bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural properties of subgroups of stars associated with open clusters
Authors: Gregorio-Hetem Jane , Hetem Annibal 
Published: August 2024

ABSTRACT
Recent studies have identified star clusters with multiple components based on accurate spatial distributions and/or proper motions from Gaia Data Release 3 (DR3), utilizing diverse diagnostics to gain an understanding of subgroup evolution. These findings motivated us to search for subgroups among the objects examined in our previous work, which employed fractal statistics. The present study considers seven open clusters that exhibit significant dispersion in age and/or proper motion distributions, suggesting that they are not single clusters. In order to characterize the stellar groups, we calculate the membership probability using Bayesian multidimensional analysis by fitting the observed proper motion distribution of the candidates. A probability distribution is also used to determine the distance of the cluster, which is obtained from the mean value of the distance modes. The photometry from Gaia DR3 is compared with evolutionary models to estimate the cluster age and total mass. In our sample, double components are found only for Markarian 38 and NGC 2659. The other five clusters are confirmed as being single. The structural parameters, such as $\mathcal {Q}$, $\Lambda _{\rm MSR}$, and $\Sigma _{\rm LDR}$, are compared with results from N-body simulations to investigate how the morphology of the stellar clustering evolves. The new results, for a more complete sample of cluster members, provide a better definition of the distribution type (central concentration or substructured region) inferred from the $\overline{m} - \overline{s}$ plot.
Gravitational interactions of binary systems in the massive planetesimal disc
Authors: López María C , Brunini A 
Published: August 2024

ABSTRACT
The prevalence of binary systems within our Solar system has become a common phenomenon, with over 500 systems identified. However, the connection that exists between the different dynamic mechanisms that give rise to their intricate orbital structure and the durability of these systems over time continues to be the subject of intense research. Encouraged by several works indicating that the number of binaries would have been much greater at the beginning of the outer Solar system, in our study we delve into the dynamical evolution of binary objects within the primordial populations of the massive disc of planetesimals between 15 and 30 au. By concentrating specifically on gravitational disturbances caused by neighbouring bodies, the research aims to investigate the effects on orbital dynamics resulting from the presence of binary objects to different extents within the studied populations. The results of our experiments indicate that populations with different binary fractions would not engender significantly divergent changes in the orbits of the study objects after 100 Myr of evolution. The survival of these systems, only considering a scenario of encounters and collisions between neighbours, would not have occurred in large quantities, being even lower in the outermost regions of the disc (25–30 au).
FLORAH: a generative model for halo assembly histories
Authors: Nguyen Tri , Modi Chirag , Yung L Y Aaron , Somerville Rachel S 
Published: August 2024

ABSTRACT
The mass assembly history (MAH) of dark matter haloes plays a crucial role in shaping the formation and evolution of galaxies. MAHs are used extensively in semi-analytic and empirical models of galaxy formation, yet current analytic methods to generate them are inaccurate and unable to capture their relationship with the halo internal structure and large-scale environment. This paper introduces florah (FLOw-based Recurrent model for Assembly Histories), a machine-learning framework for generating assembly histories of ensembles of dark matter haloes. We train florah on the assembly histories from the Gadget at Ultra-high Redshift with Extra Fine Time-steps and vsmdplN-body simulations and demonstrate its ability to recover key properties such as the time evolution of mass and concentration. We obtain similar results for the galaxy stellar mass versus halo mass relation and its residuals when we run the Santa Cruz semi-analytic model on florah-generated assembly histories and halo formation histories extracted from an N-body simulation. We further show that florah also reproduces the dependence of clustering on properties other than mass (assembly bias), which is not captured by other analytic methods. By combining multiple networks trained on a suite of simulations with different redshift ranges and mass resolutions, we are able to construct accurate main progenitor branches with a wide dynamic mass range from $z=0$ up to an ultra-high redshift $z \approx 20$, currently far beyond that of a single N-body simulation. florah is the first step towards a machine learning-based framework for planting full merger trees; this will enable the exploration of different galaxy formation scenarios with great computational efficiency at unprecedented accuracy.
SNAD catalogue of M-dwarf flares from the Zwicky Transient Facility
Authors: Voloshina A S , Lavrukhina A D , Pruzhinskaya M V , Malanchev K L , Ishida E E O , Krushinsky V V , Aleo P D , Gangler E , Kornilov M V , Korolev V S , Russeil E , Semenikhin T A , Sreejith S , Volnova A A ,   (The SNAD team)
Published: August 2024

