bluuebunny/crossref_metadata_2025_split huggingface dataset:
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity
Authors: Caraballo-Ortiz Marcos A , Miura Sayaka , Sanderford Maxwell , Dolker Tenzin , Tao Qiqing , Weaver Steven , Pond Sergei L K , Kumar Sudhir 
Published: March 2022

Abstract

Motivation
Building reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic signal, confounding true evolutionary relationships. Massive global efforts of sequencing genomes and reconstructing the phylogeny of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains exemplify these difficulties since there are only hundreds of phylogenetically informative sites but millions of genomes. For such datasets, we set out to develop a method for building the phylogenetic tree of genomic haplotypes consisting of positions harboring common variants to improve the signal-to-noise ratio for more accurate and fast phylogenetic inference of resolvable phylogenetic features.

Results
We present the TopHap approach that determines spatiotemporally common haplotypes of common variants and builds their phylogeny at a fraction of the computational time of traditional methods. We develop a bootstrap strategy that resamples genomes spatiotemporally to assess topological robustness. The application of TopHap to build a phylogeny of 68 057 SARS-CoV-2 genomes (68KG) from the first year of the pandemic produced an evolutionary tree of major SARS-CoV-2 haplotypes. This phylogeny is concordant with the mutation tree inferred using the co-occurrence pattern of mutations and recovers key phylogenetic relationships from more traditional analyses. We also evaluated alternative roots of the SARS-CoV-2 phylogeny and found that the earliest sampled genomes in 2019 likely evolved by four mutations of the most recent common ancestor of all SARS-CoV-2 genomes. An application of TopHap to more than 1 million SARS-CoV-2 genomes reconstructed the most comprehensive evolutionary relationships of major variants, which confirmed the 68KG phylogeny and provided evolutionary origins of major and recent variants of concern.

Availability and implementation
TopHap is available at https://github.com/SayakaMiura/TopHap.

Supplementary information
Supplementary data are available at Bioinformatics online.
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins
Authors: Panneerselvam Suresh , Mishra Ruchir , Berry Colin , Crickmore Neil , Bonning Bryony C 
Published: March 2022

Abstract
Pesticidal proteins derived from the bacterium Bacillus thuringiensis, have provided the bases for a diverse array of pest management tools ranging from natural products used in organic agriculture, to modern biotechnological approaches. With advances in genome sequencing technologies and protein structure determination, an increasing number of pesticidal proteins from myriad bacterial species have been identified. The Bacterial Pesticidal Protein Resource Center (BPPRC) has been established to provide informational and analytical resources on the wide range of pesticidal proteins derived from bacteria that have potential utility for arthropod management. In association with a revised nomenclature for these proteins, BPPRC contains a database that allows users to browse and download sequences. Users can search the database for the best matches to sequences of interest and can incorporate their own sequences into basic informatic analyses. These analyses include the ability to draw and export guide trees from either whole protein sequences or, in the case of the three-domain Cry proteins, from individual domains. The associated website also provides a portal for users to submit protein sequences for naming. The BPPRC provides a single authoritative source of information to which all stakeholders can be referred including academics, government regulatory bodies and research and development personnel in the industrial sector. The database provides information on more than 1060 pesticidal proteins derived from 13 species of bacteria, including insecticidal activities for a subset of these proteins.
Database URL: www.bpprc.org and www.bpprc-db.org/
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database
Authors: Nachtegael Charlotte , Gravel Barbara , Dillen Arnau , Smits Guillaume , Nowé Ann , Papadimitriou Sofia , Lenaerts Tom 
Published: March 2022

