julilili42/papers huggingface dataset:
Targeted introduction of heritable point mutations into the plant mitochondrial genome
2022-03-17

Abstract The development of technologies for the genetic manipulation of mitochondrial genomes remains a major challenge. Here we report a method for the targeted introduction of mutations into plant mitochondrial DNA (mtDNA) that we refer to as transcription activator-like effector nuclease (TALEN) gene-drive mutagenesis (GDM), or TALEN-GDM. The method combines TALEN-induced site-specific cleavage of the mtDNA with selection for mutations that confer resistance to the TALEN cut. Applying TALEN-GDM to the tobacco mitochondrial nad9 gene, we isolated a large set of mutants carrying single amino acid substitutions in the Nad9 protein. The mutants could be purified to homochondriomy and stably inherited their edited mtDNA in the expected maternal fashion. TALEN-GDM induces both transitions and transversions, and can access most nucleotide positions within the TALEN binding site. Our work provides an efficient method for targeted mitochondrial genome editing that produces genetically stable, homochondriomic and fertile plants with specific point mutations in their mtDNA.
Long Term Variability of Cygnus X-1. IV. Spectral Evolution 1999-2004
2022-03-17

(abbreviated abstract) We present the long term spectral evolution of the Galactic black hole candidate Cygnus X-1 in the X-rays and at 15GHz using ~200 pointed observations taken between early 1999 and late 2004 with RXTE and the Ryle radio telescope. The X-ray spectra are remarkably well described by a simple broken power law spectrum with an exponential cutoff. Physically motivated Comptonization models, e.g., compTT or eqpair, can reproduce this simplicity. Broken power law models reveal a significant linear correlation between the photon index of the lower energy power law and the hardening of the power law at approximately 10keV. Comptonization models show that the bolometric flux of a soft excess (e.g., disk component) is strongly correlated with the compactness ratio of the Comptonizing medium. We also find that the fraction of the time spent in low radio emission/soft X-ray spectral states has increased from ~10% in 1996-2000 to ~34% since early 2000. Radio flares typically occur during state transitions and failed state transitions. There is also a strong correlation between the 10-50keV X-ray flux and the radio luminosity of the source. We demonstrate that rather than there being distinctly separated states, in contrast to the timing properties the spectrum of Cyg X-1 shows variations between extremes of properties, with clear cut examples of spectra at every intermediate point in the observed spectral correlations.
3D-radiation hydro simulations of disk-planet interactions: I. Numerical algorithm and test cases
2022-03-17

We study the evolution of an embedded protoplanet in a circumstellar disk using the 3D-Radiation Hydro code TRAMP, and treat the thermodynamics of the gas properly in three dimensions. The primary interest of this work lies in the demonstration and testing of the numerical method. We show how far numerical parameters can influence the simulations of gap opening. We study a standard reference model under various numerical approximations. Then we compare the commonly used locally isothermal approximation to the radiation hydro simulation using an equation for the internal energy. Models with different treatments of the mass accretion process are compared. Often mass accumulates in the Roche lobe of the planet creating a hydrostatic atmosphere around the planet. The gravitational torques induced by the spiral pattern of the disk onto the planet are not strongly affected in the average magnitude, but the short time scale fluctuations are stronger in the radiation hydro models. An interesting result of this work lies in the analysis of the temperature structure around the planet. The most striking effect of treating the thermodynamics properly is the formation of a hot pressure--supported bubble around the planet with a pressure scale height of H/R ~ 0.5 rather than a thin Keplerian circumplanetary accretion disk. We also observe an outflow of gas above and below the planet during the gap opening phase.
A pharmacogenomic assessment of psychiatric adverse drug reactions to levetiracetam
2022-03-17

