gebhart/patrepeval huggingface dataset:
Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine (2018)

RNA-sequencing (RNA-seq) measures RNA abundance in a biological sample but does not provide temporal information about the sequenced RNAs. Metabolic labeling can be used to distinguish newly made RNAs from pre-existing RNAs. Mutations induced from chemical recoding of the hydrogen bonding pattern of the metabolic label can reveal which RNAs are new in the context of a sequencing experiment. These nucleotide recoding strategies have been developed for a single uridine analogue, 4-thiouridine (s<sup>4</sup>U), limiting the scope of these experiments. Here we report the first use of nucleoside recoding with a guanosine analogue, 6-thioguanosine (s<sup>6</sup>G). Using TimeLapse sequencing (TimeLapse-seq), s<sup>6</sup>G can be recoded under RNA-friendly oxidative nucleophilic-aromatic substitution conditions to produce adenine analogues (substituted 2-aminoadenosines). We demonstrate the first use of s<sup>6</sup>G recoding experiments to reveal transcriptome-wide RNA population dynamics.
Causes of death and autopsy findings in a large study cohort of individuals with Cornelia de Lange syndrome and review of the literature (2011)

To identify causes of death (COD) in propositi with Cornelia de Lange syndrome (CdLS) at various ages, and to develop guidelines to improve management and avoid morbidity and mortality, we retrospectively reviewed a total of 426 propositi with confirmed clinical diagnoses of CdLS in our database who died in a 41-year period between 1966 and 2007. Of these, 295 had an identifiable COD reported to us. Clinical, laboratory, and complete autopsy data were completed on 41, of which 38 were obtainable, an additional 19 had autopsies that only documented the COD, and 45 propositi had surgical, imaging, or terminal event clinical documentation of their COD. Proband ages ranged from fetuses (21-40 weeks gestation) to 61 years. A literature review was undertaken to identify all reported causes of death in CdLS individuals. In our cohort of 295 propositi with a known COD, respiratory causes including aspiration/reflux and pneumonias were the most common primary causes (31%), followed by gastrointestinal disease, including obstruction/volvulus (19%). Congenital anomalies accounted for 15% of deaths and included congenital diaphragmatic hernia and congenital heart defects. Acquired cardiac disease accounted for 3% of deaths. Neurological causes and accidents each accounted for 8%, sepsis for 4%, cancer for 2%, renal disease for 1.7%, and other causes, 9% of deaths. We also present 21 representative clinical cases for illustration. This comprehensive review has identified important etiologies contributing to the morbidity and mortality in this population that will provide for an improved understanding of clinical complications, and management for children and adults with CdLS.
Magnetic resonance multitasking for multidimensional assessment of cardiovascular system: Development and feasibility study on the thoracic aorta (2020)

The MT-MACS technique provides high-quality, multidimensional images for a comprehensive assessment of the thoracic aorta. Technical feasibility was demonstrated in healthy subjects and patients with thoracic aortic diseases. Further clinical validation is warranted.
Bifurcation-based adiabatic quantum computation with a nonlinear oscillator network (2016)

The dynamics of nonlinear systems qualitatively change depending on their parameters, which is called bifurcation. A quantum-mechanical nonlinear oscillator can yield a quantum superposition of two oscillation states, known as a Schrodinger cat state, via quantum adiabatic evolution through its bifurcation point. Here we propose a quantum computer comprising such quantum nonlinear oscillators, instead of quantum bits, to solve hard combinatorial optimization problems. The nonlinear oscillator network finds optimal solutions via quantum adiabatic evolution, where nonlinear terms are increased slowly, in contrast to conventional adiabatic quantum computation or quantum annealing, where quantum fluctuation terms are decreased slowly. As a result of numerical simulations, it is concluded that quantum superposition and quantum fluctuation work effectively to find optimal solutions. It is also notable that the present computer is analogous to neural computers, which are also networks of nonlinear components. Thus, the present scheme will open new possibilities for quantum computation, nonlinear science, and artificial intelligence.
Glass Compositions for Producing Pressure and Temperature Insensitive Optical Fiber Coatings and Optical Fibers Therefrom. (1985)

Abstract : This invention relates generally to glass compositions and more particularly to low compressibility, low expansivity glass compositions for use with optical fibers. Pressure and temperature insensitive optical fibers are produced using a Ta205 based glass composition which has a high bulk modulus and a low thermal expansion coefficient. The glass composition can function as the classing in the optical fiber or as a protective coating which surrounds the cladding thereby protecting the fiber from fluctuations in temperature and pressure.
Enhanced Delivery of Insulin through Acrylamide-Modified Chitosan Containing Smart Carrier System (2022)

