gebhart/patrepeval huggingface dataset:
<i>Lactobacillus johnsonii</i> La1 Antagonizes <i>Giardia intestinalis</i> In Vivo (2005)

This study describes the in vivo activity of Lactobacillus johnsonii La1 (NCC533) in Giardia intestinalis-infected gerbils (Meriones unguiculatus). Daily administration of lactobacilli in the drinking water from 7 days before inoculation with Giardia trophozoites efficiently prevented G. intestinalis strain WB clone C6 from infecting gerbils. More specifically, shedding of fecal Giardia antigens (GSA65 protein) was diminished in the La1-treated group, and resolution of infection was observed by 21 days postinoculation. Histology and analysis of enzymatic markers of microvillus membrane integrity revealed that probiotic administration also protected against parasite-induced mucosal damage. In addition, a cellular response to Giardia antigens was stimulated in spleen cells from La1-treated gerbils. Results show for the first time the antigiardial effect of probiotic lactobacilli in vivo and provide further insight into the antagonistic properties of lactic acid bacteria against protozoa involved in intestinal infections.
Phased Array Radar Polarimetry for Weather Sensing: Challenges and Opportunities (2008)

It is becoming widely accepted that radar polarimetry provides accurate and informative weather measurements, while phased array technology can shorten data updating time. In this paper, a theory of phased array radar polarimetry is developed, and the relationship between the wave field at the radar antenna coordinate and that at the hydrometeors is established, along with the correction matrix to the scattering matrix. The challenges and opportunities for the weather sensing are discussed.
High bandwidth board-level parallel optical interconnects for server applications (2006)

Optical waveguides embedded in a printed circuit board offer a substantial increase in the achievable bandwidth density compared with todays electrical interconnects. Specific challenges and solutions to integrate optical interconnects in a printed circuit board are addressed.
Joint Crosstalk-Avoidance and Error-Correction Coding for Parallel Data\n Buses (2016)

Decreasing transistor sizes and lower voltage swings cause two distinct\nproblems for communication in integrated circuits. First, decreasing inter-wire\nspacing increases interline capacitive coupling, which adversely affects\ntransmission energy and delay. Second, lower voltage swings render the\ntransmission susceptible to various noise sources. Coding can be used to\naddress both these problems. So-called crosstalk-avoidance codes mitigate\ncapacitive coupling, and traditional error-correction codes introduce\nresilience against channel errors.\n Unfortunately, crosstalk-avoidance and error-correction codes cannot be\ncombined in a straightforward manner. On the one hand, crosstalk-avoidance\nencoding followed by error-correction encoding destroys the crosstalk-avoidance\nproperty. On the other hand, error-correction encoding followed by\ncrosstalk-avoidance encoding causes the crosstalk-avoidance decoder to fail in\nthe presence of errors. Existing approaches circumvent this difficulty by using\nadditional bus wires to protect the parities generated from the output of the\nerror-correction encoder, and are therefore inefficient.\n In this work we propose a novel joint crosstalk-avoidance and\nerror-correction coding and decoding scheme that provides higher bus\ntransmission rates compared to existing approaches. Our joint approach\ncarefully embeds the parities such that the crosstalk-avoidance property is\npreserved. We analyze the rate and minimum distance of the proposed scheme. We\nalso provide a density evolution analysis and predict iterative decoding\nthresholds for reliable communication under random bus erasures. This density\nevolution analysis is nonstandard, since the crosstalk-avoidance constraints\nare inherently nonlinear.\n
Field Testing of a New Nuclear Magnetic Resonance Logging-While-Drilling Tool (2002)