ABSTRACT
Most of the stars in the Universe are M spectral class dwarfs, which are known to be the source of bright and frequent stellar flares. In this paper, we propose new approaches to discover M-dwarf flares in ground-based photometric surveys. We employ two approaches: a modification of a traditional method of parametric fit search and a machine learning algorithm based on active anomaly detection. The algorithms are applied to Zwicky Transient Facility (ZTF) data release 8, which includes the data from the ZTF high-cadence survey, allowing us to reveal flares lasting from minutes to hours. We analyse over 35 million ZTF light curves and visually scrutinize 1168 candidates suggested by the algorithms to filter out artefacts, occultations of a star by an asteroid, and other types of known variable objects. The result of this analysis is the largest catalogue of ZTF flaring stars to date, representing 134 flares with amplitudes ranging from −0.2 to −4.6 mag, including repeated flares. Using Pan-STARRS DR2 colours, we assign a spectral subclass to each object in the sample. For 13 flares with well-sampled light curves and available geometric distances from Gaia DR3, we estimate the bolometric energy. This research shows that the proposed methods combined with the ZTF’s cadence strategy are suitable for identifying M-dwarf flares and other fast transients, allowing for the extraction of significant astrophysical information from their light curves.
Methods for constructing and evaluating consensus genomic interval sets
Authors: Rymuza Julia , Sun Yuchen , Zheng Guangtao , LeRoy Nathan J , Murach Maria , Phan Neil , Zhang Aidong , Sheffield Nathan C 
Published: August 2024

Abstract
The amount of genomic region data continues to increase. Integrating across diverse genomic region sets requires consensus regions, which enable comparing regions across experiments, but also by necessity lose precision in region definitions. We require methods to assess this loss of precision and build optimal consensus region sets. Here, we introduce the concept of flexible intervals and propose three novel methods for building consensus region sets, or universes: a coverage cutoff method, a likelihood method, and a Hidden Markov Model. We then propose three novel measures for evaluating how well a proposed universe fits a collection of region sets: a base-level overlap score, a region boundary distance score, and a likelihood score. We apply our methods and evaluation approaches to several collections of region sets and show how these methods can be used to evaluate fit of universes and build optimal universes. We describe scenarios where the common approach of merging regions to create consensus leads to undesirable outcomes and provide principled alternatives that provide interoperability of interval data while minimizing loss of resolution.
Replication fork stalling in late S-phase elicits nascent strand degradation by DNA mismatch repair
Authors: Colicino-Murbach Erica , Hathaway Caitlin , Dungrawala Huzefa 
Published: August 2024

Abstract
Eukaryotic chromosomal replication occurs in a segmented, temporal manner wherein open euchromatin and compact heterochromatin replicate during early and late S-phase respectively. Using single molecule DNA fiber analyses coupled with cell synchronization, we find that newly synthesized strands remain stable at perturbed forks in early S-phase. Unexpectedly, stalled forks are susceptible to nucleolytic digestion during late replication resulting in defective fork restart. This inherent vulnerability to nascent strand degradation is dependent on fork reversal enzymes and resection nucleases MRE11, DNA2 and EXO1. Inducing chromatin compaction elicits digestion of nascent DNA in response to fork stalling due to reduced association of RAD51 with nascent DNA. Furthermore, RAD51 occupancy at stalled forks in late S-phase is diminished indicating that densely packed chromatin limits RAD51 accessibility to mediate replication fork protection. Genetic analyses reveal that susceptibility of late replicating forks to nascent DNA digestion is dependent on EXO1 via DNA mismatch repair (MMR) and that the BRCA2-mediated replication fork protection blocks MMR from degrading nascent DNA. Overall, our findings illustrate differential regulation of fork protection between early and late replication and demonstrate nascent strand degradation as a critical determinant of heterochromatin instability in response to replication stress.
A new method for network bioinformatics identifies novel drug targets for mucinous ovarian carcinoma
Authors: Craig Olivia , Lee Samuel , Pilcher Courtney , Saoud Rita , Abdirahman Suad , Salazar Carolina , Williams Nathan , Ascher David B , Vary Robert , Luu Jennii , Cowley Karla J , Ramm Susanne , Li Mark Xiang , Thio Niko , Li Jason , Semple Tim , Simpson Kaylene J , Gorringe Kylie L , Holien Jessica K 
Published: August 2024

