bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrographic flow mapping of persistent atrial fibrillation: intra- and inter-procedure reproducibility in the absence of ‘ground truth’
Authors: Reddy Vivek Y , Kong Melissa H , Petru Jan , Maan Abhishek , Funasako Moritoshi , Minami Kentaro , Ruppersberg Peter , Dukkipati Srinivas , Neuzil Petr 
Published: November 2023

Abstract

Aims
Validating mapping systems that identify atrial fibrillation (AF) sources (focal/rotational activity) is confounded by the absence of ground truth. A key concern of prior mapping technologies is spatiotemporal instability, manifesting as poor map reproducibility. Electrographic flow (EGF) employs a novel algorithm that visualizes atrial electrical wavefront propagation to identify putative AF sources. We analysed both intra- (3 min) and inter- (&gt;3 months) procedure EGF map reproducibility.

Methods and results
In 23 persistent AF patients, after pulmonary vein isolation (PVI), EGF maps were generated from 3 serial 1 min recordings using a 64-electrode basket mapping catheter (triplets) at right and left atrial locations. Source prevalence from map triplets was compared between recordings. Per protocol, 12 patients returned for 3-month remapping (1 non-inducible): index procedure post-PVI EGF maps were compared with initial EGF remapping at 3-month redo. Intra-procedure reproducibility: analysing 224 map triplets (111 right atrium, 113 left atrium) revealed a high degree of map consistency with minimal min-to-min shifts: 97 triplets (43%), exact match of leading sources on all 3 maps; 95 triplets (42%), leading source within 1 electrode space on 2 of 3 maps; and 32 triplets (14%), chaotic leading source pattern. Average deviation in source prevalence over 60 s was low (6.4%). Inter-procedure reproducibility: spatiotemporal stability of EGF mapping &gt;3 months was seen in 16 of 18 (89%) sources mapped in 12 patients with (re)inducible AF.

Conclusion
Electrographic flow mapping generates reproducible intra- and inter-procedural maps, providing rationale for randomized clinical trials targeting these putative AF sources.
Large variance in inbreeding within the Iberian wolf population
Authors: Salado Isabel , Preick Michaela , Lupiáñez-Corpas Natividad , Fernández-Gil Alberto , Vilà Carles , Hofreiter Michael , Leonard Jennifer A 
Published: November 2023

AbstractThe gray wolf (Canis lupus) population on the Iberian Peninsula was the largest in western and central Europe during most of the 20th century, with its size apparently never under a few hundred individuals. After partial legal protection in the 1970s in Spain, the northwest Iberian population increased to about 300 to 350 packs and then stabilized. In contrast to many current European wolf populations, which have been connected through gene flow, the Iberian wolf population has been isolated for decades. Here, we measured changes in genomic diversity and inbreeding through the last decades in a geographic context. We find that the level of genomic diversity in Iberian wolves is low compared with other Eurasian wolf populations. Despite population expansion in the last 50 years, some modern wolves had very high inbreeding, especially in the recently recolonized and historical edge areas. These individuals contrast with others with low inbreeding within the same population. The high variance in inbreeding despite population expansion seems associated with small-scale fragmentation of the range that is revealed by the genetic similarity between modern and historical samples from close localities despite being separated by decades, remaining differentiated from other individuals that are just over 100 km away, a small distance for a species with great dispersal capacity inhabiting a continuous range. This illustrates that, despite its demographically stable condition, the population would probably benefit from favoring connectivity within the population as well as genetic exchange with other European wolf populations to avoid excessive fragmentation and local inbreeding depression.
Fines, nonpayment, and revenues: evidence from speeding tickets
Authors: Christian Traxler , Libor Dušek 
Published: November 2023

Abstract
We estimate the effect of the level of fines on payment compliance and revenues collected from speeding tickets. Exploiting discontinuous increases in fines at speed cutoffs and reform-induced variation in these discontinuities, we implement two complementary regression discontinuity designs. The results consistently document small payment responses: a 10% increase in the fine (i.e., the payment obligation) induces a 1.2 percentage point decline in timely payments. The implied revenue elasticity is about 0.9. Expressed in absolute terms, a one-dollar increase in the fine translates into a roughly 60-cent increase in payments collected within 15 days (JEL H27, H26, K42).
CRP-Tree: a phylogenetic association test for binary traits
Authors: Zhang Julie , Preising Gabriel A , Schumer Molly , Palacios Julia A 
Published: November 2023

