bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypercritical accretion during common envelopes in triples leading to binary black holes in the pair-instability-supernova mass gap
Authors: Moreno Méndez Enrique , De Colle Fabio , López-Cámara Diego , Vigna-Gómez Alejandro 
Published: April 2023

ABSTRACT
Hydrodynamic studies of stellar-mass compact objects (COs) in a common envelope (CE) have shown that the accretion rate onto the CO is a few orders of magnitude below the Bondi–Hoyle–Lyttleton (BHL) estimate. This is several orders of magnitude above the Eddington limit and above the limit for neutrino-cooled accretion (i.e. hypercritical accretion or HCA). Considering that a binary system inside the CE of a third star accretes material at nearly the same rate as a single object of the same total mass, we propose stellar-evolution channels which form binary black hole (BBH) systems with its component masses within the pair-instability supernova (PISN) mass gap. Our model is based on HCA onto the BBH system engulfed into the CE of a massive tertiary star. Furthermore, we propose a mass transfer mode which allows to store mass lost by the binary onto a third star. Through the use of population synthesis simulations for the evolution of BBHs and standard binary-evolution principles for the interaction with a tertiary star, we are able to produce BBHs masses consistent with those estimated for GW190521. We also discuss the massive binary system Mk34 as a possible progenitor of BBHs in the PISN gap.
Multiband gravitational wave observations of stellar binary black holes at the low to middle and high frequencies
Authors: Zhao Yuetong , Lu Youjun , Yan Changshuo , Chen Zhiwei , Ni Wei-Tou 
Published: April 2023

ABSTRACT
The ground-based gravitational wave (GW) observatories discover a population of merging stellar binary black holes (BBHs), which are promising targets for multiband observations by the low-, middle-, and high-frequency GW detectors. In this paper, we investigate the multiband GW detections of BBHs and demonstrate the advantages of such observations in improving the localization and parameter estimates of the sources. We generate mock samples of BBHs by considering different formation models as well as the merger rate density constrained by the current observations (GWTC-3). We specifically consider the astrodynamical middle-frequency interferometer GW observatory (AMIGO) in the middle-frequency band and estimate that it may detect 21–91 BBHs with signal-to-noise ratio ϱ ≥ 8 in a 4-yr observation period. The multiband observations by the low-frequency detectors [Laser Interferometer Space Antenna (LISA) and Taiji] and AMIGO may detect 5–33 BBHs with ϱLT ≥ 5 and ϱAMI ≥ 5, which can evolve to the high-frequency band within 4 yr and can be detected by the Cosmic Explorer (CE) and Einstein Telescope (ET). The joint observations of LISA-Taiji-AMIGO-ET-CE may localize the majority of the detectable BBHs in sky areas of 7 × 10−7 to 2 × 10−3 deg2, which is improved by a factor of ∼120, ∼2.4 × 105, ∼1.8 × 104, or ∼1.2 × 104, comparing with those by only adopting CE-ET, AMIGO, LISA-Taiji, or LISA-Taiji-AMIGO. These joint observations can also lead to an improvement of the measurement precision of the chirp mass (symmetric mass ratio) by a factor of ∼5.5 × 104 (33), ∼16 (8), ∼120 (90), or ∼5 (5), comparing with those by CE-ET, AMIGO, LISA-Taiji, or LISA-Taiji-AMIGO.
Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features
Authors: Czernecki Dariusz , Nourisson Antonin , Legrand Pierre , Delarue Marc 
Published: April 2023

Abstract
Family A DNA polymerases (PolAs) form an important and well-studied class of extant polymerases participating in DNA replication and repair. Nonetheless, despite the characterization of multiple subfamilies in independent, dedicated works, their comprehensive classification thus far is missing. We therefore re-examine all presently available PolA sequences, converting their pairwise similarities into positions in Euclidean space, separating them into 19 major clusters. While 11 of them correspond to known subfamilies, eight had not been characterized before. For every group, we compile their general characteristics, examine their phylogenetic relationships and perform conservation analysis in the essential sequence motifs. While most subfamilies are linked to a particular domain of life (including phages), one subfamily appears in Bacteria, Archaea and Eukaryota. We also show that two new bacterial subfamilies contain functional enzymes. We use AlphaFold2 to generate high-confidence prediction models for all clusters lacking an experimentally determined structure. We identify new, conserved features involving structural alterations, ordered insertions and an apparent structural incorporation of a uracil-DNA glycosylase (UDG) domain. Finally, genetic and structural analyses of a subset of T7-like phages indicate a splitting of the 3′–5′ exo and pol domains into two separate genes, observed in PolAs for the first time.
RNA-dependent interactome allows network-based assignment of RNA-binding protein function
Authors: Fradera-Sola Albert , Nischwitz Emily , Bayer Marie Elisabeth , Luck Katja , Butter Falk 
Published: April 2023