AbstractMucinous ovarian carcinoma (MOC) is a subtype of ovarian cancer that is distinct from all other ovarian cancer subtypes and currently has no targeted therapies. To identify novel therapeutic targets, we developed and applied a new method of differential network analysis comparing MOC to benign mucinous tumours (in the absence of a known normal tissue of origin). This method mapped the protein-protein network in MOC and then utilised structural bioinformatics to prioritise the proteins identified as upregulated in the MOC network for their likelihood of being successfully drugged. Using this protein-protein interaction modelling, we identified the strongest 5 candidates, CDK1, CDC20, PRC1, CCNA2 and TRIP13, as structurally tractable to therapeutic targeting by small molecules. siRNA knockdown of these candidates performed in MOC and control normal fibroblast cell lines identified CDK1, CCNA2, PRC1 and CDC20, as potential drug targets in MOC. Three targets (TRIP13, CDC20, CDK1) were validated using known small molecule inhibitors. Our findings demonstrate the utility of our pipeline for identifying new targets and highlight potential new therapeutic options for MOC patients.
Synonymous rpsH variants: the common denominator in Escherichia coli adapting to ionizing radiation
Authors: Stemwedel Katharina , Haase Nadin , Christ Simon , Bogdanova Natalia V , Rudorf Sophia 
Published: August 2024

Abstract
Ionizing radiation (IR) in high doses is generally lethal to most organisms. Investigating mechanisms of radiation resistance is crucial for gaining insights into the underlying cellular responses and understanding the damaging effects of IR. In this study, we conducted a comprehensive analysis of sequencing data from an evolutionary experiment aimed at understanding the genetic adaptations to ionizing radiation in Escherichia coli. By including previously neglected synonymous mutations, we identified the rpsH c.294T &gt; G variant, which emerged in all 17 examined isolates across four subpopulations. The identified variant is a synonymous mutation affecting the 30S ribosomal protein S8, and consistently exhibited high detection and low allele frequencies in all subpopulations. This variant, along with two additional rpsH variants, potentially influences translational control of the ribosomal spc operon. The early emergence and stability of these variants suggest their role in adapting to environmental stress, possibly contributing to radiation resistance. Our findings shed light on the dynamics of ribosomal variants during the evolutionary process and their potential role in stress adaptation, providing valuable implications for understanding clinical radiation sensitivity and improving radiotherapy.
Expeditious chemical synthesis of xylomannans disproves the proposed antifreeze activities
Authors: Zhu Qian , Nicolardi Simone , Wang Yuanguang , Liu Yasong , Xu Peng , Wang Jianjun , Zhu Dapeng , Yu Biao 
Published: August 2024

