gebhart/patrepeval huggingface dataset:
A microfluidic fully paper-based analytical device integrated with loop-mediated isothermal amplification and nano-biosensors for rapid, sensitive, and specific quantitative detection of infectious diseases (2022)

Bacterial meningitis, an infection of the membranes (meninges) and cerebrospinal fluid (CSF) surrounding the brain and spinal cord, is one of the major causes of death and disability worldwide. Higher case-fatality rates and short survival times have been reported in developing countries. Hence, a quick, straightforward, and low-cost approach is in great demand for the diagnosis of meningitis. In this research, a microfluidic fully paper-based analytical device (μFPAD) integrated with loop-mediated isothermal amplification (LAMP) and ssDNA-functionalized graphene oxide (GO) nano-biosensors was developed for the first time for a simple, rapid, low-cost, and quantitative detection of the main meningitis-causing bacteria, <i>Neisseria meningitidis</i> (<i>N. meningitidis</i>). The results can be successfully read within 1 hour with the limit of detection (LOD) of 6 DNA copies per detection zone. This paper device also offers versatile functions by providing a qualitative diagnostic analysis (<i>i.e.</i>, a yes or no answer), confirmatory testing, and quantitative analysis. These features make the presented μFPAD capable of a simple, highly sensitive, and specific diagnosis of <i>N. meningitis</i>. Furthermore, this microfluidic approach has great potential in the rapid detection of a wide variety of different other pathogens in low-resource settings.
Inhibition of Ricin A-Chain with Pyrrolidine Mimics of the Oxacarbenium Ion Transition State (2004)

Ricin A-chain (RTA) catalyzes the hydrolytic depurination of a specific adenosine at position 4324 of 28S rRNA. Kinetic isotope effects on the hydrolysis of a small 10mer stem-tetraloop oligonucleotide substrate established the mechanism of the reaction as D(N)*A(N), involving an oxacarbenium ion intermediate in a highly dissociative transition state. An inhibitor with a protonated 1,4-dideoxy-1,4-imino-D-ribitol moiety, a 4-azasugar mimic, at the depurination site in the tetraloop of a 14mer oligonucleotide with a 5 bp duplex stem structure had previously been shown to bind to RTA with a K(d) of 480 nM, which improved to 12 nM upon addition of adenine. Second-generation stem-tetraloop inhibitors have been synthesized that incorporate a methylene bridge between the nitrogen of a 1-azasugar mimic, namely, (3S,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidine, and substituents, including phenyl, 8-aza-9-deazaadenyl, and 9-deazaadenyl groups, that mimic the activated leaving group at the transition state. The values for the dissociation constants (K(i)) for these were 99 nM for the phenyl 10mer, 163 and 94 nM for the 8-aza-9-deazaadenyl 10- and 14mers, respectively, and 280 nM for the 9-deazaadenyl 14mer. All of these compounds are among the tightest binding molecules known for RTA. A related phenyl-substituted inhibitor with a deoxyguanosine on the 5'-side of the depurination site was also synthesized on the basis of stem-loop substrate specificity studies. This molecule binds with a K(i) of 26 nM and is the tightest binding "one-piece" inhibitor. 8-Aza-9-deaza- and 9-deazaadenyl substituents provide an increased pK(a) at N7, a protonation site en route to the transition state. The binding of these inhibitors is not improved relative to the binding of their phenyl counterpart, however, suggesting that RTA might also employ protonation at N1 and N3 of the adenine moiety to activate the substrate during catalysis. Studies with methylated adenines support this argument. That the various stem-loop inhibitors have similar potencies suggests that an optimal one-piece inhibitor remains to be identified. The second-generation inhibitors described here incorporate ribose mimics missing the 2-hydroxy group. On the basis of inhibition data and substrate specificity studies, the 2'-hydroxyl group at the depurination site seems to be critical for recruitment as well as catalysis by RTA.
Biocompatible Films: Rapid Nanoimprinting of Silk Fibroin Films for Biophotonic Applications (Adv. Mater. 15/2010) (2010)

Natural silk fibers provide the raw material to constitute biocompatible films with favorable properties for nanopatterning and device integration. The image shows a free-standing credit-card sized film constituted entirely by silk and containing a number of diffractive optics (lenses, microlens arrays, gratings, phase masks). Such elements can be obtained either by casting or rapid nanoimprinting of silk films (master courtesy of Tessera Inc.). Further details can be found in the Communication by Fiorenzo Omenetto and co-workers on p. 1746.
PinMe: Tracking a Smartphone User around the World (2017)

