gebhart/patrepeval huggingface dataset:
Synthetic SARS-CoV-2 Spike-Based DNA Vaccine Elicits Robust and Long-Lasting Th1 Humoral and Cellular Immunity in Mice (2021)

The ongoing global pandemic of coronavirus disease 2019 (COVID-19) calls for an urgent development of effective and safe prophylactic and therapeutic measures. The spike (S) glycoprotein of severe acute respiratory syndrome-coronavirus (SARS-CoV-2) is a major immunogenic and protective protein and plays a crucial role in viral pathogenesis. In this study, we successfully constructed a synthetic codon-optimized DNA-based vaccine as a countermeasure against SARS-CoV-2, denoted VIU-1005. The design was based on a codon-optimized coding sequence of a consensus full-length S glycoprotein. The immunogenicity of the vaccine was tested in two mouse models (BALB/c and C57BL/6J). Th1-skewed systemic S-specific IgG antibodies and neutralizing antibodies (nAbs) were significantly induced in both models 4 weeks after three injections with 100 μg of the VIU-1005 vaccine via intramuscular needle injection but not intradermal or subcutaneous routes. Such immunization induced long-lasting IgG and memory T cell responses in mice that lasted for at least 6 months. Interestingly, using a needle-free system, we showed an enhanced immunogenicity of VIU-1005 in which lower or fewer doses were able to elicit significantly high levels of Th1-biased systemic S-specific immune responses, as demonstrated by the significant levels of binding IgG antibodies, nAbs and IFN-γ, TNF and IL-2 cytokine production from memory CD8<sup>+</sup> and CD4<sup>+</sup> T cells in BALB/c mice. Furthermore, compared to intradermal needle injection, which failed to induce any significant immune response, intradermal needle-free immunization elicited a robust Th1-biased humoral response similar to that observed with intramuscular immunization. Together, our results demonstrate that the synthetic VIU-1005 candidate DNA vaccine is highly immunogenic and capable of inducing long-lasting Th1-skewed humoral and cellular immunity in mice. Furthermore, we show that the use of a needle-free system could enhance the immunogenicity and minimize doses needed to induce protective immunity in mice, supporting further preclinical and clinical testing of this candidate vaccine.
Joint multiview video plus depth coding (2010)

Multiview video plus depth (MVD), where per-pixel depth map sequences are associated with multiview texture video, is a promising approach for three-dimensional (3D) video solutions requiring view synthesis. The Multiview Video Coding (MVC) standard has been typically used to compress the MVD representation, resulting into the multiview texture video and the multiview depth video being in two separate MVC bitstreams. Such a coding scheme does not, however, utilize the similarities of the motion information of the multiview texture video and the multiview depth video. The joint multiview video plus depth coding (JMVDC) scheme presented in this paper uses inter-view prediction similarly to MVC as well as the inter-layer motion prediction tool of the Scalable Video Coding (SVC) standard to exploit the correlation of the motion in the texture and depth video sequences. The simulation results show that the JMVDC method achieves about 10 to 20% saving in depth bitrate compared with conventional MVC-based coding of MVD representations.
Statistical reconstruction for quantitative CT applications (2004)

This paper summarizes considerations in developing statistical reconstruction algorithms for polyenergetic X-ray CT. The algorithms are based on Poisson statistics and polyenergetic X-ray attenuation physics and object models. In single-kVp scans, object models enable estimates of the contributions of bone and soft tissue at every pixel, based on prior assumptions about the tissue properties. In dual-kVp scans, one can estimate water and bone images independently. Preliminary results with fan-beam data from two cone beam systems show better accuracy for iterative methods over FBP.
Query word deletion prediction (2003)

Web search query logs contain traces of users' search modifications. One strategy users employ is deleting terms, presumably to obtain greater coverage. It is useful to model and automate term deletion when arbitrary searches are conjunctively matched against a small hand constructed collection, such as a hand-built hierarchy, or collection of high-quality pages matched with key phrases. Queries with no matches can have words deleted till a match is obtained. We provide algorithms which perform substantially better than the baseline in predicting which word should be deleted from a reformulated query, for increasing query coverage in the context of web search on small high-quality collections.
Design and Synthesis of Peptide Tertiary Amides‐A Fusion of Peptides and Peptoids (2012)