Abstract Objective Levetiracetam (LEV) is an effective antiseizure medicine, but 10%–20% of people treated with LEV report psychiatric side‐effects, and up to 1% may have psychotic episodes. Pharmacogenomic predictors of these adverse drug reactions (ADRs) have yet to be identified. We sought to determine the contribution of both common and rare genetic variation to psychiatric and behavioral ADRs associated with LEV. Methods This case‐control study compared cases of LEV‐associated behavioral disorder ( n = 149) or psychotic reaction ( n = 37) to LEV‐exposed people with no history of psychiatric ADRs ( n = 920). All samples were of European ancestry. We performed genome‐wide association study (GWAS) analysis comparing those with LEV ADRs to controls. We estimated the polygenic risk scores (PRS) for schizophrenia and compared cases with LEV‐associated psychotic reaction to controls. Rare variant burden analysis was performed using exome sequence data of cases with psychotic reactions ( n = 18) and controls ( n = 122). Results Univariate GWAS found no significant associations with either LEV‐associated behavioural disorder or LEV‐psychotic reaction. PRS analysis showed that cases of LEV‐associated psychotic reaction had an increased PRS for schizophrenia relative to contr ols ( p = .0097, estimate = .4886). The rare‐variant analysis found no evidence of an increased burden of rare genetic variants in people who had experienced LEV‐associated psychotic reaction relative to controls. Significance The polygenic burden for schizophrenia is a risk factor for LEV‐associated psychotic reaction. To assess the clinical utility of PRS as a predictor, it should be tested in an independent and ideally prospective cohort. Larger sample sizes are required for the identification of significant univariate common genetic signals or rare genetic signals associated with psychiatric LEV ADRs.
Molecular Properties of Human Guanylate Cyclase-Activating Protein 3 (GCAP3) and Its Possible Association with Retinitis Pigmentosa
2022-03-17

The cone-specific guanylate cyclase-activating protein 3 (GCAP3), encoded by the GUCA1C gene, has been shown to regulate the enzymatic activity of membrane-bound guanylate cyclases (GCs) in bovine and teleost fish photoreceptors, to an extent comparable to that of the paralog protein GCAP1. To date, the molecular mechanisms underlying GCAP3 function remain largely unexplored. In this work, we report a thorough characterization of the biochemical and biophysical properties of human GCAP3, moreover, we identified an isolated case of retinitis pigmentosa, in which a patient carried the c.301G&gt;C mutation in GUCA1C, resulting in the substitution of a highly conserved aspartate residue by a histidine (p.(D101H)). We found that myristoylated GCAP3 can activate GC1 with a similar Ca2+-dependent profile, but significantly less efficiently than GCAP1. The non-myristoylated form did not induce appreciable regulation of GC1, nor did the p.D101H variant. GCAP3 forms dimers under physiological conditions, but at odds with its paralogs, it tends to form temperature-dependent aggregates driven by hydrophobic interactions. The peculiar properties of GCAP3 were confirmed by 2 ms molecular dynamics simulations, which for the p.D101H variant highlighted a very high structural flexibility and a clear tendency to lose the binding of a Ca2+ ion to EF3. Overall, our data show that GCAP3 has unusual biochemical properties, which make the protein significantly different from GCAP1 and GCAP2. Moreover, the newly identified point mutation resulting in a substantially unfunctional protein could trigger retinitis pigmentosa through a currently unknown mechanism.
Discrete embryonic character variation uncovers hidden ecological adaptations in lacertid lizards
2022-03-17

Abstract Embryogenesis is the first step in the ontogenetic life journey of any individual, and is thus a starting point for natural selection to cause evolutionary change. There are slight variations in the timing of embryonic development, known as heterochrony, which may eventually lead to major differences in adult anatomy. To test this hypothesis, the embryonic development of three closely related lizard species, Darevskia armeniaca , Lacerta agilis , and L. viridis , which are adapted to different habitats, was compared by analyzing discrete timing characters. Both intra‐ and interspecific variation was detected. The latter may be interpreted as embryonic pre‐adaptions to later adult lifestyles, demonstrating that developmental penetrance manifests within a few million years. Traits with large intraspecific temporal variation, such as limb‐related features, were susceptible to natural selection. In particular, the mountain‐dwelling, climbing species D. armeniaca showed embryonic preadaptions by an early developing limb anlagen. This observation demonstrated interspecific variation, which was elusive in a previous comparative study based on purely metric data of developing limb lengths, and highlighted the importance of multiple data sources to draw robust conclusions about evolutionary change. Timing differences indicated unexplored ecological adaptations of the poorly understood lifestyle of these lizards. Thus, embryonic research provides a platform to explore superficially hidden evolutionary adaptations of all organisms on Earth.
Spherical Hartree-Fock calculations with linear momentum projection before the variation.Part II: Spectral functions and spectroscopic factors
2022-03-17

