bluuebunny/crossref_metadata_2025_split huggingface dataset:
The specific angular momentum of disc galaxies and its connection with galaxy morphology, bar structure, and disc gravitational instability
Authors: Romeo Alessandro B , Agertz Oscar , Renaud Florent 
Published: October 2022

ABSTRACT
The specific angular momenta (j ≡ J/M) of stars (j⋆), gas (jgas), baryons as a whole (jb) and dark matter haloes (jh) contain clues of vital importance about how galaxies form and evolve. Using one of the largest samples of disc galaxies (S0–BCD) with high-quality rotation curves and near-infrared surface photometry, we perform a detailed comparative analysis of j that stretches across a variety of galaxy properties. Our analysis imposes tight constraints on the ‘retained’ fractions of specific angular momentum (j⋆/jh, jH i/jh, and jb/jh), as well as on their systematic trends with mass fraction and galaxy morphology, thus on how well specific angular momentum is conserved in the process of disc galaxy formation and evolution. In particular, one of the most innovative results of our analysis is the finding that galaxies with larger baryon fractions have also retained larger fractions of their specific angular momentum. Furthermore, our analysis demonstrates how challenging it is to characterize barred galaxies from a gravitational instability point of view. This is true not only for the popular Efstathiou, Lake & Negroponte bar instability criterion, which fails to separate barred from non-barred galaxies in about 55 per cent of the cases, but also for the mass-weighted Toomre parameter of atomic gas, 〈QH i〉, which succeeds in separating barred from non-barred galaxies, but only in a statistical sense.
Age-morphology dependence of the Milky Way boxy/peanut bulge seen in Mira variables
Authors: Semczuk Marcin , Dehnen Walter , Schönrich Ralph , Athanassoula E 
Published: October 2022

ABSTRACT
We analyse the distribution of Mira variable stars in the central region of the Milky Way. We find that with increasing period, i.e. decreasing age, the Miras shift towards negative Galactic longitudes ℓ. Comparing to a cosmological zoom simulation of a barred galaxy, we find that this shift with age can be explained by an age-morphology dependence of the boxy peanut/bulge. Owing to a combination of projection effects and the limitation of the range of Galactic longitudes, the near hump at ℓ &gt; 0 is more truncated for younger populations, and the far hump at ℓ &lt; 0 dominates the observed distributions.
A mechanism of bar formation in disc galaxies: Synchronization of apsidal precession
Authors: Bekki Kenji 
Published: October 2022

ABSTRACT
We discuss the mechanism(s) of bar formation in isolated and tidally interacting disc galaxies using the results of idealized collision-less N-body simulations of the galaxies. In order to better understand the mechanism, we investigate orbital eccentricities (e), epochs of apocentre passages (ta), azimuthal angles at ta (φa), precession rates (Ωpre), for individual stars, as well as bar strengths represented by relative m = 2 Fourier amplitude (A2) and bar pattern speeds (Ωbar). The main results are as follows. A significant fraction of stars with initially different φa and Ωpre in an isolated disc galaxy can have similar values within several dynamical time-scales. This synchronization of φa and Ωpre, which is referred to as apsidal precession synchronization (‘APS’) in this study, is caused by the enhanced strength of the tangential component of gravitational force. A weak seed bar (A2 &lt; 0.1) is first formed through APS in local regions of a disc, then the bar grows due to APS. In the bar growth phase (0.1 &lt; A2 &lt; 0.4), APS can proceed more efficiently due to stronger tangential force from the bar so that it can enhance the bar strength further. This positive feedback loop in APS is the key physical mechanism of bar growth in isolated stellar discs. Bar formation can be severely suppressed in discs with lower disc mass fractions and/or higher Q parameters due to much less efficient APS. APS proceeds more rapidly and more efficiently due to strong tidal perturbation in the formation of tidal bars compared to spontaneous bar formation.
Apparent counter-rotation in the torus of NGC 1068: influence of an asymmetric wind
Authors: Bannikova Elena Yu , Akerman Nina O , Capaccioli Massimo , Berczik Peter P , Akhmetov Vladimir S , Ishchenko Marina V 
Published: October 2022

