gebhart/patrepeval huggingface dataset:
Classification and reconstruction of compressed GMM signals with side information (2015)

This paper offers a characterization of performance limits for classification and reconstruction of high-dimensional signals from noisy compressive measurements, in the presence of side information. We assume the signal of interest and the side information signal are drawn from a correlated mixture of distributions/components, where each component associated with a specific class label follows a Gaussian mixture model (GMM). We provide sharp sufficient and/or necessary conditions for the phase transition of the misclassification probability and the reconstruction error in the low-noise regime. These conditions, which are reminiscent of the well-known Slepian-Wolf and Wyner-Ziv conditions, are a function of the number of measurements taken from the signal of interest, the number of measurements taken from the side information signal, and the geometry of these signals and their interplay.
A MethodtoEstimate Destination ofaWalking Person withHidden MarkovModelforSafety of HumanFriendly Robots (2008)

Inthis paper, weproposed amethodtoestimate behavioral traits aregiven attention(6). Theseareapproaches thedestination ofwalking persons fromtheir walking patterns, for basedonthedefined person's walking model, whichisbased avoidance ofcollision accidents between pedestrians androbots in oncertain assumptions about humanbehavior. Inshort, these aHuman-Robot Coexistence Environment. We adopted theHidden Markov Model(HMM)asamodeltorepresent walking patterns. We models donotexactly reflect anactual pedestrian's behavior. It constructed amodelforeachmovement pattern. A movement pattern isexpected that theaccuracy willbeimproved withmodeling wasdefined withadeparture point anddestination point ofaperson.using anactually observed movementtrajectory according to Comparing thelikelihood withtheachieved model, wediscriminated theenvironment. walking patterns forwhichthedestination isunknown. Wedidsome Basedon theaboveunderstanding, we takethetrajectory experiments inanactual environment toverify theavailability of theproposed method. Results showthatthediscrimination ratioofanobject person usinga fixed camera, andconstruct a approached 80%within 2sofobservation. learning modelofthewalking pattern described using the HiddenMarkovModel(HMM).Then, we define movement
Soliton density in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Rb</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">ZnBr</mml:mi></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math> (1986)

The modulation wave in ${\mathrm{Rb}}_{2}$${\mathrm{ZnBr}}_{4}$ is pinned over most of the incommensurate phase and $^{87}\mathrm{Rb}$ NMR line-shape analysis cannot distinguish between a true incommensurate phase and a large-period commensurate phase with N=17. The temperature variations of the soliton density, the line shape, and the spin-lattice relaxation rate speak for the coexistence of a large number of domains pinned by impurities rather than for the existence of a devil's staircase and pinning by the discreteness of the crystal lattice. The large thermal hysteresis in the soliton density demonstrates the presence of a metastable, impurity-induced ``chaotic'' phase with random intersoliton spacing which exists even far below the incommensurate-commensurate transition.
Butyrylcholinesterase and acetylcholinesterase activity and quantal transmitter release at normal and acetylcholinesterase knockout mouse neuromuscular junctions (2003)

1 The present study was performed to evaluate the presence and the physiological consequences of butyrylcholinesterase (BChE) inhibition on isolated phrenic-hemidiaphragm preparations from normal mice expressing acetylcholinesterase (AChE) and BChE, and from AChE-knockout mice (AChE(-/-)) expressing only BChE. 2 Histochemical and enzymatic assays revealed abundance of AChE and BChE in normal mature neuromuscular junctions (NMJs). 3 In normal NMJs, in which release was reduced by low Ca(2+)/high Mg(2+) medium BChE inhibition with tetraisopropylpyrophosphoramide (iso-OMPA) or bambuterol decreased ( approximately 50%) evoked quantal release, while inhibition of AChE with fasciculin-1, galanthamine (10, 20 micro M) or neostigmine (0.1-1 micro M) increased (50-80%) evoked quantal release. Inhibition of both AChE and BChE with galanthamine (80 micro M), neostigmine (3-10 micro M), O-ethylS-2-(diisopropylamino)ethyl-methylphosphono-thioate (MTP) or phospholine decreased evoked transmitter release (20-50%). 4 In AChE(-/-) NMJs, iso-OMPA pre-treatment decreased evoked release. 5 Muscarinic toxin-3 decreased evoked release in both AChE(-/-) and normal NMJs treated with low concentrations of neostigmine, galanthamine or fasciculin-1, but had no effect in normal NMJs pretreated with iso-OMPA, bambuterol, MTP and phospholine. 6 In normal and AChE(-/-) NMJs pretreatment with iso-OMPA failed to affect the time course of miniature endplate potentials and full-sized endplate potentials. 7 Overall, our results suggest that inhibition or absence of AChE increases evoked quantal release by involving muscarinic receptors (mAChRs), while BChE inhibition decreases release through direct or indirect mechanisms not involving mAChRs. BChE apparently is not implicated in limiting the duration of acetylcholine action on postsynaptic receptors, but is involved in a presynaptic modulatory step of the release process.
Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets (2002)

