bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncloaking hidden repeating fast radio bursts with unsupervised machine learning
Authors: Chen Bo Han , Hashimoto Tetsuya , Goto Tomotsugu , Kim Seong Jin , Santos Daryl Joe D , On Alvina Y L , Lu Ting-Yi , Hsiao Tiger Y-Y 
Published: October 2021

ABSTRACT
The origins of fast radio bursts (FRBs), astronomical transients with millisecond time-scales, remain unknown. One of the difficulties stems from the possibility that observed FRBs could be heterogeneous in origin; as some of them have been observed to repeat, and others have not. Due to limited observing periods and telescope sensitivities, some bursts may be misclassified as non-repeaters. Therefore, it is important to clearly distinguish FRBs into repeaters and non-repeaters, to better understand their origins. In this work, we classify repeaters and non-repeaters using unsupervised machine learning, without relying on expensive monitoring observations. We present a repeating FRB recognition method based on the Uniform Manifold Approximation and Projection (UMAP). The main goals of this work are to: (i) show that the unsupervised UMAP can classify repeating FRB population without any prior knowledge about their repetition, (ii) evaluate the assumption that non-repeating FRBs are contaminated by repeating FRBs, and (iii) recognize the FRB repeater candidates without monitoring observations and release a corresponding catalogue. We apply our method to the Canadian Hydrogen Intensity Mapping Experiment Fast Radio Burst (CHIME/FRB) data base. We found that the unsupervised UMAP classification provides a repeating FRB completeness of 95 per cent and identifies 188 FRB repeater source candidates from 474 non-repeater sources. This work paves the way to a new classification of repeaters and non-repeaters based on a single epoch observation of FRBs.
Models for metal-poor stars with different initial abundances of C, N, O, Mg, and Si. II. Application to the colour–magnitude diagrams of the globular clusters 47 Tuc, NGC 6362, M 5, M 3, M 55, and M92
Authors: VandenBerg Don A , Casagrande Luca , Edvardsson Bengt 
Published: October 2021

ABSTRACTStellar models for −2.5 ≤ [Fe/H] ≤−0.5 that have been computed for variations in the C:N:O abundance ratio (for two different values of [CNO/Fe]) are compared with HST Wide Field Camera 3 (WFC3) observations of the globular clusters (GCs) 47 Tuc, NGC 6362, M 5 M 3, M 55, and M 92. The bolometric corrections (BCs) used to transpose the models to the observed planes are based on new MARCS synthetic spectra that incorporate improved treatments of molecules that involve atoms of C, N, and O. On the assumption of well-supported distance moduli and reddenings, isochrones for [O/Fe] = 0.6 and [m/Fe] = 0.4 for the other α elements, which are favoured by binary stars in GCs, generally reproduce the main features of observed colour–magnitude diagrams (CMDs) to within ∼0.03 mag. In particular, they appear to match the spreads in the observed (MF336W − MF438W)0 colours that are spanned by CN-weak and CN-strong stars along the lower giant branch quite well, but not the bluest giants, which are suspected to be N-poor ([N/Fe] ≲ −0.5). Both the absolute (MF438W − MF606W)0 colours and the variations in these colours at a given MF606W magnitude on the giant branch are difficult to explain unless the reddest stars are C-rich ([C/Fe] ≳ +0.5). Allowing for moderate He abundance variations ($\delta \, Y \sim 0.05$) improves the fits to the observations.
The impact of metallicity-dependent dust destruction on the dust-to-metals ratio in galaxies
Authors: Priestley F D , De Looze I , Barlow M J 
Published: October 2021

