Miracle-dz/UniFAR-FTUs huggingface dataset:
Tunable complexity benchmarks for evaluating physics-informed neural networks on coupled ordinary differential equations

In this work, we assess the ability of physics-informed neural networks (PINNs) to solve increasingly-complex coupled ordinary differential equations (ODEs). We focus on a pair of benchmarks: discretized partial differential equations and harmonic oscillators, each of which has a tunable parameter that controls its complexity. Even by varying network architecture and applying a state-of-the-art training method that accounts for “difficult” training regions, we show that PINNs eventually fail to produce correct solutions to these benchmarks as their complexity-the number of equations and the size of time domain-increases. We identify several reasons why this may be the case, including insufficient network capacity, poor conditioning of the ODEs, and high local curvature, as measured by the Laplacian of the PINN loss.
A parameterization scheme of orographic gravity wave drag with two different vertical partitionings, Part 2 : Zonally averaged budget analyses based on transformed Eulerian mean method

The effects of orographic gravity wave drag (GWD) on zonal-mean fields of medium-range forecasts are analyzed by means of the transformed Eulerian-mean (TEM) method. Results show that the geostrophic adjustment to GWD behaves very differently between the stratosphere and troposphere. In the troposphere, both the tropospheric and stratospheric GWDs significantly change EliassenPalm (EP) flux divergence due to large-scale (model-resolvable) waves. The change in the EP flux divergence is much larger than the net change of tonal wind and GWDs themselves and it is almost balanced with the change in the Coriolis acceleration term due to meridional flows. Among wave activities, transient gravity waves resolved in the model are considered to play important roles in the vertical redistribution of additional wave moments due to GWD. In the stratosphere, the stratospheric GWD induces a hemispheric single cell meridional circulation. The vertical motions in this cell cause significant temperature changes. The Coriolis acceleration due to GWD-induced meridional flows is almost balanced with the GWD itself. In contrast with the troposphere, EP flux divergence is less affected by GWD. From the view of Lagrangian-mean meridional circulation, diabatic heating in the tropics and wave, mean-flow interaction due to planetary-scale waves have been recognized mainly to drive a hemispheric single cell circulation (the so-called Brewer-Dobson circulation) in the lower-stratosphere. Our results indicate that the stratospheric GWD contributes to the maintenance of the single cell circulation as well. Especially in the midlatitudes of the northern hemisphere, the GWD can be regarded as an important forcing and considerably enhances lower-stratospheric downward motions in the polar side of the subtropical jet stream. It might affect significantly the transport of trace constituents in the stratosphere.
THE FAST AND FURIOUS DECAY OF THE PECULIAR TYPE Ic SUPERNOVA 2005ek

We present extensive multi-wavelength observations of the extremely rapidly declining Type Ic supernova (SN Ic), SN 2005ek. Reaching a peak magnitude of MR = −17.3 and decaying by ∼3 mag in the first 15 days post-maximum, SN 2005ek is among the fastest Type I supernovae observed to date. The spectra of SN 2005ek closely resemble those of normal SN Ic, but with an accelerated evolution. There is evidence for the onset of nebular features at only nine days post-maximum. Spectroscopic modeling reveals an ejecta mass of ∼0.3 M☉ that is dominated by oxygen (∼80%), while the pseudo-bolometric light curve is consistent with an explosion powered by ∼0.03 M☉ of radioactive 56Ni. Although previous rapidly evolving events (e.g., SN 1885A, SN 1939B, SN 2002bj, SN 2010X) were hypothesized to be produced by the detonation of a helium shell on a white dwarf, oxygen-dominated ejecta are difficult to reconcile with this proposed mechanism. We find that the properties of SN 2005ek are consistent with either the edge-lit double detonation of a low-mass white dwarf or the iron-core collapse of a massive star, stripped by binary interaction. However, if we assume that the strong spectroscopic similarity of SN 2005ek to other SNe Ic is an indication of a similar progenitor channel, then a white-dwarf progenitor becomes very improbable. SN 2005ek may be one of the lowest mass stripped-envelope core-collapse explosions ever observed. We find that the rate of such rapidly declining Type I events is at least 1%–3% of the normal SN Ia rate.
Macroclumping as solution of the discrepancy between Hα and P v mass loss diagnostics for O-type stars

