gebhart/patrepeval huggingface dataset:
Genomic surveillance at scale is required to detect newly emerging strains at an early timepoint (2021)

Abstract Genomic surveillance in the setting of the coronavirus disease 2019 (COVID-19) pandemic has the potential to identify emerging SARS-CoV-2 strains that may be more transmissible, virulent, evade detection by standard diagnostic tests, or vaccine escapes. The rapid spread of the SARS-CoV-2 B.1.1.7 strain from southern England to other parts of the country and globe is a clear example of the impact of such strains. Early discovery of the B.1.1.7 strain was enabled through the proactive COVID-19 Genomics UK (COG-UK) program and the UK’s commitment to genomic surveillance, sequencing about 10% of positive samples. 1 In order to enact more aggressive public health measures to minimize the spread of such strains, genomic surveillance needs to be of sufficient scale to detect early emergence and expansion in the broader virus population. By modeling common performance characteristics of available diagnostic and sequencing tests, we developed a model that assesses the sampling required to detect emerging strains when they are less than 1% of all strains in a population. This model demonstrates that 5% sampling of all positive tests allows the detection of emerging strains when they are a prevalence of 0.1% to 1.0%. While each country will determine their risk tolerance for the emergence of novel strains, as vaccines are distributed and we work to end the pandemic and prevent future SARS-CoV-2 outbreaks, genomic surveillance will be an integral part of success.
Conformation and dynamics in solution of an N-quaternarized benzophenone derivative: a molecule active as UV filter (1991)

The dynamics and conformation of N,N-dimethyl-N-|3-(benzoyl-4-phenoxy)|-N-n-dodecylammonium bromide, 1, have been established in two solvents (CDCl 3 and DMSO-d 6 ) by the use of 13 C spin-lattice relaxation rates, non-selective and selective proton spin-lattice relaxation rates, and 1 H–{ 1 H} nuclear Overhauser enhancement (nOe) experiments. The data obtained are consistent with two main mean conformations for compound 1: a "linear" conformation in CDCl 3 and a folded conformation in DMSO-d 6 where the alkyl chain forms a loop toward the aromatic moiety. Key words: UV filter, carbon and proton relaxation rates, nuclear Overhauser enhancement experiments, solvent dependent conformations.
Variability of UTBB MOSFET analog figures of merit in wide frequency range (2014)

Inter-die variability of analog figures of merit of ultra-thin body and buried oxide (UTBB) FDSOI MOSFETs was studied in a wide frequency range. We demonstrate that variability in the entire frequency range is small and does not exceed 5%, which is considerably less than in previously published results on SOI FinFETs. An effect of frequency on the analog figures of merit variability is discussed and preliminary explanation is proposed.
DIRECT OBSERVATION OF LONG-RANGE MIGRATION OF SELF-INTERSTITIAL ATOMS IN STAGE I OF IRRADIATED PLATINUM (1971)

The motion of single self-interstitial atoms (SIA's) in stage I of irradiated platinum was observed directly by field ion microscopy. A specimen irradiated at a temperature of 10°K with 20-keV Pt+ ions was found to contain immobile SIA's in the bulk at this temperature, as determined via pulse-field evaporation experiments. Direct observation of specimens, irradiated with 20- or 30-keV Pt+ ions, during warming experiments from 10 to 70°K showed that a flux of SIA's crossed the surface of the specimens between 13 and 25°K. Application of a diffusion model to the data yielded a value of ∼ 0.06 eV for the enthalpy change of migration and a diffusion coefficient of ∼ 0.5 exp(−0.06 eV/kT) cm2 sec−1 for the SIA.
Atom-efficient synthesis of α-alkylidene-N-furylimines via catalytic vinylcarbene-transfer reactions to carbonyl-ene-nitrile compounds (2010)

The reaction of carbonyl-ene-nitrile compounds with propargyl carboxylates in the presence of a catalytic amount of PtCl(2) afforded the alpha-alkylidene-N-furylimines with high stereoselectivities.
The Subunits of Human Pituitary Thyroid-stimulating Hormone (1973)