The present study develops on insulin-release studies from the chitosan-amide-modified stimuli-responsive polymers formed from various fatty acids including stearic acid, oleic acid, linoleic acid, and linolenic acid. This is the continuation of an earlier reported study that investigates the insulin-release profiles of chitosan-modified fatty acid amides (without stimuli responsive polymers). Following the synthesis and characterization of many different fatty acid amides with a varying amount of unsaturation, the insulin drug loading and release effects were compared among <i>N</i>-isopropylacrylamide (NIPAm), a thermo-responsive polymer, and 2-acrylamide-2-methylpropane sulfonic acid (AMPS), a pH-responsive polymer-modified hydrogel that is expected to enhance environmental response and the controllability of release. Finally, drug release effects were studied to investigate the drug release mechanisms with the help of five different pharmacokinetic models including the zero-order, first-order, Higuchi, Korsmeyers-Peppas, and Hixson models. The results indicate that the Higuchi and Hixson models are valid in terms of the operation of the NIPAm and AMPS matrices during the delivery of insulin.
Expression of Transcripts Encoding a Parathyroid Hormone-Related Peptide in Abnormal Human Parathyroid Tissues* (1989)

A PTH-related peptide (PTHRP) has been identified and its cDNA cloned from human tumors associated with the syndrome of humoral hypercalcemia of malignancy. The human PTHRP gene has been recently isolated and found to be a complex transcriptional unit using multiple promoters and containing alternatively spliced 3' exons which result in three mRNA classes, each class encoding a PTHRP with a unique carboxy-terminus. The PTHRP gene appears to be expressed in a number of normal tissues, and PTHRP transcripts have been previously reported to be overexpressed in a small sample of human parathyroid adenomas. In the present study we surveyed RNA prepared from a total of 60 abnormal human parathyroid glands for PTHRP gene expression using a combination of Northern blotting and RNase protection techniques. Apparent overexpression of PTHRP mRNA was observed in two thirds of parathyroid adenomas, whereas no overexpression was found in 7 examples of sporadic primary hyperplasia, 5 examples of secondary hyperplasia, and 3 examples of parathyroid carcinoma. Apparent overexpression was also observed in 1 of 4 cases of multiple endocrine neoplasia type 1, 1 of 2 examples of multiple endocrine neoplasia type 2, and 1 gland considered to represent tertiary hyperparathyroidism. Northern analysis of poly(A)+ RNA prepared from three representative adenomas using region-specific probes indicated that two putative promoters are used and revealed a pattern of preferential splicing of transcripts to include the most distal 3' exon. These findings suggest that the PTHRP gene is commonly overexpressed in adenomatous parathyroid glands, but not in sporadic primary hyperplasia, that this overexpression does not seem to be dependent on the use of a single specific promoter, and that adenomatous parathyroid cells appear to preferentially use one of several alternative splicing pathways. It is presently not known whether PTHRP is secreted by abnormal parathyroid tissues and, if so, in what form.
Performance and Kinetics of a Solid Amine Sorbent for Carbon Dioxide Removal (2011)

The kinetics of the reaction between CO2 and amine/bentonite particle were estimated over the range of 303–363 K from adsorption data obtained by TGA. The weight percent of amine, reaction temperature, and particle diameter were considered as experimental variables. The sorbent maximum or equilibrium CO2 uptake was found to be linearly dependent on temperature; decreasing with increasing temperature when tested in a 100% CO2 environment. Reactivity data for amine/bentonite particle with CO2 were presented and discussed. On the basis of the isothermal TGA results, reaction order and the value of activation energy have been obtained. These kinetic parameters are similar to those reported for MEA and DEA in aqueous solutions. The kinetic model was used to predict the fractional conversion at different temperature exhibiting good agreement with experimental data.
Liver fibrosis and tissue architectural change measurement using fractal-rectified metrics and Hurst’s exponent (2006)

Our model provides the first metrical evaluations of the geometric properties of fibrosis and the quantitative architectural changes of the liver tissue. The representativeness of histological sections of the whole liver is also discussed in the light of the results obtained with the Hurst coefficient.
Channel-aided, decision-directed delay-locked loop for pilot symbol aided CDMA communications impaired by fast frequency-selective Rayleigh fading and user interference (2000)

In this paper, a channel-aided, decision-directed delay-locked loop (CADD-DLL) is investigated for pilot-symbol-aided (PSA) code-division multiple-access (CDMA) communication. It is assumed that the initial pseudonoise (PN) code acquisition is accomplished with the aid of a conventional noncoherent PN code acquisition system, and that, upon acquiring the initial PN code epoch, the PN code tracking is performed using a channel-aided, decision-directed PN code tracking mechanism. The proposed tracking loop consists of the delayed and advanced PN correlators. The correlators are followed by data and phase correction as well as amplitude matching devices, the outputs of which are subtracted to form an error signal for code tracking purposes. The performance of the proposed tracking loop is assessed in terms of the variance of PN code tracking error and the mean-time-to-loss (MTTL) for a frequency-selective Rayleigh fading channel in the presence of user-induced interference. It is demonstrated that the impact of the decision-directed mechanism on the performance is to reduce the variance of timing error for moderate levels of signal-to-noise ratio (SNR) as compared to the conventional noncoherent delay-locked loop (NC-DLL) tracking mechanism. Also, the MTTL is shown to be highly dependent on the mobile's Doppler shift.
Sparsity promoting LMS for adaptive feedback cancellation (2017)