ABSTRACT
Cold-adapted species are able to generate cryoprotective proteins and glycoproteins to prevent freezing damage. The [→4)-β-D-Manp-(1→4)-β-D-Xylp-(1→]n xylomannan from the Alaska beetle Upis ceramboides was disclosed by Walters and co-workers in 2009 as the first glycan-based antifreeze agent, which was later reported to be found in diverse taxa. Here, we report the rapid synthesis of four types of xylomannans, including the proposed antifreeze xylomannan up to a 64-mer (Type I), the regioisomeric [→3)-β-D-Manp-(1→4)-β-D-Xylp-(1→]n 16-mer (Type II), the diastereomeric [→4)-β-L-Manp-(1→4)-β-D-Xylp-(1→]n 16-mer (Type III) and the block-wise [→4)-β-D-Manp-(1→]m[→4)-β-D-Xylp-(1→]n 32-mer (Type IV), by employing a strategic iterative exponential glycan growth (IEGG) process. The nuclear magnetic resonance spectral data of the alleged natural xylomannan are in accordance only to those of the block-wise Type IV glycan and none of these synthetic xylomannans has been found to be capable of inducing thermal hysteresis. These results disprove the previous reports about the natural occurrence of antifreeze xylomannans.
Time-series satellite remote sensing reveals gradually increasing war damage in the Gaza Strip
Authors: Holail Shimaa , Saleh Tamer , Xiao Xiongwu , Xiao Jing , Xia Gui-Song , Shao Zhenfeng , Wang Mi , Gong Jianya , Li Deren 
Published: August 2024

ABSTRACT
War-related urban destruction is a significant global concern, impacting national security, social stability, people’s survival and economic development. The effects of urban geomorphology and complex geological contexts during conflicts, characterized by different levels of structural damage, are not yet fully understood globally. Here we report how integrating deep learning with data from the independently developed LuoJia3-01 satellite enables near real-time detection of explosions and assessment of different building damage levels in the Israel–Palestine conflict. We found that the damage continually increased from 17 October 2023 to 2 March 2024. We found 3747 missile craters with precision positions and sizes, and timing on vital infrastructure across five governorates in the Gaza Strip on 2 March 2024, providing accurate estimates of potential unexploded ordnance locations and assisting in demining and chemical decontamination. Our findings reveal a significant increase in damage to residential and educational structures, accounting for 58.4% of the total—15.4% destroyed, 18.7% severely damaged, 11.8% moderately damaged and 12.5% slightly damaged—which exacerbates the housing crisis and potential population displacement. Additionally, there is a 34.1% decline in the cultivated area of agricultural land, posing a risk to food security. The LuoJia3-01 satellite data are crucial for impartial conflict monitoring, and our innovative methodology offers a cost-effective, scalable approach to assess future conflicts in various global contexts. These first-time findings highlight the urgent need for an immediate ceasefire to prevent further damage and support the release of hostages and subsequent reconstruction efforts.
Every Crisis Is an Opportunity: Advancing Blood Culture Stewardship During a Blood Culture Bottle Shortage
Authors: Ryder Jonathan H , Van Schooneveld Trevor C , Diekema Daniel J , Fabre Valeria 
Published: August 2024

Abstract
The current manufacturing disruption of BACTEC blood culture bottles has drawn attention to diagnostic stewardship around blood culture utilization. In this perspective, we offer strategies for implementing blood culture stewardship using a graded approach based on a hospital's blood culture bottle supply. These strategies should inform plans to mitigate the impact of the shortage on patient care and reinforce fundamental principles of blood culture stewardship.
Pulmonary embolism with thrombus in transit across a patent foramen ovale
Authors: Iyengar Sumedh , Stolear Anton , Dulgher Maxim , Ahmed Ashraf , Shkolnik Evgeny , Zarich Stuart 
Published: August 2024

Abstract
Thromboembolism-in-transit, specifically impending paradoxical embolism (IPDE), is a rare and life-threatening condition with limited reported cases. We present a case of a 51-year-old male with obstructive sleep apnea, initially diagnosed with deep vein thrombosis and pulmonary embolism. Further evaluation revealed a saddle pulmonary embolus extending into the right atrium, straddling a patent foramen ovale (PFO), confirmed by transesophageal echocardiogram. Despite a critical left anterior descending coronary artery stenosis, surgical thrombectomy, PFO closure, and coronary artery bypass grafting were successfully performed. Thromboembolism-in-transit poses diagnostic challenges, and there is a lack of consensus on the optimal treatment strategy. Surgical interventions, including embolectomy and PFO closure, have shown promise, while thrombolytic therapy remains controversial. This case underscores the importance of tailored management in the absence of standardized guidelines, emphasizing the need for further research to establish evidence-based protocols for this uncommon but potentially fatal condition.
Spatial survival analysis accounts for female-biased breeding dispersal and provides realistic estimates of true annual survival in migratory warblers
Authors: Mumme Ronald L 
Published: August 2024