Abstract Downhole nuclear magnetic resonance (NMR) measurements are evolving into a powerful formation evaluation tool, providing unique and critical information including formation porosity, pore-size distributions, bound-fluid volume (BFV), free-fluid volume (FFV), permeability, and fluid properties. Obtaining this information while drilling can have a significant impact on drilling and completion decisions. In addition, low rates of penetration common in many drilling environments can be advantageous in improving the NMR measurement statistics. This paper describes results gained during field tests of a new NMR logging-while-drilling (LWD) tool that has been designed to run in any standard measurement-while-drilling (MWD) bottomhole assembly. The new tool presents no special operational complications in terms of mechanical specifications or wellsite hardware and software, and it has been tested successfully in both real-time and recorded modes in a wide range of formations and drilling conditions. A key consideration in the design of this tool has been to deliver an NMR measurement of wireline quality with a minimum of interference to the drilling process. To this end, the tool is usable in various modes of operation (stabilized, unstabilized, while drilling, while reaming, etc.). The detrimental effects of tool motion on the NMR measurement are minimized through the hardware design. Motion-effects modeling and log examples address these issues. Having the capability of acquiring data in the conventional T2 mode, this tool offers a familiar interpretation strategy for those users accustomed to evaluating wireline NMR data along with a significant advantage in statistical precision over a T1 acquisition mode.
Locally-Centralized Certificate Validation and its Application in Desktop Virtualization Systems (2020)

To validate a certificate, a user needs to install the certificate of the root certification authority (CA) and download the certificate revocation information (CRI). Although operating systems and browsers manage the certificate trust list (CTL) of publicly-trusted root CAs for global users, locally-trusted root CAs still play an important role and it is difficult for a user to manage its CTL properly by itself. Meanwhile, the CRI access is inefficient, sometimes even unavailable, and causes privacy leakage. We revisit these problems by analyzing the TLS sessions within an organization. To the best of our knowledge, we are the first to analyze CTL management and CRI access on the scale of medium-sized organizations. Based on the analysis, a locally-centralized design is proposed to manage the CTLs of all users by IT administrators and access the CRI services for all users, within an organization. We apply this design to desktop virtualization systems to demonstrate its applicability, and build vCertGuard with oVirt and KVM-QEMU. In vCertGuard, the CTLs of all virtual machines (VMs) are managed in the VM monitors (VMMs). In the CTL, the self-signed certificates of publicly-trusted root CAs are properly configured, while each locally-trusted certificate chain is specified one by one. vCertGuard accesses the CRI services for all VMs, and the downloaded CRI is cached and shared among VMs. Because most TLS servers are visited by multiple users of an organization, it reduces the cost of CRI access. Experimental results of the prototype system show that vCertGuard maintains the CTLs with a negligible overhead, and significantly improves the performance of CRI access.
IgG-Paraoxonase-1 Fusion Protein for Targeted Drug Delivery across the Human Blood−Brain Barrier (2008)

Paraoxonase (PON)-1 is the most potent human protein with organophosphatase activity against organophosphate (OP) toxins. OP compounds readily cross the blood-brain barrier (BBB) and have lethal mechanisms of action within the brain. The production of a brain penetrating form of human PON1, which crosses the BBB, is possible with the re-engineering of the enzyme as a fusion protein with a monoclonal antibody (mAb) against the human insulin receptor (HIR). The HIRMAb crosses the BBB via the endogenous insulin receptor, and acts as a molecular Trojan horse to ferry the PON1 into brain. The human PON1 was fused to the carboxyl terminus of the heavy chain of the chimeric HIRMAb. COS cells were dual transfected with the heavy chain gene and the light chain gene, and the HIRMAb-PON1 fusion protein was affinity purified with protein A chromatography. Western blotting with antibodies to human IgG or human PON1 showed the heavy chain of the HIRMAb-PON1 fusion protein was 40 kDa larger than the heavy chain of the chimeric HIRMAb. The ED50 of binding to the HIR extracellular domain was 0.55 +/- 0.07 nM and 1.1 +/- 0.1 nM, respectively, for the chimeric HIRMAb and the HIRMAb-PON1 fusion protein. The PON1 enzyme activity of the fusion protein was approximately 25% of the enzyme activity in human plasma, based on a fluorometric enzymatic assay. In conclusion, human PON1 has been re-engineered as an IgG-organophosphatase fusion protein that penetrates the human BBB.
Security Vulnerabilities in Hybrid Flow-Specific Traffic-Adaptive Medium Access Control (2012)

