bluuebunny/crossref_metadata_2025_split huggingface dataset:
PHASTEST: faster than PHASTER, better than PHAST
Authors: Wishart David S , Han Scott , Saha Sukanta , Oler Eponine , Peters Harrison , Grant Jason R , Stothard Paul , Gautam Vasuk 
Published: May 2023

Abstract
PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids. PHASTEST also supports rapid annotation and interactive visualization of all other genes (protein coding regions, tRNA/tmRNA/rRNA sequences) in bacterial genomes. Given that bacterial genome sequencing has become so routine, the need for fast tools to comprehensively annotate bacterial genomes has become progressively more important. PHASTEST not only offers faster and more accurate prophage annotations than its predecessors, it also provides more complete whole genome annotations and much improved genome visualization capabilities. In standardized tests, we found that PHASTEST is 31% faster and 2–3% more accurate in prophage identification than PHASTER. Specifically, PHASTEST can process a typical bacterial genome in 3.2 min (raw sequence) or in 1.3 min when given a pre-annotated GenBank file. Improvements in PHASTEST’s ability to annotate bacterial genomes now make it a particularly powerful tool for whole genome annotation. In addition, PHASTEST now offers a much more modern and responsive visualization interface that allows users to generate, edit, annotate and interactively visualize (via zooming, rotating, dragging, panning, resetting), colourful, publication quality genome maps. PHASTEST continues to offer popular options such as an API for programmatic queries, a Docker image for local installations, support for multiple (metagenomic) queries and the ability to perform automated look-ups against thousands of previously PHAST-annotated bacterial genomes. PHASTEST is available online at https://phastest.ca.
Knockout of protein phosphatase 1 in Leishmania major reveals its role during RNA polymerase II transcription termination
Authors: Kieft Rudo , Zhang Yang , Yan Haidong , Schmitz Robert J , Sabatini Robert 
Published: May 2023

Abstract
The genomes of kinetoplastids are organized into polycistronic transcription units that are flanked by a modified DNA base (base J, beta-D-glucosyl-hydroxymethyluracil). Previous work established a role of base J in promoting RNA polymerase II (Pol II) termination in Leishmania major and Trypanosoma brucei. We recently identified a PJW/PP1 complex in Leishmania containing a J-binding protein (JBP3), PP1 phosphatase 1, PP1 interactive-regulatory protein (PNUTS) and Wdr82. Analyses suggested the complex regulates transcription termination by recruitment to termination sites via JBP3-base J interactions and dephosphorylation of proteins, including Pol II, by PP1. However, we never addressed the role of PP1, the sole catalytic component, in Pol II transcription termination. We now demonstrate that deletion of the PP1 component of the PJW/PP1 complex in L. major, PP1-8e, leads to readthrough transcription at the 3’-end of polycistronic gene arrays. We show PP1-8e has in vitro phosphatase activity that is lost upon mutation of a key catalytic residue and associates with PNUTS via the conserved RVxF motif. Additionally, purified PJW complex with associated PP1-8e, but not complex lacking PP1-8e, led to dephosphorylation of Pol II, suggesting a direct role of PNUTS/PP1 holoenzymes in regulating transcription termination via dephosphorylating Pol II in the nucleus.
WebQUAST: online evaluation of genome assemblies
Authors: Mikheenko Alla , Saveliev Vladislav , Hirsch Pascal , Gurevich Alexey 
Published: May 2023

AbstractSelecting proper genome assembly is key for downstream analysis in genomics studies. However, the availability of many genome assembly tools and the huge variety of their running parameters challenge this task. The existing online evaluation tools are limited to specific taxa or provide just a one-sided view on the assembly quality. We present WebQUAST, a web server for multifaceted quality assessment and comparison of genome assemblies based on the state-of-the-art QUAST tool. The server is freely available at https://www.ccb.uni-saarland.de/quast/. WebQUAST can handle an unlimited number of genome assemblies and evaluate them against a user-provided or pre-loaded reference genome or in a completely reference-free fashion. We demonstrate key WebQUAST features in three common evaluation scenarios: assembly of an unknown species, a model organism, and a close variant of it.
SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse
Authors: Qian Feng-Cui , Zhou Li-Wei , Li Yan-Yu , Yu Zheng-Min , Li Li-Dong , Wang Yue-Zhu , Xu Ming-Cong , Wang Qiu-Yu , Li Chun-Quan 
Published: May 2023

