julilili42/papers huggingface dataset:
PENELLOPE: The ESO data legacy program to complement the Hubble UV Legacy Library of Young Stars (ULLYSES)
2021-04-07

The evolution of young stars and disks is driven by the interplay of several processes, notably the accretion and ejection of material. These processes, critical to correctly describe the conditions of planet formation, are best probed spectroscopically. Between 2020 and 2022, about 500orbits of the Hubble Space Telescope (HST) are being devoted in to the ULLYSES public survey of about 70 low-mass ( M ⋆ ≤ 2 M ⊙ ) young (age &lt; 10 Myr) stars at UV wavelengths. Here, we present the PENELLOPE Large Program carried out with the ESO Very Large Telescope (VLT) with the aim of acquiring, contemporaneously to the HST, optical ESPRESSO/UVES high-resolution spectra for the purpose of investigating the kinematics of the emitting gas, along with UV-to-NIR X-shooter medium-resolution flux-calibrated spectra to provide the fundamental parameters that HST data alone cannot provide, such as extinction and stellar properties. The data obtained by PENELLOPE have no proprietary time and the fully reduced spectra are being made available to the whole community. Here, we describe the data and the first scientific analysis of the accretion properties for the sample of 13 targets located in the Orion OB1 association and in the σ -Orionis cluster, observed in November–December 2020. We find that the accretion rates are in line with those observed previously in similarly young star-forming regions, with a variability on a timescale of days (≲3). The comparison of the fits to the continuum excess emission obtained with a slab model on the X-shooter spectra and the HST/STIS spectra shows a shortcoming in the X-shooter estimates of ≲10%, which is well within the assumed uncertainty. Its origin can be either due to an erroneous UV extinction curve or to the simplicity of the modeling and, thus, this question will form the basis of the investigation undertaken over the course of the PENELLOPE program. The combined ULLYSES and PENELLOPE data will be key in attaining a better understanding of the accretion and ejection mechanisms in young stars.
Neural-Network Heuristics for Adaptive Bayesian Quantum Estimation
2021-04-07

Quantum metrology promises unprecedented measurement precision but suffers in\\npractice from the limited availability of resources such as the number of\\nprobes, their coherence time, or non-classical quantum states. The adaptive\\nBayesian approach to parameter estimation allows for an efficient use of\\nresources thanks to adaptive experiment design. For its practical success fast\\nnumerical solutions for the Bayesian update and the adaptive experiment design\\nare crucial. Here we show that neural networks can be trained to become fast\\nand strong experiment-design heuristics using a combination of an evolutionary\\nstrategy and reinforcement learning. Neural-network heuristics are shown to\\noutperform established heuristics for the technologically important example of\\nfrequency estimation of a qubit that suffers from dephasing. Our method of\\ncreating neural-network heuristics is very general and complements the\\nwell-studied sequential Monte-Carlo method for Bayesian updates to form a\\ncomplete framework for adaptive Bayesian quantum estimation.\\n
The European Federation for Medicinal Chemistry and Chemical Biology (EFMC) Best Practice Initiative: Phenotypic Drug Discovery
2021-04-07

Abstract Phenotypic drug discovery has a long track record of delivering innovative drugs and has received renewed attention in the last few years. The promise of this approach, however, comes with several challenges that should be addressed to avoid wasting time and resources on drugs with undesired modes of action or, worse, false‐positive hits. In this set of best practices, we go over the essential steps of phenotypic drug discovery and provide guidance on how to increase the chance of success in identifying validated and relevant chemical starting points for optimization: selecting the right assay, selecting the right compound screening library and developing appropriate hit validation assays. Then, we highlight the importance of initiating studies to determine the mode of action of the identified hits early and present the current state of the art.
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems
2021-04-07

