gebhart/patrepeval huggingface dataset:
Scalable trapped ion quantum computation with a probabilistic ion-photon mapping (2004)

We propose a method for scaling trapped ions for large-scale quantum computation and communication based on a probabilistic ion-photon mapping. Deterministic quantum gates between remotely located trapped ions can be achieved through detection of spontaneously-emitted photons, accompanied by the local Coulomb interaction between neighboring ions. We discuss gate speeds and tolerance to experimental noise for different probabilistic entanglement schemes.
Development of an ASO therapy for Angelman syndrome by targeting an evolutionarily conserved region at the start of the <i>UBE3A-AS</i> transcript (2021)

ABSTRACT Angelman syndrome is a devastating neurogenetic disorder for which there is currently no effective treatment. It is caused by mutations or epimutations affecting the expression or function of the maternally inherited allele of the ubiquitin-protein ligase E3A ( UBE3A ) gene. The paternal UBE3A allele is imprinted in neurons of the central nervous system (CNS) by the UBE3A antisense ( UBE3A-AS ) transcript, which represents the distal end of the SNHG14 transcription unit. Reactivating the expression of the paternal UBE3A allele in the CNS has long been pursued as a therapeutic option for Angelman syndrome. Here, we designed and optimized antisense oligonucleotides (ASO) targeting an evolutionarily conserved region demarcating the start of the human UBE3A-AS transcript and show that ASOs targeting this region can reverse imprinting of UBE3A in cultured Angelman syndrome neurons and throughout the CNS of a non-human primate model. Findings from this study advanced the first investigational molecular therapy for Angelman syndrome into clinical development (ClinicalTrials.gov, NCT04259281 ). SUMMARY Here, we describe the preclinical studies supporting the first investigational molecular therapy for Angelman syndrome to advance into clinical development (ClinicalTrials.gov, NCT04259281 ).
Re‐Based Heterogeneous Catalysts for Olefin Metathesis Prepared by Surface Organometallic Chemistry: Reactivity and Selectivity (2003)

Herein we describe the catalytic activity of 1, a well-defined Re alkylidene complex supported silica, in the reaction of olefin metathesis. This system is highly active for terminal and internal olefins with initial rates up to 0.7 mol per mol Re per s. It also catalyses the self-metathesis of methyl oleate (MO) without the need of co-catalysts. The turnover numbers can reach up to 900 for MO, which is unprecedented for a heterogeneous Re-based catalyst. Moreover the use of silica as a support can bring major advantages, such as the possibility to use branched olefins like isobutene, which are usually incompatible with alumina-based supports; therefore, the formation of isoamylene from the cross-metathesis of propene and isobutene can be performed. All these results are in sharp contrast to what has been found for other silica- or alumina-supported rhenium oxide systems, which are either completely inactive (silica system) or typically need co-catalysts when functionalised olefins are used. Finally the initiation step corresponds to a cross-metathesis reaction to give a 3:1 mixture of 3,3-dimethylbutene and trans-4,4-dimethylpent-2-ene, and make this catalyst the first generation of well-defined Re-based heterogeneous catalysts.
Protein engineering of nitrilase for chemoenzymatic production of glycolic acid (2007)

A key step in a chemoenzymatic process for the production of high-purity glycolic acid (GLA) is the enzymatic conversion of glycolonitrile (GLN) to ammonium glycolate using a nitrilase derived from Acidovorax facilis 72W. Protein engineering and over-expression of this nitrilase, combined with optimized fermentation of an E. coli transformant were used to increase the enzyme-specific activity up to 15-fold and the biocatalyst-specific activity up to 125-fold. These improvements enabled achievement of the desired volumetric productivity and biocatalyst productivity for the conversion of GLN to ammonium glycolate.
A Whole-Genome Shotgun Optical Map of <i>Yersinia pestis</i> Strain KIM (2002)