Abstract
Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses (‘pathway downstream analysis’, ‘upstream regulatory analysis’ and ‘genomic region annotation’) for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, ‘TF regulatory analysis’ and ‘Sample comparative analysis’ for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs.
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations
Authors: Chareshneu Aliaksei , Midlik Adam , Ionescu Crina-Maria , Rose Alexander , Horský Vladimír , Cantara Alessio , Svobodová Radka , Berka Karel , Sehnal David 
Published: May 2023

Abstract
Segmentation helps interpret imaging data in a biological context. With the development of powerful tools for automated segmentation, public repositories for imaging data have added support for sharing and visualizing segmentations, creating the need for interactive web-based visualization of 3D volume segmentations. To address the ongoing challenge of integrating and visualizing multimodal data, we developed Mol* Volumes and Segmentations (Mol*VS), which enables the interactive, web-based visualization of cellular imaging data supported by macromolecular data and biological annotations. Mol*VS is fully integrated into Mol* Viewer, which is already used for visualization by several public repositories. All EMDB and EMPIAR entries with segmentation datasets are accessible via Mol*VS, which supports the visualization of data from a wide range of electron and light microscopy experiments. Additionally, users can run a local instance of Mol*VS to visualize and share custom datasets in generic or application-specific formats including volumes in .ccp4, .mrc, and .map, and segmentations in EMDB-SFF .hff, Amira .am, iMod .mod, and Segger .seg. Mol*VS is open source and freely available at https://molstarvolseg.ncbr.muni.cz/.
nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands
Authors: Liu Kai , Lu Xufeng , Shi Hang , Xu Xiaojun , Kong Ren , Chang Shan 
Published: May 2023

AbstractThe rapid emergence of SARS-CoV-2 variants with multi-sites mutations is considered as a major obstacle for the development of drugs and vaccines. Although most of the functional proteins essential for SARS-CoV-2 have been determined, the understanding of the COVID-19 target-ligand interactions remains a key challenge. The old version of this COVID-19 docking server was built in 2020, and free and open to all users. Here, we present nCoVDock2, a new docking server to predict the binding modes for targets from SARS-CoV-2. First, the new server supports more targets. We replaced the modeled structures with newly resolved structures and added more potential targets of COVID-19, especially for the variants. Second, for small molecule docking, Autodock Vina was upgraded to the latest version 1.2.0, and a new scoring function was added for peptide or antibody docking. Third, the input interface and molecular visualization were updated for a better user experience. The web server, together with an extensive help and tutorial, are freely available at: https://ncovdock2.schanglab.org.cn.
Rapid Emergence of Potentially Transmissible Severe Acute Respiratory Syndrome Coronavirus 2 With Resistance to Combination Monoclonal Antibody Therapy
Authors: Jacobs Jana L , Haidar Ghady , Naqvi Asma , McCormick Kevin D , Sobolewski Michele , Treat Benjamin R , Heaps Amy L , Simpson Jordan , Kramer Kailey Hughes , McCreary Erin , Bariola J Ryan , Klamar-Blain Cynthia , Macatangay Bernard J C , Dimitrov Dimiter , Li Wei , Marino Christopher C , Raptis Anastasios , Sethi Rahil , Chandran Uma , Barratt-Boyes Simon , Parikh Urvi M , Mellors John W 
Published: May 2023

