julilili42/papers huggingface dataset:
Disparate Dynamics of Gene Body and cis-Regulatory Element Evolution Illustrated for the Senescence-Associated Cysteine Protease Gene SAG12 of Plants
2021-07-06

Gene regulation networks precisely orchestrate the expression of genes that are closely associated with defined physiological and developmental processes such as leaf senescence in plants. The Arabidopsis thaliana senescence-associated gene 12 (AtSAG12) encodes a cysteine protease that is (i) involved in the degradation of chloroplast proteins and (ii) almost exclusively expressed during senescence. Transcription factors, such as WRKY53 and WRKY45, bind to W-boxes in the promoter region of AtSAG12 and play key roles in its activation. Other transcription factors, such as bZIPs, might have accessory functions in their gene regulation, as several A-boxes have been identified and appear to be highly overrepresented in the promoter region compared to the whole genome distribution but are not localized within the regulatory regions driving senescence-associated expression. To address whether these two regulatory elements exhibiting these different properties are conserved in other closely related species, we constructed phylogenetic trees of the coding sequences of orthologs of AtSAG12 and screened their respective 2000 bp promoter regions for the presence of conserved cis-regulatory elements, such as bZIP and WRKY binding sites. Interestingly, the functional relevant upstream located W-boxes were absent in plant species as closely related as Arabidopsis lyrata, whereas an A-box cluster appeared to be conserved in the Arabidopsis species but disappeared in Brassica napus. Several orthologs were present in other species, possibly because of local or whole genome duplication events, but with distinct cis-regulatory sites in different locations. However, at least one gene copy in each family analyzed carried one W-box and one A-box in its promoter. These gene differences in SAG12 orthologs are discussed in the framework of cis- and trans-regulatory factors, of promoter and gene evolution, of genetic variation, and of the enhancement of the adaptability of plants to changing environmental conditions.
Tailoring Tautomerization of Single Phthalocyanine Molecules through Modification of Chromophore Photophysics by the Purcell Effect of an Optical Microcavity
2021-07-06

Over the years, probing and controlling tautomerization has attracted significant attention because of its fundamental importance in various chemical and biological phenomena. So far, light, force, electrons, and electric field have been employed to alter the tautomerization characteristics in porphyrin and phthalocyanine derivatives. Here, we show that engineering the photophysics of molecules through interaction with the vacuum electromagnetic field in an optical microcavity can be used to control the tautomerization of single phthalocyanine molecules. Compared to the molecules embedded in a polymer matrix in open space, the average fluorescence lifetime inside the resonant microcavity decreases significantly due to the Purcell effect. The decreased lifetime reduces the possibility of a molecule entering into the triplet state, i.e., the photoactive tautomerization channel. As a result, the photoinduced tautomerization in phthalocyanine can be significantly altered. Our results demonstrate that the weak coupling between the excited state of a molecule and the vacuum electromagnetic field via a cavity mode can lead to significant changes in photoreactivity.
Internality and the internalisation of failure: Evidence from a novel task
2021-07-06

A critical facet of adjusting one’s behaviour after succeeding or failing at a task is assigning responsibility for the ultimate outcome. Humans have trait- and state-like tendencies to implicate aspects of their own behaviour (called ‘internal’ ascriptions) or facets of the particular task or Lady Luck (’chance’). However, how these tendencies interact with actual performance is unclear. We designed a novel task in which subjects had to learn the likelihood of achieving their goals, and the extent to which this depended on their efforts. High internality (Levenson I-score) was associated with decision making patterns that are less vulnerable to failure. Our computational analyses suggested that this depended heavily on the adjustment in the perceived achievability of riskier goals following failure. We found beliefs about chance not to be explanatory of choice behaviour in our task. Beliefs about powerful others were strong predictors of behaviour, but only when subjects lacked substantial influence over the outcome. Our results provide an evidentiary basis for heuristics and learning differences that underlie the formation and maintenance of control expectations by the self.
The Three Choruses of Plato’s Laws and their Function in the Dialogue
2021-07-06

Abstract This article questions a longtime credo concerning Plato’s Laws , namely that the three choruses introduced in Book 2 are institutions of the dialogue’s political project. A detailed analysis of relevant passages shows that the evidence is insufficent. Rather, it is argued, this part of Book 2 is essentially plurivalent: on three separate semantic layers, the choruses illustrate political, moral-psychological and key educational issues of the Laws . Apart from explaining the disappearance of the choruses after Book 2, the proposed reading aims to bring to light an impressively artful philosophical and literary strategy of Plato’s.
Fear Memory Retrieval Is Associated With a Reduction in AMPA Receptor Density at Thalamic to Amygdala Intercalated Cell Synapses
2021-07-06