ABSTRACT
The ratio of the mass of interstellar dust to the total mass of metals (the dust-to-metals/DTM ratio) tends to increase with metallicity. This can be explained by the increasing efficiency of grain growth in the interstellar medium (ISM) at higher metallicities, with a corollary being that the low DTM ratios seen at low metallicities are due to inefficient stellar dust production. This interpretation assumes that the efficiency of dust destruction in the ISM is constant, whereas it might be expected to increase at low metallicity; the decreased cooling efficiency of low-metallicity gas should result in more post-shock dust destruction via thermal sputtering. We show that incorporating a sufficiently strong metallicity dependence into models of galaxy evolution removes the need for low stellar dust yields. The contribution of stellar sources to the overall dust budget may be significantly underestimated, and that of grain growth overestimated, by models assuming a constant destruction efficiency.
Modular Evolution of theDrosophilaMetabolome
Authors: Harrison Benjamin R , Hoffman Jessica M , Samuelson Ariana , Raftery Daniel , Promislow Daniel E L 
Published: October 2021

AbstractComparative phylogenetic studies offer a powerful approach to study the evolution of complex traits. Although much effort has been devoted to the evolution of the genome and to organismal phenotypes, until now relatively little work has been done on the evolution of the metabolome, despite the fact that it is composed of the basic structural and functional building blocks of all organisms. Here we explore variation in metabolite levels across 50 My of evolution in the genus Drosophila, employing a common garden design to measure the metabolome within and among 11 species of Drosophila. We find that both sex and age have dramatic and evolutionarily conserved effects on the metabolome. We also find substantial evidence that many metabolite pairs covary after phylogenetic correction, and that such metabolome coevolution is modular. Some of these modules are enriched for specific biochemical pathways and show different evolutionary trajectories, with some showing signs of stabilizing selection. Both observations suggest that functional relationships may ultimately cause such modularity. These coevolutionary patterns also differ between sexes and are affected by age. We explore the relevance of modular evolution to fitness by associating modules with lifespan variation measured in the same common garden. We find several modules associated with lifespan, particularly in the metabolome of older flies. Oxaloacetate levels in older females appear to coevolve with lifespan, and a lifespan-associated module in older females suggests that metabolic associations could underlie 50 My of lifespan evolution.
Clinical course of COVID-19 infection in paediatric familial Mediterranean fever patients
Authors: Kaya Akca Ummusen , Sener Seher , Balık Zeynep , Gurlevik Sibel , Oygar Pembe Derin , Atalay Erdal , Cuceoglu Muserref Kasap , Basaran Ozge , Batu Ezgi Deniz , Teksam Ozlem , Bilginer Yelda , Ozsurekci Yasemin , Ozen Seza 
Published: October 2021

ABSTRACT

Objective
To evaluate the course of coronavirus-19 (COVID-19) infection in paediatric familial Mediterranean fever (FMF) patients and to investigate the risk factors for COVID-19 infection.

Methods
Medical records of 100 consecutive paediatric FMF patients and their COVID-19 infection status were evaluated. Age- and gender-matched control group consisted of 51 patients with positive results for severe acute respiratory syndrome coronavirus 2.

Results
Twenty-five of 100 paediatric FMF patients were detected to have COVID-19 infection. A history of contact with a COVID-19 case was present in ∼95% of patients in both the FMF and control groups with COVID-19 infection. Asymptomatic infection was detected in two patients in the paediatric FMF group (8.0%) and 17 patients in the control group (33.3%) (P = .017). Mild disease was observed in 23 paediatric FMF patients (92.0%) and 28 control patients (54.9%) (P = .001), whereas moderate disease was present in only 6 control patients (11.7%) (0 vs 11.7%, P = .074). Severe or critical disease was not observed in any patients.