Abstract Computational models of biological systems can exploit a broad range of rapidly developing approaches, including novel experimental approaches, bioinformatics data analysis, emerging modelling paradigms, data standards and algorithms. A discussion about the most recent advances among experts from various domains is crucial to foster data-driven computational modelling and its growing use in assessing and predicting the behaviour of biological systems. Intending to encourage the development of tools, approaches and predictive models, and to deepen our understanding of biological systems, the Community of Special Interest (COSI) was launched in Computational Modelling of Biological Systems (SysMod) in 2016. SysMod’s main activity is an annual meeting at the Intelligent Systems for Molecular Biology (ISMB) conference, which brings together computer scientists, biologists, mathematicians, engineers, computational and systems biologists. In the five years since its inception, SysMod has evolved into a dynamic and expanding community, as the increasing number of contributions and participants illustrate. SysMod maintains several online resources to facilitate interaction among the community members, including an online forum, a calendar of relevant meetings and a YouTube channel with talks and lectures of interest for the modelling community. For more than half a decade, the growing interest in computational systems modelling and multi-scale data integration has inspired and supported the SysMod community. Its members get progressively more involved and actively contribute to the annual COSI meeting and several related community workshops and meetings, focusing on specific topics, including particular techniques for computational modelling or standardisation efforts.
Brain age prediction using fMRI network coupling in youths and associations with psychiatric symptoms
2021-04-07

Abstract Objective Magnetic resonance imaging (MRI) has shown that estimated brain age is deviant from chronological age in various common brain disorders. Brain age estimation could be useful for investigating patterns of brain maturation and integrity, aiding to elucidate brain mechanisms underlying these heterogeneous conditions. Here, we examined functional brain age in two large samples of children and adolescents and its relation to mental health. Methods We used resting-state fMRI data from the Philadelphia Neurodevelopmental Cohort (PNC; n=1126, age range 8-22 years) to estimate functional connectivity between brain networks, and utilized these as features for brain age prediction. We applied the prediction model to 1387 individuals (age range 8-22 years) in the Healthy Brain Network sample (HBN). In addition, we estimated brain age in PNC using a cross-validation framework. Next, we tested for associations between brain age gap and various aspects of psychopathology and cognitive performance. Results Our model was able to predict age in the independent test samples, with a model performance of r=0.54 for the HBN test set, supporting consistency in functional connectivity patterns between samples and scanners. Linear models revealed a significant association between brain age gap and psychopathology in PNC, where individuals with a lower estimated brain age, had a higher overall symptom burden. These associations were not replicated in HBN. Discussion Our findings support the use of brain age prediction from fMRI-based connectivity. While requiring further extensions and validations, the approach may be instrumental for detecting brain phenotypes related to intrinsic connectivity and could assist in characterizing risk in non-typically developing populations.
Risk and protective factors of college students’ psychological well-being during the COVID-19 pandemic: emotional stability, mental health, and household resources
2021-04-07

Colleges and universities have increasingly worried in recent decades about college students’ wellbeing, with the COVID-19 pandemic aggravating these concerns. Our study provides empirical evidence of changes to undergraduate emotional sentiments and psychological wellbeing from before to after the onset of the pandemic. In addition, we explore whether certain risk factors (i.e., prior mental health impairments, trait emotional stability) and protective factors (i.e., subjective socioeconomic status, parental education, household resources) predicted students’ emotions and their intra-individual changes due to the pandemic onset. We compared experience sampling method data from 120 students from before and after the pandemic onset, examining intra-individual trajectories.There was only little change in students’ emotions. Prior mental health impairment and trait emotional stability predicted students’ emotions, averaged across time points, but not emotion changes. Few associations with emotions were found for subjective socioeconomic status and parental education, but study-related household-resources predicted levels and changes in emotions.
Crystal structure, Magnetic and Photoluminescence Properties of GdW6Cl15, TbW6Cl15, and EuW6Cl14
2021-04-07