The hole--spectral functions and from these the spectroscopic factors have been calculated in an Galilei--invariant way for the ground state wave functions resulting from spherical Hartree--Fock calculations with projection onto zero total linear momentum before the variation for the nuclei 4He, 12C, 16O, 28Si, 32S and 40Ca. The results are compared to those of the conventional approach which uses the ground states resulting from usual spherical Hartree--Fock calculations subtracting the kinetic energy of the center of mass motion before the variation and to the results obtained analytically with oscillator occupations.
Predicting native Chinese readers’ perception of sentence boundaries in written Chinese texts
2022-03-17

Abstract The notion of sentencehood in Mandarin Chinese is much less well-defined than in many other languages, with a block of clauses often joined by commas without conjunctions and with the period often occurring at the end of a block of clauses to indicate meaning completeness rather than the completeness of a sentential structure. The potential factors that may affect native Chinese speakers’ judgment of meaning completeness and perception of sentence boundaries have not yet been systematically examined. In light of this research gap, this study investigates the factors that may play a role in native Chinese speakers’ sentence boundary perception. To this end, we conducted text re-punctuation experiments in two separate groups, a training group and a testing group, using different stimuli texts. The stimuli texts were annotated with multiple levels of linguistic information to identify potentially relevant variables that could affect the participants’ sentence boundary perception. Logistic regression and the Bayesian statistical methods were applied to test the potential effects of multiple variables on the participants’ responses. The logistic regression model trained on the data from the training group achieved a high level of accuracy in predicting the responses by the testing group. The model revealed a more important role of semantic information than syntactic information in the participants’ sentence boundary perception. The implications of our findings for understanding the perception of Chinese sentence boundaries are discussed.
Mastery-Approach Goals: A Large-Scale Cross-Cultural Analysis of Antecedents and Consequences
2022-03-17

Mastery-approach (MAP) goals, focusing on developing competence and acquiring task mastery, is posited to be the most optimal, beneficial type of achievement goal for academic and life outcomes. Although there is meta-analytic evidence supporting this finding, such evidence does not allow us to conclude that the extant MAP goal findings generalize across cultures. Meta-analyses have often suffered from over-representation of Western, educated, industrialized, rich, and democratic (WEIRD) samples, reliance on bivariate correlations, and lack the ability to directly control individual-level background variables. To address these limitations, this study used nationally representative data from 80 societies (N= 612,004 adolescents) to examine the relations of MAP goals to four personality antecedents (workmastery, competitiveness, fear of failure, and mindset) and 16 consequences (i.e., task-specific motivational, achievement-related, and well-being outcomes), and tested the cross-cultural generalizability of these relations. Results showed that MAP goals were: (a) grounded primarily in positive (workmastery, competitiveness) but not negative achievement motives (fear of failure, fixed mindset); (b) most strongly predictive of well-being outcomes (e.g., life satisfaction, resilience), followed by adaptative motivational (e.g., enjoyment, perceived competent) and achievement-related (e.g., test performance, educational aspirations) outcomes; (c) weakly negatively associated with maladaptive outcomes (perceived task difficulty); and (d) uniquely predictive of various consequences, controlling for the personality antecedents and covariates. Further, the results of four different approaches provide consistent, strong support for cross-cultural generalizability of these relations, which has practical implications regarding the benefits of MAP goal pursuit in daily life and directions for educational intervention in a global context.
A New Approach for Boundary Recognition in Geometric Sensor Networks
2022-03-17