Catalytic group II introns are mobile retroelements that invade cognate intronless genes via retrohoming, where the introns reverse splice into double-stranded DNA (dsDNA) targets. They can also retrotranspose to ectopic sites at low frequencies. Whereas our previous studies with a bacterial intron, Ll.LtrB, supported frequent use of RNA targets during retrotransposition, recent experiments with a retrotransposition indicator gene indicate that DNA, rather than RNA, is a prominent target, with both dsDNA and single-stranded DNA (ssDNA) as possibilities. Thus retrotransposition occurs in both transcriptional sense and antisense orientations of target genes, and is largely independent of homologous DNA recombination and of the endonuclease function of the intron-encoded protein, LtrA. Models based on both dsDNA and ssDNA targeting are presented. Interestingly, retrotransposition is biased toward the template for lagging-strand DNA synthesis, which suggests the possibility of the replication folk as a source of ssDNA. Consistent with some use of ssDNA targets, many retrotransposition sites lack nucleotides critical for the unwinding of target duplex DNA. Moreover, in vitro the intron reverse spliced into ssDNA more efficiently than dsDNA substrates for some of the retrotransposition sites. Furthermore, many bacterial group II introns reside on the lagging-strand template, hinting at a role for DNA replication in intron dispersal in nature.
Methyl 2-Methylthioacrylate (2001)

[43228-10-0] C5H8O2S (MW 132.20) InChI = 1S/C5H8O2S/c1-4(8-3)5(6)7-2/h1H2,2-3H3 InChIKey = QCGQAWBHALUDCD-UHFFFAOYSA-N (versatile and reactive Michael acceptor2-5) Physical Data: bp 78 °C/12 mmHg. Solubility: sol Et2O, THF, EtOH, and most organic solvents. Analysis of Reagent Purity: IR, NMR, GLC. Preparative Methods: prepared either by the reaction of methyl 2-chloroacrylate1a or methyl 2-bromoacrylate1b with Methanethiol in the presence of Triethylamine and N,N‐Dimethylformamide. It is also obtained1c quantitatively by chlorination of methyl 2-alkylthiopropionates (alkyl = Me/Et) with Sulfuryl Chloride at 0 °C followed by dehydrochlorination using refluxing chloroform. For preparation of alkyl 2-alkylsulfonylacrylates and its uses, see Gipstein.8 Handling, Storage, and Precautions: since the reagent is an acrylate, it should be stored under N2 in the refrigerator and should be inhibited with ionol or 100 ppm of hydroquinone monomethyl ether. Use in a fume hood.
Role of mast cells in tumor growth. (2007)

The growth of malignant tumors is determined in large part by the proliferative capacity of the tumor cells. Clinical observations and animal experiments have established that tumor cells elicit immune responses. Histopathologic studies show that many tumors are surrounded by mononuclear cell and mast cell infiltrates. Mast cells are ubiquitous in the body and are critical for allergic reactions. Increasing evidence indicates that mast cells secrete proinflammatory cytokines and are involved in neuro-inflammatory processes and cancer. Mast cells accumulate in the stroma surrounding certain tumors, especially mammary adenocarcinoma, and the molecules they secrete can benefit the tumor. However, mast cells can also increase at the site of tumor growth and participate in tumor rejection. Mast cells may be recruited by tumor-derived chemoattractants and selectively secrete molecules such as growth factors, histamine, heparin, VEGF, and IL-8, as well as proteases that permit the formation of new blood vessels and metastases. Tumor mast cell intersections play regulatory and modulatory roles affecting various aspects of tumor growth. Discovery of these new roles of mast cells further complicates the understanding of tumor growth. This review focuses on the strategic importance of mast cells to the progression of tumors, and proposes a revised immune effector mechanism of mast cell involvement in tumor growth.
Chlamydospore-like cell-inducing substances of fungi: Close correlation between chemical reactivity with methylamine and biological activity. (1988)