Abstract
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples and it is usually estimated from molecular sequence data at a locus or from other type of genetic data. We propose a model for trait evolution inspired by the Chinese Restaurant Process that includes a parameter that controls the degree of preferential attachment, that is, the tendency of nodes in the tree to subtend from nodes of the same type. This model with no preferential attachment is equivalent to a structured coalescent model with simultaneous migration and coalescence events and serves as a null model. We derive a test for phylogenetic binary trait association with linear computational complexity and empirically demonstrate that it is more powerful than some other methods. We apply our test to study the phylogenetic association of some traits in swordtail fish, breast cancer, yellow fever virus, and influenza A H1N1 virus. R-package implementation of our methods is available at https://github.com/jyzhang27/CRPTree.
Extensive suprasternal dehiscence reconstruction with NPWT and advancement flaps following cardiac surgery
Authors: Juhasz Boglarka , Tamas Robert 
Published: November 2023

Abstract
Treatment of suprasternal wound infection (SSWI) following cardiac surgery is not a clearly developed procedure. We report our female patient’s secondary SSWI treatment following bypass surgery. An obese female patient with unstable angina underwent an urgent, uneventful off-pump coronary artery bypass operation. An SSWI appeared within a week. After negative pressure wound therapy (NPWT), the sternum was rewired. In the previously irradiated territory of the left breast necrosis formed, a plastic surgeon reconstructed a defect. This procedure failed NPWT was restarted again, and a secondary reconstructive plastic surgery intervention was necessary. Despite extensive tissue mobilization, the central part of the reconstructive area necrotized, and we had to cover it with a split thickness skin mash graft. The irradiation therapy increases the incidence of suprasternal and/or sternal infection. It was possible to manage large soft tissue defects with bilateral and rotational advancement flaps.
Great lengths: a review of website preservation activities at three American Universities with digital humanities centers
Authors: VandeCreek Drew 
Published: November 2023

Abstract
Sustaining grant funded digital humanities websites has become a major challenge in the field. Three American universities with digital humanities centers kept eight of nine websites funded by the United States National Endowment for the Humanities (1996–2003) online to 2022. Center personnel made website preservation a part of everyday operations without additional funds devoted to the task. Web software developed rapidly in this period, however and center staff members’ efforts often did not succeed in providing necessary updates. Funded materials became increasingly obsolete. The extent of center personnel’s efforts, compared with their results, suggests that their approach itself will in many cases prove unsustainable. In one case, a university shifted responsibility for a popular website to its library. The library completely rebuilt it, only to find that the resource had again become obsolete less than 10 years later. Reconstruction should therefore be understood as an ongoing process, and its cost and complexity suggest that many online resources will not benefit from it. A new approach converting websites to a static state can facilitate sustainability at lower cost, but it also requires resources for implementation. Two American funding agencies have recently made grants available for website preservation and reconstruction. Similar organizations in other parts of the world have not followed suit and should consider doing so. In the absence of a comprehensive effort to identify and evaluate legacy websites for preservation, the competitive process of securing grant awards can begin to determine which legacy websites will survive.
Decoding dissociation of sequence-specific protein–DNA complexes with non-equilibrium simulations
Authors: van Heesch Thor , Bolhuis Peter G , Vreede Jocelyne 
Published: November 2023

Abstract
Sequence-specific protein–DNA interactions are crucial in processes such as DNA organization, gene regulation and DNA replication. Obtaining detailed insights into the recognition mechanisms of protein–DNA complexes through experiments is hampered by a lack of resolution in both space and time. Here, we present a molecular simulation approach to quantify the sequence specificity of protein–DNA complexes, that yields results fast, and is generally applicable to any protein–DNA complex. The approach is based on molecular dynamics simulations in combination with a sophisticated steering potential and results in an estimate of the free energy difference of dissociation. We provide predictions of the nucleotide specific binding affinity of the minor groove binding Histone-like Nucleoid Structuring (H-NS) protein, that are in agreement with experimental data. Furthermore, our approach offers mechanistic insight into the process of dissociation. Applying our approach to the major groove binding ETS domain in complex with three different nucleotide sequences identified the high affinity consensus sequence, quantitatively in agreement with experiments. Our protocol facilitates quantitative prediction of protein–DNA complex stability, while also providing high resolution insights into recognition mechanisms. As such, our simulation approach has the potential to yield detailed and quantitative insights into biological processes involving sequence-specific protein–DNA interactions.
Pot1 promotes telomere DNA replication via the Stn1-Ten1 complex in fission yeast
Authors: Carvalho Borges Pâmela C , Bouabboune Chaïnez , Escandell Jose Miguel , Matmati Samah , Coulon Stéphane , Ferreira Miguel Godinho 
Published: November 2023