Wireless network security is a daunting challenge as researchers analyze the vulnerabilities of wireless medium access control schemes such as IEEE 802.11, Bluetooth, and IEEE 802.16. While these wireless protocols employ traditional contention and non-contention approaches, recent work has identified the delay and throughput performance advantages of a flow-specific medium access hybrid solution for wireless networks such as the traffic-adaptive Cooperative Wireless Sensor Medium Access Control (CWS-MAC) protocol. Accordingly, this paper addresses the security of wireless networks employing these hybrid, flow-specific schemes by analyzing the vulnerabilities in traffic-adaptive CWS-MAC, many of which are applicable to hybrid medium access schemes in general. Critical vulnerabilities are identified that expose the protocol to denial of service, energy exhaustion and "greedy" attacks. The effect of attacks exploiting these vulnerabilities are shown to include decreased throughput and increased delay in both the contention and non-contention modes as well as increased per node energy consumption.
The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine (2012)

Over 15 years ago, the ability to electrically detect and characterize individual polynucleotides as they are driven through a single protein ion channel was suggested as a potential method for rapidly sequencing DNA, base-by-base, in a ticker tape-like fashion. More recently, a variation of this method was proposed in which a nanopore would instead detect single nucleotides cleaved sequentially by an exonuclease enzyme in close proximity to one pore entrance. We analyze the exonuclease/nanopore-based DNA sequencing engine using analytical theory and computer simulations that describe nucleotide transport. The available data and analytical results suggest that the proposed method will be limited to reading <80 bases, imposed, in part, by the short lifetime each nucleotide spends in the vicinity of the detection element within the pore and the ability to accurately discriminate between the four mononucleotides.
Integrated Circuit Implementation for a GaN HFETs Driver Circuit (2008)

The paper presents the design of an integrated circuit (IC) for a 10MHz low power-loss driver for GaN HFETs. While the main elements of the topology were introduced in a previous work, here the authors focus on the design of the IC and present preliminary results and considerations. The driver circuit proposed, based upon new two-stage positive-to-negative level shifters and resonant topology, has been designed and implemented using the cost-effective Smart Voltage extension (SVX) technique. Detailed analysis of the design process as well as a full set of simulations, reported in the paper, fully demonstrate the possibility to exploit the advantages of GaN devices by means of a smart and convenient implementation.
A graph-based approach for distributed parameter coordination in wireless communication networks (2012)

This paper addresses distributed parameters coordination methods for wireless communication systems founded on message-passing algorithms on graphs. This work provides evaluations on the potential of such an approach in a wireless communication network, and compares its performance and convergence properties with those of a baseline selfish/greedy approach. Simulation results for an example application, i.e. frequency reuse planning, is presented and discussed. The results show that graph-based techniques generally have higher probability of reaching (near) optimal solution than the greedy approach, though its rate of convergence tends to be slower and the message size is typically larger. Methods of improving the rate of convergence of graph-based distributed coordination techniques and reducing the associated message size are therefore important topics for future studies.
Supporting Uncompressed HD Video Streaming without Retransmissions over 60GHz Wireless Networks (2008)

