bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthetic virions reveal fatty acid-coupled adaptive immunogenicity of SARS-CoV-2 spike glycoprotein
Authors: Staufer Oskar , Gupta Kapil , Hernandez Bücher Jochen Estebano , Kohler Fabian , Sigl Christian , Singh Gunjita , Vasileiou Kate , Yagüe Relimpio Ana , Macher Meline , Fabritz Sebastian , Dietz Hendrik , Cavalcanti Adam Elisabetta Ada , Schaffitzel Christiane , Ruggieri Alessia , Platzman Ilia , Berger Imre , Spatz Joachim P. 
Published: February 2022

AbstractSARS-CoV-2 infection is a major global public health concern with incompletely understood pathogenesis. The SARS-CoV-2 spike (S) glycoprotein comprises a highly conserved free fatty acid binding pocket (FABP) with unknown function and evolutionary selection advantage1,2. Deciphering FABP impact on COVID-19 progression is challenged by the heterogenous nature and large molecular variability of live virus. Here we create synthetic minimal virions (MiniVs) of wild-type and mutant SARS-CoV-2 with precise molecular composition and programmable complexity by bottom-up assembly. MiniV-based systematic assessment of S free fatty acid (FFA) binding reveals that FABP functions as an allosteric regulatory site enabling adaptation of SARS-CoV-2 immunogenicity to inflammation states via binding of pro-inflammatory FFAs. This is achieved by regulation of the S open-to-close equilibrium and the exposure of both, the receptor binding domain (RBD) and the SARS-CoV-2 RGD motif that is responsible for integrin co-receptor engagement. We find that the FDA-approved drugs vitamin K and dexamethasone modulate S-based cell binding in an FABP-like manner. In inflammatory FFA environments, neutralizing immunoglobulins from human convalescent COVID-19 donors lose neutralization activity. Empowered by our MiniV technology, we suggest a conserved mechanism by which SARS-CoV-2 dynamically couples its immunogenicity to the host immune response.
All-optical dissipative discrete time crystals
Authors: Taheri Hossein , Matsko Andrey B. , Maleki Lute , Sacha Krzysztof 
Published: February 2022

AbstractTime crystals are periodic states exhibiting spontaneous symmetry breaking in either time-independent or periodically-driven quantum many-body systems. Spontaneous modification of discrete time-translation symmetry in periodically-forced physical systems can create a discrete time crystal (DTC) constituting a state of matter possessing properties like temporal rigid long-range order and coherence, which are inherently desirable for quantum computing and information processing. Despite their appeal, experimental demonstrations of DTCs are scarce and significant aspects of their behavior remain unexplored. Here, we report the experimental observation and theoretical investigation of DTCs in a Kerr-nonlinear optical microcavity. Empowered by the self-injection locking of two independent lasers with arbitrarily large frequency separation simultaneously to two same-family cavity modes and a dissipative Kerr soliton, this versatile platform enables realizing long-awaited phenomena such as defect-carrying DTCs and phase transitions. Combined with monolithic microfabrication, this room-temperature system paves the way for chip-scale time crystals supporting real-world applications outside sophisticated laboratories.
Local and global crosstalk among heterochromatin marks drives DNA methylome patterning in Arabidopsis
Authors: To Taiko Kim , Yamasaki Chikae , Oda Shoko , Tominaga Sayaka , Kobayashi Akie , Tarutani Yoshiaki , Kakutani Tetsuji 
Published: February 2022

AbstractTransposable elements (TEs) are robustly silenced by multiple epigenetic marks, but dynamics of crosstalk among these marks remains enigmatic. In Arabidopsis, TEs are silenced by cytosine methylation in both CpG and non-CpG contexts (mCG and mCH) and histone H3 lysine 9 methylation (H3K9me). While mCH and H3K9me are mutually dependent for their maintenance, mCG and mCH/H3K9me are independently maintained. Here, we show that establishment, rather than maintenance, of mCH depends on mCG, accounting for the synergistic colocalization of these silent marks in TEs. When mCG is lost, establishment of mCH is abolished in TEs. mCG also guides mCH in active genes, though the resulting mCH/H3K9me is removed thereafter. Unexpectedly, targeting efficiency of mCH depends on relative, rather than absolute, levels of mCG within the genome, suggesting underlying global negative controls. We propose that local positive feedback in heterochromatin dynamics, together with global negative feedback, drive robust and balanced DNA methylome patterning.
Structural basis of neuropeptide Y signaling through Y1 receptor
Authors: Park Chaehee , Kim Jinuk , Ko Seung-Bum , Choi Yeol Kyo , Jeong Hyeongseop , Woo Hyeonuk , Kang Hyunook , Bang Injin , Kim Sang Ah , Yoon Tae-Young , Seok Chaok , Im Wonpil , Choi Hee-Jung 
Published: February 2022