ABSTRACT
The recent ALMA maps together with observations of H2O maser emission seem to suggest the presence of a counter-rotation in the obscuring torus of NGC 1068. We propose to explain this phenomenon as due to the influence of a wind, considered as radiation pressure, and the effects of torus orientation. In order to test this idea: 1. we make N-body simulation of a clumpy torus taking into account mutual forces between particles (clouds); 2. we apply ray-tracing algorithm with the beams from the central engine to choose the clouds in the torus throat that can be under direct influence of the accretion disk emission; 3. we use semi-analytical model to simulate the influence of the asymmetrical radiation pressure (wind) forced on the clouds in the torus throat. An axis of such a wind is tilted with respect to the torus symmetry axis; 4. we orient the torus relative to an observer and again apply ray-tracing algorithm. In this step the beams go from an observer to the optically thick clouds that allows us to take into account the mutual obscuration of clouds; 5. after projecting on the picture plane, we impose a grid on the resulting cloud distribution and find the mean velocity of clouds in each cells to mimic the ALMA observational maps. By choosing the parameters corresponding to NGC 1068 we obtain the model velocity maps that emulate the effect of an apparent counter-rotation and can explain the discovery made by ALMA.
3D modelling of the impact of stellar activity on tidally locked terrestrial exoplanets: atmospheric composition and habitability
Authors: Ridgway R J , Zamyatina M , Mayne N J , Manners J , Lambert F H , Braam M , Drummond B , Hébrard E , Palmer P I , Kohary K 
Published: October 2022

ABSTRACT
Stellar flares present challenges to the potential habitability of terrestrial planets orbiting M dwarf stars through inducing changes in the atmospheric composition and irradiating the planet’s surface in large amounts of ultraviolet light. To examine their impact, we have coupled a general circulation model with a photochemical kinetics scheme to examine the response and changes of an Earth-like atmosphere to stellar flares and coronal mass ejections. We find that stellar flares increase the amount of ozone in the atmosphere by a factor of 20 compared to a quiescent star. We find that coronal mass ejections abiotically generate significant levels of potential bio-signatures such as N2O. The changes in atmospheric composition cause a moderate decrease in the amount of ultraviolet light that reaches the planets surface, suggesting that while flares are potentially harmful to life, the changes in the atmosphere due to a stellar flare act to reduce the impact of the next stellar flare.
Aromatic chloroosmacyclopentatrienes
Authors: Chu Zhenwei , He Guomei , Shi Chuan , Hua Yuhui , Huang Yaxi , Chen Jiangxi , Xie Hujun , Jia Guochen 
Published: October 2022

ABSTRACT
Aromatic metallacycles are of considerable current interest. Reported aromatic metallacycles are mainly those with carbon, nitrogen, oxygen and sulfur. In this work, we report the synthesis and characterization of aromatic chloroosmacyclopentatrienes, which represent the first structurally confirmed metallaaromatic with a chlorine atom in its framework. Single-crystal X-ray diffraction studies show that these planar chloroosmacyclopentatrienes possess a very short Os–ClC distance suggesting M=ClC bond character.
Multiple waves of viral invasions in Symbiodiniaceae algal genomes
Authors: Benites L Felipe , Stephens Timothy G , Bhattacharya Debashish 
Published: October 2022

AbstractDinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
Antenatal Milk Expression as a Lactation Support Intervention for Parents of Infants With Severe Birth Defects
Authors: Davis Jessica A. , Glasser Melissa , Clemens Michele , Eichhorn Barbara , Vats Kalyani , Demirci Jill R. 
Published: October 2022

Background:
A diet high in parent's own milk (parental milk) is a lifesaving intervention for critically ill infants. Lactating parents whose infants are born with birth defects that require surgical repair (surgical infants) shortly after birth often struggle to initiate and maintain a milk supply that meets their infant's nutritional needs. Antenatal milk expression has been identified as a safe, feasible, and potentially effective strategy that promotes parents' direct chest/breastfeeding or milk expression (lactation) confidence and helps parents attain their lactation goals. Two cases are presented to illustrate the potential for using antenatal milk expression as a lactation support intervention for parents of surgical infants.

Case Presentation:
Cases were drawn from a pilot study exploring the feasibility of implementing antenatal milk expression among pregnant parents of surgical infants. Participants were healthy women recruited after 30 weeks of gestation who received a fetal diagnosis of a complex congenital heart defect. Despite variability in clinical course and length of stay, parental milk was provided for the duration of each infant's hospitalization. Participant perceptions of antenatal milk expression varied.

Conclusion:
More research is needed to evaluate the feasibility, efficacy, and parent or provider perceptions of antenatal milk expression as a lactation support intervention for parents of surgical infants.
Practical Strategies in Reconstruction of Soft-Tissue Sarcoma
Authors: Aten David M. , Chang Edward I. 
Published: October 2022

Learning Objectives:
After studying this article, the participant should be able to: 1. Discuss the natural history and pathophysiology of sarcoma. 2. Summarize the most up-to-date multidisciplinary management of soft-tissue sarcoma. 3. Provide a synopsis of reconstructive modalities based on anatomical location. 4. Highlight some novel strategies for treatment of lymphedema and phantom limb pain that are common sequelae following treatment and resection of soft-tissue sarcomas.