The amygdala plays a crucial role in attaching emotional significance to environmental cues. Its intercalated cell masses (ITC) are tight clusters of GABAergic neurons, which are distributed around the basolateral amygdala complex. Distinct ITC clusters are involved in the acquisition and extinction of conditioned fear responses. Previously, we have shown that fear memory retrieval reduces the AMPA/NMDA ratio at thalamic afferents to ITC neurons within the dorsal medio-paracapsular cluster. Here, we investigate the molecular mechanisms underlying the fear-mediated reduction in the AMPA/NMDA ratio at these synapses and, in particular, whether specific changes in the synaptic density of AMPA receptors underlie the observed change. To this aim, we used a detergent-digested freeze-fracture replica immunolabeling technique (FRIL) approach that enables to visualize the spatial distribution of intrasynaptic AMPA receptors at high resolution. AMPA receptors were detected using an antibody raised against an epitope common to all AMPA subunits. To visualize thalamic inputs, we virally transduced the posterior thalamic complex with Channelrhodopsin 2-YFP, which is anterogradely transported along axons. Using face-matched replica, we confirmed that the postsynaptic elements were ITC neurons due to their prominent expression of μ-opioid receptors. With this approach, we show that, following auditory fear conditioning in mice, the formation and retrieval of fear memory is linked to a significant reduction in the density of AMPA receptors, particularly at spine synapses formed by inputs of the posterior intralaminar thalamic and medial geniculate nuclei onto identified ITC neurons. Our study is one of the few that has directly linked the regulation of AMPA receptor trafficking to memory processes in identified neuronal networks, by showing that fear-memory induced reduction in AMPA/NMDA ratio at thalamic-ITC synapses is associated with a reduced postsynaptic AMPA receptor density.
Exponential speedup of incoherent tunneling via dissipation
2021-07-06

We study the escape rate of a particle in a metastable potential in presence of a dissipative bath coupled to the momentum of the particle. Using the semiclassical bounce technique, we find that this rate is exponentially enhanced. In particular, the influence of momentum dissipation depends on the slope of the barrier that the particle is tunneling through. We investigate also the influence of dissipative baths coupled to the position, and to the momentum of the particle, respectively. In this case the rate exhibits a non-monotonic behavior as a function of the dissipative coupling strengths. Remarkably, even in presence of position dissipation, momentum dissipation can enhance exponentially the escape rate in a large range of the parameter space. The influence of the momentum dissipation is also witnessed by the substantial increase of the average energy loss during inelastic (environment-assisted) tunneling.
Deep observations of Kepler's SNR with H.E.S.S.
2021-07-06

Kepler’s supernova remnant (SNR) which is produced by the most recent naked-eye supernova in our Galaxy is one of the best studied SNRs, but its gamma-ray detection has eluded us so far. Observations with modern imaging atmospheric Cherenkov telescopes (IACT) have enlarged the knowledge about nearby SNRs with ages younger than 500 years by establishing Cassiopeia A and Tycho’s SNRs as very high energy (VHE) gamma-ray sources and setting a lower limit on the distance to Kepler’s SNR. This SNR is significantly more distant than the other two and expected to be one of the faintest gamma-ray sources within reach of the IACT arrays of this generation. We report strong evidence for a VHE signal from Kepler’s SNR based on deep observations of the High Energy Stereoscopic System (H.E.S.S.) with an exposure of 152 hours, including 122 hours accumulated in 2017-2020. We further discuss implications of this result for cosmic-ray acceleration in young SNRs.
Impaired discrimination of a subanesthetic dose of ketamine in a maternal immune activation model of schizophrenia risk
2021-07-06

Background: Animal models of psychiatric diseases suffer from a lack of reliable methods for accurate assessment of subjective internal states in nonhumans. This gap makes translation of results from animal models to patients particularly challenging. Aims/methods: Here, we used the drug-discrimination paradigm to allow rats that model a risk factor for schizophrenia (maternal immune activation, MIA) to report on the subjective internal state produced by a subanesthetic dose of the N-methyl-D-aspartate (NMDA) receptor antagonist ketamine. Results/outcomes: The MIA rats’ discrimination of ketamine was impaired relative to controls, both in the total number of rats that acquired and the asymptotic level of discrimination accuracy. This deficit was not due to a general inability to learn to discriminate an internal drug cue or internal state generally, as MIA rats were unimpaired in the learning and acquisition of a morphine drug discrimination and were as sensitive to the internal state of satiety as controls. Furthermore, the deficit was not due to a decreased sensitivity to the physiological effects of ketamine, as MIA rats showed increased ketamine-induced locomotor activity. Finally, impaired discrimination of ketamine was only seen at subanesthetic doses which functionally correspond to psychotomimetic doses in humans. Conclusion: These data link changes in NMDA responses to the MIA model. Furthermore, they confirm the utility of the drug-discrimination paradigm for future inquiries into the subjective internal state produced in models of schizophrenia and other developmental diseases.
Life on leaves : uncovering temporal dynamics in Arabidopsis’ leaf microbiota
2021-07-06