Combinatorial libraries of peptides and peptoids (N‐alkylated oligoglycines) have been shown to be a good source of protein ligands. However, each of these compound classes has significant limitations with regard to the development of metabolically stable, high affinity and selectivity drug leads or tool compounds. Peptides are sensitive to enzymatic cleavage and are poorly bioavailable, while peptoids are relatively floppy molecules, which limits the affinity with which they recognize a target protein. To facilitate our screening effort, we describe here a synthetic route to generate large libraries of P eptide T ertiary A mides (PTAs). These compounds merge many of the favorable properties of peptides and peptoids. Large Libraries of PTAs are anticipated to be a superior source of leads for the development of useful pharmacological reagents. This work was supported by the NHLBI (NO1‐HV‐00242) and a transformational RO1 grant from the NIH GM090294.
Secreted Factors from Human Vestibular Schwannomas Can Cause Cochlear Damage (2015)

Vestibular schwannomas (VSs) are the most common tumours of the cerebellopontine angle. Ninety-five percent of people with VS present with sensorineural hearing loss (SNHL); the mechanism of this SNHL is currently unknown. To establish the first model to study the role of VS-secreted factors in causing SNHL, murine cochlear explant cultures were treated with human tumour secretions from thirteen different unilateral, sporadic VSs of subjects demonstrating varied degrees of ipsilateral SNHL. The extent of cochlear explant damage due to secretion application roughly correlated with the subjects' degree of SNHL. Secretions from tumours associated with most substantial SNHL resulted in most significant hair cell loss and neuronal fibre disorganization. Secretions from VSs associated with good hearing or from healthy human nerves led to either no effect or solely fibre disorganization. Our results are the first to demonstrate that secreted factors from VSs can lead to cochlear damage. Further, we identified tumour necrosis factor alpha (TNFα) as an ototoxic molecule and fibroblast growth factor 2 (FGF2) as an otoprotective molecule in VS secretions. Antibody-mediated TNFα neutralization in VS secretions partially prevented hair cell loss due to the secretions. Taken together, we have identified a new mechanism responsible for SNHL due to VSs.
Acousto-optic fastscan delay with scan rates exceeding 30 kHz and sub-20-attosecond precision (2013)

Here we introduce a novel concept of an ultimate fastscan delay with sub-20 as precision and scan rates of tens of kHz. It is based on an acousto-optic programmable dispersive filter and exploits the propagation of the acoustic wave between successive optical pulses.
MAC Centered Cooperation - Synergistic Design of Network Coding,\n Multi-Packet Reception, and Improved Fairness to Increase Network Throughput (2011)

We design a cross-layer approach to aid in develop- ing a cooperative\nsolution using multi-packet reception (MPR), network coding (NC), and medium\naccess (MAC). We construct a model for the behavior of the IEEE 802.11 MAC\nprotocol and apply it to key small canonical topology components and their\nlarger counterparts. The results obtained from this model match the available\nexperimental results with fidelity. Using this model, we show that fairness\nallocation by the IEEE 802.11 MAC can significantly impede performance; hence,\nwe devise a new MAC that not only substantially improves throughput, but\nprovides fairness to flows of information rather than to nodes. We show that\ncooperation between NC, MPR, and our new MAC achieves super-additive gains of\nup to 6.3 times that of routing with the standard IEEE 802.11 MAC. Furthermore,\nwe extend the model to analyze our MAC's asymptotic and throughput behaviors as\nthe number of nodes increases or the MPR capability is limited to only a single\nnode. Finally, we show that although network performance is reduced under\nsubstantial asymmetry or limited implementation of MPR to a central node, there\nare some important practical cases, even under these conditions, where MPR, NC,\nand their combination provide significant gains.\n
Partial Evaluation for Distributed XPath Query Processing and Beyond (2012)

