations of the reactor, using published kinetics, map the acceptable domain of operation and the optimal set of operating parameters. The simulations exhibit slow‐moving thermal fronts and the steady‐state operation domains bounded by stationary fronts, separating domains of upstream and downstream‐moving fronts. Front velocity depends on thermal coupling and hydrogen separation. An analytical approximation for the thermal front velocity in a thermally balanced reactor has been developed. © 2008 American Institute of Chemical Engineers AIChE J, 2008
Comparison of noninvasive and remote temperature estimation employing magnetic nanoparticles in DC and AC applied fields (2012)

This paper examines the advantages and disadvantages of noninvasive and remote temperature estimation employing magnetic nanoparticles (MNPs) in DC and AC applied fields. A Langevin function that describes the magnetization of the MNPs in different applied magnetic fields is investigated to obtain a noninvasive and remote measurement of on-site temperature using MNPs. Several nonlinear functions, in which temperature and concentration are independent variances, are found by discretizing the Langevin function model of the magnetization of MNPs. Then, the temperature estimation range from 310 K to 350 K is transformed to the solution of the nonlinear function using the temperature independence of the saturation magnetization of the MNPs.
A Trisubstituted Benzimidazole Cell Division Inhibitor with Efficacy against Mycobacterium tuberculosis (2014)

Trisubstituted benzimidazoles have demonstrated potency against Gram-positive and Gram-negative bacterial pathogens. Previously, a library of novel trisubstituted benzimidazoles was constructed for high throughput screening, and compounds were identified that exhibited potency against M. tuberculosis H37Rv and clinical isolates, and were not toxic to Vero cells. A new series of 2-cyclohexyl-5-acylamino-6-N, N-dimethylaminobenzimidazoles derivatives has been developed based on SAR studies. Screening identified compounds with potency against M. tuberculosis. A lead compound from this series, SB-P17G-A20, was discovered to have an MIC of 0.16 mg/mL and demonstrated efficacy in the TB murine acute model of infection based on the reduction of bacterial load in the lungs and spleen by 1.7360.24 Log 10 CFU and 2.686Log 10 CFU, respectively, when delivered at 50 mg/kg by intraperitoneal injection (IP) twice daily (bid). The activity of SB-P17G-A20 was determined to be concentration dependent and to have excellent stability in mouse and human plasma, and liver microsomes. Together, these studies demonstrate that SB-P17G-A20 has potency against M. tuberculosis clinical strains with varying susceptibility and efficacy in animal models of infection, and that trisubstituted benzimidazoles continue to be a platform for the development of novel inhibitors with efficacy.
The Scalable Address Resolution Protocol (SARP) for Large Data Centers (2015)

This document introduces the Scalable Address Resolution Protocol (SARP), an architecture that uses proxy gateways to scale large data center networks. SARP is based on fast proxies that significantly reduce switches' Filtering Database (FDB) table sizes and reduce impact of ARP and Neighbor Discovery (ND) on network elements in an environment where hosts within one subnet (or VLAN) can spread over various locations. SARP is targeted for massive data centers with a significant number of Virtual Machines (VMs) that can move across various physical locations.
Advanced Detectors for Active Neutron Dosemeters (1997)

Different options were investigated in the development of active neutron dosemeters for personnel and area monitoring. In particular, two different classes of detectors, superheated emulsions and silicon diodes, were studied as radiation sensors for such devices. The detectors were analysed with respect to their neutron sensitivity and their overall suitability for practical dosimetry. Superheated emulsions proved adequate in terms of their dose equivalent response and their photon discrimination: future work should now focus on the development of a rugged device. Significant improvements were also achieved with the diode sensors, although more research will be necessary for the design of a simple, single structure readily usable as a neutron dosemeter.