Lunatoic acid A and (-)-mitorubrinic acid have been isolated as chlamydospore-like cellinducing substances from Cochliobolus lunatus. (+)-Sclerotiorin, (+)-rotiorin, citrinin and sclerin were shown to have the same activity. Although they share no common structural feature, all these active substances react with methylamine. The reaction products do not have this activity. The reaction curves showed a positive correlation between the chemical reactivity of chlamydospore-like cell-inducing substances with methylamine and their biological activities.
Transgenic mice that express a mini-gene version of the human gene for type I procollagen (COL1A1) develop a phenotype resembling a lethal form of osteogenesis imperfecta. (1991)

A mini-gene version of the human gene for a pro-alpha 1(I) chain of type I procollagen (COL1A1) was prepared that contained -2.5 kilobases of the promoter region and the 5'- and 3'-ends of the gene but lacked a large central region containing 41 exons. The construct was modeled after a sporadic in-frame deletion of the human gene that produced a lethal variant of osteogenesis imperfecta, because it caused synthesis of shortened pro-alpha 1(I) chains that associated with normal pro-alpha 1(I) and pro-alpha 2(I) chains and caused degradation of both the shortened and normal pro-alpha chains through a process called procollagen suicide. The mini-gene was used to prepare transgenic mice. Eight of 15 transgenic mice expressed varying levels of the gene. All except one of the Fo founders were phenotypically normal, but several of the founders were apparently mosaic since they produced F1 progeny that died shortly after birth with a distinctive phenotype. The phenotype included extensive fractures of ribs and long bones similar to the fractures seen in lethal variants of osteogenesis imperfecta. Mice with the lethal phenotype expressed much higher levels of the mini-gene than transgenic mice without the lethal phenotype. Experiments with cultured skin fibroblasts from the transgenic mice demonstrated that shortened pro-alpha 1(I) chains synthesized from the mini-gene became disulfide-linked to pro-alpha 1(I) chains synthesized from the endogenous mouse gene. The results demonstrate that a mutated type I procollagen gene based on the model of procollagen suicide can be used to produce a severe phenotype of osteogenesis imperfecta that is genetically transmitted.
Rapid generation of novel models of RAG1 deficiency by CRISPR/Cas9-induced mutagenesis in murine zygotes (2016)

Mutations in the Recombination Activating Gene 1 (RAG1) can cause a wide variety of clinical and immunological phenotypes in humans, ranging from absence of T and B lymphocytes to occurrence of autoimmune manifestations associated with expansion of oligoclonal T cells and production of autoantibodies. Although the mechanisms underlying this phenotypic heterogeneity remain poorly understood, some genotype-phenotype correlations can be made. Currently, mouse models of Rag deficiency are restricted to RAG1-/- mice and to knock-in models carrying severe missense mutations. The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 system is a novel and powerful gene-editing strategy that permits targeted introduction of DNA double strand breaks with high efficiency through simultaneous delivery of the Cas9 endonuclease and a guide RNA (gRNA). Here, we report on CRISPR-based, single-step generation and characterization of mutant mouse models in which gene editing was attempted around residue 838 of RAG1, a region whose functional role had not been studied previously.
18F-FDG-uptake and molecular markers of hypoxia and inflammation in atherosclerotic plaques of the internal carotid arteries of human subjects (2012)