Abstract
Prolonged coronavirus disease 2019 may generate new viral variants. We report an immunocompromised patient treated with monoclonal antibodies who experienced rebound of viral RNA and emergence of an antibody-resistant (&gt;1000-fold) variant containing 5 mutations in the spike gene. The mutant virus was isolated from respiratory secretions, suggesting the potential for secondary transmission.
The adaptive significance of off-lek sociality in birds: A synthetic review, with evidence for the reproductive benefits hypothesis in Long-wattled Umbrellabirds
Authors: Anderson H Luke , Olivo Jorge , Karubian Jordan 
Published: May 2023

Abstract
Anecdotal evidence suggests that lekking birds exhibit considerable variation in form and degree of sociality away from the lek, yet this phenomenon has received very little theoretical or empirical research attention. Here, we provide the first synthetic literature review of off-lek sociality in birds and develop a conceptual framework for the potential adaptive function of off-lek sociality across lekking taxa. We then present a case study of the Long-wattled Umbrellabird (Cephalopterus penduliger), where we find support for the hypothesis that off-lek sociality is primarily driven by male reproductive incentives for coordinating lek attendance during the breeding season. During periods of high lekking activity, male umbrellabirds depart the lek in highly coordinated groups and maintain larger off-lek social groups relative to periods of low lekking activity. These seasonal differences in off-lek sociality do not occur in females, are not explained by patterns of foraging behavior, and are expected to confer individual-level benefits for participating males. Both the literature review and empirical study of umbrellabirds suggest that off-lek interactions and behavioral strategies may shape sexual selection processes at leks in important ways. Further research into this historically understudied area of lekking species’ behavioral ecology will likely deepen our understanding of the evolutionary dynamics of lek mating.
Conclusions
Authors: Michelson David A. 
Published: May 2023

Abstract
This final chapter suggests how the study of East Syrian contemplative reading can serve as framework for future scholarship. The chapter begins by summarizing the findings of the book as a whole in the form of answers to the questions about Syriac contemplative reading posed in Chapter 1. Next, the chapter demonstrates how the East Syrian tradition of contemplative reading offers a new historical context for the study of Isaac of Nineveh, John of Dalyatha, and other mystical authors in later centuries in the Church of the East. The chapter notes the wider legacies and implications of the East Syrian contemplative reading tradition. The works of ʿEnanishoʿ and Dadishoʿ circulated in Sogdian, West Syrian, Melkite, and Ethiopian monastic libraries where the East Syrian theology of contemplative ascetic reading was adapted to new contexts. Moreover, the East Syrian practice offers comparative insights into the closely related traditions of Latin lectio divina as well as Greek and Slavonic hesychasm. Finally, the chapter concludes by calling for other scholars to examine what this tradition could reveal about connections between Jewish, Christian, and Muslim mystical theologies in medieval Mesopotamia.
The Origin of Ultramafic Complexes with Melilitolites and Carbonatites: A Petrological Comparison of the Gardiner (E Greenland) and Kovdor (Russia) Intrusions
Authors: Gudelius Dominik , Marks Michael W , Markl Gregor , Nielsen Troels F D , Kolb Jochen , Walter Benjamin 
Published: May 2023