Abstract
RNA-binding proteins (RBPs) form highly diverse and dynamic ribonucleoprotein complexes, whose functions determine the molecular fate of the bound RNA. In the model organism Sacchromyces cerevisiae, the number of proteins identified as RBPs has greatly increased over the last decade. However, the cellular function of most of these novel RBPs remains largely unexplored. We used mass spectrometry-based quantitative proteomics to systematically identify protein–protein interactions (PPIs) and RNA-dependent interactions (RDIs) to create a novel dataset for 40 RBPs that are associated with the mRNA life cycle. Domain, functional and pathway enrichment analyses revealed an over-representation of RNA functionalities among the enriched interactors. Using our extensive PPI and RDI networks, we revealed putative new members of RNA-associated pathways, and highlighted potential new roles for several RBPs. Our RBP interactome resource is available through an online interactive platform as a community tool to guide further in-depth functional studies and RBP network analysis (https://www.butterlab.org/RINE).
Reconstructing the landscape of gut microbial species across 29,000 diverse individuals
Authors: Segota Igor , Watrous Jeramie D , Kantz Edward D , Nallamshetty Shriram , Tiwari Saumya , Cheng Susan , Jain Mohit , Long Tao 
Published: April 2023

Abstract
The human gut microbiome has been linked to health and disease. Investigation of the human microbiome has largely employed 16S amplicon sequencing, with limited ability to distinguish microbes at the species level. Herein, we describe the development of Reference-based Exact Mapping (RExMap) of microbial amplicon variants that enables mapping of microbial species from standard 16S sequencing data. RExMap analysis of 16S data captures ∼75% of microbial species identified by whole-genome shotgun sequencing, despite hundreds-fold less sequencing depth. RExMap re-analysis of existing 16S data from 29,349 individuals across 16 regions from around the world reveals a detailed landscape of gut microbial species across populations and geography. Moreover, RExMap identifies a core set of fifteen gut microbes shared by humans. Core microbes are established soon after birth and closely associate with BMI across multiple independent studies. RExMap and the human microbiome dataset are presented as resources with which to explore the role of the human microbiome.
The RNA export factor TbMex67 connects transcription and RNA export in Trypanosoma brucei and sets boundaries for RNA polymerase I
Authors: Pozzi Berta , Naguleswaran Arunasalam , Florini Francesca , Rezaei Zahra , Roditi Isabel 
Published: April 2023

Abstract
TbMex67 is the major mRNA export factor known to date in trypanosomes, forming part of the docking platform within the nuclear pore. To explore its role in co-transcriptional mRNA export, recently reported in Trypanosoma brucei, pulse labelling of nascent RNAs with 5-ethynyl uridine (5-EU) was performed with cells depleted of TbMex67 and complemented with a dominant-negative mutant (TbMex67-DN). RNA polymerase (Pol) II transcription was unaffected, but the procyclin loci, which encode mRNAs transcribed by Pol I from internal sites on chromosomes 6 and 10, showed increased levels of 5-EU incorporation. This was due to Pol I readthrough transcription, which proceeded beyond the procyclin and procyclin-associated genes up to the Pol II transcription start site on the opposite strand. Complementation by TbMex67-DN also increased Pol I-dependent formation of R-loops and γ-histone 2A foci. The DN mutant exhibited reduced nuclear localisation and binding to chromatin compared to wild-type TbMex67. Together with its interaction with chromatin remodelling factor TbRRM1 and Pol II, and transcription-dependent association of Pol II with nucleoporins, our findings support a role for TbMex67 in connecting transcription and export in T. brucei. In addition, TbMex67 stalls readthrough by Pol I in specific contexts, thereby limiting R-loop formation and replication stress.
A novel Cas9 fusion protein promotes targeted genome editing with reduced mutational burden in primary human cells
Authors: Carusillo Antonio , Haider Sibtain , Schäfer Raul , Rhiel Manuel , Türk Daniel , Chmielewski Kay O , Klermund Julia , Mosti Laura , Andrieux Geoffroy , Schäfer Richard , Cornu Tatjana I , Cathomen Toni , Mussolino Claudio 
Published: April 2023