Abstract Leaves are primarily responsible for the plant’s photosynthetic activity. Thus, changes in the phyllosphere microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. In this context, identifying the processes and microorganisms that drive the changes in the leaf microbiota over a plant’s lifetime is crucial. In this study we analyzed the temporal dynamics in the leaf microbiota of Arabidopsis thaliana , integrating both compositional changes and changes in microbe-microbe interactions via the study of microbial networks. Field-grown Arabidopsis were used to follow leaf bacterial, fungal and oomycete communities, throughout the plant’s growing season (extending from November to March), over three consecutive years. Our results revealed the existence of conserved time patterns, with microbial communities and networks going through a stabilization phase (decreasing diversity and variability) at the beginning of the plant’s growing season. Despite a high turnover in these communities, we identified 19 ‘core’ taxa persisting in Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network ‘hubs’ and ‘hubs’ alternate with time. Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting it could be possible to predict and drive these microbial communities to desired states.
Search for dark matter annihilation towards the inner Milky Way halo with the H.E.S.S. Inner Galaxy Survey
2021-07-06

The presence of dark matter (DM) is suggested by a wealth of astrophysical and cosmological measurements. However, its underlying nature is yet unknown. Among the most promising candidates are weakly interacting massive particles (WIMPs): particles with mass and coupling strength at the electroweak scale and thermally produced in the early universe have a present relic density consistent with that observed today. WIMP self annihilation would produce Standard Model particles including gamma-rays, which have been long-time recognized as a prime messenger to indirectly detect dark matter signals. The centre of the Milky Way is predicted as the brightest source of DM annihilations. The H.E.S.S. collaboration is currently performing a survey of the inner region of the Milky Way, the Inner Galaxy Survey (IGS), intended to achieve the best sensitivity to faint and diffuse emissions in a region of several degrees around the Galactic Centre. We analyzed 2014-2020 observations taken with the five-telescope array to search for a DM annihilation signal. With the current dataset of about 550 hours, we found no significant excess and therefore derived strong constraints on the velocity-weighted annihilation cross-section. TeV thermal WIMPs can be probed in different annihilation channels.
Improving motor imagery classification during induced motor perturbations
2021-07-07

Abstract Objective. Motor imagery is the mental simulation of movements. It is a common paradigm to design brain-computer interfaces (BCIs) that elicits the modulation of brain oscillatory activity similar to real, passive and induced movements. In this study, we used peripheral stimulation to provoke movements of one limb during the performance of motor imagery tasks. Unlike other works, in which induced movements are used to support the BCI operation, our goal was to test and improve the robustness of motor imagery based BCI systems to perturbations caused by artificially generated movements. Approach. We performed a BCI session with ten participants who carried out motor imagery of three limbs. In some of the trials, one of the arms was moved by neuromuscular stimulation. We analysed 2-class motor imagery classifications with and without movement perturbations. We investigated the performance decrease produced by these disturbances and designed different computational strategies to attenuate the observed classification accuracy drop. Main results. When the movement was induced in a limb not coincident with the motor imagery classes, extracting oscillatory sources of the movement imagination tasks resulted in BCI performance being similar to the control (undisturbed) condition; when the movement was induced in a limb also involved in the motor imagery tasks, the performance drop was significantly alleviated by spatially filtering out the neural noise caused by the stimulation. We also show that the loss of BCI accuracy was accompanied by weaker power of the sensorimotor rhythm. Importantly, this residual power could be used to predict whether a BCI user will perform with sufficient accuracy under the movement disturbances. Significance. We provide methods to ameliorate and even eliminate motor related afferent disturbances during the performance of motor imagery tasks. This can help improving the reliability of current motor imagery based BCI systems.
How to Find Aquifer Statistics Utilizing Pumping Tests? Two Field Studies Using welltestpy
2021-07-07

Abstract We present a workflow to estimate geostatistical aquifer parameters from pumping test data using the Python package welltestpy . The procedure of pumping test analysis is exemplified for two data sets from the Horkheimer Insel site and from the Lauswiesen site, Germany. The analysis is based on a semi‐analytical drawdown solution from the upscaling approach Radial Coarse Graining, which enables to infer log‐transmissivity variance and horizontal correlation length, beside mean transmissivity, and storativity, from pumping test data. We estimate these parameters of aquifer heterogeneity from type‐curve analysis and determine their sensitivity. This procedure, implemented in welltestpy , is a template for analyzing any pumping test. It goes beyond the possibilities of standard methods, for example, based on Theis' equation, which are limited to mean transmissivity and storativity. A sensitivity study showed the impact of observation well positions on the parameter estimation quality. The insights of this study help to optimize future test setups for geostatistical aquifer analysis and provides guidance for investigating pumping tests with regard to aquifer statistics using the open‐source software package welltestpy .
Universal relations for binary neutron star mergers with long-lived remnants
2021-07-07