Abstract

Improving the understanding of the oligogenic nature of diseases requires access to high-quality, well-curated Findable, Accessible, Interoperable, Reusable (FAIR) data. Although first steps were taken with the development of the Digenic Diseases Database, leading to novel computational advancements to assist the field, these were also linked with a number of limitations, for instance, the ad hoc curation protocol and the inclusion of only digenic cases. The OLIgogenic diseases DAtabase (OLIDA) presents a novel, transparent and rigorous curation protocol, introducing a confidence scoring mechanism for the published oligogenic literature. The application of this protocol on the oligogenic literature generated a new repository containing 916 oligogenic variant combinations linked to 159 distinct diseases. Information extracted from the scientific literature is supplemented with current knowledge support obtained from public databases. Each entry is an oligogenic combination linked to a disease, labelled with a confidence score based on the level of genetic and functional evidence that supports its involvement in this disease. These scores allow users to assess the relevance and proof of pathogenicity of each oligogenic combination in the database, constituting markers for reporting improvements on disease-causing oligogenic variant combinations. OLIDA follows the FAIR principles, providing detailed documentation, easy data access through its application programming interface and website, use of unique identifiers and links to existing ontologies.

Database URL
https://olida.ibsquare.be
ESC/EAS guidelines for the detection, prevention, and treatment of individuals at risk of a first myocardial infarction: effect of 5 years of updates and the new SCORE2
Authors: Sulman David , Zeitouni Michel , Silvain Johanne , Kerneis Mathieu , Guedeney Paul , Barthélémy Olivier , Brugier Delphine , Sabouret Pierre , Lattuca Benoit , Mertens Emilie , Posson Julianne , Procopi Niki , Salloum Tomy , Collet Jean-Philippe , Montalescot Gilles 
Published: March 2022

Abstract

Aims
The European Society of Cardiology (ESC) has released three consecutive guidelines within 5 years addressing cardiovascular prevention, risk scores, and cholesterol treatment. This study aims to evaluate whether the 2021 ESC guidelines improved the eligibility of individuals for primary prevention statin therapy before their first ST-segment elevation myocardial infarction (STEMI), and for intensive lipid-lowering treatments in secondary prevention.

Methods and results
The cardiovascular risk category of 2757 consecutive individuals admitted for a first STEMI was evaluated to assess whether they would have been eligible for primary prevention statins according to 2021 vs. 2019 and 2016 ESC guidelines. Eligibility for intensive lipid-lowering therapy in secondary prevention was assessed according to the real-life follow-up low-density lipoprotein cholesterol (LDL-C) and the expected follow-up LDL-C. More individuals would have been eligible for primary prevention statins according to 2021 and 2019 vs. 2016 guidelines (61.8% vs. 38.7% vs. 23.6%, P &lt; 0.01), a finding observed in both men (62.3% vs. 35.0% vs. 24.9%, P &lt; 0.01) and women (60.2% vs. 50.7% vs. 19.3%, P = 0.18). Only 27% of individuals reached the LDL-C objective of 55 mg/L in secondary prevention: using the ESC stepwise approach, 61.7% were eligible for higher doses of statins, 26.2% for ezetimibe, and 12.1% for a proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitor (PCSK9i). Based on expected LDL-C reductions, eligibility for a PCSK9i in secondary prevention was greater with 2021 vs. 2016 guidelines (44.5% vs. 22.5%, P &lt; 0.01).

Conclusion
The 2021 ESC guidelines improved the detection and treatment of individuals at risk for a first myocardial infarction. In secondary prevention, 70% of patients kept LDL-C levels above 55 mg/dL: increasing the statin dose and adding ezetimibe were the most frequently recommended therapeutic actions.
EU General Court considers the importance of trade mark specification: one product, one category (unless it’s a composite product)
Authors: Sztoldman Agnieszka 
Published: March 2022

Abstract
The EU General Courts revoked Sony’s ‘VITA’ word trade mark registration due to non-use and considered the importance of trade mark registration at the outset, as well as the business’ use and promotion of the registered trade mark for assessing whether this trade mark is genuinely used in the European Union during the relevant period.
Acquiescence or national rules of limitation? Polish Supreme Court addresses time limit for pursuing EUTM’s continuous infringement
Authors: Sztoldman Agnieszka 
Published: March 2022

Abstract
The Polish Supreme Court has dispelled doubts about the national statute of limitation for non-pecuniary claims arising from continuous infringements. Even though the case involved Audi AG’s frontline EU trade mark (EUTM), the Supreme Court decided on a limitation period under national law, not the EUTM acquiescence.
Broad-band emission from a kilonova ejecta-pulsar wind Nebula system: late-time X-ray afterglow rebrightening of GRB 170817A
Authors: Ren J , Dai Z G 
Published: March 2022