This article proposes algorithms for evaluating XPath queries over an XML tree that is partitioned horizontally and vertically, and is distributed across a number of sites. The key idea is based on partial evaluation: it is to send the whole query to each site that partially evaluates the query, in parallel, and sends the results as compact (Boolean) functions to a coordinator that combines these to obtain the result. This approach possesses the following performance guarantees. First, each site is visited at most twice for data-selecting XPath queries, and only once for Boolean XPath queries. Second, the network traffic is determined by the answer to the query, rather than the size of the tree. Third, the total computation is comparable to that of centralized algorithms on the tree stored in a single site, regardless of how the tree is fragmented and distributed. We also present a MapReduce algorithm for evaluating Boolean XPath queries, based on partial evaluation. In addition, we provide algorithms to evaluate XPath queries on very large XML trees, in a centralized setting. We show both analytically and empirically that our techniques are scalable with large trees and complex XPath queries. These results, we believe, illustrate the usefulness and potential of partial evaluation in distributed systems as well as centralized XML stores for evaluating XPath queries and beyond.
Sketching streams through the net: distributed approximate query tracking (2005)

Emerging large-scale monitoring applications require continuous tracking of complex data-analysis queries over collections of physically-distributed streams. Effective solutions have to be simultaneously space/time efficient (at each remote monitor site), communication efficient (across the underlying communication network), and provide continuous, guaranteed-quality approximate query answers. In this paper, we propose novel algorithmic solutions for the problem of continuously tracking a broad class of complex aggregate queries in such a distributed-streams setting. Our tracking schemes maintain approximate query answers with provable error guarantees, while simultaneously optimizing the storage space and processing time at each remote site, and the communication cost across the network. They rely on tracking general-purpose randomized sketch summaries of local streams at remote sites along with concise prediction models of local site behavior in order to produce highly communication- and space/time-efficient solutions. The result is a powerful approximate query tracking framework that readily incorporates several complex analysis queries (including distributed join and multi-join aggregates, and approximate wavelet representations), thus giving the first known low-overhead tracking solution for such queries in the distributed-streams model. 1
Deletion or Substitution within the a Platelet-Derived Growth Factor Receptor Kinase Insert Domain: Effects on Functional Coupling with Intracellular Signaling Pathways (1991)

The tyrosine kinase domains of the platelet-derived growth factor (PDGF) and colony-stimulating factor-1 (CSF-1)/c-fms receptors are interrupted by kinase inserts (ki) which vary in length and amino acid sequence. To define the role of the ki in the human alpha PDGF receptor (alpha PDGFR), we generated deletion mutants, designated alpha R delta ki-1 and alpha R delta ki-2, which lacked 80 (710 to 789) and 95 (695 to 789) amino acids of the 104-amino-acid ki region, respectively. Their functional characteristics were compared with those of the wild-type alpha PDGFR following introduction into a naive hematopoietic cell line, 32D. Biochemical responses, including PDGF-stimulated PDGFR tyrosine phosphorylation, phosphatidylinositol (PI) turnover, and receptor-associated PI-3 kinase activity, were differentially impaired by the deletions. Despite a lack of any detectable receptor-associated PI-3 kinase activity, 32D cells expressing alpha R delta ki-1 showed only partially impaired chemotactic and mitogenic responses and were capable of sustained proliferation in vitro and in vivo under conditions of autocrine stimulation by the c-sis product. 32D transfectants expressing the larger ki deletion (alpha R delta ki-2) showed markedly decreased or abolished biochemical and biological responses. However, insertion of the highly unrelated smaller c-fms (685 to 750) ki domain into alpha R delta ki-2 restored each of these activities to wild-type alpha PDGFR levels. Since the CSF-1R does not normally induce PI turnover, the ability of the c-fms ki domain to reconstitute PI turnover in the alpha R delta ki-2 transfectant provides evidence that the ki domain of the alpha PDGFR does not directly couple with this pathway. Taken together, all od these bindings imply that their ki domains have evolved to play very similar roles in the known signaling functions PDGF and CSF-1 receptors.
Deep Sub-Wavelength Plasmonic Lasers (2010)

We show that a hybrid of semiconductor nanowire and metallic surface modes produces an efficient laser device with λ2/100 mode area and discuss the broader impact of plasmon-based light sources and integrated optical components.
Treatment of tumors with 5-radioiodo-2 sup 1 -deoxyuridine (1991)