With the pervasive use of smartphones that sense, collect, and process valuable information about the environment, ensuring location privacy has become one of the most important concerns in the modern age. A few recent research studies discuss the feasibility of processing sensory data gathered by a smartphone to locate the phone's owner, even when the user does not intend to share his location information, e.g., when the user has turned off the Global Positioning System (GPS) on the device. Previous research efforts rely on at least one of the two following fundamental requirements, which impose significant limitations on the adversary: (i) the attacker must accurately know either the user's initial location or the set of routes through which the user travels and/or (ii) the attacker must measure a set of features, e.g., device acceleration, for different potential routes in advance and construct a training dataset. In this paper, we demonstrate that neither of the above-mentioned requirements is essential for compromising the user's location privacy. We describe PinMe, a novel user-location mechanism that exploits non-sensory/sensory data stored on the smartphone, e.g., the environment's air pressure and device's timezone, along with publicly-available auxiliary information, e.g., elevation maps, to estimate the user's location when all location services, e.g., GPS, are turned off. Unlike previously-proposed attacks, PinMe neither requires any prior knowledge about the user nor a training dataset on specific routes. We demonstrate that PinMe can accurately estimate the user's location during four activities (walking, traveling on a train, driving, and traveling on a plane). We also suggest several defenses against the proposed attack.
A Perceptron-Inspired Technique for Hardware Obfuscation (2018)

Outsourcing the manufacture of integrated circuits (IC) boosts efficiency in terms of production timeline and minimizing expenditures. However, it results in security challenges, as there is uncertainty in the reliability of the foundry that is responsible for the IC fabrication. With the primary objective to safeguard the process of outsourcing the chip, this work presents an innovative manufacturing approach that partially imitates the neural network perceptron, obfuscating the hardware design. The proposed technique not only obfuscates the design functionality but immunes the IC against Trojan insertion.
Development of a mechanical strain amplifying transducer with Bragg grating sensor for low-amplitude strain sensing (2017)

© 2017 IOP Publishing Ltd. Vibration-based damage identification is a well-known method to support health monitoring of civil engineering structures. Damage in such structures can be identified by measuring changes of the natural frequencies, damping factors or modal displacements of the structure. However, this approach suffers from the low sensitivity of these natural frequencies and modal displacements to certain types of damage. Modal strains and curvatures can be more sensitive to local damage, but direct monitoring of these quantities with sufficient spatial resolution is not possible with current measurement techniques due to the very small strain levels (sub-microstrain) caused by ambient or operational excitation. To deal with this issue, we propose a novel mechanical transducer equipped with an optical fiber Bragg grating (FBG) sensor that enhances the sensitivity to strain with a factor larger than 30. The principle of operation of the transducer exploits a symmetric cantilever structure that enlarges the strain experienced by the FBG sensor compared to the strain applied to the transducer itself. We carried out dynamic and static tests to verify the ability of the strain-amplifying transducers to measure small-amplitude strain levels and to evidence the potential for carrying out FBG based modal strain measurements on concrete civil engineering structures.
The structure of rosmariquinone — A new antioxidant isolated from<i>Rosmarinus officinalis L.</i> (1985)

Abstract A new diterpene, named rosmariquinone, was isolated from the leaves of Rosmarinus officinalis L. The leaves were first extracted using methanol and, upon further purification, this extract yielded rosmariquinone. Structure elucidation of the antioxidant was done using IR, MS, 1 H‐NMR and 13 C‐NMR.
Rubber–Clay Nanocomposites Based on Butyl and Halobutyl Rubbers (2011)

This chapter contains sections titled: Introduction Types of Clays Useful in Butyl Rubber–Clay Nanocomposites Compatibilizer Systems for Butyl Rubber–Clay Nanocomposites Methods of Preparation of Butyl Rubber–Clay Nanocomposites Properties and Applications of Butyl Rubber–Clay Nanocomposites Conclusions References
Effect of blood upon the selective ablation of atherosclerotic plaque witha pulsed dye laser (1990)

Laser angioplasty systems with laser energy preferentially absorbed by atherosclerotic plaque may offer a safe method of plaque removal. This study evaluated the effect of blood upon selective energy absorption using a pulsed dye laser at 480 nm. Intra-arterial laser irradiation of normal rabbit femoral arteries demonstrated a perforation threshold energy with blood perfusion of 13.1 mJ per pulse compared to 87.9 mJ with saline (P less than .0001), indicating a deleterious effect in the presence of blood. An adverse effect upon arterial healing at 3 days was noted in sheep following intra-arterial irradiation during blood but not saline perfusion. Normal and atherosclerotic human aorta ablation thresholds differed significantly (P less than .0002) under saline (plaque: 20 mJ and normal: 120 mJ) but the difference under blood (plaque: 5 mJ and normal: 20 mJ) was not significant. We conclude that absorption of laser energy by blood can reduce the effect of differential absorption by endogenous chromophores in normal and pathologic vascular tissues and, therefore, removal of blood may be a prerequisite for selective ablation of atherosclerotic plaques.
Smart Health System to Detect Dementia Disorders Using Virtual Reality (2021)