We present a novel universal relation for binary neutron star mergers with\\nlong-lived neutron star remnants: inspired by recent work based on numerical\\nrelativity simulations, we propose a novel approach using perturbative\\ncalculations that allow us to relate the pre-merger neutron star binary tidal\\ndeformability to the effective compactness of the post-merger remnant. Our\\nresults allow for the prediction of the stellar parameters of a long-lived\\nremnant neutron star from the study of gravitational waves emitted during the\\npre-merger phase.\\n
Rhodocenium Functionalization Enabled by Half‐Sandwich Capping, Zincke Reaction, Diazoniation and Sandmeyer Chemistry
2021-07-07

Abstract In continuation of our exploration of metallocenium chemistry we report here on innovative ways toward monofunctionalized rhodocenium salts applying half‐sandwich capping reactions of cyclopentadienyl rhodium(III) halide synthons with cyclopentadienyl ylides containing pyridine, phosphine or dinitrogen leaving groups, followed by Zincke and Sandmeyer reactions. Thereby amino, diazonio, bromo, azido and iodo rhodocenium salts containing valuable functional groups are accessible for the first time. Target compounds were characterized by spectroscopic ( 1 H/ 13 C/ 103 Rh‐NMR, IR, HR‐MS), structural (single crystal XRD) and electrochemical (CV) methods and their properties were compared to those of isoelectronic cobaltocenium compounds. These new functionalized rhodocenium complexes significantly expand the so far extremely limited chemical space of rhodocenium salts with promising options for the future development in the area of rhodocenium chemistry.
Broad and Efficient Activation of Memory CD4+ T Cells by Novel HAdV- and HCMV-Derived Peptide Pools
2021-07-07

Reactivation of Human Cytomegalovirus (HCMV) and Human Adenovirus (HAdV) in immunocompromised patients following stem cell transplantation (SCT) or solid organ transplantation (SOT) is associated with high morbidity and mortality. The adoptive transfer of virus-specific CD8 + and CD4 + T cells has been shown to re-establish the antiviral T-cell response and improve clinical outcome. The viral load in immunocompromised patients can efficiently be reduced solely by the infusion of virus-specific CD4 + T cells. The identification of CD4 + T-cell epitopes has mainly focused on a limited number of viral proteins that were characterized as immunodominant. Here, we used in silico prediction to determine promiscuous CD4 + T-cell epitopes from the entire proteomes of HCMV and HAdV. Immunogenicity testing with enzyme-linked immuno spot (ELISpot) assays and intracellular cytokine staining (ICS) revealed numerous novel CD4 + T-cell epitopes derived from a broad spectrum of viral antigens. We identified 17 novel HCMV-derived and seven novel HAdV-derived CD4 + T-cell epitopes that were recognized by &amp;gt; 50% of the assessed peripheral blood mononuclear cell (PBMC) samples. The newly identified epitopes were pooled with previously published, retested epitopes to stimulate virus-specific memory T cells in PBMCs from numerous randomly selected blood donors. Our peptide pools induced strong IFNγ secretion in 46 out of 48 (HCMV) and 31 out of 31 (HAdV) PBMC cultures. In conclusion, we applied an efficient method to screen large viral proteomes for promiscuous CD4 + T-cell epitopes to improve the detection and isolation of virus-specific T cells in a clinical setting.
An ultrasound study of frequency and co-articulation
2021-07-07

&lt;p&gt;Anticipatory coarticulation has been reported to be affected by word form frequency. However, it remains unclear whether frequency effect also modulates carry-over (perseverative) coarticulation. To investigate the interaction of word form frequency effect and carry-over/anticipatory coarticulations, ultrasound imaging was performed on the articulation of the vowel [a:] in German verbs. Effects of coarticulation were induced by controlling the verb&rsquo;s suffixes and preceding pronouns. Contrary to the standard tongue contour analysis, we analyzed whole ultrasound images using Generalized Additive Models. We found more fronted tongue root, lower tongue body, and higher tongue tip in low-frequency words. By contrast, high-frequency words showed a more rounded tongue shape. This was reflected by the middle part of the tongue to be higher and the tongue root more retracted in high frequency words in comparison to low frequency words. These findings indicate more optimized tongue movements for higher frequency words.&lt;/p&gt;