190 Objectives To study whether glycolytic activity measured non-invasively by 18F-FDG-PET/CT imaging is associated with gene expression of selected markers of hypoxia and inflammation in patients with atherosclerosis of the internal carotid artery. Methods 18 patients scheduled for carotid endarterectomy consented to receiving a combined 18F-FDG-PET/CT scan. Following the PET/CT plaques were removed and using quantitative polymerase chain reaction (qPCR) we determined mRNA levels of hypoxia-inducible factor 1α (HIF1α), glucose transporter 3 (GLUT3), carbonic anhydrase 2 (CA2) and cluster of differentiation 68 (CD68). By associating 3mm image slices to corresponding physical slices of the excised lesions we compared gene expression patterns to glycolytic activity regionally across all patients on a slice by slice basis. Measures of standardized uptake values (SUVmean and SUVmax) were noted and compared to gene expression data. Immunohistochemistry was applied to confirm protein target expression. Results Gene expression of molecular markers associated with hypoxia and inflammation correlated with 18F-FDG-uptake and thus glycolysis. A final model of multivariate regression applying backward elimination of least significant factors supported HIF1α, CA2 and CD68 as contributing independent factors of 18F-FDG-uptake measured both as SUVmean (p Conclusions Glycolysis measured quantitatively with 18F-FDG PET in atherosclerotic carotid lesions in patients correlate with both inflammatory activity as indicated by macrophage infiltration and with hypoxia as indicated by expression of genes related to hypoxia
Analysis of the deflection system for a magnetic-field-immersed magnicon amplifier (1992)

A linear analysis of the electron-beam deflection system in a magnicon amplifier is presented. The system consists of identical cavities, one driven and the remainder passive, separated by a drift space and immersed in an axial magnetic field. The cavities contain a rotating TM/sub 110/ mode. The length of each cavity is pi nu /sub z// omega , and that of the drift space is pi nu /sub z// omega /sub c/, where omega is the RF frequency, omega /sub c/ is the relativistic gyrofrequency in the guide field, and nu /sub z/ is the mean axial velocity of the beam electrons. The linearized electron orbits are obtained for arbitrary initial axial velocity, radial coordinate, and magnetic field. The small-signal gain and the phase shift are determined. The special case where omega /sub c// omega =2 has unique features and is discussed in detail. For the NRL magnicon design, a power gain of 10 dB per passive cavity is feasible. Results from numerical modeling of a magnicon with two passive cavities are presented. Operation of the output cavity at the fundamental and higher harmonics of the input drive frequency is briefly discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
THE TECHNIC OF ADRENALECTOMY IN DOGS (1938)

Numerous writers have described technics for adrenalectomy, but little stress has been laid upon preserving the integrity of the splanchnic nerves. Having had occasion to use many adrenalectomized dogs in the assay of various adrenal preparations, we became dissatisfied with the operative technic previously employed, and were led to evolve a more satisfactory method, which is described herewith. It is now routine in our laboratory. Sequela of adrenalectomy. Between 1932 and 1935, 56 dogs of mongrel varieties were adrenalectomized in this laboratory, of which only 24 survived, 32 dying within the 48 hours following one-stage bilateral adrenalectomy. The two-stage operation was totally unsuccessful. Death, which was preceded by drowsiness, retching and vomiting, muscular weakness, slow respiration and pulse rate, and rapid fall of temperature, could be postponed 2 to 4 hours at most by the intravenous injection of NaCl, NaHCO3 and glucose, or by Ringer’s solution. In one dog in adrenal insufficiency, 100 mg...
Investigation of Asphaltene Association with Vapor Pressure Osmometry and Interfacial Tension Measurements (2000)

Molar masses of both n-pentane-extracted and n-heptane-extracted Athabasca asphaltenes were measured in toluene or 1,2-dichlorobenzene with a vapor pressure osmometer (VPO). The initial asphaltene molar mass, at concentrations below 0.5 kg/m3, is ≈1800 g/mol. The asphaltene molar mass is found to increase with asphaltene concentration until a limiting value is reached at a concentration between 10 and 20 kg/m3. The limiting value ranges from 4000 to 10 000 g/mol and depends on the solvent, temperature, and asphaltene fraction. The results suggest that asphaltenes form aggregates of 2−6 molecules in aromatic solvents. Interfacial tensions of asphaltenes in toluene or 1,2-dichlorobenzene versus water were measured for asphaltene concentrations from 0.3 to 100 kg/m3 using a drop volume tensiometer. The interfacial tension decreases linearly with concentration, indicating that no micelles are formed. Hence, the aggregation observed with VPO does not appear to be micellization. Similar results are obtained for Cold Lake asphaltenes.
Deletion of the DNA Ligase IV Gene in Candida glabrata Significantly Increases Gene-Targeting Efficiency (2015)