ABSTRACT
We study the broad-band radiation behaviour of a kilonova ejecta-pulsar wind nebula (PWN) system. In this model, we jointly fit the observations of AT 2017gfo in UV-optical-IR bands and the late-time X-ray afterglow of GRB 170817A. Our work shows that a PWN powered by the remnant neutron star (NS) post GW170817 event could affect the optical transient AT 2017gfo and re-brighten the late-time X-ray afterglow of GRB 170817A. The PWN radiation will regulate the trend of future X-ray observations from a flattening to a steep decline until some other sources (e.g. a kilonova afterglow) become dominant. The restricted ranges of the central NS parameters in this work are consistent with the previous works based on the observations of AT 2017gfo only. In addition, the new fitting result indicates that the NS wind is highly magnetized. We point out that the radio and X-ray emission from a kilonova ejecta-PWN system could be an important electromagnetic feature of binary NS mergers when a long-lived remnant NS is formed. Therefore, observations of a kilonova ejecta-PWN system will provide important information to inferring the nature of a merger remnant.
Herscheldiscovery of far-infrared emission from the hotspot D in the radio galaxy Cygnus A
Authors: Sunada Yuji , Isobe Naoki , Tashiro Makoto S , Kino Motoki , Koyama Shoko , Nakahara Satomi 
Published: March 2022

ABSTRACTThe far-infrared counterpart of hotspot D, the terminal hotspot of the eastern jet hosted by the radio galaxy Cygnus A, is detected with Herschel Aperture photometry of the source performed in 5 photometric bands covering the wavelength range of 70–350 $\mu$m. After removing the contamination from another nearby hotspot, E, the far-infrared intensity of hotspot D is derived as 83 ± 13 and 269 ± 66 mJy at 160 and 350 $\mu$m, respectively. Since the far-infrared spectrum of the object smoothly connects to the radio one, the far-infrared emission is attributed to the synchrotron radiation from the radio-emitting electron population. The radio-to-near-infrared spectrum is confirmed to exhibit a far-infrared break feature at the frequency of $\nu _\mathrm{br}=2.0^{+1.2}_{-0.8} \times 10^{12}$ Hz. The change in energy index at the break (Δα = 0.5) is interpreted as the impact of radiative cooling on an electron distribution sustained by continuous injection from diffusive shock acceleration. By ascribing the derived break to this cooling break, the magnetic field, B, in the hotspot is determined as a function of its radius, R within a uniform one-zone model combined with the strong relativistic shock condition. An independent B–R constraint is obtained by assuming the X-ray spectrum is wholly due to synchrotron self-Compton emission. By combining these conditions, the two parameters are tightly determined as B = 120–150 μG and R = 1.3–1.6 kpc. A further investigation into the two conditions indicates the observed X-ray flux is highly dominated by the synchrotron self-Compton emission.
Characteristics of small protoplanetary disc warps in kinematic observations
Authors: Young Alison K , Alexander Richard , Rosotti Giovanni , Pinte Christophe 
Published: March 2022

ABSTRACT
Many circumstellar discs appear to have misaligned central regions that give rise to shadows seen in scattered light observations. Small warps (&lt;20° misalignment) are probably more common but are also more difficult to detect than the large misalignments studied previously. We present the characteristics of CO emission that may be used to identify a small disc warp, found from synthetic 13CO maps of a model misaligned circumbinary disc. The spectra are not symmetrical, so fitting a Keplerian model is not appropriate and can hide a warp or lead to spurious features such as spirals appearing in the residuals. We quantify the observed warp structure by fitting sinusoids to concentric annuli of the disc. From this we can trace the radial variation of the peak velocity and of the azimuth of the peak velocity, i.e. the twist. At near face-on inclinations, these radial profiles reveal the warp structure. The twist remains detectable at moderate inclinations (iouter disc ≲ 35°) in the absence of radial flows but the measured inclination must be accurate to ≲ 5° to allow detection of the radial variation. The observed twist does not provide a direct measure of the warp structure because of its dependence on optical depth. The warp causes broad asymmetries in the channel maps that span several channels and that are distinct from localized features caused by embedded planets and gravitational instability. We suspect that kinematic evidence of warps may have been missed and we suggest a few examples where the data may be revisited.
Copper-mediated β-amyloid toxicity and its chelation therapy in Alzheimer's disease
Authors: Singh Sandeep Kumar , Balendra Vyshnavy , Obaid Ahmad A , Esposto Josephine , Tikhonova Maria A , Gautam Naveen Kumar , Poeggeler Burkhard 
Published: March 2022