Abstract Ternary compounds with the [ M 6 X 14 ] 2− ( M =Mo, W; X =Cl, Br, I) cluster have been established with several counter cations. Herein, we report examples of the ternary rare‐earth ( RE ) compounds RE W 6 Cl 15 and RE W 6 Cl 14 . Preparations of the compounds GdW 6 Cl 15 , TbW 6 Cl 15 and EuW 6 Cl 14 are accomplished by solid‐state reactions of W 6 Cl 12 and RE Cl 3 ( RE =Gd, Tb), or EuCl 2 at 575 °C in fused silica tubing. GdW 6 Cl 15 and TbW 6 Cl 15 crystallize in the space group C 2 /c and EuW 6 Cl 14 in Pn , isotypic to BiW 6 Cl 15 (REW 6 Cl 15 ) and PbMo 6 Cl 15 (EuW 6 Cl 14 ) according to X‐ray powder diffraction. Crystal structures are discussed in the light of related compounds, and properties such as magnetism and photoluminescence are reported.
Long-term results of the custom- made hip endoprostheses Evolution K® and Adaptiva®: A prospective cohort study
2021-04-07

The aim of our study is to evaluate clinical long-term results and determine changes in periprosthetic bone density of the custom-made hip prostheses Evolution-K® and Adaptiva®. Periprosthetic bone density were evaluated by means of DEXA (LunariDXA- Prodigy® bone densitometer) with a long-term follow-up of 16 (15-18) years (Evolution-K®) in 24 patients and 13 (13-15) years (Adaptiva®) in 41 patients. Evolution- K® had a survival rate of 92% and yielded 79/100 points in Harris Hip Score, a mediocre result. Adaptiva® had a survival rate of 99% and achieved a good score of 88/100 points. Bone density measurements demonstrated the greatest loss of bone density in the proximal regions of interest (ROI) for both prosthesis types (Evolution-K®: -25.8% ROI 1, -40.3% ROI 7; -8.3% ROI 2, -10.4% ROI 6; Adaptiva®: -29.8% ROI 7, -6.8% ROI 6, +14.3% ROI 3, +3.1% ROI 4). Adaptiva® yielded a good clinical result as compared to Evolution-K® with only average clinical results. Both prostheses clearly showed signs of “stress shielding”. Here, the Adaptiva® achieved reduced bone density loss as compared to the Evolution-K®.
Do embodied effects reflect the consequences rather than the causes of meaning? - "Ja!"
2021-04-07

It has been shown that a movement in a direction incongruent with the spatial semantics of words typically requires more time than movements that are directionally congruent. Two explanations have been proposed for this effect. Either a word's meaning is understood by using an internal model to simulate a word's meaning -- and incogruent directionality needs time to be resolved. Or words simply serve to reduce hearers' uncertainty about future states of the world, facilitating actions that prepare for them. However, since previous experiments have focused on actions that are directly involved in the exploration of space, they provide evidence for both hypotheses. Experiment 1 of the present study avoids this shortcoming. We investigated the basic downwards directed articulatory gesture producing a high-frequency German word, "ja" (`yes'), in response to reading words with vertical semantics. This task is thus completely unrelated to the semantics of the words. We show that tongue movements are systematically modulated by verticality ratings collected from the same speakers. To investigate the source of the effect, we performed two additional, linguistically unrelated experiments. Experiment 2 demonstrates anti-phasic coupling between tongue body movements and vertical arm and leg movements. Experiment 3 investigates tongue body movements prior to head movements and uncovers preparatory tongue raising to head raising in contrast to head lowering. Taken together, the results indicate that the changes in "ja" associated with vertical semantics most likely emerge from anticipating a head movement in the direction of the spatial target associated with the read word in order to optimize the body position for subsequent actions. Thus, the results support the assumption that words reduce the uncertainty about future states of the world.
Gravitational Wave Glitches in Chaotic Extreme-Mass-Ratio Inspirals
2021-04-08

The Kerr geometry admits the Carter symmetry, which ensures that the geodesic equations are integrable. It is shown that gravitational waveforms associated with extreme-mass-ratio inspirals involving a nonintegrable compact object display "glitch" phenomena, where the frequencies of gravitational waves increase abruptly, when the orbit crosses certain spacetime regions known as Birkhoff islands. The presence or absence of these features in data from upcoming space-borne detectors will therefore allow not only for tests of general relativity but also of fundamental spacetime symmetries.
Cell-Type-Specific Dynamics of Calcium Activity in Cortical Circuits over the Course of Slow-Wave Sleep and Rapid Eye Movement Sleep
2021-04-08