Yersinia pestis is the causative agent of the bubonic, septicemic, and pneumonic plagues (also known as black death) and has been responsible for recurrent devastating pandemics throughout history. To further understand this virulent bacterium and to accelerate an ongoing sequencing project, two whole-genome restriction maps (XhoI and PvuII) of Y. pestis strain KIM were constructed using shotgun optical mapping. This approach constructs ordered restriction maps from randomly sheared individual DNA molecules directly extracted from cells. The two maps served different purposes; the XhoI map facilitated sequence assembly by providing a scaffold for high-resolution alignment, while the PvuII map verified genome sequence assembly. Our results show that such maps facilitated the closure of sequence gaps and, most importantly, provided a purely independent means for sequence validation. Given the recent advancements to the optical mapping system, increased resolution and throughput are enabling such maps to guide sequence assembly at a very early stage of a microbial sequencing project.
Spin-Phonon-Photon Strong Coupling in a Piezomechanical Nanocavity (2022)

We introduce a hybrid tripartite quantum system for strong coupling between a semiconductor spin, a mechanical phonon, and a microwave photon. Consisting of a piezoelectric resonator with an integrated diamond strain concentrator, this system achieves microwave-acoustic and spin-acoustic coupling rates $\sim$MHz or greater, allowing for simultaneous ultra-high cooperativities ($\sim 10^3$ and $\sim 10^2$, respectively). From finite-element modeling and master equation simulations, we estimate photon-to-spin quantum state transfer fidelities exceeding 0.97 based on separately demonstrated device parameters. We anticipate that this device will enable hybrid quantum architectures that leverage the advantages of both superconducting circuits and solid-state spins for information processing, memory, and networking.
Polyamide–polyether copolymers: A new family of impact‐resistant thermoplastics (1983)

Abstract A new family of thermoplastic polyamide–polyether copolymers that display outstanding impact resistance and are especially useful as hot melt adhesives are described. These polymers are prepared by copolymerizationof polymerized fatty acid derivatives (dimer diamines) and poly(oxyalkylene) diamines with the typical polyamide monomers sebacic acid and piperazine. Impact resistance is apparently achieved through synergistic interaction between the dimer and the polyether portions of the polymers.
Direct UV writing of Bragg grating channel waveguides in a single step process (2003)

We present a development of Direct UV writing that allows simultaneous definition of channel waveguides with or without Bragg gratings in a single process in photosensitivity locked planar silica-on-silicon samples.
A user-independent sensor gesture interface for embedded device (2011)

Sensor based gesture interaction gains increasing attention in ubiquitous computing; however most algorithms suffer from large database for training and user dependency limitation. This paper summarize the gesture generating model, and propose a new physical analysis based gesture recognition method which can fulfill user-independent no-training gesture recognition. It utilizes principle component analysis for energy distribution analysis to bypass the gratitude influence, and extracts the physical characteristics of the gesture trajectory for classification. In our real-time gesture recognition system, first the acceleration data of a gesture is collected through Bluetooth interface between Wii-Remote and PC; then the energy distribution shape is calculated, then several physical trajectory characteristic is organized as motion feature cascade classification. The proposed method is compared with the published method under the Nokia dataset, whose recognition accuracy could achieve 97.35% for user-independent situation.
Rapid Low Temperature Bonding of Silicon to Steel for MEMS Sensors (2004)

We have developed a rapid silicon to steel bonding process used to attach silicon microsensors onto steel. The specific application is to bond silicon based strain sensors to steel structures for real time strain sensing. Steel samples are electroplated with eutectic Pb/Sn alloy (Mp 183°C) and are bonded to silicon dice coated with Cr/Au or Cr/Cu/Ni/PbSn layers. Bonding took place in the inert environment of a rapid thermal annealing (RTA) oven at 220°C for about 20 seconds, which caused minimal damage to the steel samples. The silicon to steel bond survived &gt;1000με of static loading at the steel surface and 1000 cycles of &gt;1000με cyclic strain at the steel surface without failure. Corrosion resistance of the silicon to steel bond was tested by immersion in various oils and salt solutions, and the bonding method thus far has been successful.
Reaction of pyrroles with naphthoquinones. Synthesis of new pyrrolylnaphthoquinone dyes (2000)

