gebhart/patrepeval huggingface dataset:
A platform for glycoengineering a polyvalent pneumococcal bioconjugate vaccine using E. coli as a host (2019)

Chemical synthesis of conjugate vaccines, consisting of a polysaccharide linked to a protein, can be technically challenging, and in vivo bacterial conjugations (bioconjugations) have emerged as manufacturing alternatives. Bioconjugation relies upon an oligosaccharyltransferase to attach polysaccharides to proteins, but currently employed enzymes are not suitable for the generation of conjugate vaccines when the polysaccharides contain glucose at the reducing end, which is the case for ~75% of Streptococcus pneumoniae capsules. Here, we use an O-linking oligosaccharyltransferase to generate a polyvalent pneumococcal bioconjugate vaccine with polysaccharides containing glucose at their reducing end. In addition, we show that different vaccine carrier proteins can be glycosylated using this system. Pneumococcal bioconjugates are immunogenic, protective and rapidly produced within E. coli using recombinant techniques. These proof-of-principle experiments establish a platform to overcome limitations of other conjugating enzymes enabling the development of bioconjugate vaccines for many important human and animal pathogens.
Validation of Distributed SDN Control Plane Under Uncertain Failures (2019)

The design of distributed control plane is an essential part of SDN. While there is an urgent need for verifying the control plane, little, however, is known about how to validate that the control plane offers assurable performance, especially across various failures. Such validation is hard due to two fundamental challenges. First, the number of potential failure scenarios could be exponential or even non-enumerable. Second, it is still an open problem to model the performance change when the control plane employs different failure recovery strategies. In this paper, we first characterize the validation of the distributed control plane as a robust optimization problem and further propose a robust validation framework to verify whether a control plane provides assurable performance across various failure scenarios and multiple failure recovery strategies. Then, we prove that identifying an optimal recovery strategy is NP-hard after developing an optimization model of failure recovery. Accordingly, we design two efficient failure recovery strategies, which can well approximate the optimal strategy and further exhibit good performance against potential failures. Furthermore, we design the capacity augmentation scheme when the control plane fails to accommodate the worst failure scenario even with the optimal failure recovery strategy. We have conducted extensive evaluations based on an SDN test bed and large-scale simulations over real network topologies. The evaluation results show the efficiency and effectiveness of the proposed validation framework.
Neural Stem Cells Harvested from Live Brains by Antibody‐Conjugated Magnetic Nanoparticles (2013)

It stems from the magnetism: The extraction of stem/progenitor cells from the brain of live animals is possible using antibodies conjugated to magnetic nanoparticles (Ab-MNPs). The Ab-MNPs are introduced to a rat's brain with a superfine micro-syringe. The stem cells attach to the Ab-MNPs and are magnetically isolated and removed. They can develop into neurospheres and differentiate into different types of cells outside the subject body. The rat remains alive and healthy.
Uplink power control based on receiver noise measurementsin satellitecommunication systems (1996)

The authors describe a novel procedure for uplink power control in a multicarrier satellite communication system. The purpose of uplink power control is to compensate for rain attenuation so that all carriers are at the same power level at the input of the satellite nonlinear amplifier. The presence and amount of rain attenuation is predicted by continuous monitoring of the receiver noise power. Attractive features of the proposed scheme include its conceptual simplicity, ease of implementation, applicability to a wide variety of scenarios, and avoidance of the undesirable overhead, coordination, and delay requirements associated with previously used methods.
Improved Methods for the Synthesis of Irbesartan, an Antihypertensive Active Pharmaceutical Ingredient (2007)

Abstract New methods for the preparation of irbesartan 1 have been described. The dehydration and tetrazole formation in one step from substituted cyclopentane derivative 7 with tributyltin chloride and sodium azide is described. Selective hydrolysis of nitrile 3 with HCl has also been described in the preparation of N‐acylaminocyclopentane‐2‐carboxylic acid 4, which is the key intermediate for the preparation of irbesartan. The impurity profiling of irbesartan has also been discussed.
Investigation of Coal Tar Mobility at a Former MGP Site (2009)