AbstractNeuropeptide Y (NPY) is highly abundant in the brain and involved in various physiological processes related to food intake and anxiety, as well as human diseases such as obesity and cancer. However, the molecular details of the interactions between NPY and its receptors are poorly understood. Here, we report a cryo-electron microscopy structure of the NPY-bound neuropeptide Y1 receptor (Y1R) in complex with Gi1 protein. The NPY C-terminal segment forming the extended conformation binds deep into the Y1R transmembrane core, where the amidated C-terminal residue Y36 of NPY is located at the base of the ligand-binding pocket. Furthermore, the helical region and two N-terminal residues of NPY interact with Y1R extracellular loops, contributing to the high affinity of NPY for Y1R. The structural analysis of NPY-bound Y1R and mutagenesis studies provide molecular insights into the activation mechanism of Y1R upon NPY binding.
Humoral and cellular responses after a third dose of SARS-CoV-2 BNT162b2 vaccine in patients with lymphoid malignancies
Authors: Re Daniel , Seitz-Polski Barbara , Brglez Vesna , Carles Michel , Graça Daisy , Benzaken Sylvia , Liguori Stéphane , Zahreddine Khaled , Delforge Margaux , Bailly-Maitre Béatrice , Verrière Benjamin , Chamorey Emmanuel , Barrière Jérôme 
Published: February 2022

AbstractPatients with hematological malignancies have impaired immune response after two doses of BNT162b2 (Pfizer/BioNTech) vaccine against SARS-CoV-2. Here, in this observational study (registration number HDH F20210324145532), we measure SARS-CoV-2 anti-Spike antibodies, neutralizing antibodies and T-cell responses after immune stimulation with a third dose (D3) of the same vaccine in patients with chronic lymphocytic leukemia (n = 13), B cell non-Hodgkin lymphoma (n = 14), and multiple myeloma (n = 16)). No unexpected novel side effects are reported. Among 25 patients with positive anti-S titers before D3, 23 (92%) patients increase their anti-S and neutralizing antibody titer after D3. All 18 (42%) initially seronegative patients remain negative. D3 increases the median IFN-γ secretion in the whole cohort and induces IFN-γ secretion in a fraction of seronegative patients. Our data thus support the use of a third vaccine dose amongst patients with lymphoid malignancies, even though some of them will still have vaccine failure.
Antibody responses and correlates of protection in the general population after two doses of the ChAdOx1 or BNT162b2 vaccines
Authors: Wei Jia , Pouwels Koen B. , Stoesser Nicole , Matthews Philippa C. , Diamond Ian , Studley Ruth , Rourke Emma , Cook Duncan , Bell John I. , Newton John N. , Farrar Jeremy , Howarth Alison , Marsden Brian D. , Hoosdally Sarah , Jones E. Yvonne , Stuart David I. , Crook Derrick W. , Peto Tim E. A. , Walker A. Sarah , Eyre David W. ,   the COVID-19 Infection Survey team, Thomas Tina , Ayoubkhani Daniel , Black Russell , Felton Antonio , Crees Megan , Jones Joel , Lloyd Lina , Sutherland Esther , Pritchard Emma , Vihta Karina-Doris , Doherty George , Kavanagh James , Chau Kevin K. , Hatch Stephanie B. , Ebner Daniel , Ferreira Lucas Martins , Christott Thomas , Dejnirattisai Wanwisa , Mongkolsapaya Juthathip , Cameron Sarah , Tamblin-Hopper Phoebe , Wolna Magda , Brown Rachael , Cornall Richard , Screaton Gavin , Lythgoe Katrina , Bonsall David , Golubchik Tanya , Fryer Helen , Cox Stuart , Paddon Kevin , James Tim , House Thomas , Robotham Julie , Birrell Paul , Jordan Helena , Sheppard Tim , Athey Graham , Moody Dan , Curry Leigh , Brereton Pamela , Jarvis Ian , Godsmark Anna , Morris George , Mallick Bobby , Eeles Phil , Hay Jodie , VanSteenhouse Harper , Lee Jessica , White Sean , Evans Tim , Bloemberg Lisa , Allison Katie , Pandya Anouska , Davis Sophie , Conway David I. , MacLeod Margaret , Cunningham Chris 
Published: February 2022

