bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine-learning prediction for mean motion resonance behaviour – The planar case
Authors: Li Xin , Li Jian , Xia Zhihong Jeff , Georgakarakos Nikolaos 
Published: January 2022

ABSTRACT
Most recently, machine learning has been used to study the dynamics of integrable Hamiltonian systems and the chaotic 3-body problem. In this work, we consider an intermediate case of regular motion in a non-integrable system: the behaviour of objects in the 2:3 mean motion resonance with Neptune. We show that, given initial data from a short 6250 yr numerical integration, the best-trained artificial neural network (ANN) can predict the trajectories of the 2:3 resonators over the subsequent 18 750 yr evolution, covering a full libration cycle over the combined time period. By comparing our ANN’s prediction of the resonant angle to the outcome of numerical integrations, the former can predict the resonant angle with an accuracy as small as of a few degrees only, while it has the advantage of considerably saving computational time. More specifically, the trained ANN can effectively measure the resonant amplitudes of the 2:3 resonators, and thus provides a fast approach that can identify the resonant candidates. This may be helpful in classifying a huge population of KBOs to be discovered in future surveys.
Detectability of the gravitational redshift effect from the asymmetric galaxy clustering
Authors: Saga Shohei , Taruya Atsushi , Rasera Yann , Breton Michel-Andrès 
Published: January 2022

ABSTRACT
It has been recently recognized that the observational relativistic effects, mainly arising from the light propagation in an inhomogeneous universe, induce the dipole asymmetry in the cross-correlation function of galaxies. In particular, the dipole asymmetry at small scales is shown to be dominated by the gravitational redshift effects. In this paper, we exploit a simple analytical description for the dipole asymmetry in the cross-correlation function valid at quasi-linear regime. In contrast to the previous model, a new prescription involves only 1D integrals, providing a faster way to reproduce the results obtained by Saga et al. Using the analytical model, we discuss the detectability of the dipole signal induced by the gravitational redshift effect from upcoming galaxy surveys. The gravitational redshift effect at small scales enhances the signal-to-noise ratio (S/N) of the dipole, and in most of the cases considered, the S/N is found to reach a maximum at z ≈ 0.5. We show that current and future surveys such as DESI and SKA provide an idealistic data set, giving a large S/N of 10–20. Two potential systematics arising from off-centred galaxies are also discussed (transverse Doppler effect and diminution of the gravitational redshift effect), and their impacts are found to be mitigated by a partial cancellation between two competitive effects. Thus, the detection of the dipole signal at small scales is directly linked to the gravitational redshift effect, and should provide an alternative route to test gravity.
Automatic algorithm to obtain v sin i values via Fourier transform in the BeSOS database
Authors: Solar Martín , Arcos Catalina , Curé Michel , Levenhagen Ronaldo S , Araya Ignacio 
Published: January 2022

ABSTRACT
Be stars are found to rotate close to their critical rotation and therefore they are considered an important laboratory for the study of stellar rotation. In this context, we obtain the projected rotational velocity of a sample of classical Be southern stars in the BeSOS database via Fourier transforms in an automated way for several absorption lines at different epochs. A Gaussian profile is fitted to eight observed photospheric He i lines in order to select automatically from the profile the spectral signal given by areas under the curve of 95.45, 98.75, and 99.83 per cent, to obtain vsin i via the Fourier transform technique. The values obtained are in global agreement with the literature. Analysing only one line is not enough to set the vsin i value: depending on the line, the value in most cases is underestimated with respect to λ4471. When gravity-darkening effects are included, apparent values increase by ∼10 per cent. The resolution of the instrument Pontificia Universidad Catolica High Echelle Resolution Optical Spectrograph (PUCHEROS) used for BeSOS spectra ($R \sim 17\, 000$) constrains the theoretical lower bound possible to vsin i ∼ 100  km s−1. The procedure has limitations, using a linear limb-darkening function with ε = 0.6 for classical Be stars rotating close to the break-up velocity without gravity-darkening corrections, which cannot be negligible. Previous works measure vsin i values using just one spectral line and here we demonstrate that with more lines the results can vary. This could be due to the photospheric distribution of atomic transitions in classical Be stars.
Stellar response after stripping as a model for common-envelope outcomes
Authors: Vigna-Gómez Alejandro , Wassink Michelle , Klencki Jakub , Istrate Alina , Nelemans Gijs , Mandel Ilya 
Published: January 2022