The presence of coal tar in the subsurface of former manufactured gas plant sites poses an environmental hazard and a potential threat to public health. Coal tar can release various chemical compounds that are transported into the groundwater. Before any efforts can be made to remove coal tar from contaminated subsurface soils, it is recommended to characterize coal tar properties and composition and to delineate the residual saturation point between mobile and immobile coal tar. This paper presents a new innovative field device, the Res-SAT field tool, and laboratory procedures that can be used to determine the saturation-capillary pressure relationship for a soil-water coal-tar system and the critical pressure for coal tar mobility.
Mechanism of the Vascular Action of Parathyroid Hypertensive Factor (1994)

Journal of Cardiovascular Pharmacology™ is a peer reviewed, multidisciplinary journal that publishes original articles and pertinent review articles on basic and clinical aspects of cardiovascular pharmacology. Appropriate subjects include new drug development and evaluation, physiological and pharmacological bases of drug action, metabolism, drug interactions and side effects, clinical results with new and established agents and novel methods. The focus is on pharmacology in its broadest applications, incorporating not only traditional approaches, but new approaches to the development of pharmacological agents and the prevention and treatment of cardiovascular diseases.
Optical LDPC decoders for beyond 100 Gbits/s optical transmission (2009)

We present an optical low-density parity-check (LDPC) decoder suitable for implementation above 100 Gbits/s, which provides large coding gains when based on large-girth LDPC codes. We show that a basic building block, the probabilities multiplier circuit, can be implemented using a Mach-Zehnder interferometer, and we propose corresponding probabilistic-domain sum-product algorithm (SPA). We perform simulations of a fully parallel implementation employing girth-10 LDPC codes and proposed SPA. The girth-10 LDPC(24015,19212) code of the rate of 0.8 outperforms the BCH(128,113)xBCH(256,239) turbo-product code of the rate of 0.82 by 0.91 dB (for binary phase-shift keying at 100 Gbits/s and a bit error rate of 10(-9)), and provides a net effective coding gain of 10.09 dB.
Assessing mechanical properties of tissue phantoms with non-contact optical coherence elastography and Michelson interferometric vibrometry (2015)

Purpose : Elastography is an emerging method for detecting the pathological changes in tissue biomechanical properties caused by various diseases. In this study, we have compared two methods of noncontact optical elastography for quantifying Young’s modulus of tissue-mimicking agar phantoms of various concentrations: a laser Michelson interferometric vibrometer and a phase-stabilized swept source optical coherence elastography system. Methods : The elasticity of the phantoms was estimated from the velocity of air-pulse induced elastic waves as measured by these two techniques. Results : The results show that both techniques were able to accurately assess the elasticity of the samples as compared to uniaxial mechanical compression testing. Conclusion : The laser Michelson interferometric vibrometer is significantly more cost-effective, but it cannot directly provide the elastic wave temporal profile, nor can it offer in-depth information.
Holistic Discourse Coherence Annotation for Noisy Essay Writing (2013)

This paper reviews annotation schemes used for labeling discourse coherence in well-formed and noisy (essay) data, and it describes a system that we have developed for automated holistic scoring of essay coherence. We review previous, related work on unsupervised computational approaches to evaluating discourse coherence and focus on a taxonomy of discourse coherence schemes classified by their different goals and types of data. We illustrate how a holistic approach can be successfully used to build systems for noisy essay data, across domains and populations. We discuss the model features related to human scoring guide criteria for essay scoring, and the importance of using model features relevant to these criteria for the purpose of generating meaningful scores and feedback for students and test-takers. To demonstrate the effectiveness of a holistic annotation scheme, we present results of system evaluations.
IGroup (2006)

