gebhart/patrepeval huggingface dataset:
A cocktail of three virulent bacteriophages prevents Vibrio cholerae infection in animal models (2017)

Effective prevention strategies will be essential in reducing disease burden due to bacterial infections. Here we harness the specificity and rapid-acting properties of bacteriophages as a potential prophylaxis therapy for cholera, a severely dehydrating disease caused by Vibrio cholerae. To this end, we test a cocktail of three virulent phages in two animal models of cholera pathogenesis (infant mouse and rabbit models). Oral administration of the phages up to 24 h before V. cholerae challenge reduces colonization of the intestinal tract and prevents cholera-like diarrhea. None of the surviving V. cholerae colonies are resistant to all three phages. Genome sequencing and variant analysis of the surviving colonies indicate that resistance to the phages is largely conferred by mutations in genes required for the production of the phage receptors. For acute infections, such as cholera, phage prophylaxis could provide a strategy to limit the impact of bacterial disease on human health.
Spectrally efficient sensing protocol for cognitive relay systems (2009)

We propose sensing protocols for a cognitive dual-hop relay system where transmission from source (S) to destination (D) is accomplished over two phases with the assistance of a relay (R). A naive sensing protocol is to perform sensing at S and R before the respective transmission phase. This leads to substantial loss in spectral efficiency. We propose a sensing protocol where sensing is only performed at S when R is transmitting to D after canceling out the self-interference component that is known a priori. Theoretical analysis and numerical simulation validate that our proposed scheme achieves higher spectral efficiency than the naive sensing scheme while maintaining detection performance.
Nonlinear Equalization for TDMR Channels Using Neural Networks (2019)

This paper presents new structure and adaptation criterion for equalization of two-dimensional magnetic recording channels, as opposed to typical linear equalizer with minimum mean square error (MMSE) as adaptation criterion. To compensate for the nonlinear channel noise, we propose a neural network based nonlinear equalizer and show it outperforms linear equalizer under the same criterion. To achieve minimum bit error rate (BER) at the detector output, we propose to adapt the equalizer with cross entropy between the true probability of the bit and detector's estimate of it. We show minimizing the cross entropy enables maximum likelihood adaptation, and results in lower detector BER than the MSE criterion. Several variations of nonlinear equalizer structures with cross entropy criterion are investigated. Compared to linear MMSE equalizer, the proposed scheme can provide up to 22.76% detector BER reduction with only 6x increase in complexity.
Bridging β‐Cyclodextrin Prevents Self‐Inclusion, Promotes Supramolecular Polymerization, and Promotes Cooperative Interaction with Nucleic Acids (2018)

A bridge to assemble: Cyclodextrins bridged with an ammonium linker bearing a hydrophobic substituent can efficiently form supramolecular polymers and avoid the competing self-inclusion and head-to-head processes. Furthermore, the self-assembling cyclodextrin derivative interacts in a highly cooperative manner with DNA, as demonstrated by compaction experiments. It also interacts cooperatively with siRNA and allows its transfection.
Carbocyclic analogs of thymine nucleosides and related 1‐substituted thymines (1981)

Abstract The carbocyclic analogs of thymidine (IXf), 1‐β‐ribofuranosylthymine (IXg), and 1‐β‐3′‐deoxyribofuranosyl‐thymine (IXe) were synthesized by incorporating modifications into the Shaw method of synthesizing 2,4‐(1 H ,3 H )pyrimidinediones via acryloylureas. Simpler analogs of thymine nucleosides were also prepared by this method. The carbocyclic analog of thymidine displayed modest activity against Leukemia L1210 in vivo. It differs from a compound prepared previously by a Prins reaction.
Platelet contractile force (PCF) and clot elastic modulus (CEM) are elevated in diabetic patients with chest pain (2002)

PCF and CEM are elevated in diabetic chest pain patients. The significance of these laboratory findings awaits additional clinical studies.
Total biosynthesis of the cyclic AMP booster forskolin from Coleus forskohlii (2017)