Abstract
Precise genome editing requires the resolution of nuclease-induced DNA double strand breaks (DSBs) via the homology-directed repair (HDR) pathway. In mammals, this is typically outcompeted by non-homologous end-joining (NHEJ) that can generate potentially genotoxic insertion/deletion mutations at DSB sites. Because of higher efficacy, clinical genome editing has been restricted to imperfect but efficient NHEJ-based approaches. Hence, strategies that promote DSB resolution via HDR are essential to facilitate clinical transition of HDR-based editing strategies and increase safety. Here we describe a novel platform that consists of a Cas9 fused to DNA repair factors to synergistically inhibit NHEJ and favor HDR for precise repairing of Cas-induced DSBs. Compared to canonical CRISPR/Cas9, the increase in error-free editing ranges from 1.5-fold to 7-fold in multiple cell lines and in primary human cells. This novel CRISPR/Cas9 platform accepts clinically relevant repair templates, such as oligodeoxynucleotides (ODNs) and adeno-associated virus (AAV)-based vectors, and has a lower propensity to induce chromosomal translocations as compared to benchmark CRISPR/Cas9. The observed reduced mutational burden, resulting from diminished indel formation at on- and off-target sites, provides a remarkable gain in safety and advocates this novel CRISPR system as an attractive tool for therapeutic applications depending on precision genome editing.
An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening
Authors: Xiang Manli , Xia Kaijiang , Chen Bingyi , Luo Zhiteng , Yu Ying , Jiang Lili , Zhou Huihao 
Published: April 2023

Abstract
Tryptophanyl-tRNA synthetase (TrpRS) links tryptophan to tRNATrp, thereby playing an indispensable role in protein translation. Unlike most class I aminoacyl-tRNA synthetases (AARSs), TrpRS functions as a homodimer. Herein, we captured an ‘open-closed’ asymmetric structure of Escherichia coli TrpRS (EcTrpRS) with one active site occupied by a copurified intermediate product and the other remaining empty, providing structural evidence for the long-discussed half-of-the-sites reactivity of bacterial TrpRS. In contrast to its human counterpart, bacterial TrpRS may rely on this asymmetric conformation to functionally bind with substrate tRNA. As this asymmetric conformation is probably a dominant form of TrpRS purified from bacterial cells, we performed fragment screening against asymmetric EcTrpRS to support antibacterial discovery. Nineteen fragment hits were identified, and 8 of them were successfully cocrystallized with EcTrpRS. While a fragment named niraparib bound to the L-Trp binding site of the ‘open’ subunit, the other 7 fragments all bound to an unprecedented pocket at the interface between two TrpRS subunits. Binding of these fragments relies on residues specific to bacterial TrpRS, avoiding undesired interactions with human TrpRS. These findings improve our understanding of the catalytic mechanism of this important enzyme and will also facilitate the discovery of bacterial TrpRS inhibitors with therapeutic potential.
AlloReverse: multiscale understanding among hierarchical allosteric regulations
Authors: Zha Jinyin , Li Qian , Liu Xinyi , Lin Weidong , Wang Tingting , Wei Jiacheng , Zhang Ziliang , Lu Xun , Wu Jing , Ni Duan , Song Kun , Zhang Liang , Lu Xuefeng , Lu Shaoyong , Zhang Jian 
Published: April 2023