Uncompressed HD (high-definition) video delivery over wireless personal area networks (WPANs) is a challenging problem because of the limited bandwidth and variations in channel. The most straight forward technique to recover from channel errors is to retransmit corrupted packets. However, retransmissions introduce significant delay/jitter and require additional bandwidth. Therefore, retransmissions may be unsuitable for uncompressed video streaming. In this paper, we develop, simulate, and evaluate an millimeter- wave (mmWave) system for supporting uncompressed video streams up to 3-Gbps without any retransmissions. New features of the mmWave system incorporates: (i) UEP (unequal error protection) where different video bits (MSBs and LSBs) are protected differently, (ii) a multiple-CRC to determine whether MSB or/and LSB portions are in error, (iii) RS code swapping (RSS), an error concealment scheme which can conceal some errors in video pixels. Simulations using real uncompressed HD images indicate that the proposed mmWave system can maintain good average PSNR (peak-signal-to-noise-ratio) under poor channel conditions, achieving what is generally accepted as a good picture quality with PSNR values greater than 40 dB. Moreover, the proposed system results in less fluctuating PSNR values.
A Mathematical Formulation and Solution of the CoPhMoRe Inverse Problem for Helically Wrapping Polymer Corona Phases on Cylindrical Substrates (2015)

Corona phase molecular recognition (CoPhMoRe) is a new technique that generates a nanoparticle-coupled polymer phase, capable of recognizing a specific molecule with high affinity and selectivity. CoPhMoRe has been successfully demonstrated using polymer wrapped single walled carbon nanotubes, resulting in molecular recognition complexes, to date, for dopamine, estradiol, riboflavin, and l-thyroxine, utilizing combinatorial library screening. A rational alternative design to this empirical library screening is to solve the mathematical formulation that we introduce as the CoPhMoRe inverse problem. This inverse problem seeks a linear function representing the position of monomers or functional groups along a polymer backbone that results in a 3-dimensional structure capable of recognizing a specific molecule when mapped to a nanoparticle surface. The potential solution space for such an inverse problem is infinite in general, but for the specific constraint of a helically wrapping polymer, mapped to a cylindrical nanoparticle, we show in this work that two types of inverse problems are exactly solvable. In one case, the polymer pitch and composition can be designed to allow for the specific binding of a small molecule analyte in the occluded space on the nanotube surface. In the other, a larger macromolecule can interact with a deformed helix, which partially conforms to it. A simplified, coarse-grained molecular model of a helically wrapping polymer demonstrates the inhomogeneous binding potential formed by a wrapping with a given pitch. Calculating the potential maps for various pitch values illustrates that there is an optimal pitch that enables the selective and specific binding of the target analyte. An additional coarse-grained model of a helical wrapping by a polymer consisting of alternating hydrophobic–hydrophilic segments demonstrates the resulting deformed helix corona around the nanotube, which forms accessible binding pockets between the hydrophilic loops. While these are the idealized forms of actual CoPhMoRe phases, the formation and solution of such inverse problems may serve to reduce the dimensionality of library screening for CoPhMoRe discoveries, as well as provide a theoretical basis for understanding certain types of CoPhMoRe recognition.
A regulatory network for the efficient control of transgene expression (2000)

This system permits tight long-term regulation when stably introduced into cell lines. The underlying principles of this network system should have general applications in biotechnology and gene therapy.
Improving Inspection of Turnouts (2013)

Railway system and track inspection has been the subject of significant research and implementation technology to monitor track conditions and provide timely and accurate information to government agencies, suppliers, and railroads. However, the implementation of new technology is lacking in the area of turnouts and their key components. Turnouts, a design discontinuity in the railroad track structure, represent a change in track geometry as well as in the stiffness of the track structure. High levels of force are generated as a vehicle negotiates the turnout, which results in rapid degradation of the turnout and causes train derailments. Derailments in turnouts represent more than 20 percent of track-caused accidents. While other areas of track structure use the visual and automated inspections required by the Federal Railroad Administration (FRA), turnouts still rely on walking inspections whose key provisions are qualitative rather than quantitative. The National Academy of Sciences (NAS) is sponsoring a project to look at international inspection tools and practices and their potential application for United States freight and passenger railways. While many of these technologies are still in the research, development, or early implementation stages, they represent significant potential for complementing today's visual and manual inspection processes with automated technology in order to provide accurate information about turnout condition.
Beta-mannosylceramide represents a new class of NKT agonists that induces tumor immunity by a novel IFN-γ-independent mechanism. (89.7) (2010)