Summary:
The management of soft-tissue sarcoma presents unique challenges to the reconstructive surgeon. The optimal management mandates a multidisciplinary approach; however, reconstruction must take into account the extent of the resection and exposed vital structures, but often occurs in the setting of adjuvant treatments including chemotherapy and radiation therapy. Reconstruction is based on the extent of the defect and the location of the primary tumor. As such, an evidence-based, algorithmic approach following the reconstructive ladder is warranted to minimize the risks of complications and maximize success, which varies from head and neck to torso to breast to extremity sarcomas. Aside from reconstruction of the defect, advances in the surgical treatment of lymphedema and neuropathic pain resulting from treatment and extirpation of soft-tissue sarcoma are critical to maintain function and patients’ quality of life.
The hippocampus contributes to retroactive stimulus associations during trace fear conditioning
Authors: Puhger Kyle , Crestani Ana P. , Diniz Cassiano R. A. F. , Wiltgen Brian J. 
Published: October 2022

SummaryBinding events that occur at different times is essential for memory formation. In trace fear conditioning, animals associate a tone and footshock despite no temporal overlap. The hippocampus is thought to mediate this learning by maintaining a memory of the tone until shock occurrence, however evidence for sustained hippocampal tone representations is lacking. Here we demonstrate a retrospective role for the hippocampus in trace fear conditioning. Bulk calcium imaging revealed sustained increases in CA1 activity after footshock that were not observed after tone termination. Optogenetic silencing of CA1 immediately after footshock impaired subsequent memory. Additionally, footshock increased the number of sharp wave-ripples compared to baseline during conditioning. Therefore, post-shock hippocampal activity likely supports learning by reactivating and linking latent tone and shock representations. These findings highlight an underappreciated function of post-trial hippocampal activity in enabling retroactive temporal associations during new learning, as opposed to persistent maintenance of stimulus representations.
Graph Regularized Probabilistic Matrix Factorization for Drug-Drug Interactions Prediction
Authors: Jain Stuti , Chouzenoux Emilie , Kumar Kriti , Majumdar Angshul 
Published: October 2022

AbstractCo-administration of two or more drugs simultaneously can result in adverse drug reactions. Identifying drug-drug interactions (DDIs) is necessary, especially for drug development and for repurposing old drugs. DDI prediction can be viewed as a matrix completion task, for which matrix factorization (MF) appears as a suitable solution. This paper presents a novel Graph Regularized Probabilistic Matrix Factorization (GRPMF) method, which incorporates expert knowledge through a novel graph-based regularization strategy within an MF framework. An efficient and sounded optimization algorithm is proposed to solve the resulting non-convex problem in an alternating fashion. The performance of the proposed method is evaluated through the DrugBank dataset, and comparisons are provided against state-of-the-art techniques. The results demonstrate the superior performance of GRPMF when compared to its counterparts.
Segment Based Pattern Analysis Reveals a Persistent Regular Rhythm in the Motion Artifact Record of the MIT-BIH Noise Stress Test Database
Authors: Hopenfeld Bruce 
Published: October 2022

AbstractBackgroundThe MIT-BIH Noise Stress Test Database (NSTDB) is a publicly available resource for testing QRS detection algorithms. Serial QRS detection algorithms applied to the NSTDB have apparently failed to detect the presence of a possible heartbeat like rhythm associated with peaks that the NSTDB classifies as noise. The failure to detect this rhythm may arise from the difficulty associated with interpreting noisy RR interval time series produced by serial QRS detection schemes.Algorithm Summary and ExperimentTo extract rhythm information from noisy peak time/RR interval time series, a peak space signal is created with triangular pulses centered on peaks located by a serial QRS detection algorithm such as Pan-Tompkins. The peak space signal is autocorrelated over 20 s segments and the primary (non-origin) peak in the autocorrelation signal is located. In the presence of reasonably regular sinus rhythm, this peak corresponds to a fundamental RR interval present throughout the 20 s segment. This peak time processing method was applied to the Pan-Tompkins QRS detections in the motion artifact record of the NSTDB. To compare the results to a different algorithm capable of detecting patterns at the segment level, a previously described pattern-based heartbeat detection scheme (Temporal Pattern Search, or “TEPS”) was applied in both single and multiple channel modes to the NSTDB motion artifact record.ResultsBoth the Pan-Tompkins/autocorrelation method and TEPS detected a persistent rhythm around 1000-1050 ms in both channels throughout the entirety of the motion artifact record. The RR interval correlation between Pan-Tompkins/autocorrelation and single channel TEPS was 0.8 and 0.7 in channels 1 and 2 respectively with p values of 0.
Category trumps shape as an organizational principle of object space in the human occipitotemporal cortex
Authors: Yargholi Elahe’ , de Beeck Hans Op 
Published: October 2022