Abstract The subunits, α and β, of human thyroid-stimulating hormone (TSH) from the pituitary have been obtained by the same procedures utilized for the preparation of bovine TSH subunits, namely, dissociation in 1 m propionic acid and separation by gel filtration. The amino acid composition of human TSH-α indicates that this subunit is identical or nearly so with the α subunits of human luteinizing hormone and human chorionic gonadotropin. The NH2-terminal residue is valine and it appears that human TSH-α is shortened at its amino end by 7 residues relative to bovine TSH-α; a similar relationship has been shown by others for human LH-α relative to the ovine or bovine subunit. The β subunit of human TSH differs markedly in amino acid composition from those of the two human gonadotropins, particularly with respect to tyrosine, isoleucine, valine, proline, arginine, and lysine. The carbohydrate analyses for the 2 subunits are given. A major difference between human and bovine TSH is the presence of sialic acid in the former, nearly all in the α subunit. Immunological comparisons by double diffusion show that antisera to the intact hormone or its α subunit cross-react with homologous TSH and with the human gonadotropins but that the antiserum against the β subunit is specific for thyroid-stimulating hormone. The human subunits were shown, by gel electrophoresis and bioassay, to form intra- and interspecies recombinants with complementary subunits from other glycoprotein hormones.
The JRC-Acquis: A multilingual aligned parallel corpus with 20+ languages (2006)

We present a new, unique and freely available parallel corpus containing European Union (EU) documents of mostly legal nature. It is available in all 20 official EUanguages, with additional documents being available in the languages of the EU candidate countries. The corpus consists of almost 8,000 documents per language, with an average size of nearly 9 million words per language. Pair-wise paragraph alignment information produced by two different aligners (Vanilla and HunAlign) is available for all 190+ language pair combinations. Most texts have been manually classified according to the EUROVOC subject domains so that the collection can also be used to train and test multi-label classification algorithms and keyword-assignment software. The corpus is encoded in XML, according to the Text Encoding Initiative Guidelines. Due to the large number of parallel texts in many languages, the JRC-Acquis is particularly suitable to carry out all types of cross-language research, as well as to test and benchmark text analysis software across different languages (for instance for alignment, sentence splitting and term extraction).
Exact angle‐mute pattern for a transversely isotropic medium with vertical symmetry axis and its implication in offset‐to‐angle transform (2011)

Computing an accurate angle mute pattern is vital to the offset‐to‐angle transform of prestack seismic data. Here, we use a ray‐based approach to calculate this angle‐mute pattern. From any given zero‐offset time sample, we ray‐trace through the medium to the corresponding source and receiver locations and compute the ray‐path length, travel time, offset for a given central angle. We then increase and decrease the angle value in each side of the central angle and calculate the corresponding ray‐path length, travel time, offset until the difference in ray‐path length of central angle and present angle is equal to one‐fourth of the wavelength in each‐side. The traces within this offset range retain the energy reflected from the given central angle, and the corresponding offset range defines the angle‐mute pattern. A constrained cubic‐spline interpolation is then designed within this angle‐mute pattern to obtain the times corresponding to those offsets and are partially stacked to obtain the corresponding zero‐offset angle domain response. The method allows us to compute both primary (P‐P) and converted wave (P‐SV) angle gathers. Additionally, by computing an exact ray‐path length, we can apply an exact geometric spreading compensation to the computed gathers. This present approach calculates angle gathers that are accurate out to large angles in a horizontally stratified transversely isotropic medium with a vertical symmetry axis (VTI medium). By calculating the exact angle‐mute pattern and total ray‐path length in a VTI medium both for P‐P and P‐SV reflections, we are able to preserve the accurate energy associated with the respective rays. The angle‐mute pattern in an anisotropic medium is significantly different from that calculated for the same medium if it is considered isotropic. Accurate angle gathers out to large angles from observed seismic data can be used in a multicomponent prestack waveform inversion to match with synthetic angle gathers. In addition, the velocity and anisotropic parameters of the medium can be obtained by changing the elastic parameters and ray‐tracing in a AVO sensitive semblance type analysis. These results, if not exact but close, can eventually be used as initial model to any linear or non‐linear seismic inversion scheme.
MicroRNAs as modulators and biomarkers of inflammatory and neuropathic pain conditions (2014)