Abstract
In many alkaline complexes, large amounts of ultramafic rocks occur together with carbonatites, melilitolites and other alkaline silicate rocks. There is an ongoing debate if and how these contrasting lithologies were formed by differentiation of a common, mantle-derived silicate magma or rather by metasomatic processes between carbonatite and country rocks. In order to find petrological evidence for one or the other, two key examples, the Gardiner (E Greenland) and Kovdor (Russia) complexes are compared in this study. Despite their similar tectonic setting and succession of rock types, they show significant differences in the texture and mineral composition of ultramafic rocks. Ultramafic rocks from Kovdor include calcite- and biotite-rich dunites and pyroxenites without typical cumulate textures. They consist of Ni-poor forsterite, Cr-poor diopside and Ni-Cr-poor spinel and are possibly metasomatic reaction products between mantle-derived carbonatite melts and silicic host rocks. Similar ultramafic rocks are associated with carbonatites e. g. at Palabora (South Africa), Afrikanda (Russia), and Salitre (Brazil). In contrast, the ultramafic rocks from Gardiner show well-preserved cumulate textures and consist of Ni-rich forsterite, Cr-rich diopside as well as Cr-Ni-Ti-rich spinel and also contain F-Cl-rich apatite. They record an increase in aSiO2 from dunite to pyroxenite at similar fO2 (ΔFMQ ~ +1.2, with FMQ = fayalite-magnetite-quartz buffer), indicating that these rocks represent cumulates of an evolving, moderately oxidized mafic melt derived from a Ti-rich mantle source, similar to other rocks of the North Atlantic igneous province. In contrast to systems like Kovdor where carbonatite metasomatism is likely dominant, Ti-rich parental silicate magmas can abundantly crystallize Ti phases, as recorded by massive perovskite cumulates in Gardiner melilitolites. This can effectively scavenge HFSE from the magmatic system early in its evolution and likely explains HFSE-barren carbonatites at Gardiner, while those from Kovdor are highly HFSE-enriched. In summary, the results of our study provide strong textural and mineral chemical evidence that ultramafic rocks in alkaline complexes can be of both cumulate and metasomatic origin; the specific type has an important bearing on their HFSE enrichment and on the types of ores present in such complexes.
The transcriptional hub SHORT INTERNODES1 integrates hormone signals to orchestrate rice growth and development
Authors: Duan Erchao , Lin Qibing , Wang Yihua , Ren Yulong , Xu Huan , Zhang Yuanyan , Wang Yunlong , Teng Xuan , Dong Hui , Wang Yupeng , Jiang Xiaokang , Chen Xiaoli , Lei Jie , Yang Hang , Chen Rongbo , Jiang Ling , Wang Haiyang , Wan Jianmin 
Published: May 2023

Abstract
Plants have evolved sophisticated mechanisms to coordinate their growth and stress responses via integrating various phytohormone signaling pathways. However, the precise molecular mechanisms orchestrating integration of the phytohormone signaling pathways remain largely obscure. In this study, we found that the rice (Oryza sativa) short internodes1 (shi1) mutant exhibits typical auxin-deficient root development and gravitropic response, brassinosteroid (BR)-deficient plant architecture and grain size as well as enhanced abscisic acid (ABA)-mediated drought tolerance. Additionally, we found that the shi1 mutant is also hyposensitive to auxin and BR treatment but hypersensitive to ABA. Further, we showed that OsSHI1 promotes the biosynthesis of auxin and BR by activating the expression of OsYUCCAs and D11, meanwhile dampens ABA signaling by inducing the expression of OsNAC2, which encodes a repressor of ABA signaling. Furthermore, we demonstrated that 3 classes of transcription factors, AUXIN RESPONSE FACTOR 19 (OsARF19), LEAF AND TILLER ANGLE INCREASED CONTROLLER (LIC), and OsZIP26 and OsZIP86, directly bind to the promoter of OsSHI1 and regulate its expression in response to auxin, BR, and ABA, respectively. Collectively, our results unravel an OsSHI1-centered transcriptional regulatory hub that orchestrates the integration and self-feedback regulation of multiple phytohormone signaling pathways to coordinate plant growth and stress adaptation.
A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii
Authors: Lau Chun Sing , Dowle Adam , Thomas Gavin H , Girr Philipp , Mackinder Luke C M 
Published: May 2023