Abstract The reaction of 1,4‐naphthoquinone (1) with N ‐alkylpyrroles (2) gives a mixture of 2‐(pyrrol‐2‐yl)‐1,4‐naphthoquinones (3) and 2,5‐bis(1,4‐naphthoquinon‐2‐yl)pyrroles (4). The yields and the ratios of these two products depend greatly on the experimental conditions. The reaction has been extended to 5‐hydroxy‐1,4‐naphthoquinone (juglone, 5) and 1,2‐naphthoquinone (6). New pyrrolylnaphthoquinones are obtained.
Model-based synthesis of plucked string instruments by using a class of scattering recurrent networks (2000)

A physical modeling method for electronic music synthesis of plucked-string tones by using recurrent networks is proposed. A scattering recurrent network (SRN) which is used to analyze string dynamics is built based on the physics of acoustic strings. The measured vibration of a plucked string is employed as the training data for the supervised learning of the SRN. After the network is well trained, it can be regarded as the virtual model for the measured string and used to generate tones which can be very close to those generated by its acoustic counterpart. The "virtual string" corresponding to the SRN can respond to different "plucks" just like a real string, which is impossible using traditional synthesis techniques such as frequency modulation and wavetable. The simulation of modeling a cello "A"-string demonstrates some encouraging results of the new music synthesis technique. Some aspects of modeling and synthesis procedures are also discussed.
Safety and Vision Outcomes of Subretinal Gene Therapy Targeting Cone Photoreceptors in Achromatopsia (2020)

ClinicalTrials.gov Identifier: NCT02610582.
Automatic audio segmentation using a measure of audio novelty (2002)

The paper describes methods for automatically locating points of significant change in music or audio, by analyzing local self-similarity. This method can find individual note boundaries or even natural segment boundaries such as verse/chorus or speech/music transitions, even in the absence of cues such as silence. This approach uses the signal to model itself, and thus does not rely on particular acoustic cues nor requires training. We present a wide variety of applications, including indexing, segmenting, and beat tracking of music and audio. The method works well on a wide variety of audio sources.
Practical Device for Precise Cutting of Costal Cartilage Grafts to Uniform Thickness (2011)

Our study demonstrates the precision of using a mechanical slicing device to section costal cartilage to a clinically relevant and uniform thickness. This mechanized technology may increase accuracy and reduce carving time required for using costal cartilage tissue in head and neck reconstruction.
Inactivation of Herpes Simplex Viruses by Nonionic Surfactants (1978)

Nonionic surface-active agents possessing ether or amide linkages between the hydrophillic and hydrophobic portions of the molecule rapidly inactivated the infectivity of herpes simplex viruses. The activity stemmed from the ability of nonionic surfactants to dissolve lipid-containing membranes. This was confirmed by observing surfactant destruction of mammalian cell plasma membranes and herpes simplex virus envelopes. Proprietary vaginal contraceptive formulations containing nonionic surfactants also inactivated herpes simplex virus infectivity. This observation suggests that nonionic surfactants in appropriate formulation could effectively prevent herpes simplex virus transmission.
Characterization of an <i>Agrobacterium tumefaciens</i> <scp>d</scp> -Psicose 3-Epimerase That Converts <scp>d</scp> -Fructose to <scp>d</scp> -Psicose (2006)

The noncharacterized gene previously proposed as the D-tagatose 3-epimerase gene from Agrobacterium tumefaciens was cloned and expressed in Escherichia coli. The expressed enzyme was purified by three-step chromatography with a final specific activity of 8.89 U/mg. The molecular mass of the purified protein was estimated to be 132 kDa of four identical subunits. Mn2+ significantly increased the epimerization rate from D-fructose to D-psicose. The enzyme exhibited maximal activity at 50 degrees C and pH 8.0 with Mn2+. The turnover number (k(cat)) and catalytic efficiency (k(cat)/Km) of the enzyme for D-psicose were markedly higher than those for d-tagatose, suggesting that the enzyme is not D-tagatose 3-epimerase but D-psicose 3-epimerase. The equilibrium ratio between D-psicose and D-fructose was 32:68 at 30 degrees C. D-Psicose was produced at 230 g/liter from 700-g/liter D-fructose at 50 degrees C after 100 min, corresponding to a conversion yield of 32.9%.
Understanding Diagnostic Testing for Periodontal Diseases (1995)