Smart health technology includes physical sensors, intelligent sensors, and output advice to help monitor patients' health and adjust their behavior. Virtual reality (VR) plays an increasingly larger role to improve health outcomes, being used in a variety of medical specialties including robotic surgery, diagnosis of some difficult diseases, and virtual reality pain distraction for severe burn patients. Smart VR health technology acts as a decision support system in the diseases diagnostic test of patients as they perform real world tasks in virtual reality (e.g., navigation). In this study, a non-invasive, cognitive computerized test based on 3D virtual environments for detecting the main symptoms of dementia (memory loss, visuospatial defects, and spatial navigation) is proposed. In a recent study, the system was tested on 115 real patients of which thirty had a dementia, sixty-five were cognitively healthy, and twenty had a mild cognitive impairment (MCI). The performance of the VR system was compared with Mini-Cog test, where the latter is used to measure cognitive impaired patients in the traditional diagnosis system at the clinic. It was observed that visuospatial and memory recall scores in both clinical diagnosis and VR system of dementia patients were less than those of MCI patients, and the scores of MCI patients were less than those of the control group. Furthermore, there is a perfect agreement between the standard methods in functional evaluation and navigational ability in our system where P-value in weighted Kappa statistic= 100% and between Mini-Cog-clinical diagnosis vs. VR scores where P-value in weighted Kappa statistic= 93%.
Relieving the wireless infrastructure: When opportunistic networks meet guaranteed delays (2011)

Major wireless operators are nowadays facing network capacity issues in striving to meet the growing demands of mobile users. At the same time, 3G-enabled devices increasingly benefit from ad hoc radio connectivity (e.g., Wi-Fi). In this context of hybrid connectivity, we propose Push-and-track, a content dissemination framework that harnesses ad hoc communication opportunities to minimize the load on the wireless infrastructure while guaranteeing tight delivery delays. It achieves this through a control loop that collects user-sent acknowledgements to determine if new copies need to be reinjected into the network through the 3G interface. Push-and-Track includes multiple strategies to determine how many copies of the content should be injected, when, and to whom. The short delay-tolerance of common content, such as news or road traffic updates, make them suitable for such a system. Based on a realistic large-scale vehicular dataset from the city of Bologna composed of more than 10,000 vehicles, we demonstrate that Push-and-Track consistently meets its delivery objectives while reducing the use of the 3G network by over 90%.
Selective evaporation of focusing fluid in two-fluid hydrodynamic print head. (2014)

The work performed in this project has demonstrated the feasibility to use hydrodynamic focusing of two fluid steams to create a novel micro printing technology for electronics and other high performance applications. Initial efforts focused solely on selective evaporation of the sheath fluid from print stream provided insight in developing a unique print head geometry allowing excess sheath fluid to be separated from the print flow stream for recycling/reuse. Fluid flow models suggest that more than 81 percent of the sheath fluid can be removed without affecting the print stream. Further development and optimization is required to demonstrate this capability in operation. Print results using two-fluid hydrodynamic focusing yielded a 30 micrometers wide by 0.5 micrometers tall line that suggests that the cross-section of the printed feature from the print head was approximately 2 micrometers in diameter. Printing results also demonstrated that complete removal of the sheath fluid is not necessary for all material systems. The two-fluid printing technology could enable printing of insulated conductors and clad optical interconnects. Further development of this concept should be pursued.
Sequential Oxidative and Reductive Bleaching of Wool in a Single Bath (1990)

A new bleaching process applicable to wool was developed in which an oxidative step (hydrogen peroxide) is combined with a subsequent reductive step (thiourea, thiourea dioxide, or sodium hydroxymethanesulfinate) in a single-bath process. Ox idative followed by reductive bleaching is normally a two- or three-step treatment done in separate baths. Effective bleaching with reduced time and equipment use is achieved by the new single-bath process with a specific order of reagent addition. Although the reductive stage of such a single-bath process may be achieved by the complete decomposition of unspent hydrogen peroxide and then addition of reductive substances such as thiourea dioxide or sodium hydroxymethanesulfinate with necessary pH adjustment, one may take advantage of the unspent hydrogen peroxide to form a reductive substance in situ by reaction with thiourea followed by an appropriate pH adjustment to 7-8. In all the cases above, greatly superior bleaching with less physical damage is achieved with the new process compared with conventional single- or multi- bath processes.
PGD and aneuploidy screening for 24 chromosomes by genome-wide SNP analysis: seeing the wood and the trees (2011)