Context. Recent studies of O-type stars have demonstrated that discrepant mass-loss rates are obtained when different diagnostic methods are employed. Fitting the unsaturated UV resonance lines (e.g., P v) gives drastically lower values than obtained from the Hα emission. Wind inhomogeneity (so-called “clumping”) may be the main cause of this discrepancy. Aims. In a previous paper, we presented 3D Monte-Carlo calculations for the formation of scattering lines in a clumped stellar wind. In the present paper we select five O-type supergiants (from O4 to O7) and test whether the reported discrepancies can be resolved this way. Methods. In the first step, the analyses started with simulating the observed spectra with Potsdam Wolf-Rayet (PoWR) non-LTE model atmospheres. The mass-loss rates are adjusted to fit to the observed Hα emission lines best. For the unsaturated UV resonance lines (i.e., P v) we then applied our 3D Monte-Carlo code, which can account for wind clumps of any optical depths (“macroclumping”), a non-void interclump medium, and a velocity dispersion inside the clumps. The ionization stratifications and underlying photospheric spectra were adopted from the PoWR models. The properties of the wind clumps were constrained by fitting the observed resonance line profiles. Results. Our results show that with the mass-loss rates that fit Hα (and other Balmer and He ii lines), the UV resonance lines (especially the unsaturated doublet of P v) can also be reproduced with no problem when macroclumping is taken into account. There is no need to artificially reduce the mass-loss rates or to assume a subsolar phosphorus abundance or an extremely high clumping factor, unlike what was claimed by other authors. These consistent mass-loss rates are lower by a factor of 1.3 to 2.6, compared to the mass-loss rate recipe from Vink et al. Conclusions. Macroclumping resolves the previously reported discrepancy between Hα and P v mass-loss diagnostics.
HDAC inhibitors suppress protein poly(ADP-ribosyl)ation and DNA repair protein levels and phosphorylation status in hematologic cancer cells: implications for their use in combination with PARP inhibitors and chemotherapeutic drugs

The therapeutic efficacy of histone deacetylase inhibitors (HDACi) for hematologic malignancies and solid tumors is attributed to their ability to remodel chromatin, normalize dysregulated gene expression, and inhibit repair of damaged DNA. Studies on the interactions of HDACi with PARP inhibitors in hematologic cancers are limited, especially when combined with chemotherapeutic agents. Exposure of hematologic cancer cell lines and patient-derived cell samples to various HDACi resulted in a significant caspase-independent inhibition of protein PARylation, mainly catalyzed by PARP1. HDACi affected the expression of PARP1 at the transcription and/or post-translation levels in a cell line-dependent manner. HDACi-mediated inhibition of PARylation correlated with decreased levels and phosphorylation of major proteins involved in DNA repair. Combination of HDAC and PARP1 inhibitors provided synergistic cytotoxicity, which was further enhanced when combined with a chemotherapeutic regimen containing gemcitabine, busulfan and melphalan as observed in lymphoma cell lines. Our results indicate that the anti-tumor efficacy of HDACi is partly due to down-regulation of PARylation, which negatively affects the status of DNA repair proteins. This repair inhibition, combined with the high levels of oxidative and DNA replication stress characteristic of cancer cells, could have conferred these hematologic cancer cells not only with a high sensitivity to HDACi but also with a heightened dependence on PARP and therefore with extreme sensitivity to combined HDACi/PARPi treatment and, by extension, to their combination with conventional DNA-damaging chemotherapeutic agents. The observed synergism of these drugs could have a major significance in improving treatment of these cancers.
Cognitive effort-based decision-making across experimental and daily life indices in younger and older adults.