Abstract
Telomeres are nucleoprotein complexes that protect the chromosome-ends from eliciting DNA repair while ensuring their complete duplication. Pot1 is a subunit of telomere capping complex that binds to the G-rich overhang and inhibits the activation of DNA damage checkpoints. In this study, we explore new functions of fission yeast Pot1 by using a pot1-1 temperature sensitive mutant. We show that pot1 inactivation impairs telomere DNA replication resulting in the accumulation of ssDNA leading to the complete loss of telomeric DNA. Recruitment of Stn1 to telomeres, an auxiliary factor of DNA lagging strand synthesis, is reduced in pot1-1 mutants and overexpression of Stn1 rescues loss of telomeres and cell viability at restrictive temperature. We propose that Pot1 plays a crucial function in telomere DNA replication by recruiting Stn1-Ten1 and Polα-primase complex to telomeres via Tpz1, thus promoting lagging-strand DNA synthesis at stalled replication forks.
The function of BCL11B in base excision repair contributes to its dual role as an oncogene and a haplo-insufficient tumor suppressor gene
Authors: Vickridge Elise , Faraco Camila C F , Lo Fanny , Rahimian Hedyeh , Liu Zi Yang , Tehrani Payman S , Djerir Billel , Ramdzan Zubaidah M , Leduy Lam , Maréchal Alexandre , Gingras Anne-Claude , Nepveu Alain 
Published: November 2023

Abstract
Genetic studies in mice and human cancers established BCL11B as a haploinsufficient tumor suppressor gene. Paradoxically, BCL11B is overexpressed in some human cancers where its knockdown is synthetic lethal. We identified the BCL11B protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro DNA repair assays demonstrated that both BCL11B and a small recombinant BCL11B213-560 protein lacking transcription regulation potential can stimulate the enzymatic activities of two base excision repair (BER) enzymes: NTHL1 and Pol β. In cells, BCL11B is rapidly recruited to sites of DNA damage caused by laser microirradiation. BCL11B knockdown delays, whereas ectopic expression of BCL11B213-560 accelerates, the repair of oxidative DNA damage. Inactivation of one BCL11B allele in TK6 lymphoblastoid cells causes an increase in spontaneous and radiation-induced mutation rates. In turn, ectopic expression of BCL11B213-560 cooperates with the RAS oncogene in cell transformation by reducing DNA damage and cellular senescence. These findings indicate that BCL11B functions as a BER accessory factor, safeguarding normal cells from acquiring mutations. Paradoxically, it also enables the survival of cancer cells that would otherwise undergo senescence or apoptosis due to oxidative DNA damage resulting from the elevated production of reactive oxygen species.
Ensembl 2024
Authors: Harrison Peter W , Amode M Ridwan , Austine-Orimoloye Olanrewaju , Azov Andrey G , Barba Matthieu , Barnes If , Becker Arne , Bennett Ruth , Berry Andrew , Bhai Jyothish , Bhurji Simarpreet Kaur , Boddu Sanjay , Branco Lins Paulo R , Brooks Lucy , Ramaraju Shashank Budhanuru , Campbell Lahcen I , Martinez Manuel Carbajo , Charkhchi Mehrnaz , Chougule Kapeel , Cockburn Alexander , Davidson Claire , De Silva Nishadi H , Dodiya Kamalkumar , Donaldson Sarah , El Houdaigui Bilal , Naboulsi Tamara El , Fatima Reham , Giron Carlos Garcia , Genez Thiago , Grigoriadis Dionysios , Ghattaoraya Gurpreet S , Martinez Jose Gonzalez , Gurbich Tatiana A , Hardy Matthew , Hollis Zoe , Hourlier Thibaut , Hunt Toby , Kay Mike , Kaykala Vinay , Le Tuan , Lemos Diana , Lodha Disha , Marques-Coelho Diego , Maslen Gareth , Merino Gabriela Alejandra , Mirabueno Louisse Paola , Mushtaq Aleena , Hossain Syed Nakib , Ogeh Denye N , Sakthivel Manoj Pandian , Parker Anne , Perry Malcolm , Piližota Ivana , Poppleton Daniel , Prosovetskaia Irina , Raj Shriya , Pérez-Silva José G , Salam Ahamed Imran Abdul , Saraf Shradha , Saraiva-Agostinho Nuno , Sheppard Dan , Sinha Swati , Sipos Botond , Sitnik Vasily , Stark William , Steed Emily , Suner Marie-Marthe , Surapaneni Likhitha , Sutinen Kyösti , Tricomi Francesca Floriana , Urbina-Gómez David , Veidenberg Andres , Walsh Thomas A , Ware Doreen , Wass Elizabeth , Willhoft Natalie L , Allen Jamie , Alvarez-Jarreta Jorge , Chakiachvili Marc , Flint Bethany , Giorgetti Stefano , Haggerty Leanne , Ilsley Garth R , Keatley Jon , Loveland Jane E , Moore Benjamin , Mudge Jonathan M , Naamati Guy , Tate John , Trevanion Stephen J , Winterbottom Andrea , Frankish Adam , Hunt Sarah E , Cunningham Fiona , Dyer Sarah , Finn Robert D , Martin Fergal J , Yates Andrew D 
Published: November 2023