Conclusion
Paediatric FMF patients receiving colchicine had no moderate COVID-19 disease compared to the control group. We suggest that colchicine use may tune down the severity of the disease even if it does not prevent COVID-19 infection.
ProteomicsDB: toward a FAIR open-source resource for life-science research
Authors: Lautenbacher Ludwig , Samaras Patroklos , Muller Julian , Grafberger Andreas , Shraideh Marwin , Rank Johannes , Fuchs Simon T , Schmidt Tobias K , The Matthew , Dallago Christian , Wittges Holger , Rost Burkhard , Krcmar Helmut , Kuster Bernhard , Wilhelm Mathias 
Published: October 2021

Abstract
ProteomicsDB (https://www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research. In this update, we present our efforts to continuously develop and expand ProteomicsDB. The major focus over the last two years was improving the findability, accessibility, interoperability and reusability (FAIR) of the data as well as its implementation. For this purpose, we release a new application programming interface (API) that provides systematic access to essentially all data in ProteomicsDB. Second, we release a new open-source user interface (UI) and show the advantages the scientific community gains from such software. With the new interface, two new visualizations of protein primary, secondary and tertiary structure as well an updated spectrum viewer were added. Furthermore, we integrated ProteomicsDB with our deep-neural-network Prosit that can predict the fragmentation characteristics and retention time of peptides. The result is an automatic processing pipeline that can be used to reevaluate database search engine results stored in ProteomicsDB. In addition, we extended the data content with experiments investigating different human biology as well as a newly supported organism.
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
Authors: Perez-Riverol Yasset , Bai Jingwen , Bandla Chakradhar , García-Seisdedos David , Hewapathirana Suresh , Kamatchinathan Selvakumar , Kundu Deepti J , Prakash Ananth , Frericks-Zipper Anika , Eisenacher Martin , Walzer Mathias , Wang Shengbo , Brazma Alvis , Vizcaíno Juan Antonio 
Published: October 2021

AbstractThe PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas.
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms
Authors: Decker Katherine T , Gao Ye , Rychel Kevin , Al Bulushi Tahani , Chauhan Siddharth M , Kim Donghyuk , Cho Byung-Kwan , Palsson Bernhard O 
Published: October 2021

AbstractThe transcriptional regulatory network in prokaryotes controls global gene expression mostly through transcription factors (TFs), which are DNA-binding proteins. Chromatin immunoprecipitation (ChIP) with DNA sequencing methods can identify TF binding sites across the genome, providing a bottom-up, mechanistic understanding of how gene expression is regulated. ChIP provides indispensable evidence toward the goal of acquiring a comprehensive understanding of cellular adaptation and regulation, including condition-specificity. ChIP-derived data's importance and labor-intensiveness motivate its broad dissemination and reuse, which is currently an unmet need in the prokaryotic domain. To fill this gap, we present proChIPdb (prochipdb.org), an information-rich, interactive web database. This website collects public ChIP-seq/-exo data across several prokaryotes and presents them in dashboards that include curated binding sites, nucleotide-resolution genome viewers, and summary plots such as motif enrichment sequence logos. Users can search for TFs of interest or their target genes, download all data, dashboards, and visuals, and follow external links to understand regulons through biological databases and the literature. This initial release of proChIPdb covers diverse organisms, including most major TFs of Escherichia coli, and can be expanded to support regulon discovery across the prokaryotic domain.
PDBe-KB: collaboratively defining the biological context of structural data
Authors:   PDBe-KB consortium, Varadi Mihaly , Anyango Stephen , Armstrong David , Berrisford John , Choudhary Preeti , Deshpande Mandar , Nadzirin Nurul , Nair Sreenath S , Pravda Lukas , Tanweer Ahsan , Al-Lazikani Bissan , Andreini Claudia , Barton Geoffrey J , Bednar David , Berka Karel , Blundell Tom , Brock Kelly P , Carazo Jose Maria , Damborsky Jiri , David Alessia , Dey Sucharita , Dunbrack Roland , Recio Juan Fernandez , Fraternali Franca , Gibson Toby , Helmer-Citterich Manuela , Hoksza David , Hopf Thomas , Jakubec David , Kannan Natarajan , Krivak Radoslav , Kumar Manjeet , Levy Emmanuel D , London Nir , Macias Jose Ramon , Srivatsan Madhusudhan M , Marks Debora S , Martens Lennart , McGowan Stuart A , McGreig Jake E , Modi Vivek , Parra R Gonzalo , Pepe Gerardo , Piovesan Damiano , Prilusky Jaime , Putignano Valeria , Radusky Leandro G , Ramasamy Pathmanaban , Rausch Atilio O , Reuter Nathalie , Rodriguez Luis A , Rollins Nathan J , Rosato Antonio , Rubach Paweł , Serrano Luis , Singh Gulzar , Skoda Petr , Sorzano Carlos Oscar S , Stourac Jan , Sulkowska Joanna I , Svobodova Radka , Tichshenko Natalia , Tosatto Silvio C E , Vranken Wim , Wass Mark N , Xue Dandan , Zaidman Daniel , Thornton Janet , Sternberg Michael , Orengo Christine , Velankar Sameer 
Published: October 2021