We describe a new approach for dealing with the following central problem in the self-organization of a geometric sensor network: Given a polygonal region R, and a large, dense set of sensor nodes that are scattered uniformly at random in R. There is no central control unit, and nodes can only communicate locally by wireless radio to all other nodes that are within communication radius r, without knowing their coordinates or distances to other nodes. The objective is to develop a simple distributed protocol that allows nodes to identify themselves as being located near the boundary of R and form connected pieces of the boundary. We give a comparison of several centrality measures commonly used in the analysis of social networks and show that restricted stress centrality is particularly suited for geometric networks; we provide mathematical as well as experimental evidence for the quality of this measure.
Sum rules of single-particle spectral functions in hot asymmetric nuclear matter
2022-03-17

The neutron and proton single-particle spectral functions in asymmetric nuclear matter fulfill energy weighted sum rules. The validity of these sum rules within the self-consistent Green's function approach is investigated. The various contributions to these sum rules and their convergence as a function of energy provide information about correlations induced by the realistic interaction between the nucleons. These features are studied as a function of the asymmetry of nuclear matter.
On embeddings of homogeneous spaces with small boundary
2022-03-17

We study equivariant embeddings with small boundary of a given homogeneous space , where is a connected, linear algebraic group with trivial Picard group and only trivial characters, and is an extension of a connected Grosshans subgroup by a torus. Under certain maximality conditions, like completeness, we obtain finiteness of the number of isomorphism classes of such embeddings, and we provide a combinatorial description the embbeddings and their morphisms. The latter allows a systematic treatment of examples and basic statements on the geometry of the equivariant embeddings of a given homogeneous space .
Positively and negatively excited random walks on integers, with branching processes
2022-03-17

We consider excited random walks on the integers with a bounded number of i.i.d. cookies per site which may induce drifts both to the left and to the right. We extend the criteria for recurrence and transience by M. Zerner and for positivity of speed by A.-L. Basdevant and A. Singh to this case and also prove an annealed central limit theorem. The proofs are based on results from the literature concerning branching processes with migration and make use of a certain renewal structure.
Recurrence and transience of excited random walks on $\\Z^d$ and strips
2022-03-17

We investigate excited random walks on and on planar strips which have a drift in a given direction. The strength of the drift may depend on a random i.i.d. environment and on the local time of the walk. We give exact criteria for recurrence and transience, thus generalizing results by Benjamini and Wilson for once-excited random walk on and by the author for multi-excited random walk on .
Destabilizing the Fundamental Mode of Black Holes: The Elephant and the Flea
2022-03-18

Recent work applying the notion of pseudospectrum to gravitational physics showed that the quasinormal mode spectrum of black holes is unstable, with the possible exception of the longest-lived (fundamental) mode. The fundamental mode dominates the expected signal in gravitational wave astronomy, and there is no reason why it should have privileged status. We compute the quasinormal mode spectrum of two model problems where the Schwarzschild potential is perturbed by a small "bump" consisting of either a Pöschl-Teller potential or a Gaussian, and we show that the fundamental mode is destabilized under generic perturbations. We present phase diagrams and study a simple double-barrier toy problem to clarify the conditions under which the spectral instability occurs.
GaBoDS: The Garching-Bonn Deep Survey -- I. Anatomy of galaxy clusters in the background of NGC 300
2022-03-18

The Garching-Bonn Deep Survey (GaBoDS) is a virtual 12 square degree cosmic shear and cluster lensing survey, conducted with the WFI@2.2m MPG/ESO telescope at La Silla. It consists of shallow, medium and deep random fields taken in R-band in subarcsecond seeing conditions at high galactic latitude. A substantial amount of the data was taken from the ESO archive, by means of a dedicated ASTROVIRTEL program. In the present work we describe the main characteristics and scientific goals of GaBoDS. Our strategy for mining the ESO data archive is introduced, and we comment on the Wide Field Imager data reduction as well. In the second half of the paper we report on clusters of galaxies found in the background of NGC 300, a random archival field. We use weak gravitational lensing and the red cluster sequence method for the selection of these objects. Two of the clusters found were previously known and already confirmed by spectroscopy. Based on the available data we show that there is significant evidence for substructure in one of the clusters, and an increasing fraction of blue galaxies towards larger cluster radii. Two other mass peaks detected by our weak lensing technique coincide with red clumps of galaxies. We estimate their redshifts and masses.
α‐hemolysin of Staphylococcus aureus impairs thrombus formation
2022-03-18