AbstractAntibody responses are an important part of immunity after Coronavirus Disease 2019 (COVID-19) vaccination. However, antibody trajectories and the associated duration of protection after a second vaccine dose remain unclear. In this study, we investigated anti-spike IgG antibody responses and correlates of protection after second doses of ChAdOx1 or BNT162b2 vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the United Kingdom general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by the second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, whereas declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2–3 months after two ChAdOx1 doses, for 5–8 months after two BNT162b2 doses in those without prior infection and for 1–2 years for those unvaccinated after natural infection. A third booster dose might be needed, prioritized to ChAdOx1 recipients and those more clinically vulnerable.
A FAIR and AI-ready Higgs boson decay dataset
Authors: Chen Yifan , Huerta E. A. , Duarte Javier , Harris Philip , Katz Daniel S. , Neubauer Mark S. , Diaz Daniel , Mokhtar Farouk , Kansal Raghav , Park Sang Eon , Kindratenko Volodymyr V. , Zhao Zhizhen , Rusack Roger 
Published: February 2022

AbstractTo enable the reusability of massive scientific datasets by humans and machines, researchers aim to adhere to the principles of findability, accessibility, interoperability, and reusability (FAIR) for data and artificial intelligence (AI) models. This article provides a domain-agnostic, step-by-step assessment guide to evaluate whether or not a given dataset meets these principles. We demonstrate how to use this guide to evaluate the FAIRness of an open simulated dataset produced by the CMS Collaboration at the CERN Large Hadron Collider. This dataset consists of Higgs boson decays and quark and gluon background, and is available through the CERN Open Data Portal. We use additional available tools to assess the FAIRness of this dataset, and incorporate feedback from members of the FAIR community to validate our results. This article is accompanied by a Jupyter notebook to visualize and explore this dataset. This study marks the first in a planned series of articles that will guide scientists in the creation of FAIR AI models and datasets in high energy particle physics.
Whole genome sequences of 234 indigenous African chickens from Ethiopia
Authors: Gheyas Almas , Vallejo-Trujillo Adriana , Kebede Adebabay , Dessie Tadelle , Hanotte Olivier , Smith Jacqueline 
Published: February 2022

AbstractIndigenous chickens predominate poultry production in Africa. Although preferred for backyard farming because of their adaptability to harsh tropical environments, these populations suffer from relatively low productivity compared to commercial lines. Genome analyses can unravel the genetic potential of improvement of these birds for both production and resilience traits for the benefit of African poultry farming systems. Here we report whole-genome sequences of 234 indigenous chickens from 24 Ethiopian populations distributed under diverse agro-climatic conditions. The data represents over eight terabytes of paired-end sequences from the Ilumina HiSeqX platform with an average coverage of about 57X. Almost 99% of the sequence reads could be mapped against the chicken reference genome (GRCg6a), confirming the high quality of the data. Variant calling detected around 15 million SNPs, of which about 86% are known variants (i.e., present in public databases), providing further confidence on the data quality. The dataset provides an excellent resource for investigating genetic diversity and local environmental adaptations with important implications for breed improvement and conservation purposes.
Thinking out loud, an open-access EEG-based BCI dataset for inner speech recognition
Authors: Nieto Nicolás , Peterson Victoria , Rufiner Hugo Leonardo , Kamienkowski Juan Esteban , Spies Ruben 
Published: February 2022

AbstractSurface electroencephalography is a standard and noninvasive way to measure electrical brain activity. Recent advances in artificial intelligence led to significant improvements in the automatic detection of brain patterns, allowing increasingly faster, more reliable and accessible Brain-Computer Interfaces. Different paradigms have been used to enable the human-machine interaction and the last few years have broad a mark increase in the interest for interpreting and characterizing the “inner voice” phenomenon. This paradigm, called inner speech, raises the possibility of executing an order just by thinking about it, allowing a “natural” way of controlling external devices. Unfortunately, the lack of publicly available electroencephalography datasets, restricts the development of new techniques for inner speech recognition. A ten-participant dataset acquired under this and two others related paradigms, recorded with an acquisition system of 136 channels, is presented. The main purpose of this work is to provide the scientific community with an open-access multiclass electroencephalography database of inner speech commands that could be used for better understanding of the related brain mechanisms.
A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary
Authors: Xu Bu , Li Fuyan , Cai Lanlan , Zhang Rui , Fan Lu , Zhang Chuanlun 
Published: February 2022