ABSTRACT
Binary neutron stars have been observed as millisecond pulsars, gravitational-wave sources, and as the progenitors of short gamma-ray bursts and kilonovae. Massive stellar binaries that evolve into merging double neutron stars are believed to experience a common-envelope episode. During this episode, the envelope of a giant star engulfs the whole binary. The energy transferred from the orbit to the envelope by drag forces or from other energy sources can eject the envelope from the binary system, leading to a stripped short-period binary. In this paper, we use one-dimensional single stellar evolution to explore the final stages of the common-envelope phase in progenitors of neutron star binaries. We consider an instantaneously stripped donor star as a proxy for the common-envelope phase and study the star’s subsequent radial evolution. We determine a range of stripping boundaries that allow the star to avoid significant rapid re-expansion and that thus represent plausible boundaries for the termination of the common-envelope episode. We find that these boundaries lie above the maximum compression point, a commonly used location of the core/envelope boundary. We conclude that stars may retain fractions of a solar mass of hydrogen-rich material even after the common-envelope episode. If we consider orbital energy as the only energy source available, all of our models would overfill their Roche lobe after ejecting the envelope, whose binding energy includes gravitational, thermal, radiation, and recombination energy terms.
Surface tension of cosmic voids as a possible source for dark energy
Authors: Yusofi E , Khanpour M , Khanpour B , Ramzanpour M A , Mohsenzadeh M 
Published: January 2022

ABSTRACT
The cosmological constant is estimated by considering the surface tension of supervoids in a void-dominated cosmic fluid by which we can get a possible source of dark energy. Looking at voids as bubbles, we define the concept of surface tension which is shown to have an almost constant value for supervoids that are enclosed by superclusters. The surface tensions of voids are computed by dimensional method for galaxies and superclusters with different values for each group. At large scale which vast voids are dominant the positive cosmological constants obtained of order (≃ +10−52 m−2), which are very close to those given by Planck.
Placing Ancient DNA Sequences into Reference Phylogenies
Authors: Martiniano Rui , De Sanctis Bianca , Hallast Pille , Durbin Richard 
Published: January 2022

Abstract
Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.
A Peroxide-Responding sRNA Evolved from a Peroxidase mRNA
Authors: Krieger Madeline C , Dutcher H Auguste , Ashford Andrew J , Raghavan Rahul 
Published: January 2022

Abstract
Small RNAs (sRNAs) are important gene regulators in bacteria, but it is unclear how new sRNAs originate and become part of regulatory networks that coordinate bacterial response to environmental stimuli. Using a covariance modeling-based approach, we analyzed the presence of hundreds of sRNAs in more than a thousand genomes across Enterobacterales, a bacterial order with a confluence of factors that allows robust genome-scale sRNA analyses: several well-studied organisms with fairly conserved genome structures, an established phylogeny, and substantial nucleotide diversity within a narrow evolutionary space. We discovered that a majority of sRNAs arose recently, and uncovered protein-coding genes as a potential source from which new sRNAs arise. A detailed investigation of the emergence of OxyS, a peroxide-responding sRNA, revealed that it evolved from a fragment of a peroxidase messenger RNA. Importantly, although it replaced the ancestral peroxidase, OxyS continues to be part of the ancestral peroxide-response regulon, indicating that an sRNA that arises from a protein-coding gene would inherently be part of the parental protein’s regulatory network. This new insight provides a fresh framework for understanding sRNA origin and regulatory integration in bacteria.
Exosomes released from Sertoli cells contribute to the survival of Leydig cells through CCL20 in rats
Authors: Ma Yi , Zhou Yan , Zou Sha-Sha , Sun Yun , Chen Xiang-Feng 
Published: January 2022

Abstract
Reciprocal communication between Sertoli and Leydig cells occurs in the testes; however, the detailed mechanisms involved are not completely understood. Exosomes can communicate within neighboring or distant cells to regulate cell function. Our aim was to determine whether exosomes released from Sertoli cells can regulate the survival of Leydig cells. We found that exosomes released from rat primary Sertoli cells could be internalized by Leydig cells in vitro, and promote the survival of Leydig cells, as assessed by optical density at 450 nm, compared to untreated control (mean ± SD: 0.95 ± 0.04 vs 0.79 ± 0.03, P &lt; 0.05). When the exosomes were injected into the interstitial area of rat testis, they could also be internalized by Leydig cells in vivo. To investigate if exosomes released from Sertoli cells can reach Leydig cells in vivo, exosomes were injected into the efferent duct, from where they entered the interstitial space from seminiferous tubules, which indicated that they may cross the blood–testis barrier (BTB). Further in vitro studies found that exosomes released from Sertoli cells significantly increased CC-chemokine ligand 20 (Ccl20) mRNA (mean ± SD: 2.79 ± 0.08 vs 0.98 ± 0.04, P &lt; 0.01) and protein (mean ± SD: 1.08 ± 0.06 vs 0.53 ± 0.05 ng/ml, P &lt; 0.01) levels in Leydig cells, compared to the untreated Leydig cells. CCL20 promoted the phosphorylation of AKT (protein kinase B) in Leydig cells, compared to untreated control (mean ± SD: 0.074 ± 0.002 vs 0.051 ± 0.002, P &lt; 0.01). In conclusion, our results demonstrated that exosomes released by Sertoli cells may cross the BTB and promote the survival of Leydig cells. The findings may add new evidence for Sertoli–Leydig cell communication.
Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel
Authors: Kolář Michal H , Nagy Gabor , Kunkel John , Vaiana Sara M , Bock Lars V , Grubmüller Helmut 
Published: January 2022