Abstract
Phase separation underpins many biologically important cellular events such as RNA metabolism, signaling, and CO2 fixation. However, determining the composition of a phase-separated organelle is often challenging due to its sensitivity to environmental conditions, which limits the application of traditional proteomic techniques like organellar purification or affinity purification mass spectrometry to understand their composition. In Chlamydomonas reinhardtii, Rubisco is condensed into a crucial phase-separated organelle called the pyrenoid that improves photosynthetic performance by supplying Rubisco with elevated concentrations of CO2. Here, we developed a TurboID-based proximity labeling technique in which proximal proteins in Chlamydomonas chloroplasts are labeled by biotin radicals generated from the TurboID-tagged protein. By fusing 2 core pyrenoid components with the TurboID tag, we generated a high-confidence pyrenoid proxiome that contains most known pyrenoid proteins, in addition to new pyrenoid candidates. Fluorescence protein tagging of 7 previously uncharacterized TurboID-identified proteins showed that 6 localized to a range of subpyrenoid regions. The resulting proxiome also suggests new secondary functions for the pyrenoid in RNA-associated processes and redox-sensitive iron–sulfur cluster metabolism. This developed pipeline can be used to investigate a broad range of biological processes in Chlamydomonas, especially at a temporally resolved suborganellar resolution.
Cholesterol twists the transmembrane Di-Gly region of amyloid-precursor protein
Authors: Wang David Tzu-Wei , Tang Tiffany Y C , Kuo Chun-Ting , Yu Yun-Ting , Chen Eric H L , Lee Ming-Tao , Tsai Ruei-Fong , Chen Hung-Ying , Chiang Yun-Wei , Chen Rita P Y 
Published: May 2023

Abstract
Nearly 95% of Alzheimer's disease (AD) occurs sporadically without genetic linkage. Aging, hypertension, high cholesterol content, and diabetes are known nongenomic risk factors of AD. Aggregation of Aβ peptides is an initial event of AD pathogenesis. Aβ peptides are catabolic products of a type I membrane protein called amyloid precursor protein (APP). Aβ40 is the major product, whereas the 2-residue-longer version, Aβ42, induces amyloid plaque formation in the AD brain. Since cholesterol content is one risk factor for sporadic AD, we aimed to explore whether cholesterol in the membrane affects the structure of the APP transmembrane region, thereby modulating the γ-secretase cutting behavior. Here, we synthesized several peptides containing the APP transmembrane region (sequence 693–726, corresponding to the Aβ22–55 sequence) with one or two Cys mutations for spin labeling. We performed three electron spin resonance experiments to examine the structural changes of the peptides in liposomes composed of dioleoyl phosphatidylcholine and different cholesterol content. Our results show that cholesterol increases membrane thickness by 10% and peptide length accordingly. We identified that the di-glycine region of Aβ36–40 (sequence VGGVV) exhibits the most profound change in response to cholesterol compared with other segments, explaining how the presence of cholesterol affects the γ-secretase cutting site. This study provides spectroscopic evidence showing how cholesterol modulates the structure of the APP transmembrane region in a lipid bilayer.
Discourses of growth in megaproject-based urban development: a comparative study of Poland and Finland
Authors: Rek-Woźniak Magdalena 
Published: May 2023

Abstract
The paper aims to add to the debate on the varieties of neoliberalism and the homogenizing effects of megaproject-based urban development. It examines the acculturation of the growth imperative as the master discourse that supports the development and implementation of two projects aimed at transforming the centers of Tampere, Finland, and Łódź, Poland. The selected cities shared similar traits as industrial centers in the past, but their current socioeconomic situation is entirely different. Tampere holds the title of “Finland’s most likeable city,” while rapidly depopulating Łódź was labeled the “Polish Detroit.” Nevertheless, both municipalities became attracted by the idea of boosting their development through implementing large-scale infrastructural investments to reshape their centers. Inspired by discursive institutionalism, which defines discourse as a set of policy ideas and values, and interactive policy communication and formulation processes, the paper reconstructs and compares the strategic visions of Tampere’s “Five Star City Centre” and “The New Centre of Łódź.” It demonstrates how the proponents of the projects discursively forced consent around proposed ideas. Namely, it shows how the issues of complexity, risk, and potential conflict of the two megaprojects have been addressed. On a conceptual level, the paper shows how policy convergence can be discursively facilitated in different socioeconomic, cultural, and political circumstances.