Abstract
The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.
Tumour Treating Fields in Glioblastoma: Is the treatment tolerable, effective, and practical in UK Patients?
Authors: Olubajo Farouk , Thorpe Antonia , Davis Charles , Crofton Anna , Mills Samantha J , Jenkisnon Michael , Watts Colin , Price Stephen , Brodbelt Andrew 
Published: October 2021

Abstract

Aims
Tumour Treating Fields (TTF) in combination with standard therapy, prolongs survival in patients with Glioblastoma (GBM). The aim of the current study was to assess the feasibility of integrating TTF into a standard UK neuro-oncology service with a focus on patient tolerability, compliance, and treatment delivery.

Method
A prospective study was performed of UK patients with IDH 1 Wild Type, MGMT Unmethylated GBM treated with TTF, in conjunction with conventional therapy. Patient compliance data, device-specific tolerability questions, and an evaluation of disease progression and survival were collected. Monthly quality of life (QoL) questionnaires (EORTC QLQ-C30 with BN-20) examined the trend of global health, psychosocial function and symptom progression.

Results
Nine patients were enrolled with a median age of 47 (7 males; 2 females). Overall, compliance with TTF was 89% (range 16% - 97%). Only one patient failed to comply with treatment. Patients tolerated the device with minimal side effects. Eight patients described mild to moderate skin irritation, whilst all patients were keen to recommend the device to other patients (100%). Most patients found the weight and size of the device to be its biggest drawback (72%). Progression-free survival was 5.5 months and median overall survival 14.9 months.

Conclusion
TTF was well tolerated amongst a small cohort of UK patients, who were able to comply with treatment without any significant complication. QoL questionnaires showed no sustained deterioration in global health, physical and emotional function until the final months of life, when disease burden was greatest.
Physiological responses to acute fasting: implications for intermittent fasting programs
Authors: Stratton Matthew T , Albracht-Schulte Kembra , Harty Patrick S , Siedler Madelin R , Rodriguez Christian , Tinsley Grant M 
Published: October 2021

Abstract
Intermittent fasting (IF) is a dietary strategy that involves alternating periods of abstention from calorie consumption with periods of ad libitum food intake. There is significant interest in the body of literature describing longitudinal adaptations to IF. Less attention has been given to the acute physiological responses that occur during the fasting durations that are commonly employed by IF practitioners. Thus, the purpose of this review was to examine the physiological responses – including alterations in substrate metabolism, systemic hormones, and autophagy – that occur throughout an acute fast. Literature searches were performed to locate relevant research describing physiological responses to acute fasting and short-term starvation. A single fast demonstrated the ability to alter glucose and lipid metabolism within the initial 24 hours, but variations in protein metabolism appeared to be minimal within this time frame. The ability of an acute fast to elicit significant increases in autophagy is still unknown. The information summarized in this review can be used to help contextualize existing research and better inform development of future IF interventions.
Genetic structure in the nonbreeding range ofrufaRed Knots suggests distinct Arctic breeding populations
Authors: Verkuil Yvonne I , Tavares Erika , González Patricia M , Choffe Kristen , Haddrath Oliver , Peck Mark , Niles Lawrence J , Baker Allan J , Piersma Theunis , Conklin Jesse R 
Published: October 2021