OBJECTIVES The study investigated whether cognitive effort decision-making measured via a neuroeconomic paradigm that manipulated framing (gain vs. loss outcomes), could predict daily life engagement in mentally demanding activities in both younger and older adults. METHOD Younger and older adult participants (N=310) completed the Cognitive Effort Discounting paradigm (Cog-ED), under both gain and loss conditions, to provide an experimental index of cognitive effort costs for each participant in each framing condition. A subset of participants (N=230) also completed a seven-day Ecological Momentary Assessment (EMA) protocol measuring engagement in mentally demanding daily life activities. RESULTS In a large, online sample, we replicated a robust increase in cognitive effort costs among older, relative to younger, adults. Additionally, costs were found to be reduced in the loss relative to gain frame, although these effects were only reliable at high levels of task difficulty and were not moderated by age. Critically, participants who had lower effort costs in the gain frame tended to report engaging in more mentally demanding daily life activities, but the opposite pattern was observed in the loss frame. Further analyses demonstrated the specificity of reward-related cognitive motivation in predicting daily life mentally demanding activities. DISCUSSION Together, these results suggest that cognitive effort costs, as measured through behavioral choice patterns in a neuroeconomic decision-making task, can be used to predict and explain engagement in mentally demanding activities during daily life among both older and younger adults.
Cosmological Models with No Big Bang

In the late 1990s, observations of Type Ia supernovae led to the astounding discovery that the universe is expanding at an accelerating rate. The explanation of this anomalous acceleration has been one of the great problems in physics since that discovery. In this article we propose cosmological models that can explain the cosmic acceleration without introducing a cosmological constant into the standard Einstein field equation, negating the necessity for the existence of dark energy. There are four distinguishing features of these models: 1) the speed of light and the gravitational "constant" are not constant, but vary with the evolution of the universe, 2) time has no beginning and no end, 3) the spatial section of the universe is a 3-sphere, and 4) the universe experiences phases of both acceleration and deceleration. One of these models is selected and tested against current cosmological observations of Type Ia supernovae, and is found to fit the redshift-luminosity distance data quite well.
Structural basis of three different transcription activation strategies adopted by a single regulator SoxS

Abstract Transcription activation is established through extensive protein–protein and protein–DNA interactions that allow an activator to engage and remodel RNA polymerase. SoxS, a global transcription activator, diversely regulates subsets of stress response genes with different promoters, but the detailed SoxS-dependent transcription initiation mechanisms remain obscure. Here, we report cryo-EM structures of three SoxS-dependent transcription activation complexes (SoxS-TACI, SoxS-TACII and SoxS-TACIII) comprising of Escherichia coli RNA polymerase (RNAP), SoxS protein and three representative classes of SoxS-regulated promoters. The structures reveal that SoxS monomer orchestrates transcription initiation through specific interactions with the promoter DNA and different conserved domains of RNAP. In particular, SoxS is positioned in the opposite orientation in SoxS-TACIII to that in SoxS-TACI and SoxS-TACII, unveiling a novel mode of transcription activation. Strikingly, two universally conserved C-terminal domains of alpha subunit (αCTD) of RNAP associate with each other, bridging SoxS and region 4 of σ70. We show that SoxS interacts with RNAP directly and independently from DNA, remodeling the enzyme to activate transcription from cognate SoxS promoters while repressing transcription from UP-element containing promoters. Our data provide a comprehensive summary of SoxS-dependent promoter architectures and offer new insights into the αCTD contribution to transcription control in bacteria.
A search for H i and OH absorption in z ≳ 3 CO emitters

We present the results of a survey for HI 21-cm and OH 18-cm absorption in seven strong CO emitters at z > 3. Despite reaching limits comparable to those required to detect 21-cm absorption at lower redshifts, we do not detect either transition in any of the objects searched. We believe that this is due to the high redshift selection causing all of our targets to have ultra-violet luminosities above the critical value, where all of the atomic gas in the host galaxy disk is suspected to be ionised. However, not only are all of our targets bright in CO emission, but detection of CO above the critical UV luminosity is generally not uncommon. This suggests that the molecular gas is shielded from the radiation or is physically remote from the source of the continuum emission, as it appears to be from CO observations of high redshift radio galaxies.
Sex-Specific Differences in Patients With Psoriatic Arthritis: A Systematic Review