In hearing aids (HAs), the acoustic coupling between the microphone and the receiver results in the system becoming unstable under certain conditions and causes artifacts commonly referred to as whistling or howling. The least mean square (LMS) class of algorithms is commonly used to mitigate this by providing adaptive feedback cancellation (AFC). The speech quality after AFC and the amount of added stable gain (ASG) with AFC are used to assess these algorithms. In this paper, we introduce a variant of the LMS that promotes sparsity in estimating the acoustic feedback path. By using the l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> norm as a diversity measure, the approach does not enforce, but takes advantage of sparsity when it exists. The performance in terms of speech quality, misalignment, and ASG of the proposed algorithm is compared with other proportionate-type LMS algorithms which also leverage sparsity in the feedback path. We demonstrate faster convergence compared with those algorithms, quality improvement of about 0.25 (on a 0-1 objective scale of the hearing-aid speech quality index (HASQI)), and about 5 dB ASG improvement compared with the normalized LMS (NLMS).
Topological analysis of trabecular bone MR images (2000)

Recently, imaging techniques have become available which permit nondestructive analysis of the three-dimensional (3-D) architecture of trabecular bone (TB), which forms a network of interconnected plates and rods. Most osteoporotic fractures occur at locations rich in TB, which has spurred the search for architectural parameters as determinants of bone strength. Here, the authors present a new approach to quantitative characterization of the 3-D microarchitecture of TB, based on digital topology. The method classifies each voxel of the 3-D structure based on the connectivity information of neighboring voxels. Following conversion of the 3-D digital image to a skeletonized surface representation containing only one-dimensional (1-D) and two-dimensional (2-D) structures, each voxel is classified as a curve, surface, or junction. The method has been validated by means of synthesized images and has subsequently been applied to TB images from the human wrist. The topological parameters were found to predict Young's modulus (YM) for uniaxial loading, specifically, the surface-to-curve ratio was found to be the single strongest predictor of YM (r/sup 2/=0.69). Finally, the method has been applied to TB images from a group of patients showing very large variations in topological parameters that parallel much smaller changes in bone volume fraction (BVF).
Innovation in the Treatment of Uremia: Proceedings from the Cleveland Clinic Workshop: Renal Cell Therapy and Beyond (2009)

Although current dialysis techniques have transformed acute and chronic renal failure from uniformly fatal clinical disorders into treatable diseases, these therapies replace only the water and solute clearance function of the kidney and have reached a point where little further therapeutic improvement can be anticipated. In addition to their metabolic and endocrine functions, renal tubule cells presumably play an important role in the systemic inflammatory balance by participating in the complex and dynamic network of leukocyte action and pro- and anti-inflammatory cytokines. Loss of this function may result in a propensity to develop systemic inflammatory response syndrome (SIRS), multiorgan dysfunction, and a high risk of death in acute kidney injury (AKI), and may relate to chronic inflammatory state in end-stage renal disease (ESRD). A renal tubule cell assist device (RAD) containing animal or human renal tubule cells has been recently developed with the purpose of integrating the functions of tubule cells with the filtration function of current dialysis to offer a more complete renal replacement therapy. The viability and functionality of this device were confirmed in in vitro experiments and large animal studies, and recently the RAD's clinical therapeutic benefit was demonstrated with a series of FDA-approved human trials. Another novel synthetic membrane extracorporeal device that binds and inhibits circulating leukocytes has been developed with the purpose of reducing microvascular damage promoted primarily via activated circulating leukocytes in AKI and SIRS. This device, called a selective cytopheretic inhibitory device, mimics immunomodulation and duplicates RAD efficiency in preliminary studies. Both devices may become comprehensive treatments, replacing full renal function and correcting inflammatory imbalance in patients with acute and chronic renal disorders.
New Type Thermal Printing Head Using Thin Film (1976)

This paper describes the development of a new type thermal printing head. The main features of this paper are as follows. 1) The heating element is a Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> N thin-film resistor coated with a SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> -Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> double layer. The SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> layer prevents oxidation of Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> N; the Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> layer, which rubs directly against the heat-sensitive paper, is hard enough to resist abrasion. 2) A theoretical calculation revealed that the thermal time constant can be controlled by changing the thickness of the heat insulating layer. It was found that a glazed alumina ceramic substrate has the most suitable thermal properties. 3) A beam-lead diode array and a crossover structure have been developed to satisfy the electrical interface requirements of both the thermal printing head and the external logic.
Properties and Limits of the Minimum-norm Differential Beamformers with Circular Microphone Arrays (2019)