Forskolin is a unique structurally complex labdane-type diterpenoid used in the treatment of glaucoma and heart failure based on its activity as a cyclic AMP booster. Commercial production of forskolin relies exclusively on extraction from its only known natural source, the plant <i>Coleus forskohlii</i>, in which forskolin accumulates in the root cork. Here, we report the discovery of five cytochrome P450s and two acetyltransferases which catalyze a cascade of reactions converting the forskolin precursor 13<i>R</i>-manoyl oxide into forskolin and a diverse array of additional labdane-type diterpenoids. A minimal set of three P450s in combination with a single acetyl transferase was identified that catalyzes the conversion of 13<i>R</i>-manoyl oxide into forskolin as demonstrated by transient expression in <i>Nicotiana benthamiana</i>. The entire pathway for forskolin production from glucose encompassing expression of nine genes was stably integrated into <i>Saccharomyces cerevisiae</i> and afforded forskolin titers of 40 mg/L.
TrInc: small trusted hardware for large distributed systems (2009)

A simple yet remarkably powerful tool of selfish and malicious participants in a distributed system is “equivocation”: making conflicting statements to others. We present TrInc, a small, trusted component that combats equivocation in large, distributed systems. Consisting fundamentally of only a non-decreasing counter and a key, TrInc provides a new primitive: unique, once-in-alifetime attestations. We show that TrInc is practical, versatile, and easily applicable to a wide range of distributed systems. Its deployment is viable because it is simple and because its fundamental components—a trusted counter and a key—are already deployed in many new personal computers today. We demonstrate TrInc’s versatility with three detailed case studies: attested append-only memory (A2M), PeerReview, and BitTorrent. We have implemented TrInc and our three case studies using real, currently available trusted hardware. Our evaluation shows that TrInc eliminates most of the trusted storage needed to implement A2M, significantly reduces communication overhead in PeerReview, and solves an open incentives issue in BitTorrent. Microbenchmarks of our TrInc implementation indicate directions for the design of future trusted hardware. 1
Encapsulation of enzymes and cells in sol-gel matrices for biosensor applications (1999)

Porous silicate materials made by low temperature sol-gel process are promising host matrices for encapsulation of biomolecules. Their mechanical strength, chemical inertness, hydrophilic nature, and above all, their optical transparency makes them an exciting platform for development of biosensors. To date, researchers have focused on sol-gel routes using alkoxides for encapsulation of biomolecules. However, formation of alcohol as a byproduct is an undesired complication as it can have detrimental effect on the activity of entrapped biomolecules. We have developed a novel sol-gel process to encapsulate biological molecules (such as enzymes, antibodies and cells) that uses neutral pH, room temperature, and does not generate alcohol as a byproduct. The process uses sodium silicate as precursor and is carried out in two steps--preparation of a low pH silicate sol followed by gelation at neutral pH in a buffer containing biomolecules. We developed a novel homogeneous immunoassay for 2,4,6-trinitrotoluene (TNT), and have encapsulated the immunoassay reagents in sol-gel matrices to product dispersible biosensors for the detection of TNT. Using the sol-gel doped with immunoassay reagents, we can detect TNT at low ppm levels. We also report encapsulation of E. Coli cells expressing the enzyme organophosphorus hydrolase on the cell surface in sol-gel matrices. The cell- doped sol-gel material can be used to develop biosensors for detection of organophosphates.
Semantics-Preserving Parallelization of Stochastic Gradient Descent (2018)

Stochastic gradient descent (SGD) is a well-known method for regression and classification tasks. However, it is an inherently sequential algorithm - at each step, the processing of the current example depends on the parameters learned from previous examples. Prior approaches to parallelizing linear learners using SGD, such as Hogwild! and AllReduce, do not honor these dependencies across threads and thus can potentially suffer poor convergence rates and/or poor scalability. This paper proposes SymSGD, a parallel SGD algorithm that, to a first-order approximation, retains the sequential semantics of SGD. Each thread learns a local model in addition to a model combiner, which allows local models to be combined to produce the same result as what a sequential SGD would have produced. This paper evaluates SymSGD's accuracy and performance on 6 datasets on a shared-memory machine shows up-to 11x speedup over our heavily optimized sequential baseline on 16 cores and 2.2x, on average, faster than Hogwild!.
Corneal Epithelial Wound Healing on Bilayer Composite Hydrogels (1995)