Abstract
The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.
Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds
Authors: Bose Tanaya , Fridkin Gil , Davidovich Chen , Krupkin Miri , Dinger Nikita , Falkovich Alla H , Peleg Yoav , Agmon Ilana , Bashan Anat , Yonath Ada 
Published: January 2022

AbstractAlthough the mode of action of the ribosomes, the multi-component universal effective protein-synthesis organelles, has been thoroughly explored, their mere appearance remained elusive. Our earlier comparative structural studies suggested that a universal internal small RNA pocket-like segment called by us the protoribosome, which is still embedded in the contemporary ribosome, is a vestige of the primordial ribosome. Herein, after constructing such pockets, we show using the "fragment reaction" and its analyses by MALDI-TOF and LC–MS mass spectrometry techniques, that several protoribosome constructs are indeed capable of mediating peptide-bond formation. These findings present strong evidence supporting our hypothesis on origin of life and on ribosome's construction, thus suggesting that the protoribosome may be the missing link between the RNA dominated world and the contemporary nucleic acids/proteins life.
Prediction and pan-cancer analysis of mammalian transcripts involved in target directed miRNA degradation
Authors: Simeone Ines , Rubolino Carmela , Noviello Teresa Maria Rosaria , Farinello Diego , Cerulo Luigi , Marzi Matteo Jacopo , Nicassio Francesco 
Published: January 2022

AbstractIt is currently unknown how many RNA transcripts are able to induce degradation of microRNAs (miRNA) via the mechanism known as target-directed miRNA degradation (TDMD). We developed TDMDfinder, a computational pipeline that identifies ‘high confidence’ TDMD interactions in the Human and Mouse transcriptomes by combining sequence alignment and feature selection approaches. Our predictions suggested that TDMD is widespread, with potentially every miRNA controlled by endogenous targets. We experimentally tested 37 TDMDfinder predictions, of which 17 showed TDMD effects as measured by RT-qPCR and small RNA sequencing, linking the miR-17, miR-19, miR-30, miR-221, miR-26 and miR-23 families to novel endogenous TDMDs. In some cases, TDMD was found to affect different members of the same miRNA family selectively. Features like complementarity to the miRNA 3′ region, bulge size and hybridization energy appeared to be the main factors determining sensitivity. Computational analyses performed using the multiomic TCGA platform substantiated the involvement of many TDMD transcripts in human cancer and highlighted 36 highly significant interactions, suggesting TDMD as a new potential oncogenic mechanism. In conclusion, TDMDfinder provides the first inventory of bona fide human and mouse TDMDs. Available as a free webtool, TDMDfinder allows users to search for any TDMD interaction of interest by customizing its selection criteria.
NBS1-CtIP–mediated DNA end resection suppresses cGAS binding to micronuclei
Authors: Abdisalaam Salim , Mukherjee Shibani , Bhattacharya Souparno , Kumari Sharda , Sinha Debapriya , Ortega Janice , Li Guo-Min , Sadek Hesham A , Krishnan Sunil , Asaithamby Aroumougame 
Published: January 2022

Abstract
Cyclic guanosine monophosphate–adenosine monophosphate synthase (cGAS) is activated in cells with defective DNA damage repair and signaling (DDR) factors, but a direct role for DDR factors in regulating cGAS activation in response to micronuclear DNA is still poorly understood. Here, we provide novel evidence that Nijmegen breakage syndrome 1 (NBS1) protein, a well-studied DNA double-strand break (DSB) sensor—in coordination with Ataxia Telangiectasia Mutated (ATM), a protein kinase, and Carboxy-terminal binding protein 1 interacting protein (CtIP), a DNA end resection factor—functions as an upstream regulator that prevents cGAS from binding micronuclear DNA. When NBS1 binds to micronuclear DNA via its fork-head–associated domain, it recruits CtIP and ATM via its N- and C-terminal domains, respectively. Subsequently, ATM stabilizes NBS1’s interaction with micronuclear DNA, and CtIP converts DSB ends into single-strand DNA ends; these two key events prevent cGAS from binding micronuclear DNA. Additionally, by using a cGAS tripartite system, we show that cells lacking NBS1 not only recruit cGAS to a major fraction of micronuclear DNA but also activate cGAS in response to these micronuclear DNA. Collectively, our results underscore how NBS1 and its binding partners prevent cGAS from binding micronuclear DNA, in addition to their classical functions in DDR signaling.
The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7
Authors: Maldotti Mara , Lauria Andrea , Anselmi Francesca , Molineris Ivan , Tamburrini Annalaura , Meng Guohua , Polignano Isabelle Laurence , Scrivano Mirko Giuseppe , Campestre Fabiola , Simon Lisa Marie , Rapelli Stefania , Morandi Edoardo , Incarnato Danny , Oliviero Salvatore 
Published: January 2022