A phytochemical study of the methylene chloride/methanol (1/1) extract of the leaves of Glossocalyx brevipes Benth. (Monimiaceae) afforded three new derivatives of homogentisic acid, methyl 2-(1'beta-geranyl-5'beta-hydroxy-2'-oxocyclohex-3'-enyl)acetate (1), 2-(1'beta-geranyl-5'beta-hydroxy-2'-oxocyclohex-3'-enyl)acetic acid (2), methyl 2-(1'beta-geranyl-5'beta-hydroxy-4'beta-methoxy-2'-oxocyclohexyl)acetate (3), and two known alkaloids, aristololactam BII and liriodenine. Compounds 1 and 2 and liriodenine showed modest in vitro activity against Plasmodium falciparum.
Stochastic Metallic-Glass Cellular Structures Exhibiting Benchmark Strength (2008)

By identifying the key characteristic "structural scales" that dictate the resistance of a porous metallic glass against buckling and fracture, stochastic highly porous metallic-glass structures are designed capable of yielding plastically and inheriting the high plastic yield strength of the amorphous metal. The strengths attainable by the present foams appear to equal or exceed those by highly engineered metal foams such as Ti-6Al-4V or ferrous-metal foams at comparable levels of porosity, placing the present metallic-glass foams among the strongest foams known to date.
Leukocyte segmentation and classification in blood-smear images (2005)

The detection and classification of leukocytes in blood smear images is a routine task in medical diagnosis. In this paper we present a fully automated approach to leukocyte segmentation that is robust with respect to cell appearance and image quality. A set of features is used to describe cytoplasm and nucleus properties. Pairwise SVM classification is used to discriminate between different cell types. Evaluation on a set of 1166 images (13 classes) resulted in 95% correct segmentations and 75% to 99% correct classification (with reject option).
Blood flow velocity imaging of malignant melanoma by micro multipoint laser Doppler velocimetry (2010)

We have developed a laser Doppler velocimeter to measure blood flow, the micromultipoint laser Doppler velocimeter (μ-MLDV). This equipment can measure absolute velocity and, based on this, can display the course of blood vessels. In this study, we attempted to perform blood flow velocity imaging of malignant melanoma transplanted to the mouse ear. We found that blood flow velocity of the formed blood vessels originating in the melanoma was much greater than that of the capillary vessels in normal skin. Furthermore, the form of the tumor was clearly visible from the blood flow velocity image. These experimental results suggest that μ-MLDV has potential as a diagnostic method for distinguishing benign nevi from malignant melanomas.
Random phase encryption in reflection-type holographic memory (2004)

A reflection-type holographic memory system with data security is presented. Binary data frames are recorded as encrypted volume holograms by use of random phase mask in a reference arm. Experimental results of recording and reconstruction by the correct and an incorrect phase mask are presented.
A self-forming dual-phase membrane for high-temperature electrochemical CO<sub>2</sub> capture (2017)

We report here a dual-phase mixed CO<sub>3</sub><sup>2−</sup>- and e<sup>−</sup>-conducting CO<sub>2</sub> capture membrane self-formed at high temperatures from NiO and molten carbonate.
Virantmycin, a new antiviral antibiotic produced by a strain of Streptomyces. (1981)

Virantmycin, a novel chlorine-containing antiviral antibiotic, has been isolated from Streptomyces nitrosporeus No. AM-2722. The active substance in culture broth is isolated as colorless needles by solvent extraction followed by high performance liquid chromatography on silicic acid. The molecular formula is C19H26NO3Cl (molecular weight 351) from the elemental analysis and mass spectrum. The antibiotic possesses antifungal activity and potent inhibitory activity against various RNA and DNA viruses.
Fabrication of freestanding heteroepitaxial diamond substrate via micropatterns and microneedles (2016)

Abstract The fabrication of a high-quality freestanding diamond substrate was successfully demonstrated via heteroepitaxy by introducing diamond micropatterns and microneedles in the early stage of growth. Micropatterns contributed to a marked reduction in the number of dislocations induced by epitaxial lateral overgrowth, and microneedles relaxed heteroepitaxial strain. Raman spectroscopy indicated the absence of nondiamond carbon inclusions in the obtained freestanding substrate. The full width at half maximum of the X-ray rocking curve for diamond (004) reflections was 0.07°, the lowest value for heteroepitaxial diamond that has been reported so far. The results provide novel insights toward realizing large-diameter single-crystalline diamond substrates.
Physical properties of extended-chain high-density polyethylene (1974)