The post-transcriptional regulator molecules, microRNAs, have emerged as important biomarkers and modulators of numerous pathophysiological processes including oncogenesis and cardiovascular diseases. Recently, a significant number of dysregulations in microRNAs have been reported in patients suffering from painful disorders such as complex regional pain syndrome, cystitis-induced chronic pain and irritable bowel disorder, in both affected tissues and the circulation. Moreover, microRNAs are known to be involved in pain processing based on several recent findings in animal models of inflammatory and neuropathic pain. The basis of this review was to cover and summarize available articles in English encompassing "microRNA and pain". In animal pain models widespread microRNA modulation is present and manifests on multiple levels i.e.: the dorsal root ganglia, the spinal dorsal horn and the brain. Numerous functional in vivo studies have found that dysregulated microRNAs are involved in the post-transcriptional modulation of genes implicated in pain generation and maintenance. Lastly, a few animal studies have delivered promising results as to the possibility of applying microRNAs as therapeutics to alleviate established pain and several clinical studies have highlighted the potential in applying microRNAs as biomarkers in painful conditions such as complex regional pain syndrome and fibromyalgia. This review briefly introduces the basics of microRNAs, their biogenesis and function, and mainly focuses on the recent advances made in understanding the role of microRNAs in relation to pain processing and painful conditions. It also provides an overview of widely diverse methodological approaches and results with a potential for future implications of microRNAs in the diagnosis and treatment of pain.
Dynamic model of dual layer neural network for vertebrate retina (1989)

A neural network model was formulated to describe the spatiotemporal properties of the photoreceptor and horizontal cell responses to light in the vertebrate retina. The model consists of two layers, one of which represents the photoreceptor syncytium and the other the horizontal cell syncytium. Each syncytium is an array of elemental neurons, each of which is expressed by the coupling resistance between neighboring cells and membrane impedance. Corresponding elements of each syncytium interact reciprocally with synaptic weighting functions. The analytical solutions of the voltage responses to extrinsically applied current, which corresponds to the light-induced current, were obtained in the frequency domain. The model provides a computational framework of the early visual processing in the vertebrate retina.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Stability of Attitudes to the Ethical Issues Raised by the Return of Incidental Genomic Research Findings in Children: A Follow-Up Study (2015)

The opinions of parents regarding genomic research remain stable over time. Guidelines on the return of results should incorporate these findings.
Dense Non-Rigid Structure from Motion: A Manifold Viewpoint (2020)

Non-Rigid Structure-from-Motion (NRSfM) problem aims to recover 3D geometry of a deforming object from its 2D feature correspondences across multiple frames. Classical approaches to this problem assume a small number of feature points and, ignore the local non-linearities of the shape deformation, and therefore, struggles to reliably model non-linear deformations. Furthermore, available dense NRSfM algorithms are often hurdled by scalability, computations, noisy measurements and, restricted to model just global deformation. In this paper, we propose algorithms that can overcome these limitations with the previous methods and, at the same time, can recover a reliable dense 3D structure of a non-rigid object with higher accuracy. Assuming that a deforming shape is composed of a union of local linear subspace and, span a global low-rank space over multiple frames enables us to efficiently model complex non-rigid deformations. To that end, each local linear subspace is represented using Grassmannians and, the global 3D shape across multiple frames is represented using a low-rank representation. We show that our approach significantly improves accuracy, scalability, and robustness against noise. Also, our representation naturally allows for simultaneous reconstruction and clustering framework which in general is observed to be more suitable for NRSfM problems. Our method currently achieves leading performance on the standard benchmark datasets.
Isolation and Characterization of NUC70, a Cytoplasmic, Hematopoietic Apoptotic Endonuclease (1998)