Our findings might be of clinical relevance for S. aureus induced endocarditis. Stabilizing the aortic-valve thrombi by inhibiting Hla-induced impairment of platelets might reduce the risk for septic (micro-)embolization.
Cavity-driven Rabi oscillations between Rydberg states of atoms trapped on a superconducting atom chip
2022-03-18

Hybrid quantum systems involving cold atoms and microwave resonators can enable cavity-mediated infinite-range interactions between atomic spin systems and realize atomic quantum memories and transducers for microwave-to-optical conversion. To achieve strong coupling of atoms to on-chip microwave resonators, it was suggested to use atomic Rydberg states with strong electric-dipole transitions. Here we report on the experimental realization of coherent coupling of a Rydberg transition of ultracold atoms, trapped on an integrated superconducting atom chip, to the microwave field of an on-chip coplanar waveguide resonator. Close to the chip surface, stray electric fields lead to inhomogeneous Rydberg level shifts, which would hinder coherent interactions of atoms in a cloud with the Rydberg excitation lasers and the microwave cavity field. We, however, use optical excitation of a Rydberg state of atoms in a narrow layer with nearly constant electric field, which allows for resonant coupling of the atoms to the cavity microwave field on an appropriate Rydberg transition. We also achieve state-selective detection of the energetically close Rydberg states. We then observe and characterize cavity-driven Rabi oscillations between a pair of atomic Rydberg states. The residual damping of the oscillations is dominated by the spread of Rabi frequencies of atoms in different positions of the resonant cavity mode, as revealed by our model. Despite the technical challenges, our studies demonstrate the feasibility of coherent-state manipulation of Rydberg atoms interacting with superconducting circuits, paving the way for realization of capable hybrid quantum systems.
Light Stimulation of Neurons on Organic Photocapacitors Induces Action Potentials with Millisecond Precision
2022-03-18

Abstract Nongenetic optical control of neurons is a powerful technique to study and manipulate the function of the nervous system. This research has benchmarked the performance of organic electrolytic photocapacitor (OEPC) optoelectronic stimulators at the level of single mammalian cells: human embryonic kidney (HEK) cells with heterologously expressed voltage‐gated K + channels and hippocampal primary neurons. OEPCs act as extracellular stimulation electrodes driven by deep red light. The electrophysiological recordings show that millisecond light stimulation of OEPC shifts conductance‐voltage plots of voltage‐gated K + channels by ≈ 30 mV. Models are described both for understanding the experimental findings at the level of K + channel kinetics in HEK cells, as well as elucidating interpretation of membrane electrophysiology obtained during stimulation with an electrically floating extracellular photoelectrode. A time‐dependent increase in voltage‐gated channel conductivity in response to OEPC stimulation is demonstrated. These findings are then carried on to cultured primary hippocampal neurons. It is found that millisecond time‐scale optical stimuli trigger repetitive action potentials in these neurons. The findings demonstrate that OEPC devices enable the manipulation of neuronal signaling activities with millisecond precision. OEPCs can therefore be integrated into novel in vitro electrophysiology protocols, and the findings can inspire in vivo applications.
INTEGRAL Spectrometer SPI's GRB detection capabilities. GRBs detected inside SPI's FoV and with the anticoincidence system ACS
2022-03-18

The spectrometer SPI, one of the two main instruments of the INTEGRAL spacecraft, offers significant gamma-ray burst detection capabilities. In its 35 deg (full width) field of view SPI is able to localise gamma-ray bursts at a mean rate of ~ 0.8/month. With its large anticoincidence shield of 512 kg of BGO crystals SPI is able to detect gamma-ray bursts quasi omni-directionally with a very high sensitivity. Burst alerts of the anticoincidence shield are distributed by the INTEGRAL Burst Alert System. In the first 8 months of the mission about 0.8/day gamma-ray burst candidates and 0.3/day gamma-ray burst positions were obtained with the anticoincidence shield by interplanetary network triangulations with other spacecrafts.