Abstract Type I NKT cells are a unique lymphocyte population which recognize lipid antigens presented by the non-classical MHC-like molecule CD1d. Activation of type I NKT cells by α-galactosylceramide (α-GC) induces tumor immunity by IFN-γ dependent mechanisms. In this study, we characterized how modifications of the sugar head group of α-GC impacted tumor protection in an in vivo mouse model of lung metastasis. β-mannosylceramide (β-ManCer), but not α-mannosylceramide or α-fucosylceramide, induced strong type I NKT cell-dependent tumor immunity. Because this is the first report of a β-linked glycosylcermide capable of inducing significant type I NKT cell-mediated tumor protection, we further characterized the mechanism by which β-ManCer induced tumor elimination. Interestingly, unlike α-GC and its analogs which protected through IFN-γ dependent mechanisms, β-ManCer induced very little cytokine production both in vitro and in vivo and retained protection in the absence of IFN-γ. Rather, β-ManCer protected through a TNF-α and nitric oxide synthase-dependent mechanism novel for NKT cells. Simultaneous administration of sub-therapeutic doses of β-ManCer and α-GC resulted in synergistic reduction in tumor burden, supporting the conclusion that these glycolipids work through different mechanisms. The distinct mechanism of action of β-ManCer and its ability to synergize with α-GC suggest that β-ManCer is the first representative of a new class of type I NKT cell agonists.
High temperature magnetic sphere/needle rheometer (1989)

A magnetic sphere/needle rheometer, which is capable of measuring viscosities between ≂3×10−3 and 5×104 Pas at temperatures up to 380 °C, has been developed. The temperature dependence of the melt viscosity of a polyethylene sample is also reported.
Focal edge association to glaucoma diagnosis (2011)

Glaucoma is an optic nerve disease resulting in the loss of vision. There are two common types of glaucoma: open angle glaucoma and angle closure glaucoma. Glaucoma type classification is important in glaucoma diagnosis. Clinically, ophthalmologists examine the iridocorneal angle between iris and cornea to determine the glaucoma type as well as the degree of closure. However, manual grading of the iridocorneal angle images is subjective and often time consuming. In this paper, we propose focal edge for automated iridocorneal angle grading. The iris surface is located to determine focal region and focal edges. The association between focal edges and angle grades is built through machine learning. A modified grading system with three grades is adopted. The experimental results show that the proposed method can correctly classify 87.3% open angle and 88.4% closed angle. Moreover, it can correctly classify 75.0% grade 1 and 77.4% grade 0 for angle closure cases.
Computerized analysis of mammographic parenchymal patterns for assessing breast cancer risk: Effect of ROI size and location (2004)

The long-term goal of our research is to develop computerized radiographic markers for assessing breast density and parenchymal patterns that may be used together with clinical measures for determining the risk of breast cancer and assessing the response to preventive treatment. In our earlier studies, we found that women at high risk tended to have dense breasts with mammographic patterns that were coarse and low in contrast. With our method, computerized texture analysis is performed on a region of interest (ROI) within the mammographic image. In our current study, we investigate the effect of ROI size and ROI location on the computerized texture features obtained from 90 subjects (30 BRCA1/BRCA2 gene-mutation carriers and 60 age-matched women deemed to be at low risk for breast cancer). Mammograms were digitized at 0.1 mm pixel size and various ROI sizes were extracted from different breast regions in the craniocaudal (CC) view. Seventeen features, which characterize the density and texture of the parenchymal patterns, were extracted from the ROIs on these digitized mammograms. Stepwise feature selection and linear discriminant analysis were applied to identify features that differentiate between the low-risk women and the BRCA1/BRCA2 gene-mutation carriers. ROC analysis was used to assess the performance of the features in the task of distinguishing between these two groups. Our results show that there was a statistically significant decrease in the performance of the computerized texture features, as the ROI location was varied from the central region behind the nipple. However, we failed to show a statistically significant decrease in the performance of the computerized texture features with decreasing ROI size for the range studied.