Candida glabrata is reported as the second most prevalent human opportunistic fungal pathogen in the United States. Over the last decades, its incidence increased, whereas that of Candida albicans decreased slightly. One of the main reasons for this shift is attributed to the inherent tolerance of C. glabrata toward the commonly used azole antifungal drugs. Despite a close phylogenetic distance to Saccharomyces cerevisiae, homologous recombination works with poor efficiency in C. glabrata compared to baker's yeast, in fact limiting targeted genetic alterations of the pathogen's genome. It has been shown that nonhomologous DNA end joining is dominant over specific gene targeting in C. glabrata. To improve the homologous recombination efficiency, we have generated a strain in which the LIG4 gene has been deleted, which resulted in a significant increase in correct gene targeting. The very specific function of Lig4 in mediating nonhomologous end joining is the reason for the absence of clear side effects, some of which affect the ku80 mutant, another mutant with reduced nonhomologous end joining. We also generated a LIG4 reintegration cassette. Our results show that the lig4 mutant strain may be a valuable tool for the C. glabrata research community.
The catalytic mechanism for NO production by the mitochondrial enzyme, sulfite oxidase (2019)

Recently, Guenter Schwarz and colleagues published an elegant study in the <i>Biochemical Journal</i> (2019) <b>476</b>, 1805-1815 which combines kinetic and spectroscopic studies with protein engineering to provide a mechanism for sulfite oxidase (SO)-catalyzed nitrite reduction that yields nitric oxide (NO). This work is noteworthy as it demonstrates that (i) for NO generation, both sulfite and nitrite must bind to the same molybdenum (Mo) center; (ii) upon sulfite reduction, Mo is reduced from +6 (Mo<sup>VI</sup>) to +4 (Mo<sup>IV</sup>) and Mo<sup>IV</sup> reduces nitrite to NO yielding Mo<sup>V</sup>; (iii) the heme moiety, linked to the Mo-center by an 11 amino acid residue tether, gets reduced by intramolecular electron transfer (IET) resulting in Mo<sup>V</sup> being oxidized to Mo<sup>VI</sup>; (iv) the reduced heme transfers its electron to a second nitrite molecule converting it to NO; (v) the authors demonstrate steady-state NO production in the presence of the natural electron acceptor cytochrome <i>c</i>; (vi) Finally, the authors use protein engineering to shorten the heme tether to reduce the heme-Mo-center distance with the aim of increasing NO production. Consequently, the rate of IET to cytochrome <i>c</i> is decreased but the enzymatic turnover rate for NO production is increased by ∼10-fold. This paper is unique as it provides strong evidence for a novel mechanism for steady-state NO production for human mitochondrial SO and serves as a potential template for studying NO production mechanisms in other enzymes by integrating the information gained from enzyme kinetics with EPR and UV/vis spectroscopy and protein engineering.
Convolutional Analysis Operator Learning: Acceleration, Convergence, Application, and Neural Networks. (2018)

Convolutional operator learning is increasingly gaining attention in many signal processing and computer vision applications. Learning kernels has mostly relied on so-called local approaches that extract and store many overlapping patches across training signals. Due to memory demands, local approaches have limitations when learning kernels from large datasets -- particularly with multi-layered structures, e.g., convolutional neural network (CNN) -- and/or applying the learned kernels to high-dimensional signal recovery problems. The so-called global approach has been studied within the synthesis signal model, e.g., convolutional dictionary learning, overcoming the memory problems by careful algorithmic designs. This paper proposes a new convolutional analysis operator learning (CAOL) framework in the global approach, and develops a new convergent Block Proximal Gradient method using a Majorizer (BPG-M) to solve the corresponding block multi-nonconvex problems. To learn diverse filters within the CAOL framework, this paper introduces an orthogonality constraint that enforces a tight-frame (TF) filter condition, and a regularizer that promotes diversity between filters. Numerical experiments show that, for tight majorizers, BPG-M significantly accelerates the CAOL convergence rate compared to the state-of-the-art method, BPG. Numerical experiments for sparse-view computational tomography show that CAOL using TF filters significantly improves reconstruction quality compared to a conventional edge-preserving regularizer. Finally, this paper shows that CAOL can be useful to mathematically model a CNN, and the corresponding updates obtained via BPG-M coincide with core modules of the CNN.