Objective A systematic review of published literature was conducted to collate evidence on sex-specific differences in clinical characteristics, disease activity, and patient-reported outcomes (PROs) in psoriatic arthritis (PsA), including response to treatment. Methods Searches of MEDLINE, Embase, and the Cochrane Database of Systematic Reviews were performed in November 2020 for observational studies of adults with PsA reporting outcomes by sex (published from January 1, 2015, to November 13, 2020). In addition, hand searches of systematic literature reviews and (network) metaanalysis bibliographies were performed. Searches of ClinicalTrials.gov and congress abstracts from the European Alliance of Associations for Rheumatology, the American College of Rheumatology (ACR), and the American Academy of Dermatology (2019-2020) were also carried out. Eligible studies with 100 or more patients prespecified a comparison by sex and reported clinical characteristics and/or disease activity. Data extracted included patient characteristics, study design, baseline clinical characteristics, and disease activity results, including PROs. Results Database searching yielded 3283 unique records; 31 publications of 27 unique studies were included. The review found generally higher rates of peripheral disease in women, including higher tender joint counts. There was some evidence of more axial disease in men, plus greater skin disease burden. There were consistently no differences in Dermatology Life Quality Index scores, though across other PROs, women had worse scores, including pain and fatigue. Women had poorer responses to treatment, indicated by outcome measures such as ACR responses and minimal disease activity. Conclusion This review indicates that important differences exist between the sexes in PsA. However, the limited evidence for this conclusion underlines the need for additional research in this area.
Catastrophic chromosome fragmentation probes the nucleoid structure and dynamics in Escherichia coli

Abstract Escherichia coli cells treated with a combination of cyanide (CN) and hydrogen peroxide (HP) succumb to catastrophic chromosome fragmentation (CCF), detectable in pulsed-field gels as >100 double-strand breaks per genome equivalent. Here we show that CN + HP-induced double-strand breaks are independent of replication and occur uniformly over the chromosome,—therefore we used CCF to probe the nucleoid structure by measuring DNA release from precipitated nucleoids. CCF releases surprisingly little chromosomal DNA from the nucleoid suggesting that: (i) the nucleoid is a single DNA-protein complex with only limited stretches of protein-free DNA and (ii) CN + HP-induced breaks happen within these unsecured DNA stretches, rather than at DNA attachments to the central scaffold. Mutants lacking individual nucleoid-associated proteins (NAPs) release more DNA during CCF, consistent with NAPs anchoring chromosome to the central scaffold (Dps also reduces the number of double-strand breaks directly). Finally, significantly more broken DNA is released once ATP production is restored, with about two-thirds of this ATP-dependent DNA release being due to transcription, suggesting that transcription complexes act as pulleys to move DNA loops. In addition to NAPs, recombinational repair of double-strand breaks also inhibits DNA release by CCF, contributing to a dynamic and complex nucleoid structure.
Anisotropic flow and flow fluctuations for Au plus Au at root s(NN)=200 GeV in a multiphase transport model

Anisotropic flow coefficients and their fluctuations are investigated for Au + Au collisions at center-of-mass energy root s(NN) = 200 GeV by using a multiphase transport model with string melting scenario. Experimental results of azimuthal anisotropies by means of the two- and four-particle cumulants are generally well reproduced by the model including both parton cascade and hadronic rescatterings. Event-by-event treatments of the harmonic flow coefficients v(n) (for n = 2, 3, and 4) are performed, in which event distributions of vn for different orders are consistent with Gaussian shapes over all centrality bins. Systematic studies on centrality, transverse momentum (p(T)), and pseudorapidity (eta) dependencies of anisotropic flows and quantitative estimations of the flow fluctuations are presented. The p(T) and eta dependencies of absolute fluctuations for both v(2) and v(3) follow trends similar to their flow coefficients. Relative fluctuation of triangular flow v(3) is slightly centrality dependent, which is quite different from that of elliptic flow v(2). It is observed that parton cascade has a large effect on the flow fluctuations, but hadronic scatterings make little contribution to the flow fluctuations, which indicates flow fluctuations are mainly modified during partonic evolution stage.
Global survey of star clusters in the Milky Way - I. The pipeline and fundamental parameters in the second quadrant