AbstractAn understanding of the migratory connectivity between breeding and nonbreeding areas is fundamental to the management of long-distance migrants under pressure from habitat change along their flyways. Here we describe evidence for genetic structure within the nonbreeding range of the endangered Arctic-Canadian rufa subspecies of Red Knots (Calidris canutus). Using blood and tissue samples from the major nonbreeding regions in Argentina (Tierra del Fuego and Río Negro), northern Brazil (Maranhão), and southeastern USA (Florida), we estimated genetic structure in 514 amplified fragment length polymorphism (AFLP) loci, applying cluster assignment analyses in DAPC, assignPOP, and STRUCTURE. Using a priori location information, individuals could be correctly re-assigned to their nonbreeding regions, which validated that the assignment accuracy of the data was sufficient. Without using a priori location information, we detected 3–5 genotype clusters, and posterior assignment probabilities of samples to these genotype clusters varied among the three regions. Lastly a chi-square test confirmed that allele frequencies varied significantly among nonbreeding regions, rejecting the hypothesis that samples were drawn from a single gene pool. Our findings hint at undescribed structure within the Red Knot rufa breeding range in the Canadian Arctic and indicate that each rufa nonbreeding area in this study hosts a different subsample of these breeding populations. The observation that nonbreeding sites of rufa Red Knots contain different genetic pools argues for separate conservation management of these sites.
Democratic Law and the Erosion of Common Law
Authors: Valentine Shiffrin Seana 
Published: October 2021

Abstract
This chapter explores the democratic character of the common law by examining the implied contractual duty of good faith and its dismissive treatment by the US Supreme Court in Northwest v. Ginsberg, a 2014 preemption decision. The decision was mistaken because it failed to recognize law’s morally indispensable role of publicly articulating and interpreting our shared moral commitments, treating law instead as a mere means of resolving disputes. The chapter also celebrates the democratic character of common law, which, although articulated by judges, responds to reasons and problems emerging from the citizenry and attends to moral expectations embodied in customary practices. The chapter underscores the importance of common law (and the doctrine of good faith) in publicly articulating reasons and drawing on the underlying values that law serves, democratic functions that are lost when litigation is replaced by private arbitration and overlooked by a narrow focus on elections.
Thylakoid attachment to the plasma membrane in Synechocystis sp. PCC 6803 requires the AncM protein
Authors: Ostermeier Matthias , Heinz Steffen , Hamm Julia , Zabret Jure , Rast Anna , Klingl Andreas , Nowaczyk Marc M , Nickelsen Jörg 
Published: October 2021

Abstract
Thylakoids are the highly specialized internal membrane systems that harbor the photosynthetic electron transport machinery in cyanobacteria and in chloroplasts. In Synechocystis sp. PCC 6803, thylakoid membranes (TMs) are arranged in peripheral sheets that occasionally converge on the plasma membrane (PM) to form thylakoid convergence membranes (TCMs). TCMs connect several thylakoid sheets and form local contact sites called thylapses between the two membrane systems, at which the early steps of photosystem II (PSII) assembly occur. The protein CurT is one of the main drivers of TCM formation known so far. Here, we identify, by whole-genome sequencing of a curT− suppressor strain, the protein anchor of convergence membranes (AncM) as a factor required for the attachment of thylakoids to the PM at thylapses. An ancM− mutant is shown to have a photosynthetic phenotype characterized by reductions in oxygen-evolution rate, PSII accumulation, and PS assembly. Moreover, the ancM− strain exhibits an altered thylakoid ultrastructure with additional sheets and TCMs detached from the PM. By combining biochemical studies with fluorescence and correlative light-electron microscopy-based approaches, we show that AncM is an integral membrane protein located in biogenic TCMs that form thylapses. These data suggest an antagonistic function of AncM and CurT in shaping TM ultrastructure.