Extended-chain high-density polyethylene prepared through crystallization at high pressure is substantially stiffer and somewhat stronger than normal folded-chain HDPE. With weight-average molecular weight in the range normal for molding or extrusion resins, the extended-chain material is inductile and brittle; but with molecular weight near 2,000,000, the resin can be rigid and tough. This rigid, tough material can be converted to articles through some of the solid-state processes developed for metals. The volume–temperature behavior of HDPE at 5000 atmospheres appears to reflect a polymorphic transition between orthorhombic and triclinic phases.
Underwater Source-Level Estimation using Sparsity-Cognizant Source-Location Mapping (2014)

Abstract : This work focused on estimating the acoustic source gains of broadband sources in a shallow-water environment. The results show that accurate acoustic source gain estimation is possible if the sources were correctly localized. Knowledge about the environment was a fundamental enabler for the acoustic source gain estimation. When dealing with multiple sources, the source gain estimation does not perform as well, but if localization was achieved, then it is still able to give accurate results at higher signal-to-noise ratios. Future research will explore how this algorithm performs on real data set(s) and in the presence of environmental uncertainty.
Global DNA Hypomethylation in Liver Cancer Cases and Controls: A Phase I Preclinical Biomarker Development Study (2007)

A correlation between global genomic DNA methylation patterns and type of liver tissue was observed. These results add to the accumulating body of evidence suggesting that global DNA hypomethylation may be a useful biomarker to distinguish between liver cancer cases and controls.
Simple method for making a hyperboloid lens (1980)

A simple lathe for making hyperboloid lenses has been developed. A cutting tool revolves around the vertical tool spindle, and its edge forms a hyperboloid of one sheet of revolution. A plastic rod is chucked on the main spindle and set at right angles to the hyperboloid of one sheet of revolution formed by the edge of the cutting tool. Plastic rods are easily cut into hyperboloid lenses within 10 min. This simple lathe is very useful for preparing experimental optical systems with small aberration in the laboratory.
A piezoelectric frequency-increased power generator for scavenging low-frequency ambient vibration (2010)

This paper presents the design, fabrication, and testing of a piezoelectric inertial micro power generator for scavenging low-frequency non-periodic vibrations. A mechanism up-converts the ambient vibration frequency to a higher internal operation frequency, in order to achieve better electromechanical coupling and efficiency: enhancing the generators performance at very low frequencies (< 30 Hz). The generator incorporates a bulk piezoelectric ceramic machined using ultrafast laser ablation. The fabricated device generated a peak power of 100 ¿W and an average power of 3.25 ¿W from an input acceleration of 9.8 m/s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at 10 Hz. The device operates over a frequency range of 24 Hz. The internal volume of the generator is 1.2 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> .
Hybrid Laser Printing of 3D, Multiscale, Multimaterial Hydrogel Structures (2019)

Fabrication of multiscale, multi-material three-dimensional (3D) structures at high resolution is difficult using current technologies. This is especially significant when working with hydrated and mechanically weak hydrogel materials. In this work, a new hybrid laser printing (HLP) technology is reported to print complex, multiscale, multimaterial, 3D hydrogel structures with microscale resolution. This technique of fabrication utilizes sequential additive and subtractive modes of material fabrication, that are typically considered as mutually exclusive due to differences in their material processing conditions. Further, compared to current laser writing systems that enforce stringent processing depth limits, HLP is shown to fabricate structures at any depth inside the material. As a proof-of-principle, a Mayan Pyramid with embedded cube-frame is printed using model synthetic polyethylene glycol diacrylate (PEGDA) hydrogel. Printing of ready-to-use open-well chips with embedded microchannels is also demonstrated using PEGDA and gelatin methacrylate (GelMA) hydrogels for potential applications in biomedical sciences. Next, HLP is used in additive and additive modes to print multiscale 3D structures spanning in size from centimeter to micrometers within minutes, which is followed by printing of 3D, multi-material, multiscale structures using this technology. Overall, this work demonstrates that HLP's fabrication versatility can potentially offer a unique opportunity for a range of applications in optics and photonics, biomedical sciences, microfluidics, soft robotics, etc.