Endonucleolytic DNA fragmentation is the common end point and the prevailing indicator of apoptosis. We have identified a 70-kDa endonuclease (NUC70) that is activated in drug-induced apoptosis of human hematopoietic cells. We purified NUC70 to homogeneity and generated a rabbit polyclonal antibody to distinguish it from previously identified nucleases. Biochemical characterization of isolated NUC70 demonstrates that it is Ca2+/Mg2+-dependent and active over a pH range of 6-8. When incubated with isolated HeLa nuclei, NUC70 was capable of generating internucleosomal DNA fragmentation. This endonucleolytic activity was inhibited by Zn2+, aurintricarboxylic acid, N-ethylmaleimide, spermine, and iodoacetamide. Western immunoblots using the anti-NUC70 antibody and DNA-SDS-polyacrylamide gel electrophoresis assays indicate that NUC70 expression and activity is restricted to human hematopoietic cells. No such activity was detected in human epithelial cell lines or murine hematopoietic cells. We also observed no difference in levels of NUC70 expression between apoptotic and nonapoptotic cells, suggesting that activation of NUC70 may be by posttranslational modification. We demonstrate that NUC70 activity is diminished in cells pretreated with the caspase inhibitors z-DEVD-fmk, z-VAD-fmk, and Z-CH2-Asp-DCB. Time course studies of cytoplasmic and nuclear endonuclease activities during apoptosis show that NUC70 is a cytoplasmic endonuclease that is translocated to the nucleus after the initiation of apoptosis. We confirmed this with immunostaining studies using anti-NUC70 antibody. These results demonstrate that NUC70 is an endogenous cytoplasmic endonuclease that is activated during apoptosis in a caspase-dependent mechanism.
An assessment on feasibility of flotation as a secondary clarifier of an activated sludge process (2008)

An experimental study was carried out to evaluate the potential of flotation process for the secondary clarifier of an activated sludge process. Flotation techniques, applied in this study, include electrofloation (EF) which generated fine bubbles smaller than 35 µm in average and diffuser flotation (DF) which generated fine bubbles smaller than 55 µm in average. The batch experiments were done with activated sludge displaying various characteristics. It was shown that the efficiency of solids/liquid separation was reduced as the diluted sludge volume index (DSVI30) of activated sludge increased. The dependency, however, gradually decreased as the gas to solids (G/S) ratio increased. Thickening efficiency of EF was more than 2∼10 times and DF process was more than 1.5∼5 times as compared with gravity sedimentation (GS). Stable sludge blanket was maintained regardless of sludge settleability when the G/S ratio was 0.019 in the EF. On the other hand, Serious deterioration in the sludge blanket was observed in the DF depends on G/S ratio and sludge settleability. And For EF and DF, the suspended solids concentration of effluent was not nearly influenced on settleability of activated sludge and more clear than GS. A biological nutrient removal (BNR) process, combined with EF as a secondary clarifier was operated for three months. The mean MLSS (mixed liquid suspended solids) concentration in the reactor and mean solids concentration of return sludge were estimated to be 5,340 mg/L and 16,770 mg/L, respectively. The water quality of effluent was considerably stable and low value was accomplished, that was, standard suspended solids concentration 0.07 ± 0.51 mg/L and standard turbidity 1.44 ± 0.56 NTU. The EF could be applicable for enhancement of efficiency of activated sludge system as well as improvement of the water quality of effluent.
Immediate Generation of Jump-and-Hit Motions by a Pneumatic Humanoid Robot Using a Lookup Table of Learned Dynamics (2021)

This letter focuses on the jump-and-hit motion of a humanoid robot, wherein a robot instantaneously jumps forward and hits a flying ball in the air, similar to how human players behave in volleyball games. We propose a Immediate Motion generation using a Lookup table of learned dynamics (IMoLo) for generating the motions of a pneumatic humanoid robot. To test this method, we developed a humanoid robot called “Liberobot” with eight joints applying structure-integrated pneumatic cable cylinders. Using simulations, the prediction errors of the robot hand positions during the jump-and-hit motions measured via nonlinear interpolation when using IMoLo was smaller than without it in cases having a small number of training trials. In the experiments, the robot jumped and hit the flying ball 16 times out of 20 trials using the proposed motion generation method. The results indicate that a pneumatic humanoid robot using IMoLo can instantaneously perform dynamic whole-body motions, such as jump-and-hit motions, with a changing target within a specified time. Our humanoid robot is the first pneumatic humanoid robot capable of executing such dynamic motions.
Characterization of patch antennae for PD detection in power cables (2007)