In this paper, we propose, IGroup, an efficient and effective algorithm that organizes Web image search results into clusters. IGroup is different from all existing Web image search results clustering algorithms that only cluster the top few images using visual or textual features. Our proposed algorithm first identifies several query-related semantic clusters based on a key phrases extraction algorithm originally proposed for clustering general Web search results. Then, all the resulting images are separated and assigned to corresponding clusters. As a result, all the resulting images are organized into a clustering structure with semantic level. To make the best use of the clustering results, a new user interface (UI) is proposed. Different from existing Web image search interfaces, which show only a limited number of suggested query terms or representative image thumbnails of some clusters, the proposed interface displays both representative thumbnails and appropriate titles of semantically coherent image clusters. Comprehensive user studies have been completed to evaluate both the clustering algorithm and the new UI.
A Three-Component Biomarker Panel for Prediction of Dengue Hemorrhagic Fever (2012)

Dengue virus infections are a major cause of morbidity in tropical countries. Early detection of dengue hemorrhagic fever (DHF) may help identify individuals that would benefit from intensive therapy. Predictive modeling was performed using 11 laboratory values of 51 individuals (38 DF and 13 DHF) obtained on initial presentation using logistic regression. We produced a robust model with an area under the curve of 0.9615 that retained IL-10 levels, platelets, and lymphocytes as the major predictive features. A classification and regression tree was developed on these features that were 86% accurate on cross-validation. The IL-10 levels and platelet counts were also identified as the most informative features associated with DHF using a Random Forest classifier. In the presence of polymerase chain reaction-proven acute dengue infections, we suggest a complete blood count and rapid measurement of IL-10 can assist in the triage of potential DHF cases for close follow-up or clinical intervention improving clinical outcome.
Scalable music recommendation by search (2007)

The growth of music resources on personal devices and Internet radio has increased the need for music recommendations. In this paper, aiming at providing an efficient and general solution, we present a search-based solution for scalable music recommendations. In this solution a music piece is first transformed to a music signature sequence in which each signature characterizes the timbre of a local music clip. Based on such signatures, a scale-sensitive method is then proposed to index the music pieces for similarity search, using the locality sensitive hashing (LSH). The scale-sensitive method can numerically find the appropriate parameters for indexing various scales of music collections, and thus can guarantee a proper number of nearest neighbors are found in search. In the recommendation stage, representative signatures from snippets of a seed piece are extracted as query terms, to retrieve pieces with similar melodies for suggestions. We also design a relevance-ranking function to sort the search results, based on the criteria that include matching ratio, temporal order, term weight, and matching confidence. Finally, with the search results, we propose a strategy to generate a dynamic playlist which can automatically expand with time. Evaluations of several music collections at various scales showed that our approach achieves encouraging results in terms of recommendation satisfaction and system scalability.
A Grazing Incidence Monochromator With A Varied-Space Plane Grating For Synchrotron Radiation (1984)

A grazing incidence monochromator to scan the 5 - 100 Å wavelength range of synchrotron radiation is designed by taking advantage of the focusing property of a varied-space plane grating ruled with a numerically controlled ruling engine. The plane grating monochromator uses only two plane surfaces for reflection optics so that high throughput in the soft x-ray region is expected.
Structural characterization of monoclonal antibodies targeting C-terminal Ser<sup>404</sup> region of phosphorylated tau protein (2019)

Targeting tau with immunotherapies is currently the most common approach taken in clinical trials of patients with Alzheimer’s disease. The most prominent pathological feature of tau is its hyperphosphorylation, which may cause the protein to aggregate into toxic assemblies that collectively lead to neurodegeneration. Of the phospho-epitopes, the region around Ser396/Ser404 has received particular attention for therapeutic targeting because of its prominence and stability in diseased tissue. Herein, we present the antigen-binding fragment (Fab)/epitope complex structures of three different monoclonal antibodies (mAbs) that target the pSer404 tau epitope region. Most notably, these structures reveal an antigen conformation similar to a previously described pathogenic tau epitope, pSer422, which was shown to have a β-strand structure that may be linked to the seeding core in tau oligomers. In addition, we have previously reported on the similarly ordered conformation observed in a pSer396 epitope, which is in tandem with pSer404. Our data are the first Fab structures of mAbs bound to this epitope region of the tau protein and support the existence of proteopathic tau conformations stabilized by specific phosphorylation events that are viable targets for immune modulation.
Figure S2 from <i>In Vivo</i> Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The <i>ϕ</i>-Index (2023)