Abstract
The link between bio-metals, Alzheimer's disease (AD), and its associated protein, amyloid-β (Aβ), is very complex and one of the most studied aspects currently. Alzheimer's disease, a progressive neurodegenerative disease, is proposed to occurs due to the misfolding and aggregation of Aβ. Dyshomeostasis of metal ions and their interaction with Aβ has largely been implicated in AD. Copper plays a crucial role in amyloid-β toxicity, and AD development potentially occurs through direct interaction with the copper-binding motif of APP and different amino acid residues of Aβ. Previous reports suggest that high levels of copper accumulation in the AD brain result in modulation of toxic Aβ peptide levels, implicating the role of copper in the pathophysiology of AD. In this review, we explore the possible mode of copper ion interaction with Aβ, which accelerates the kinetics of fibril formation and promote amyloid-β mediated cell toxicity in Alzheimer's disease and the potential use of various copper chelators in the prevention of copper-mediated Aβ toxicity.
PARP inhibitors trap PARP2 and alter the mode of recruitment of PARP2 at DNA damage sites
Authors: Lin Xiaohui , Jiang Wenxia , Rudolph Johannes , Lee Brian J , Luger Karolin , Zha Shan 
Published: March 2022

Abstract
Dual-inhibitors of PARP1 and PARP2 are promising anti-cancer drugs. In addition to blocking PARP1&2 enzymatic activity, PARP inhibitors also extend the lifetime of DNA damage-induced PARP1&2 foci, termed trapping. Trapping is important for the therapeutic effects of PARP inhibitors. Using live-cell imaging, we found that PARP inhibitors cause persistent PARP2 foci by switching the mode of PARP2 recruitment from a predominantly PARP1- and PAR-dependent rapid exchange to a WGR domain-mediated stalling of PARP2 on DNA. Specifically, PARP1-deletion markedly reduces but does not abolish PARP2 foci. The residual PARP2 foci in PARP1-deficient cells are DNA-dependent and abrogated by the R140A mutation in the WGR domain. Yet, PARP2-R140A forms normal foci in PARP1-proficient cells. In PARP1-deficient cells, PARP inhibitors - niraparib, talazoparib, and, to a lesser extent, olaparib - enhance PARP2 foci by preventing PARP2 exchange. This trapping of PARP2 is independent of auto-PARylation and is abolished by the R140A mutation in the WGR domain and the H415A mutation in the catalytic domain. Taken together, we found that PARP inhibitors trap PARP2 by physically stalling PARP2 on DNA via the WGR-DNA interaction while suppressing the PARP1- and PAR-dependent rapid exchange of PARP2.
Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain
Authors: Chen Shirui , Liu Wei , Naganuma Masahiro , Tomari Yukihide , Iwakawa Hiro-oki 
Published: March 2022