Patch antennae suitable for partial discharge detection in power cables have been characterized through laboratory experiments carried out in the time and frequency domain, as well as through PD testing. The results reported in this paper show that helicoidal antennae wrapped around the cable at a distance of few meters from the defect site can provide sensitivities and bandwidth that can allow effective detection of PD in accessories or short cable links.
Unconventional Origin of Metal Ion Rescue in the Hammerhead Ribozyme Reaction:  Mn2+-Assisted Redox Conversion of 2‘-Mercaptocytidine to Cytidine (2000)

A specific oxygen atom in RNA is identified as a ligand for a metal ion when sulfur substitution of that atom shifts the metal ion specificity of the RNA-mediated process to a more thiophilic metal. Extensive discussion and debate have centered around whether a metal ion activates the 2‘-oxygen nucleophile during the phosphotransesterification reaction catalyzed by the hammerhead ribozyme (HH). To test this possibility, we probed the metal ion specificity of HH reactions using a substrate that contained 2‘-mercaptocytidine at the cleavage site. This substrate is generated in situ from a disulfide-protected precursor by treatment with tris(carboxyethyl)phosphine (TCEP). In HH reactions with this substrate, phosphotransesterification does not occur when Mg2+ is present as the only divalent cation but does occur in the presence of Mn2+. These results are consistent with a direct interaction between the metal ion and the nucleophile. However, further analysis reveals that this switch in metal ion specificity does not arise because Mn2+ coordinates sulfur more readily than Mg2+ does, but because under the assay conditions, the 2‘-mercaptocytidine residue is converted to a mixture of cytidyl-1-β-d-arabinofuranoside and cytidyl-1-β-d-ribofuranoside, the natural substrate for the ribozyme. This conversion occurs in the absence of HH ribozyme, requires Mn2+ (or Co2+), O2, and TCEP, and is inhibited by a free radical scavenger. The mechanism presumably involves a multistep free radical process, in which the key step is homolytic fission of the C2‘-sulfur bond induced by TCEP. The putative 2‘-carbon radical then reacts with an oxygen species to produce the cytidyl-1-β-d-arabinofuranoside and ribocytidine products. To our knowledge, this chemical transformation is unprecedented in the literature and represents a new reaction for nucleic acids. If O2 is excluded from the HH reactions, the 2‘-sulfur is not modified in the presence of Mn2+ but is still blocked in the phosphotransesterification reaction, both in the forward direction as the mercapto (−SH) group or in the reverse direction as part of a cyclic phosphorothiolate. Although we are unable to provide evidence for metal ion activation of the nucleophile in the HH ribozyme reaction, this work establishes the groundwork for further use of 2‘-mercaptonucleotides in biochemical analyses.
Blind Image Restoration with Flow Based Priors (2020)

Image restoration has seen great progress in the last years thanks to the advances in deep neural networks. Most of these existing techniques are trained using full supervision with suitable image pairs to tackle a specific degradation. However, in a blind setting with unknown degradations this is not possible and a good prior remains crucial. Recently, neural network based approaches have been proposed to model such priors by leveraging either denoising autoencoders or the implicit regularization captured by the neural network structure itself. In contrast to this, we propose using normalizing flows to model the distribution of the target content and to use this as a prior in a maximum a posteriori (MAP) formulation. By expressing the MAP optimization process in the latent space through the learned bijective mapping, we are able to obtain solutions through gradient descent. To the best of our knowledge, this is the first work that explores normalizing flows as prior in image enhancement problems. Furthermore, we present experimental results for a number of different degradations on data sets varying in complexity and show competitive results when comparing with the deep image prior approach.
Handel: Messiah (1991)

A keyboard virtuoso and composer of the highest calibre, George Frideric Handel was also a practical musician and entrepreneur. He owned at least an interest in the production companies that presented his operas and oratorios and he also frequently acted as an impresario, organising and promoting his own concerts. None of his compositions was graven on stone; he considered them all subject to revision, not only to improve them, but also to meet the practical requirements of particular performances. He often altered works to suit the capabilities of available performers.
Supplemental Material and Methods from An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines (2023)

&lt;p&gt;Supplemental Methods descriptions and supplemental references supporting this additional text.&lt;/p&gt;