Abstract
The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear (1,2). We found 122 lncRNAs that interacts directly with p300. In depth analysis of one of these, lncSmad7, is required to maintain ESC self-renewal and it interacts to the C-terminal domain of p300. lncSmad7 also contains predicted RNA-DNA Hoogsteen forming base pairing. Combined Chromatin Isolation by RNA precipitation followed by sequencing (ChIRP-seq) together with CRISPR/Cas9 mutagenesis of the target sites demonstrate that lncSmad7 binds and recruits p300 to enhancers in trans, to trigger enhancer acetylation and transcriptional activation of its target genes. Thus, these results unveil a new mechanism by which p300 is recruited to the genome.
Surgical and anatomic factors predict development of leptomeningeal disease in patients with melanoma brain metastases
Authors: Lowe Stephen R , Wang Christopher P , Brisco Amanda , Whiting Junmin , Arrington John , Ahmed Kamran , Yu Michael , Robinson Timothy , Oliver Daniel , Etame Arnold , Tran Nam , Beer Furlan Andre , Sahebjam Solmaz , Mokhtari Sepideh , Piña Yolanda , Macaulay Robert , Forsyth Peter , Vogelbaum Michael A , Liu James K C 
Published: January 2022

Abstract

Background
Leptomeningeal disease (LMD) is a devastating complication of systemic malignancy, of which there is an unclear etiology. The aim of this study is to determine if surgical or anatomic factors can predict LMD in patients with metastatic melanoma.

Methods
A retrospective chart review was performed of 1162 patients treated at single institution for melanoma brain metastases (MBM). Patients with fewer than 3 months follow-up or lacking appropriate imaging were excluded. Demographic information, surgical, and anatomic data were collected.

Results
Eight hundred and twenty-seven patients were included in the final review. On multivariate analysis for the entire cohort, female gender, dural-based and intraventricular metastasis, and tumor bordering CSF spaces were associated with increased risk of LMD. Surgical resection was not significant for risk of LMD. On multivariate analysis of patients who have undergone surgical resection of a metastatic tumor, dural-based and intraventricular metastasis, ventricular entry during surgery, and metastasis in the infratentorial space were associated with increased risk of LMD. On multivariate analysis of patients who did not undergo surgery, chemotherapy after initial diagnosis and metastasis bordering CSF spaces were associated with increased risk of LMD.

Conclusion
In a single-institution cohort of MBM, we found that surgical resection alone did not result in an increased risk of LMD. Anatomical factors such as dural-based and intraventricular metastasis were significant for developing LMD, as well as entry into a CSF space during surgical resection. These data suggest a strong correlation between anatomic location and tumor cell seeding in relation to the development of LMD.
Weldable and closed-loop recyclable monolithic dynamic covalent polymer aerogels
Authors: Zhang Xinhai , Zhao Jun , Liu Kai , Li Guangfeng , Zhao Dong , Zhang Zhaoming , Wan Junjun , Yang Xue , Bai Ruixue , Wang Yongming , Zhang Wei , Yan Xuzhou 
Published: January 2022

ABSTRACT
Owing to their low density, high porosity and unique micro-nanostructures, aerogels are attractive for application in various fields; however, they suffer from shrinkage and/or cracking during preparation, mechanical brittleness, low production efficiency and non-degradation. Herein, we introduce the concept of dynamic covalent polymer chemistry to produce a new class of aerogels—referred to as DCPAs. The resulting lightweight DCPAs have the potential to be prepared on a large scale and feature high porosity (90.7%–91.3%), large degrees of compression (80% strain) and bending (diametral deflection of 30 mm) without any cracks, as well as considerable tensile properties (an elongation with a break at 32.7%). In addition, the DCPAs showcase the emergent characteristics of weldability, repairability, degradability and closed-loop recyclability that are highly desirable for providing versatile material platforms, though hardly achieved by traditional aerogels. Taking advantage of their robust porous structures, we demonstrate the potential of DCPAs for applications in thermal insulation and emulsion separation. These findings reveal that the dynamic covalent bond strategy would be generalized for the production of a new generation of aerogels with customized features for functioning in the field of intelligent and sustainable materials.