Abstract
Monocot DICER-LIKE3 (DCL3) and DCL5 produce distinct 24-nt small interfering RNAs (siRNAs), heterochromatic siRNAs (hc-siRNAs) and phased secondary siRNAs (phasiRNAs), respectively. The former small RNAs are linked to silencing of transposable elements and heterochromatic repeats, and the latter to reproductive processes. It is assumed that these DCLs evolved from an ancient ‘eudicot-type’ DCL3 ancestor, which may have produced both types of siRNAs. However, how functional differentiation was achieved after gene duplication remains elusive. Here, we find that monocot DCL3 and DCL5 exhibit biochemically distinct preferences for 5′ phosphates and 3′ overhangs, consistent with the structural properties of their in vivo double-stranded RNA substrates. Importantly, these distinct substrate specificities are determined by the PAZ domains of DCL3 and DCL5, which have accumulated mutations during the course of evolution. These data explain the mechanism by which these DCLs cleave their cognate substrates from a fixed end, ensuring the production of functional siRNAs. Our study also indicates how plants have diversified and optimized RNA silencing mechanisms during evolution.
The role of China's terrestrial carbon sequestration 2010–2060 in offsetting energy-related CO2 emissions
Authors: Huang Yao , Sun Wenjuan , Qin Zhangcai , Zhang Wen , Yu Yongqiang , Li Tingting , Zhang Qing , Wang Guocheng , Yu Lingfei , Wang Yijie , Ding Fan , Zhang Ping 
Published: March 2022

Abstract
Energy consumption dominates annual CO2 emissions in China. It is essential to significantly reduce CO2 emissions from energy consumption to reach national carbon neutrality by 2060, while the role of terrestrial carbon sequestration in offsetting energy-related CO2 emissions cannot be underestimated. Natural climate solutions (NCS), including improvements in terrestrial carbon sequestration, represent readily deployable options to offset anthropogenic greenhouse gas emissions. However, the extent to which China's terrestrial carbon sequestration in the future, especially when target-oriented managements (TOMs) are implemented, can help to mitigate energy-related CO2 emissions is far from certain. By synthesizing available findings and using several parameter-sparse empirical models that have been calibrated and/or fitted against contemporary measurements, we assessed China's terrestrial carbon sequestration over 2010–2060 and its contribution to offsetting national energy-related CO2 emissions. We show that terrestrial C sequestration in China will increase from 0.375 ± 0.056 (mean ± standard deviation) Pg C yr−1 in the 2010s to 0.458 ± 0.100 Pg C yr−1 under RCP2.6 and 0.493 ± 0.108 Pg C yr−1 under the RCP4.5 scenario in the 2050s, when TOMs are implemented. The majority of carbon sequestration comes from forest, accounting for 67.8–71.4% of the total amount. China's terrestrial ecosystems can offset 12.2–15.0% and 13.4–17.8% of energy-related peak CO2 emissions in 2030 and 2060, respectively. The implementation of TOMs contributes 11.9% of the overall terrestrial carbon sequestration in the 2020s and 23.7% in the 2050s. The most likely strategy to maximize future NCS effectiveness is a full implementation of all applicable cost-effective NCS pathways in China. Our findings highlight the role of terrestrial carbon sequestration in offsetting energy-related CO2 emissions and put forward future needs in the context of carbon neutrality.
Dual-compressed photoacoustic single-pixel imaging
Authors: Guo Yuning , Li Baowen , Yin Xiaobo 
Published: March 2022

ABSTRACT
Photoacoustic imaging, an acoustic imaging modality with potentially optical resolution in an optical turbid medium, has attracted great attention. However, the convergence of wavefront optimization and raster scanning in computational photoacoustic imaging leads to the challenge of fast mapping, especially for a spatial resolution approaching the acoustic deep-subwavelength regime. As a sparse sampling paradigm, compressive sensing has been applied in numerous fields to accelerate data acquisition without significant quality losses. In this work, we propose a dual-compressed approach for photoacoustic surface tomography that enables high-efficiency imaging with 3D spatial resolution unlimited by the acoustics in a turbid environment. The dual-compressed photoacoustic imaging with single-pixel detection, enabled by spatially optical modulation with synchronized temporally photoacoustic coding, allows decoding of the fine optical information from the modulated acoustic signal even when the variance of original photoacoustic signals is weak. We perform a proof-of-principle numerical demonstration of dual-compressed photoacoustic imaging, that resolves acoustic sub-acoustic-wavelength details with a significantly reduced number of measurements, revealing the potential for dynamic imaging. The dual-compressed concept, which transforms unobtrusive spatial difference into spatio-temporal detectable information, can be generalized to other imaging modalities to realize efficient, high-spatial-resolution imaging.