Probability computations are used to characterize new periodontal diagnostic tests and are an integral facet of risk assessment for periodontal diseases. However, misinterpretation of these data can result in confusion and erroneous conclusions regarding the relationship of test results to the presence or absence of disease in a subject, or to episodes of periodontal destruction at specific sites. This paper was written to provide clinicians with a primer to help in understanding calculations used to evaluate diagnostic tests and risk assessment.
Ranking on graph data (2006)

In ranking, one is given examples of order relationships among objects, and the goal is to learn from these examples a real-valued ranking function that induces a ranking or ordering over the object space. We consider the problem of learning such a ranking function when the data is represented as a graph, in which vertices correspond to objects and edges encode similarities between objects. Building on recent developments in regularization theory for graphs and corresponding Laplacian-based methods for classification, we develop an algorithmic framework for learning ranking functions on graph data. We provide generalization guarantees for our algorithms via recent results based on the notion of algorithmic stability, and give experimental evidence of the potential benefits of our framework.
Water-Soluble Biodegradable Polyphosphazenes Containing <i>N</i>-Ethylpyrrolidone Groups (2005)

Novel water-soluble biodegradable polyphosphazenes are described. Polymers are constructed on the basis of a biodegradable polyphosphazene backbone to mimic the structure of poly(vinylpyrrolidone), PVP. Poly{di[2-(2-oxo-1-pyrrolidinyl)ethoxy]phosphazene}, PYRP, and its copolymers containing biologically active carboxylatophenoxy side groups have been synthesized. The ability of these polymers to degrade in aqueous environment at 37 °C is demonstrated by light scattering-GPC and NMR studies. The degradation is manifested by the gradual decrease in the molecular weight and release of the side group −1-(2-hydroxyethyl)-2-pyrrolidone. It has been shown that the incorporation of N-ethylpyrrolidone containing side groups in the polymer structure can modulate degradation profiles of phosphazene copolymers. The kinetics of hydrolytic degradation and the effect of pH on the degradation rate have been investigated.
Applicability of SSTDR Analysis of Complex Loads (2019)

Spread spectrum time domain reflectometry (SSTDR) can be used to measure complex impedances in live electrical systems by evaluating the shape and magnitude of the reflected signature. A range of capacitors or inductors can be identified, but above and below this range, they cannot be distinguished from open or short circuits. This range depends on the frequency band of the reflectometry system and characteristic impedance of the transmission line. This can be used to characterize changes in complex impedance for the purpose of fault detection in complex loads, such as PV panels and systems.
Completeley optical coincidence logic employing a dye laser (1975)

We report the theory and experimental demonstration of a laser device which performs the functions of binary arithmetic completely optically. The coincidence circuit employs polarization coding of the logic variables and is based upon the bistable polarization behavior of a dye laser in a birefringent cavity.
Using PLT Data To Estimate the Size of Natural Fractures (2009)

Abstract In naturally fractured reservoirs, determining fracture properties, such as size and permeability, is difficult due to the limited data about the fractures. The primary information that is available, mainly from image logs or core, is known only at the wellbore; however, the fractures can be local to the wellbore region, or they can extend hundreds of feet from the well. If fractures can be characterized more accurately, then flow paths and flow behaviors in the reservoir can be better delineated. Thus, rates and declines in primary production and breakthrough times of injected fluids can be better estimated, and the field can be developed more efficiently. The goal of our work has been to combine dynamic data with static data to better characterize fracture properties, especially the size of fractures away from the wellbore. PLT information can be used in conjunction with static data to more accurately define fracture properties such as size and permeability. A single-well single-phase flow-simulation model is constructed with discrete fractures at each location where wellbore inflow is observed with a PLT. A program has been created to automatically perturb the lengths and heights of model fractures until their flow response matches the actual measured response (i.e. history matching PLT data by changing fracture properties). This program is designed for wells that intersect multiple fractures. The tool has been used on a number of different examples, and matches are achieved in all cases. Fracture lengths range from a few feet to thousands of feet. The optimization is efficient as it generally finds solutions after iterating through only about 20 flow simulations. To demonstrate the various capabilities of the program, different options are used in different cases. One example is matched with six different models to provide a range of uncertainty for the fracture sizes.
Protein Contents in Different Peanut Varieties and Their Relationship to Gel Property (2013)