<p>Distributions of the median Euclidean distance between the near and far ROIs for each patient according to their EGFRvIII status. We note no significant difference between the two groups (p-value=0.6728).</p>
Enhancement- and depletion-mode vertical-channel m.o.s. gated thyristors (1979)

A new gate structure is described for power thyristors which uses the m.o.s. field effect to control the anode breakover voltage. Experimental devices have been fabricated using a V-groove etched in (100) oriented wafers and forming the gate in these grooves. Both enhancement- and depletion-mode devices have been demonstrated.
Applications for Progressive Barcodes (2014)

Color barcodes offer increased density over two-dimensional barcodes, which can be taken advantage of to embed longer data strings in the same printed/displayed area. However, the color channels also offer the possibility of containing multiple, distinct sets of data in the same “hybrid” mark.The four-dimensional progressive barcode is a printed mark that does not change in size as it is used to represent different stages (or “states”) in a workflow. The addition of progressive information to a barcode allows it to change through time—supporting many different information lifecycles.1,2 This means that the use of the same barcode location for multiple barcodes through time is possible. Progressive barcodes can be also used to support two (or more) applications or services in the same object. One of these can be standards compliant and another can be proprietary or customized. Thus, a “hybrid” of two functions, represented by two planes of information, is combined in a single mark.These two planes of information include different densities of information. The first plane is binary, with high contrast between the two binary encoding (usually black and white) tiles in the barcode. The second is n-ary, and utilizes inks that are invisible to the binary barcode reading software. This is accomplished with highly saturated colors, but it can also be used with IR, UV or other “invisible” inks.In this article, the authors will demonstrate several types of applications and services that are enabled by the progressive barcode. They are most effectively deployed when there are multiple types of information payloads needed for a single object—e.g., point-of-sale and customer interrogation of the product. This also makes them useful in a variety of document/physical item workflows.
Photovoltaic properties of Cu(In,Ga)Se/sub 2/ thin film solar cell fabricated by coevaporation process (2002)

Thin film solar cells based on Cu(In,Ga)Se/sub 2/ films were fabricated, and their junction and photovoltaic properties were investigated. Ga in CuInSe/sub 2/ thin films formed by the so-called "bilayer process" was incorporated homogeneously. The fabricated cell structure was glass/Mo/Cu(In,Ga)Se/sub 2//CdS/ZnO/ITO(/MgF/sub 2/). The incorporation of Ga into CuInSe/sub 2/ films up to about 20 mol% improved the photovoltaic performance. From the study of photoluminescence, capacitance-voltage and current-voltage characteristics, it was clarified that the incorporation of Ga not only widened the bandgap energy, but also played an important role in the effect which yields hole concentration. The best cell with an AR-coating (MgF/sub 2/) exhibited an efficiency of 15.2%; Jsc=33.9 mA/cm/sup 2/, Voc=0.616 V, FF=0.730. The device performance can be improved by the development of the film with higher hole concentration, keeping the crystalline quality.
Ureteric retrieval net: comparison with stone extraction by Dormia baskets in an <i>in vitro</i> porcine model (1994)

This newly developed ureteric retrieval net has a compact design, resulting in minimal resistance during retraction. Its smooth hydrophilic outer surface enhances scooping properties against the luminal wall. The mesh is similar to that in nylon stockings--porous enough to allow flow, yet small enough to capture fragments. It can capture numerous small fragments with one scoop, but can easily disengage them if extraction is not possible. The loop encompasses the entire lumen with the 'pusher' offset to a side wall, allowing maximal space and visualization, and the device can dilate the ureter to facilitate extraction. Clinical studies are in progress to evaluate the full potential of this new device.
Three-dimensional Printing of Silver Microarchitectures Using Newtonian Nanoparticle Inks (2017)