We demonstrate that a bilayer composite hydrogel composed of corneal stroma crosslinked to poly(ethylene oxide) provides a substrate suitable for wound healing behavior of corneal epithelial cells and for formation and maintenance of a stable multilayered epithelium. Potential diffusion-limitation of nutrients or regulatory molecules across the hydrogel was investigated experimentally with a new in vitro ocular assay, using epithelial cell migration as an index of molecular diffusion limitations. Corneal epithelial cells explanted on the composite hydrogel in vitro exhibited morphology similar to those in vivo, and migrated effectively over the stromal surface. Importantly, our system yielded multilayered epithelium like that found in normal corneal tissue under conditions that closely simulate the in vivo physiologic arrangement. In addition, our results indicate that molecules of substantially greater molecular weight than glucose appear to control the cell migration rate. Thus, engineering design of this composite hydrogel system may allow it to be useful in corneal wound healing applications.
Control of Vortices by Homogeneous Fields in Asymmetric Ferroelectric and Ferromagnetic Rings (2008)

Effective Hamiltonians have been used (i) to demonstrate that the shape asymmetry of ferromagnetic rings is essential to the recently discovered switching of the chirality of their vortices by homogeneous magnetic fields, via a transition into onion states; (ii) to reveal that an electric vortex can also be controlled by a homogeneous electric field in asymmetric ferroelectric nanorings, via the formation of antiferrotoroidic pair states rather than onion states; and (iii) to provide the fundamental reason that allows such control, namely, two new interaction energies involving a vector characterizing the asymmetry, the applied field, and the toroidal moment.
Broadening mechanisms and self-consistent gain calculations for GaN quantum cascade laser structures (2018)

Carrier transport in GaN terahertz (THz) quantum cascade laser (QCL) structures is theoretically investigated using a non-equilibrium Green's function method. Although scattering due to polar optical phonons in GaN is greatly enhanced with respect to GaAs/AlGaAs THz QCLs, the phonon-induced broadening of the laser levels is found to remain much smaller than other sources of broadening arising from impurity and electron-electron scattering. The gain is calculated self-consistently accounting for the correlation effects in level broadening. Three-well based design with resonant-phonon scheme shows a peak gain of 88/cm at 10 K, and 34/cm at 280 K, which remains above the calculated loss of a double metal waveguide. The results suggest that lasing at 6.6 THz, which is beyond the traditional GaAs THz QCLs, is possible up to 280 K.
Platelets Promote Tumor Growth and Metastasis via Direct Interaction between Aggrus/Podoplanin and CLEC-2 (2013)

The platelet aggregation-inducing factor Aggrus, also known as podoplanin, is frequently upregulated in several types of tumors and enhances hematogenous metastasis by interacting with and activating the platelet receptor CLEC-2. Thus, Aggrus-CLEC-2 binding could be a therapeutic molecular mechanism for cancer therapy. We generated a new anti-human Aggrus monoclonal antibody, MS-1, that suppressed Aggrus-CLEC-2 binding, Aggrus-induced platelet aggregation, and Aggrus-mediated tumor metastasis. Interestingly, the MS-1 monoclonal antibody attenuated the growth of Aggrus-positive tumors in vivo. Moreover, the humanized chimeric MS-1 antibody, ChMS-1, also exhibited strong antitumor activity against Aggrus-positive lung squamous cell carcinoma xenografted into NOD-SCID mice compromising antibody-dependent cellular cytotoxic and complement-dependent cytotoxic activities. Because Aggrus knockdown suppressed platelet-induced proliferation in vitro and tumor growth of the lung squamous cell carcinoma in vivo, Aggrus may be involved in not only tumor metastasis but also tumor growth by promoting platelet-tumor interaction, platelet activation, and secretion of platelet-derived factors in vivo. Our results indicate that molecular target drugs inhibiting specific platelet-tumor interactions can be developed as antitumor drugs that suppress both metastasis and proliferation of tumors such as lung squamous cell carcinoma.
One-step homogeneous immunoassay for small analytes (2006)

We have developed a one-step, homogeneous noncompetitive immunoassay for small analytes using recombinant antibodies and morphine as the model analyte. A highly specific antibody against the immune complex (IC) formed between an anti-morphine antibody and morphine was selected from a naive scFv phage display library. The in vitro phage library selection procedure avoids the difficulties associated with the production of anti-IC antibodies by animal immunization. The anti-morphine and the anti-IC antibodies were labeled with a pair of fluorescence resonance energy transfer (FRET) fluorophores. In the FRET assay the labeled antibodies were incubated with saliva samples spiked with morphine, codeine, or heroin. Within 2 min, 5 ng/mL morphine, which is clearly under the recommended cutoff level, was detected without cross-reactivity to codeine or heroin. This assay principle is also widely applicable to other small analytes.
Passive Harmonic Filter Design Scheme (2011)