Sleep shapes cortical network activity, fostering global homeostatic downregulation of excitability while maintaining or even upregulating excitability in selected networks in a manner that supports memory consolidation. Here, we used two-photon calcium imaging of cortical layer 2/3 neurons in sleeping male mice to examine how these seemingly opposing dynamics are balanced in cortical networks. During slow-wave sleep (SWS) episodes, mean calcium activity of excitatory pyramidal (Pyr) cells decreased. Simultaneously, however, variance in Pyr population calcium activity increased, contradicting the notion of a homogenous downregulation of network activity. Indeed, we identified a subpopulation of Pyr cells distinctly upregulating calcium activity during SWS, which were highly active during sleep spindles known to support mnemonic processing. Rapid eye movement (REM) episodes following SWS were associated with a general downregulation of Pyr cells, including the subpopulation of Pyr cells active during spindles, which persisted into following stages of sleep and wakefulness. Parvalbumin-positive inhibitory interneurons (PV-In) showed an increase in calcium activity during SWS episodes, while activity remained unchanged during REM sleep episodes. This supports the view that downregulation of Pyr calcium activity during SWS results from increased somatic inhibition via PV-In, whereas downregulation during REM sleep is achieved independently of such inhibitory activity. Overall, our findings show that SWS enables upregulation of select cortical circuits (likely those which were involved in mnemonic processing) through a spindle-related process, whereas REM sleep mediates general downregulation, possibly through synaptic re-normalization. SIGNIFICANCE STATEMENT Sleep is thought to globally downregulate cortical excitability and, concurrently, to upregulate synaptic connections in neuron ensembles with newly encoded memory, with upregulation representing a function of sleep spindles. Using in vivo two-photon calcium imaging in combination with surface EEG recordings, we classified cells based on their calcium activity during sleep spindles. Spindle-active pyramidal (Pyr) cells persistently increased calcium activity during slow-wave sleep (SWS) episodes while spindle-inactive cells decreased calcium activity. Subsequent rapid eye movement (REM) sleep episodes profoundly reduced calcium activity in both cell clusters. Results indicate that SWS allows for a spindle-related differential upregulation of ensembles whereas REM sleep functions to globally downregulate networks.
FASTER and SCOTT&EVA trainings for adults with high-functioning autism spectrum disorder (ASD): study protocol for a randomized controlled trial
2021-04-08

Abstract Background Autism spectrum disorder (ASD) is a chronic neurodevelopmental condition with a prevalence rate above 1%, characterized by deficits in social communication and interaction; restrictive, repetitive patterns of behavior, interests, or activities; and a preference for sameness and routines. The majority of adult ASD patients suffer from comorbid conditions such as depression and anxiety. Therapy options for adult ASD patients are lacking, with presently no available evidence-based interventions in Germany. Recently, two interventions to improve social responsiveness have been published. FASTER (“Freiburger Asperger-Spezifische Therapie für ERwachsene” = Freiburg Asperger-specific therapy for adults) is a manualized group psychotherapy program including three modules on psychoeducation, stress regulation management, and non-verbal and verbal social communication training with videotaped tasks. SCOTT&amp;EVA (“Social Cognition Training Tool”, and its enhancement “Emotionen Verstehen und Ausdruecken” = understanding and expressing emotions) is a computer-based training program to enhance social cognition including video and audio material of emotional expressions and complex real-life social situations. Initial studies for both programs have shown good feasibility and efficacy. Methods Three hundred sixty adult participants with an autism spectrum disorder (ASD) will take part in a randomized controlled three-armed multi-center trial to prove the efficacy of manualized group psychotherapy and a manualized computer-based training program. Both interventions will be compared with a treatment as usual (TAU) group, aiming to establish evidence-based psychotherapy approaches for adult individuals with ASD. The primary outcome is evaluated by parents, spouses, or others who have sufficient insight into the respective participant’s social communication and interaction, and will be measured with the Social Responsiveness Scale. First, each of both interventions will be compared to TAU. If at least one of the differences is significant, both interventions will be compared against each other. The primary outcome will be measured at baseline (T0) and 4 months after baseline (T1). Discussion The trial is the first to validate psychiatric therapeutic and training interventions for adult ASD patients in Germany. A trial is needed because the prevalence of ASD in adulthood without intellectual disability is high, and no evidence-based intervention can be offered in Germany. Trial registration German Clinical Trial Register DRKS00017817 . Registered on 20 April 2020.
Numerical simulation of quantum nonequilibrium phase transitions without finite-size effects
2021-04-08