The objective of this work was to study the contribution of different peanut varieties with regard to their arachin and conarachin fractions, and their respective subunits to protein gel properties. It was found that the proteins of various cultivars could be classified into two groups according to the lack of the 35.5 kDa acidic subunit of the arachin. Two peanut cultivars, Yueyou7 and Qinglan8, had the highest content of arachin (62.3%) and conarachin (53.5%), respectively. Three indexes, namely, hardness, springiness, and cohesiveness, were used to describe the protein gel properties. An efficient approach was developed to characterize the three gel properties into one index. The correlation coefficients between the newly depicted index and the original ones were 0.87, 0.41, and 0.47, which corresponded to hardness, springiness, and cohesiveness, respectively. Principal component analysis, linear discriminant analysis, and cluster analysis were used as classification techniques. About 40 varieties were classified into three groups by principal component analysis and all group members determined by principal component analysis are in the predicted group that 100.0% of original grouped cases correctly classified by linear discriminant analysis. The result of cluster analysis had some similarities with the principal component analysis.
Robust radiation therapy optimization using simulated treatment courses for handling deformable organ motion (2020)

We describe a radiation therapy treatment plan optimization method that explicitly considers the effects of interfraction organ motion through optimization on the clinical target volume (CTV), and investigate how it compares to conventional planning using a planning target volume (PTV). The method uses simulated treatment courses generated using patient images created by a deformable registration algorithm to replicate the effects of interfraction organ motion, and performs robust optimization aiming to achieve CTV coverage under all simulated treatment courses. The method was applied to photon-mediated treatments of three prostate cases and compared to conventional, PTV-based planning with margins selected to achieve similar CTV coverage as the robustly optimized plans. Clinical goals for the CTV and healthy tissue were used in comparison between the two types of plans. Out of the two clinical goals for overdosage of the CTV, the three robustly optimized plans violated respectively 2, 2, and 0 goals in the mean over the scenarios, whereas none of the PTV plans violated these goals. Of the ten clinical goals for rectum, bladder, anal canal, and bulbus, the robustly optimized plans violated respectively 0, 1, and 1 goals in the mean, whereas the PTV plans violated 5, 7, and 4 goals. Compared to PTV-based planning, the inclusion of treatment course scenarios in the optimization has the potential to reduce the dose to healthy tissues while retaining a high probability of target coverage. This may reduce the need for adaptive replanning.
Surrogate Marker of Preclinical Tuberculosis in Human Immunodeficiency Virus Infection: Antibodies to an 88‐kDa Secreted Antigen of<i>Mycobacterium tuberculosis</i> (1997)

Antibodies to purified, size-fractionated secreted proteins of Mycobacterium tuberculosis in sera from patients with human immunodeficiency virus (HIV) infection and active tuberculosis (HIV/TB patients), and in stored sera obtained from the same patients prior to clinical manifestation of TB, were evaluated by ELISA, and the repertoire of antigens recognized was analyzed by immunoblotting. Compared with non-HIV/TB patients, HIV/TB patients had lower levels of anti-mycobacterial antibodies, and these were directed toward a restricted set of antigens. Antibodies to an 88-kDa secreted antigen were present in the sera of 74% of HIV/TB patients during the years (1.5-6) prior to manifestation of active, clinical tuberculosis, although only 66% were positive by the time tuberculosis was diagnosed. The presence of antibodies to the 88-kDa antigen can serve as a surrogate marker for identifying HIV-infected persons with active, subclinical disease who are at a high risk of developing clinical tuberculosis.
Script-agnostic reflow of text in document images (2011)

Reading text from document images can be difficult on mobile devices due to the limited screen width available on them. While there exist solutions for reflowing Latin-script texts on such devices, these solutions do not work well for images of other scripts or combinations of scripts, since they rely on script-specific characteristics or OCR. We present a technique that reflows text in document images in a manner that is agnostic to the script used to compose them. Our technique achieved over 95% segmentation accuracy for a corpus of 139 images containing text in 4 genetically-distant languages-English, Hindi, Kannada and Arabic. A preliminary user study with a prototype implementation of the technique provided evidence of some of its usability benefits.