In this article, a passive harmonic filter design scheme is proposed for offshore power distribution systems with subsea cables. Such an offshore system requires more reliable harmonic filters due to parallel resonance and the resultant large harmonic distortions in the system caused by subsea cables. The new passive harmonic filter design scheme is easy to achieve and more reliable compared to traditional pas sive harmonic filter design. It also offers a flexible power factor control to the offshore platform with generators. The stability, reliability, and flexibility of the offshore distribu tion system with the proposed filters are significantly improved. To avoid subfilter overloading, detuning capacitors and reactor taps should be provided for each subfilter in case detuning is required in the field.
Superhard Mixed Transition Metal Dodecaborides (2016)

Solid solutions of mixed metal dodecaborides of ZrB12, YB12, and ScB12 were prepared by arc-melting and studied for their mechanical properties. Zr1–xYxB12 formed an essentially perfect solid solution, closely following Vegard’s law. Zr1–xScxB12 and Y1–xScxB12 undergo a face centered-cubic to body-centered tetragonal transition at 90–95 at. % Sc as determined by powder X-ray diffraction and transmission electron microscopy. The compounds Zr0.5Y0.5B12, Zr0.5Sc0.5B12, and Y0.5Sc0.5B12 are superhard (Vickers hardness ≥ 40 GPa) and demonstrate an increase in hardness to 45.8 ± 1.3, 48.0 ± 2.1, and 45.2 ± 2.1 GPa under a load of 0.49 N, respectively, compared to 40.4 ± 1.8, 40.9 ± 1.6, and 41.7 ± 2.2 GPa for pure ZrB12, YB12, and ScB12, respectively. In addition, Zr0.5Y0.5B12, Zr0.5Sc0.5B12, and Y0.5Sc0.5B12 solid solutions show a substantial increase in oxidation resistance to approximately 630, 685, and 695 °C, respectively, when compared to other superhard metal borides (e.g., ∼400 °C for WB4) and their alloys and the traditional cutting tools material tungsten carbide (∼400 °C). Moreover, Zr0.5Y0.5B12, Zr0.5Sc0.5B12, and Y0.5Sc0.5B12 have relatively low densities of 3.52, 3.32, and 3.18 g/cm3, respectively, comparable to or even lower than that of diamond (3.52 g/cm3) and significantly lower than those of other superhard borides such as ReB2 (12.67 g/cm3) and WB4 (8.40 g/cm3) and traditional cutting tools materials, e.g., WC (15.77 g/cm3), making them of potential interest for lightweight protective coatings and/or as materials for cutting and machining.
Selective catalytic reduction of NO{sub x} with methane (1993)

The authors discovered a catalytic process that efficiently reduces NO{sub x} with CH{sub 4} in the presence of excess O{sub 2}. The new process provides an alternative approach for NO{sub x} control in the presence of excess O{sub 2} for both stationary and mobile sources. A complete conversion of NO to N{sub 2} was obtained over a Co-ZM-5 catalyst at 400{degrees}C. In fact, the presence of O{sub 2} in the feed significantly enhanced the NO{sub x} reduction activity. The catalytic activity for NO{sub x} reduction is proportional to the CH{sub 4} level in the feed and the level of Co2+ exchanged into the zeolite, Co2+ exchanged zeolite Y, however, is a poor catalyst compared to Co-ZSM-5, and CoO/Al{sub 2}O{sub 3} inactive for this reaction. On the other hand, Cu-ZSM-5, which is a unique catalyst for the direct NO decomposition, is much less active for the NO reduction by CH{sub 4} in the presence of excess O{sub 2}. In this presentation, the basic features of this catalytic process, the role of zeolite and the importance of metal center for an active catalyst will be discussed.
Reduction of lymph tissue false positives in pulmonary embolism detection (2008)