Bisignano et al. (2011) argue that, for preimplantation genetic diagnosis (PGD) of aneuploidy for all 24 chromosomes, microarray-based comparative genomic hybridization (array CGH) is superior to the use of single-nucleotide polymorphism (SNP) genotyping arrays. Published studies indicate that both technologies accurately detect aneuploidy of whole chromosomes or chromosome segments. However, given the extra theoretical resolution and parent-of-origin information provided by SNP-based approaches, these may be particularly suited to certain applications such as PGD of single-gene defects or translocation chromosome imbalance combined with comprehensive detection of aneuploidy. A consensus on how to validate aneuploidy testing and all other clinically relevant information resulting from genome-wide analysis is needed urgently.
Topic Modeling of Document Metadata for Visualizing Collaborations over Time (2016)

We describe methods for analyzing and visualizing document metadata to provide insights about collaborations over time. We investigate the use of Latent Dirichlet Allocation (LDA) based topic modeling to compute areas of interest on which people collaborate. The topics are represented in a node-link force directed graph by persistent fixed nodes laid out with multidimensional scaling (MDS), and the people by transient movable nodes. The topics are also analyzed to detect bursts to highlight "hot" topics during a time interval. As the user manipulates a time interval slider, the people nodes and links are dynamically updated. We evaluate the results of LDA topic modeling for the visualization by comparing topic keywords against the submitted keywords from the InfoVis 2004 Contest, and we found that the additional terms provided by LDA-based keyword sets result in improved similarity between a topic keyword set and the documents in a corpus. We extended the InfoVis dataset from 8 to 20 years and collected publication metadata from our lab over a period of 21 years, and created interactive visualizations for exploring these larger datasets.
First Field Trial of Distributed Fiber Optical Sensing and High-Speed Communication Over an Operational Telecom Network (2019)

To the best of our knowledge, we present the first field trial of distributed fiber optical sensing (DFOS) and high-speed communication, comprising a coexisting system, over an operation telecom network. Using probabilistic-shaped (PS) DP-144QAM, a 36.8 Tb/s with an 8.28-b/s/Hz spectral efficiency (SE) (48-Gbaud channels, 50-GHz channel spacing) was achieved. Employing DFOS technology, road traffic, i.e., vehicle speed and vehicle density, were sensed with 98.5% and 94.5% accuracies, respectively, as compared to video analytics. Additionally, road conditions, i.e., roughness level was sensed with >85% accuracy via a machine learning based classifier.
Controlling Item Exposure Conditional on Ability in Computerized Adaptive Testing (1998)

The interest in the application of large-scale adaptive testing for secure tests has served to focus attention on issues that arise when theoretical advances are made operational. One such issue is that of ensuring item and pool security in the continuous testing environment made possible by the computerized admin-istration of a test, as opposed to the more periodic testing environment typically used for linear paper-and-pencil tests. This article presents a new method of controlling the exposure rate of items conditional on ability level in this continuous testing environment. The properties of such conditional control on the exposure rates of items, when used in conjunction with a particular adaptive testing algorithm, are explored through studies with simulated data.
Molecular and Biological Characterization of a New Isolate of Guinea Pig Cytomegalovirus (2014)

Development of a vaccine against congenital infection with human cytomegalovirus is complicated by the issue of re-infection, with subsequent vertical transmission, in women with pre-conception immunity to the virus. The study of experimental therapeutic prevention of re-infection would ideally be undertaken in a small animal model, such as the guinea pig cytomegalovirus (GPCMV) model, prior to human clinical trials. However, the ability to model re-infection in the GPCMV model has been limited by availability of only one strain of virus, the 22122 strain, isolated in 1957. In this report, we describe the isolation of a new GPCMV strain, the CIDMTR strain. This strain demonstrated morphological characteristics of a typical Herpesvirinae by electron microscopy. Illumina and PacBio sequencing demonstrated a genome of 232,778 nt. Novel open reading frames ORFs not found in reference strain 22122 included an additional MHC Class I homolog near the right genome terminus. The CIDMTR strain was capable of dissemination in immune compromised guinea pigs, and was found to be capable of congenital transmission in GPCMV-immune dams previously infected with salivary gland‑adapted strain 22122 virus. The availability of a new GPCMV strain should facilitate study of re-infection in this small animal model.