Abstract
Breeding dispersal—between-season change in breeding location—is usually female-biased in birds and creates problems in accurately estimating annual survival, as conventional Cormack-Jolly-Seber (CJS) survival models cannot discriminate between mortality and undetected emigration. Recently, spatial CJS (s-CJS) models have been developed that use data on breeding dispersal within a population to account for undetected emigration and provide corrected estimates of true annual survival, a development that promises to advance avian conservation initiatives that require accurate estimates of annual survival. Using a 14-year dataset on a color-banded population of Setophaga citrina (Hooded Warbler) in northwest Pennsylvania, I examined female-biased breeding dispersal and performance of an s-CJS model in estimating true annual survival of females and males. I also compared my findings to published literature on other migratory North American warblers, a group with many species of high conservation concern. Breeding dispersal in the S. citrina study population is strongly female-biased, with median dispersal distances of 151 m for females (n = 227) and 51 m (n = 336) for males. Although most individuals disperse short distances, the observed pattern of breeding dispersal within the study site was best modeled using a heavy-tailed Cauchy dispersal kernel, a model that indicates the presence of a substantial tail of undetected long-distance dispersal, particularly in females. Using the Cauchy model, s-CJS analysis yielded realistic estimates of S. citrina true annual survival, 0.61 for both sexes, and resolved ambiguities evident in much lower estimates of apparent annual survival, 0.45 for females and 0.54 for males, derived from conventional CJS analysis. Because long-distance breeding dispersal is widespread in migratory warblers and especially frequent in females, analyses of warbler survival should employ s-CJS methods whenever possible, as estimates of apparent annual survival derived from conventional CJS methods will in most cases poorly approximate true annual survival.
It is good to be average: Ecological correlates of breeding phenology in an Arctic seabird, Alle alle (Dovekie)
Authors: Ribeiro Léa , Devogel Marion , Grissot Antoine , Kidawa Dorota , Jakubas Dariusz , Syposz Martyna , Wojczulanis-Jakubas Katarzyna 
Published: August 2024

Abstract
Recognizing the deviation in an animal’s behavior from a population mean is not only necessary to understand the evolution and stability of the whole system but also to predict the future of a population in a changing environment. Arctic seabirds are expected to exhibit high synchronization in timing of breeding at the population level, due to highly seasonal and harsh environmental conditions. Nevertheless, even in such a highly synchronized system, there are always some earlier and later breeders, and the drivers of inter-pair variation remain largely unknown. Using an 8-year dataset on Alle alle (Dovekie), a small Arctic seabird, we examined potential drivers of breeding phenology. We found that A. alle pairs were quite repeatable in their phenology, and preserved their phenological status, with their chicks hatching consistently before, during, or after the population median date for hatching, despite that the calendar position of the median shifted between years. This would suggest that timing of breeding is associated with some pair characteristics, either via properties of the nest and/or some partner’s traits. However, breeding phenology of the pair was not dependent on nest location, pair bond duration or morphological similarity of the partners. Importantly, timing of breeding was negatively associated with chick growth rate, indicating fitness consequences of phenology. A simulation in our study further suggests that the chance of fledgling survival in the context of predation may be the highest for the chicks that hatched during the peak of the hatching period. While our results suggest that the timing of the breeding is important for the reproductive outcome, further research is required to determine the drivers of the consistent breeding phenology within A. alle pairs.
Linnebo on Analyticity and Thin Existence
Authors: Povich Mark 
Published: August 2024

AbstractIn his groundbreaking book, Thin Objects, Øystein Linnebo argues for an account of neo-Fregean abstraction principles and thin existence that does not rely on analyticity or conceptual rules. It instead relies on a metaphysical notion he calls “sufficiency”. In this short discussion, I defend the analytic or conceptual-rule account of thin existence.