AbstractIncreasing data in allostery are requiring analysis of coupling relationships among different allosteric sites on a single protein. Here, based on our previous efforts on reversed allosteric communication theory, we have developed AlloReverse, a web server for multiscale analysis of multiple allosteric regulations. AlloReverse integrates protein dynamics and machine learning to discover allosteric residues, allosteric sites and regulation pathways. Especially, AlloReverse could reveal hierarchical relationships between different pathways and couplings among allosteric sites, offering a whole map of allostery. The web server shows a good performance in re-emerging known allostery. Moreover, we applied AlloReverse to explore global allostery on CDC42 and SIRT3. AlloReverse predicted novel allosteric sites and allosteric residues in both systems, and the functionality of sites was validated experimentally. It also suggests a possible scheme for combined therapy or bivalent drugs on SIRT3. Taken together, AlloReverse is a novel workflow providing a complete regulation map and is believed to aid target identification, drug design and understanding of biological mechanisms. AlloReverse is freely available to all users at https://mdl.shsmu.edu.cn/AlloReverse/ or http://www.allostery.net/AlloReverse/.
Helper-embedded satellites from an integrase clade that repeatedly targets prophage late genes
Authors: Tommasini Dario , Mageeney Catherine M , Williams Kelly P 
Published: April 2023

AbstractSatellites such as phage-induced chromosomal islands (PICIs) are mobile genetic elements relying on helper phages for their mobilization, through trans-regulatory interactions. We discovered a PICI with a more intimate cis-regulatory configuration, integrated within a late gene of its helper prophage. This helper-embedded PICI (HE-PICI) configuration delays expression of the interrupted helper late gene until the satellite excises and provides passive helper-driven components to both HE-PICI replication and late transcription. Upon induction of a helper-satellite composite, precise excision of the entire composite was observed, followed by composite replication, then satellite excision. We mapped 491 additional HE-PICIs to one of 14 sites in cognates of phage lambda late genes. Associated integrases form a single phylogenetic clade with subclades respecting the 14 site groups, exhibiting repeated tropism for prophage late genes as new integration sites evolve. Four ordered zones in a general gram-negative PICI genome organization are: an integration zone encoding integrase and AlpA, a dynamic zone encoding members of the Bro-N network of domain-swapping DNA-interactive proteins and immunity repressor RNAs, a replication zone, and a dynamic late zone in which clusters as large as 17 consecutive helper prophage late genes have been captured. Helper-embedded satellites present new dimensions in satellite/helper relationships.
Justified Epistemic Exclusions in Mathematics
Authors: Rittberg Colin Jakob 
Published: April 2023

Abstract
Who gets to contribute to knowledge production of an epistemic community? Scholarship has focussed on unjustified forms of exclusion. Here I study justified forms of exclusion by investigating the phenomenon of so-called ‘cranks’ in mathematics. I argue that workload-management concerns justify the exclusion of these outsiders from mathematical knowledge-making practices. My discussion reveals three insights. There are reasons other than incorrect mathematical argument that justify exclusions from mathematical practices. There are instances in which mathematicians are justified in rejecting even correct mathematical arguments. Finally, the way mathematicians spot mathematical crankery does not support the pejorative connotations of the ‘crank’ terminology.
Advances in osseointegration of biomimetic mineralized collagen and inorganic metal elements of natural bone for bone repair
Authors: Zhu Wenbo , Li Chao , Yao Mengxuan , Wang Xiumei , Wang Juan , Zhang Wei , Chen Wei , Lv Hongzhi 
Published: April 2023

Abstract
At this stage, bone defects caused by trauma, infection, tumor, or congenital diseases are generally filled with autologous bone or allogeneic bone transplantation, but this treatment method has limited sources, potential disease transmission and other problems. Ideal bone-graft materials remain continuously explored, and bone defect reconstruction remains a significant challenge. Mineralized collagen prepared by bionic mineralization combining organic polymer collagen with inorganic mineral calcium phosphate can effectively imitate the composition and hierarchical structure of natural bone and has good application value in bone repair materials. Magnesium, strontium, zinc and other inorganic components not only can activate relevant signaling pathways to induce differentiation of osteogenic precursor cells but also stimulate other core biological processes of bone tissue growth and play an important role in natural bone growth, and bone repair and reconstruction. This study reviewed the advances in hydroxyapatite/collagen composite scaffolds and osseointegration with natural bone inorganic components, such as magnesium, strontium and zinc.
House Price Dynamics, Optimal LTV Limits and the Liquidity Trap
Authors: Ferrero Andrea , Harrison Richard , Nelson Benjamin 
Published: April 2023