Small aperture circular microphone arrays (CMAs) have been widely used in many applications such as teleconferencing, smartspeakers, and robotics. A critical component of such arrays is the differential beamformer, which can achieve relatively high spatial gains with the same beampatterns at most frequencies. Among different differential beamforming approaches that were developed in the literature, the minimum-norm one has attracted much interest as it can deal better with sensors' self noise, sensor mismatch, and beamformer's irregularity at some frequencies due to the zeros of the Bessel functions. In our previous study, we have investigated the performance of the minimum-norm differential beamformer with uniform CMAs (UCMAs) in the 2-dimensional (2D) space where the sound sources and the sensors are assumed to be in the same plane. But in practice, this assumption is generally not true. So, in this paper, we investigate the properties and limitations of the minimum-norm differential beamformer in the 3-dimensional(3D) space. Through theoretical study as well as simulations, we show that the minimum-norm differential beamformer is effective in dealing with the problem of white noise amplification and irregularity of the beampatterns and the directivity factor (DF) if the steering angles are within or near the sensor plane, but it becomes less and less effective as the beamformer is steered away from this plane.
Interferometric Surface-Wave Acousto-Optic Time-Integrating Correlators (1980)

A structure for a coherent-interferometric acousto-optic (AO) time-integrating correlator was implemented by using a single surface acoustic wave (SAW) device with tilted transducers to reduce intermodulation terms. The SAW device was fabricated on Y-Z LiNbO3 with a center frequency of 175 MHz, a bandwidth of 60 MHz, and a time aperture of about 10 micros. The density of the photodetector array, with a potential of 120 MHz. Typical integration times are 30 to 40 ms, providing processing gains in excess of 10 to the 6th power. Such a device is useful in providing fast synchronization of communication links and in demodulating to base band and simultaneously acting as a synchronization lock monitor for moderate data rates. Where processing may be limited by Doppler shifts, a two dimensional architecture was implemented to allow full processing gain. Two one-dimensional, SAW AO time-integrating correlators and a two dimensional correlator are evaluated.
Ka-band high efficiency asymmetric MMIC power combiner for space communications (2010)

A novel Ka-band (32.05±0.25 GHz) high efficiency asymmetric waveguide four-port combiner for coherent combining of two monolithic microwave integrated circuit (MMIC) power amplifiers having unequal outputs has been successfully designed, fabricated and characterised. The measured combiner efficiency is greater than 90%, the return loss greater than 18 dB and isolation greater than 22 dB. Applications considered are NASA's space communications systems needing 8–15 W of RF power.
Leveraging the web for automating tag expansion for low-content items (2014)

Tags, as high quality semantic descriptors, are used in categorization, clustering and efficient retrieval of various items in the web corpus. Images, videos, songs and similar multimedia items are the most common items which are tagged either manually or in a semiautomatic manner. However, the tagging process becomes complicated when the content structure of an item is not interpretable. Such a problems occurs in items like scientific research datasets or documents with very little text content. In this work, we propose a generalized approach to automate tag expansion for such low-content items. We leverage intelligence of the web to generate secondary content for such items for the tag expansion process. While automating tag expansion, we also address the problem of topic drift by automating removal of the noisy tags from the set of candidate new tags. The effectiveness of the proposed approach is tested on a real world dataset. The performance of the proposed is compared with Wikipedia based nearest neighbor tagging (WikiSem) and non-negative matrix factorization (NMF) based tag expansion approaches. Based on the Mean Reciprocal Rank (MRR) metric, the proposed approach was twice as accurate as the WikiSem baseline (0.27 vs 0.13) and at least 2.25 times the NMF baselines (0.27 vs 0.12).
Ionic Liquids as Hyper-Stable Solvents for Ionic Polymer Transducers (2003)

Nafion™ membranes are known to operate as electromechanical actuators and sensors. The transduction in the material is caused by redistribution of the mobile cations in the material, which is made possible because the material is saturated with a solvent. Typically the solvent used is water, although its use limits the performance of these materials. This is due to the chemical breakdown of the water at relatively low operating voltages and the loss of the water to evaporation when these devices are operated in air, causing a corresponding loss of performance. In the current work, the use of highly stable ionic liquids to replace water is explored. Ionic liquids have the advantage of greater electrochemical stability than water, thus offering the possibility of higher actuation voltages for these materials. Also, ionic liquids are known to be non-volatile and therefore will not leach out of the polymer by evaporation as water will. This paper will present the results of some initial work with ionic liquids and will compare these materials to the same polymers solvated with water.