Aims. On the basis of the PPMXL star catalogue we performed a survey of star clusters in the second quadrant of the Milky Way. Methods. From the PPMXL catalogue of positions and proper motions we took the subset of stars with near-infrared photometry from 2MASS and added the remaining 2MASS stars without proper motions (called 2MAst, i.e. 2MASS with astrometry). We developed a data-processing pipeline including interactive human control of a standardised set of multi-dimensional diagrams to determine kinematic and photometric membership probabilities for stars in a cluster region. The pipeline simultaneously produced the astrophysical parameters of a cluster. From literature we compiled a target list of presently known open and globular clusters, cluster candidates, associations, and moving groups. From established member stars we derived spatial parameters (coordinates of centres and radii of the main morphological parts of clusters) and cluster kinematics (average proper motions and sometimes radial velocities). For distance, reddening, and age determination we used specific sets of theoretical isochrones. Tidal parameters were obtained by a fit of three-parameter King profiles to the observed density distributions of members. Results. We investigated all 871 objects in the 2nd Galactic quadrant, of which we successfully treated 642 open clusters, 2 globular clusters, and 8 stellar associations. The remaining 219 objects (24%) were recognised by us to be nonexistent clusters, duplicate entries, or clusters too faint for 2MAst. We found that our sample is complete in the 2nd quadrant up to a distance of 2 kpc, where the average surface density is 94 clusters per kpc 2 . Compared with literature values we found good agreement in spatial and kinematic data, as well as for optical distances and reddening. Small, but systematic offsets were detected in the age determination.
MAGNETOHYDRODYNAMIC TURBULENCE POWERED BY MAGNETOROTATIONAL INSTABILITY IN NASCENT PROTONEUTRON STARS

Magnetorotational instability (MRI) in a convectively stable layer around the neutrinosphere is simulated by a three-dimensional model of a supernova core. To resolve MRI-unstable modes, a thin layer approximation considering only the radial global stratification is adopted. Our intriguing finding is that the convectively stable layer around the neutrinosphere becomes fully turbulent due to the MRI and its nonlinear penetration into the strongly stratified MRI-stable region. The intensity of the MRI-driven turbulence increases with magnetic flux threading the core, but is limited by the free energy stored in the differential rotation. The turbulent neutrinosphere is a natural consequence of rotating core-collapse and could exert a positive impact on the supernova mechanism.
Incidence of mandibular osteoradionecrosis (MORN) after intensity modulated radiotherapy (IMRT) versus 3D conformal radiotherapy (3D-CRT): A systematic review

Background Analyze the incidence of MORN after head and neck radiotherapy by two novel irradiation techniques, 3DCRT and IMRT and compare the success rates of distinct authors. Material and Methods An electronic search in Pubmed (MEDLINE), Ovid, Google Scholar and Cochrane Library (Wiley), databases was conducted with the key words "Radiotherapy, Conformal"[Mesh] OR "Radiotherapy, Intensity-Modulated"[Mesh]) AND "Osteoradionecrosis"[Mesh] for all databases. The inclusion criteria randomized controlled trials (RCT), as well as prospective and retrospective cohort studies published in English; MORN patients treated with 3D-CRT y IMRT. Results 27 articles were selected from 194 initially found. 14 articles out of 27 were excluded and finally included 8 publications were included in the systematic review that were ranked according to their level of scientific evidence using the SORT criteria. Conclusions When both RT techniques were compared; IMRT revealed a lower risk incidence of MORN development and enhanced dose constraint than 3D-CRT (less than 10%), this improvement could translate into less complications post RT treatment. Key words:Radiotherapy, conformal, intensity-modulated, osteoradionecrosis.
Ultralong spin decoherence times in graphene quantum dots with a small number of nuclear spins

We study the dynamics of an electron spin in a graphene quantum dot, which is interacting with a bath of less than ten nuclear spins via the anisotropic hyperfine interaction. Due to substantial progress in the fabrication of graphene quantum dots, the consideration of such a small number of nuclear spins is experimentally relevant. This choice allows us to use exact diagonalization to calculate the long-time average of the electron spin as well as its decoherence time. We investigate the dependence of spin observables on the initial states of nuclear spins and on the position of nuclear spins in the quantum dot. Moreover, we analyze the effects of the anisotropy of the hyperfine interaction for different orientations of the spin quantization axis with respect to the graphene plane. Interestingly, we then predict remarkable long decoherence times of more than 10 ms in the limit of few nuclear spins.