Abstract
Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.
RefMetaPlant: a reference metabolome database for plants across five major phyla
Authors: Shi Han , Wu Xueting , Zhu Yan , Jiang Tao , Wang Zhengwei , Li Xuetong , Liu Jianju , Zhang Yingxue , Chen Feng , Gao Jinshan , Xu Xiaoyan , Zhang Guoqing , Xiao Ning , Feng Xianzhong , Zhang Peng , Wu Yongrui , Li Aihong , Chen Ping , Li Xuan 
Published: November 2023

Abstract
Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC–MS platform, we generated untargeted mass spectral data from &gt;150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A ‘Reference Metabolome Database for Plants’ (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like ‘LC–MS/MS Query’, ‘RefMetaBlast’ and ‘CompoundLibBlast’ for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort
Authors: Beltrán Daniel , Hospital Adam , Gelpí Josep Lluís , Orozco Modesto 
Published: November 2023

Abstract
Molecular dynamics (MD) simulations are keeping computers busy around the world, generating a huge amount of data that is typically not open to the scientific community. Pioneering efforts to ensure the safety and reusability of MD data have been based on the use of simple databases providing a limited set of standard analyses on single-short trajectories. Despite their value, these databases do not offer a true solution for the current community of MD users, who want a flexible analysis pipeline and the possibility to address huge non-Markovian ensembles of large systems. Here we present a new paradigm for MD databases, resilient to large systems and long trajectories, and designed to be compatible with modern MD simulations. The data are offered to the community through a web-based graphical user interface (GUI), implemented with state-of-the-art technology, which incorporates system-specific analysis designed by the trajectory providers. A REST API and associated Jupyter Notebooks are integrated into the platform, allowing fully customized meta-analysis by final users. The new technology is illustrated using a collection of trajectories obtained by the community in the context of the effort to fight the COVID-19 pandemic. The server is accessible at https://bioexcel-cv19.bsc.es/#/. It is free and open to all users and there are no login requirements. It is also integrated into the simulations section of the BioExcel-MolSSI COVID-19 Molecular Structure and Therapeutics Hub: https://covid.molssi.org/simulations/ and is part of the MDDB effort (https://mddbr.eu).
Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat
Authors: Zhu Anting , Liu Mengmeng , Tian Zhitao , Liu Wei , Hu Xin , Ao Min , Jia Jingqi , Shi Taotao , Liu Hongbo , Li Dongqin , Mao Hailiang , Su Handong , Yan Wenhao , Li Qiang , Lan Caixia , Fernie Alisdair R , Chen Wei 
Published: November 2023

Abstract
The importance of metabolite modification and species-specific metabolic pathways has long been recognized. However, linking the chemical structure of metabolites to gene function in order to explore the genetic and biochemical basis of metabolism has not yet been reported in wheat (Triticum aestivum). Here, we profiled metabolic fragment enrichment in wheat leaves and consequently applied chemical-tag-based semi-annotated metabolomics in a genome-wide association study in accessions of wheat. The studies revealed that all 1,483 quantified metabolites have at least one known functional group whose modification is tailored in an enzyme-catalyzed manner and eventually allows efficient candidate gene mining. A Triticeae crop-specific flavonoid pathway and its underlying metabolic gene cluster were elucidated in further functional studies. Additionally, upon overexpressing the major effect gene of the cluster TraesCS2B01G460000 (TaOMT24), the pathway was reconstructed in rice (Oryza sativa), which lacks this pathway. The reported workflow represents an efficient and unbiased approach for gene mining using forward genetics in hexaploid wheat. The resultant candidate gene list contains vast molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets and will ultimately aid in achieving wheat crop improvement.