Abstract
This paper studies the optimal design of a macro-prudential instrument, a loan-to-value (LTV) limit, and its implications for monetary policy in a model with nominal rigidities and financial frictions. The analysis accounts for both an effective lower bound on the nominal interest rate and an upper bound on the ability of LTV limits to stimulate credit demand. The welfare-based loss function features a role for macro-prudential policy to enhance risk-sharing. Optimal LTV limits are strongly countercyclical. In a house price boom-bust episode, the active use of LTV limits alleviates debt-deleveraging dynamics and prevents the economy from falling into a liquidity trap.
When Do Low-Frequency Measures Really Measure Effective Spreads? Evidence from Equity and Foreign Exchange Markets
Authors: Jahan-Parvar Mohammad R , Zikes Filip 
Published: April 2023

Abstract
We present evidence that several popular low-frequency measures of effective spread suffer from a volatility-induced bias and that volatility is the primary driver of the variation of these liquidity proxies. Using data for U.S. equities and major foreign exchange rates, we show that the bias arises when the effective spread is small relative to volatility. We document that the bias has become more acute over time and show that volatility-biased measures fail to replicate some well-known results in empirical finance. We conclude by providing guidance on the choice of low-frequency measures in empirical applications.
Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Genome-Wide Association Mapping of Bacterial Leaf Streak Resistance in Two Elite Barley Breeding Panels
Authors: Ritzinger Mitch , Sallam Ahmad H. , Smith Kevin P. , Case Austin J. , Wodarek Joseph , Curland Rebecca D. , Dill-Macky Ruth , Steffenson Brian J. 
Published: April 2023

Bacterial leaf streak (BLS), caused chiefly by the pathogen Xanthomonas translucens pv. translucens, is becoming an increasingly important foliar disease of barley in the Upper Midwest. The deployment of resistant cultivars is the most economical and practical method of control. To identify sources of BLS resistance, we evaluated two panels of breeding lines from the University of Minnesota (UMN) and Anheuser-Busch InBev (ABI) barley improvement programs for reaction to strain CIX95 in the field at St. Paul and Crookston, MN, in 2020 and 2021. The percentage of resistant lines in the UMN and ABI panels with mid-season maturity was 1.8% (6 of 333 lines) and 5.2% (13 of 251 lines), respectively. Both panels were genotyped with the barley 50K iSelect SNP array, and then a genome-wide association study was performed. A single, highly significant association was identified for BLS resistance on chromosome 6H in the UMN panel. This association was also identified in the ABI panel. Seven other significant associations were detected in the ABI panel: two each on chromosomes 1H, 2H, and 3H and one on chromosome 5H. Of the eight associations identified in the panels, five were novel. The discovery of resistance in elite breeding lines will hasten the time needed to develop and release a BLS-resistant cultivar.
SARS‐CoV‐2 ORF3a expression in brain disrupts the autophagy–lysosomal pathway, impairs sphingolipid homeostasis, and drives neuropathogenesis
Authors: Zhu Hongling , Byrnes Colleen , Lee Y. Terry , Tuymetova Galina , Duffy Hannah B. D. , Bakir Jenna Y. , Pettit Sydney N. , Angina Jabili , Springer Danielle A. , Allende Maria L. , Kono Mari , Proia Richard L. 
Published: April 2023

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection causes injury to multiple organ systems, including the brain. SARS‐CoV‐2's neuropathological mechanisms may include systemic inflammation and hypoxia, as well as direct cell damage resulting from viral infections of neurons and glia. How the virus directly causes injury to brain cells, acutely and over the long term, is not well understood. In order to gain insight into this process, we studied the neuropathological effects of open reading frame 3a (ORF3a), a SARS‐CoV‐2 accessory protein that is a key pathological factor of the virus. Forced ORF3a brain expression in mice caused the rapid onset of neurological impairment, neurodegeneration, and neuroinflammation—key neuropathological features found in coronavirus disease (COVID‐19, which is caused by SARS‐CoV‐2 infection). Furthermore, ORF3a expression blocked autophagy progression in the brain and caused the neuronal accumulation of α‐synuclein and glycosphingolipids, all of which are linked to neurodegenerative disease. Studies with ORF3‐expressing HeLa cells confirmed that ORF3a disrupted the autophagy–lysosomal pathway and blocked glycosphingolipid degradation, resulting in their accumulation. These findings indicate that, in the event of neuroinvasion by SARS‐CoV‐2, ORF3a expression in brain cells may drive neuropathogenesis and be an important mediator of both short‐ and long‐term neurological manifestations of COVID‐19.