Classical cellular automata, as for instance Domany-Kinzel cellular\\nautomata, are paradigmatic systems for the study of non-equilibrium phenomena.\\nSuch systems evolve in discrete time-steps, and are thus free of\\ntime-discretisation errors. Moreover, information about critical phenomena can\\nbe obtained by simulating the evolution of an initial seed that, at any finite\\ntime, has support only on a finite light-cone. This allows for essentially\\nnumerically exact simulations, free of finite-size errors or boundary effects.\\nHere, we show how similar advantages can be gained in the quantum regime: The\\nmany-body critical dynamics occurring in quantum cellular automata\\nwith an absorbing state can be studied directly on an infinite lattice when\\nstarting from seed initial conditions. This can be achieved efficiently by\\nsimulating the dynamics of an associated one-dimensional, non-unitary quantum\\ncellular automaton using tensor networks. We apply our method to a model\\nintroduced recently and find accurate values for universal exponents,\\nsuggesting that this approach can be a powerful tool for precisely classifying\\nnon-equilibrium universal physics in quantum systems.\\n
The lockdown effect: A counterfactual for Sweden
2021-04-08

While most countries imposed a lockdown in response to the first wave of COVID-19 infections, Sweden did not. To quantify the lockdown effect, we approximate a counterfactual lockdown scenario for Sweden through the outcome in a synthetic control unit. We find, first, that a 9-week lockdown in the first half of 2020 would have reduced infections and deaths by about 75% and 38%, respectively. Second, the lockdown effect starts to materialize with a delay of 3–4 weeks only. Third, the actual adjustment of mobility patterns in Sweden suggests there has been substantial voluntary social restraint, although the adjustment was less strong than under the lockdown scenario. Lastly, we find that a lockdown would not have caused much additional output loss.
Genetic variants of programmed cell death 1 are associated with HBV infection and liver disease progression
2021-04-08

Abstract The inhibitory effects of programmed cell death 1/programmed cell death ligand 1 (PD-1/PD-L1) modulates T-cell depletion. T-cell depletion is one of the key mechanisms of hepatitis B virus (HBV) persistence, in particular liver disease progression and the development of hepatocellular carcinoma (HCC). This case–control study aimed to understand the significance of PD-1 polymorphisms ( PD-1.5 and PD-1.9 ) association with HBV infection risk and HBV-induced liver disease progression. Genotyping of PD-1.5 and PD-1.9 variants was performed by direct Sanger sequencing in 682 HBV-infected patients including chronic hepatitis (CHB, n = 193), liver cirrhosis (LC, n = 183), hepatocellular carcinoma (HCC, n = 306) and 283 healthy controls (HC). To analyze the association of PD-1 variants with liver disease progression, a binary logistic regression, adjusted for age and gender, was performed using different genetic models. The PD-1.9 T allele and PD-1.9 TT genotype are significantly associated with increased risk of LC, HCC, and LC + HCC. The frequencies of PD-1.5 TT genotype and PD-1.5 T allele are significantly higher in HCC compared to LC patients. The haplotype CT ( PD-1.5 C and PD-1.9 T ) was significantly associated with increased risk of LC, HCC, and LC + HCC. In addition, the TC ( PD-1.5 T and PD-1.9 C ) haplotype was associated with the risk of HCC compared to non-HCC. The PD-1.5 CC, PD-1.9 TT, genotype, and the CC ( PD-1.5 C and PD-1.9) haplotype are associated with unfavorable laboratory parameters in chronic hepatitis B patients. PD-1.5 and PD1.9 are useful prognostic predictors for HBV infection risk and liver disease progression.