AbstractThe organizational principles of the object space represented in human ventral visual cortex are debated. Here we contrast two prominent proposals that, in addition to an organization in terms of animacy, propose either a representation related to aspect ratio or to the distinction between faces and bodies. We designed a critical test that dissociates the latter two categories from aspect ratio and investigated responses from human fMRI and deep neural networks (BigBiGAN). Representational similarity and decoding analyses showed that the object space in occipitotemporal cortex (OTC) and BigBiGAN was partially explained by animacy but not by aspect ratio. Data-driven approaches showed clusters for face and body stimuli and animate-inanimate separation in the representational space of OTC and BigBiGAN, but no arrangement related to aspect ratio. In sum, the findings go in favor of a model in terms of an animacy representation combined with strong selectivity for faces and bodies.
DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks
Authors: Liu Tong , Wang Zheng 
Published: October 2022

AbstractChromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can capture genome-wide chromatin interactions mediated by a specific DNA-associated protein. The ChIA-PET experiments have been applied to explore the key roles of different protein factors in chromatin folding and transcription regulation. However, compared with widely available Hi-C and ChIP-seq data, there are not many ChIA-PET datasets available in the literature. A computational method for accurately predicting ChIA-PET interactions from Hi-C and ChIP-seq data is needed that can save the efforts of performing wet-lab experiments. Here we present DeepChIA-PET, a supervised deep learning approach that can accurately predict ChIA-PET interactions by learning the latent relationships between ChIA-PET and two widely used data types: Hi-C and ChIP-seq. We trained our deep models with CTCF-mediated ChIA-PET of GM12878 as ground truth, and the deep network contains 40 dilated residual convolutional blocks. We first showed that DeepChIA-PET with only Hi-C as input significantly outperforms Peakachu, another computational method for predicting ChIA-PET from Hi-C but using random forests. We next proved that adding ChIP-seq as one extra input does improve the classification performance of DeepChIA-PET, but Hi-C plays a more prominent role in DeepChIA-PET than ChIP-seq. Our evaluation results indicate that our learned models can accurately predict not only CTCF-mediated ChIA-ET in GM12878 and HeLa but also non-CTCF ChIA-PET interactions, including RNA polymerase II (RNAPII) ChIA-PET of GM12878, RAD21 ChIA-PET of GM12878, and RAD21 ChIA-PET of K562. In total, DeepChIA-PET is an accurate tool for predicting the ChIA-PET interactions mediated by various chromatin-associated proteins from different cell types. DeepChIA-PET is publicly available athttp://dna.cs.miami.edu/DeepChIA-PET/.
Mode of inhibition of RNase P by gambogic acid and juglone
Authors: Meyers Nancy Wu , Karasik Agnes , Kaitany Kipchumba , Fierke Carol A. , Koutmos Markos 
Published: October 2022

AbstractThe first step in transfer RNA (tRNA) maturation is the cleavage of the 5’ end of precursor transfer RNA (pre-tRNA) catalyzed by ribonuclease P (RNase P). RNase P is either a ribonucleoprotein (RNP) complex with a catalytic RNA subunit or aprotein-onlyRNaseP(PRORP). In most land plants, algae, and Euglenozoa, PRORP is a single-subunit enzyme. There are currently no inhibitors of protein-only RNase P that can be used as tools for studying the biological function of this enzyme. Therefore, we screened for compounds that inhibit the activity of a model PRORP fromA. thalianaorganelles (PRORP1) using a high throughput fluorescence polarization (FP) cleavage assay. Two compounds, gambogic acid and juglone (5-hydroxy-1,4-naphthalenedione) that inhibit PRORP1 in the 1 μM range were identified and analyzed. These compounds similarly inhibit human mtRNase P, a multi-subunit protein enzyme, and are 50-fold less potent against bacterial RNA-dependent RNase P. Biochemical measurements indicate that gambogic acid is a rapid-binding, uncompetitive inhibitor that targets the PRORP1-substrate complex while juglone acts as time-dependent inhibitor of PRORP1. X-ray crystal structures of PRORP1 in complex with juglone demonstrate the formation of a covalent complex with cysteine side chains on the surface of the protein. A model consistent with the kinetic data is that juglone binds to PRORP1 rapidly to form an inactive enzyme-inhibitor (EI) complex, and then undergoes a slow step to form an inactive covalent adduct with PRORP1. These inhibitors have the potential to be developed into tools to probe PRORP structure and function relationships.