Pulmonary embolism (PE) is a serious medical condition, characterized by the partial/complete blockage of an artery within the lungs. We have previously developed a fast yet effective approach for computer aided detection of PE in computed topographic pulmonary angiography (CTPA),<sup>1</sup> which is capable of detecting both acute and chronic PEs, achieving a benchmark performance of 78% sensitivity at 4 false positives (FPs) per volume. By reviewing the FPs generated by this system, we found the most dominant type of FP, roughly one third of all FPs, to be lymph/connective tissue. In this paper, we propose a novel approach that specifically aims at reducing this FP type. Our idea is to explicitly exploit the anatomical context configuration of PE and lymph tissue in the lungs: a lymph FP connects to the airway and is located outside the artery, while a true PE should not connect to the airway and must be inside the artery. To realize this idea, given a detected candidate (i.e. a cluster of suspicious voxels), we compute a set of contextual features, including its distance to the airway based on local distance transform and its relative position to the artery based on fast tensor voting and Hessian "vesselness" scores. Our tests on unseen cases show that these features can reduce the lymph FPs by 59%, while improving the overall sensitivity by 3.4%.
Lesion assessment and radiation dose in contrast-enhanced digital breast tomosynthesis (2018)

Contrast-Enhanced Digital Breast Tomosynthesis (CEDBT) provides a three-dimensional (3D) contrast-enhancement map with co-registered anatomical information from low-energy DBT. It combines the benefits from Contrast-Enhanced Digital Mammography (CEDM) and Digital Breast Tomosynthesis (DBT), and may improve breast cancer detection and assessment of lesion morphology. We investigate the efficacy of CEDBT in the assessment of lesion contrast enhancement and margin identification, and evaluate the dose efficiency. We generate synthetic CEDM images from CEDBT data, similar to synthesis of 2D mammograms from DBT data, which may facilitate overall lesion assessment without additional radiation dose. Preliminary results from a patient study show that CEDBT depicts lesion margins better compared to CEDM, while the contrast-enhancement level for in-plane slice is not as high as in CEDM. CEDBT delivers less radiation dose compared to CEDM + DBT. Synthetic CEDM is able to provide lesion contrast-enhancement level comparable to CEDM.
Damping measurements of highly damped wavy composite structures (2001)

Wavy composite material is a composite that has been developed in recent years that uses opposing sinusoidal fiber waveforms in adjacent layers in a manner that enhances the constrained layer damping effect in the material. Analysis of the material has predicted both high damping and stiffness, which is contrary to many materials where increased damping generally leads to decreased stiffness of the material. To validate the analysis, a test system has been developed to measure both the damping and the stiffness properties of the material under axial excitation. The system has been shown to be capable of measuring frequency dependent damping coefficients of less than 1%. Tests on the wavy composite have led to a characterization of the material over a broad range of frequency and temperature that agrees well with predicted values, and allows one to design the wavy composite lay-up to give a desired performance at a given temperature and frequency. Damping measurements as high as 30% have been measured, while maintaining stiffness properties that are comparable to materials such as aluminum and titanium, using standard graphite fibers.
ACQUINE (2010)

We present ACQUINE - Aesthetic Quality Inference Engine, a publicly accessible system which allows users to upload their photographs and have them rated automatically for aesthetic quality. The system integrates a support vector machine based classifier which extracts visual features on the fly and performs real-time classification and prediction. As the first publicly available tool for automatically determining the aesthetic value of an image, this work is a significant first step in recognizing human emotional reaction to visual stimulus. In this paper, we discuss fundamentals behind this system, and some of the challenges faced while creating it. We report statistics generated from over 140,000 images uploaded by Web users. The system is demonstrated at http://acquine.alipr.com.
Inattentional Blindness for Redirected Walking Using Dynamic Foveated Rendering (2020)

Redirected walking is a Virtual Reality(VR) locomotion technique which enables users to navigate virtual environments (VEs) that are spatially larger than the available physical tracked space. In this work we present a novel technique for redirected walking in VR based on the psychological phenomenon of inattentional blindness. Based on the user's visual fixation points we divide the user's view into zones. Spatially-varying rotations are applied according to the zone's importance and are rendered using foveated rendering. Our technique is real-time and applicable to small and large physical spaces. Furthermore, the proposed technique does not require the use of stimulated saccades but rather takes advantage of naturally occurring saccades and blinks for a complete refresh of the framebuffer. We performed extensive testing and present the analysis of the results of three user studies conducted for the evaluation.