Although three-dimensional (3D) printing has recently emerged as a technology to potentially bring about the next industrial revolution, the limited selection of usable materials restricts its use to simple prototyping. In particular, metallic 3D printing with submicrometer spatial resolution is essential for the realization of 3D-printed electronics. Herein, a meniscus-guided 3D printing method that exploits a low-viscosity (∼7 mPa·s) silver nanoparticle (AgNP) ink meniscus with Newtonian fluid characteristics (which is compatible with conventional inkjet printers) to fabricate 3D silver microarchitectures is reported. Poly(acrylic acid)-capped AgNP ink that exhibits a continuous ink flow through a confined nozzle without aggregation is designed in this study. Guiding the ink meniscus with controlled direction and speed enables both vertical pulling and layer-by-layer processing, resulting in the creation of 3D microobjects with designed shapes other than those for simple wiring. Various highly conductive (>10<sup>4</sup> S·cm<sup>-1</sup>) 3D metallic patterns are demonstrated for applications in electronic devices. This research is expected to widen the range of materials that can be employed in 3D printing technology, with the aim of moving 3D printing beyond prototyping and into real manufacturing platforms for future electronics.
Imaging Mutant Huntingtin Aggregates: Development of a Potential PET Ligand (2020)

Mutant huntingtin (mHTT) protein carrying the elongated N-terminal polyglutamine (polyQ) tract misfolds and forms protein aggregates characteristic of Huntington's disease (HD) pathology. A high-affinity ligand specific for mHTT aggregates could serve as a positron emission tomography (PET) imaging biomarker for HD therapeutic development and disease progression. To identify such compounds with binding affinity for polyQ aggregates, we embarked on systematic structural activity studies; lead optimization of aggregate-binding affinity, unbound fractions in brain, permeability, and low efflux culminated in the discovery of compound <b>1</b>, which exhibited target engagement in autoradiography (ARG) studies in brain slices from HD mouse models and postmortem human HD samples. PET imaging studies with <sup>11</sup>C-labeled <b>1</b> in both HD mice and WT nonhuman primates (NHPs) demonstrated that the right-hand-side labeled ligand [<sup>11</sup>C]-<b>1R</b> (CHDI-180R) is a suitable PET tracer for imaging of mHTT aggregates. [<sup>11</sup>C]-<b>1R</b> is now being advanced to human trials as a first-in-class HD PET radiotracer.
Production of ethanol from refinery waste gases. Phase 2, technology development, annual report (1995)

Oil refineries discharge large volumes of H{sub 2}, CO, and CO{sub 2} from cracking, coking, and hydrotreating operations. This program seeks to develop a biological process for converting these waste gases into ethanol, which can be blended with gasoline to reduce emissions. Production of ethanol from all 194 US refineries would save 450 billion BTU annually, would reduce crude oil imports by 110 million barrels/year and emissions by 19 million tons/year. Phase II efforts has yielded at least 3 cultures (Clostridium ljungdahlii, Isolate O-52, Isolate C-01) which are able to produce commercially viable concentrations of ethanol from CO, CO{sub 2}, and H{sub 2} in petroleum waste gas. Single continuous stirred tank reactor studies have shown that 15-20 g/L of ethanol can be produced, with less than 5 g/L acetic acid byproduct. Culture and reactor optimization in Phase III should yield even higher ethanol concentrations and minimal acetic acid. Product recovery studies showed that ethanol is best recovered in a multi-step process involving solvent extraction/distillation to azeotrope/azeotropic distillation or pervaporation, or direct distillation to the azeotrope/azeotropic distillation or pervaporation. Projections show that the ethanol facility for a typical refinery would require an investment of about $30 million, which would be returned in less than 2 years.
Stabilizing synthetic DNA for long-term data storage with earth alkaline salts (2020)

Rapid aging tests (70 °C, 50% RH) of solid state DNA dried in the presence of various salt formulations, showed the strong stabilizing effect of calcium phosphate, calcium chloride and magnesium chloride, even at high DNA loadings (>20 wt%). A DNA-based digital information storage system utilizing the stabilizing effect of MgCl<sub>2</sub> was tested by storing a DNA file, encoding 115 kB of digital data, and the successful readout of the file by sequencing after accelerated aging.