AbstractEstuaries are one of the most important coastal ecosystems. While microbiomes and viromes have been separately investigated in some estuaries, few studies holistically deciphered the genomes and connections of viruses and their microbial hosts along an estuarine salinity gradient. Here we applied deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary, one of China’s largest estuaries with strong anthropogenic impacts. Overall, 1,205 non-redundant prokaryotic genomes with ≥50% completeness and ≤10% contamination, and 78,502 non-redundant viral-like genomes were generated from samples of three size fractions and five salinity levels. Phylogenomic analysis and taxonomy classification show that majority of these estuarine prokaryotic and viral genomes are novel at species level according to public databases. Potential connections between the microbial and viral populations were further investigated by host-virus matching. These combined microbial and viral genomes provide an important complement of global marine genome datasets and should greatly facilitate our understanding of microbe-virus interactions, evolution and their implications in estuarine ecosystems.
The effects of the COVID-19 pandemic on neuropsychiatric symptoms in dementia and carer mental health: an international multicentre study
Authors: Wei Grace , Diehl-Schmid Janine , Matias-Guiu Jordi A. , Pijnenburg Yolande , Landin-Romero Ramon , Bogaardt Hans , Piguet Olivier , Kumfor Fiona 
Published: February 2022

AbstractAs a global health emergency, the rapid spread of the novel coronavirus disease (COVID-19) led to the implementation of widespread restrictions (e.g., quarantine, physical/social distancing measures). However, while these restrictions reduce the viral spread of COVID-19, they may exacerbate behavioural and cognitive symptoms in dementia patients and increase pressure on caregiving. Here, we aimed to assess the impact of COVID-19 and related restrictions on both carers and people living with dementia across the world. We conducted an international survey (Australia, Germany, Spain, and the Netherlands) to assess the impact of COVID-19 on carers and people living with dementia. People with dementia experienced worsened neuropsychiatric symptoms since the outbreak of COVID-19, most commonly, depression, apathy, delusions, anxiety, irritability, and agitation. Regression analyses revealed that limited understanding of the COVID-19 situation and not living with the carer was associated with worsened neuropsychiatric symptoms. Carers also reported a decline in their own mental health, increased stress and reduced social networks as a result of COVID-19 and related restrictions. Regression analyses revealed uncertainty about the future and loneliness were associated with worsened carer mental health. Findings from this study will inform strategies for the development of support services and compassionate protocols that meet the evolving needs of those living with dementia and their carers.
Turbidity and fecal indicator bacteria in recreational marine waters increase following the 2018 Woolsey Fire
Authors: Cira Marisol , Bafna Anisha , Lee Christine M. , Kong Yuwei , Holt Benjamin , Ginger Luke , Cawse-Nicholson Kerry , Rieves Lucy , Jay Jennifer A. 
Published: February 2022

AbstractWildfires increase runoff and sediment yields that impact downstream ecosystems. While the effects of wildfire on stream water quality are well documented, oceanic responses to wildfire remain poorly understood. Therefore, this study investigated oceanic responses to the 2018 Woolsey Fire using satellite remote sensing and in situ data analyses. We examined 2016–2020 turbidity plume (n = 192) and 2008–2020 fecal indicator bacteria (FIB, n = 15,015) measurements at variable proximity to the Woolsey Fire. Shifts in coastal water quality were more pronounced in the “inside” region, which drained the burn area. The inside region experienced 2018–2019 plume surface area monthly means that were 10 and 9 times greater than 2016–2017 and 2017–2018 monthly means, respectively. Further, linear regressions showed that 2018–2019 three-day precipitation totals produced plumes of greater surface area. We also noted statistically significant increases in the inside region in 2018–2019 total coliform and Enterococcus monthly means that were 9 and 53 times greater than 2008–2018 monthly means, respectively. These results indicate that sediment and microbial inputs to coastal ecosystems can increase substantially post-wildfire at levels relevant to public and environmental health, and underscore the benefit of considering remote sensing and in situ measurements for water quality monitoring.
The low abundance of CpG in the SARS-CoV-2 genome is not an evolutionarily signature of ZAP
Authors: Afrasiabi Ali , Alinejad-Rokny Hamid , Khosh Azad , Rahnama Mostafa , Lovell Nigel , Xu Zhenming , Ebrahimi Diako 
Published: February 2022

AbstractThe zinc finger antiviral protein (ZAP) is known to restrict viral replication by binding to the CpG rich regions of viral RNA, and subsequently inducing viral RNA degradation. This enzyme has recently been shown to be capable of restricting SARS-CoV-2. These data have led to the hypothesis that the low abundance of CpG in the SARS-CoV-2 genome is due to an evolutionary pressure exerted by the host ZAP. To investigate this hypothesis, we performed a detailed analysis of many coronavirus sequences and ZAP RNA binding preference data. Our analyses showed neither evidence for an evolutionary pressure acting specifically on CpG dinucleotides, nor a link between the activity of ZAP and the low CpG abundance of the SARS-CoV-2 genome.
Bioinformatic and experimental characterization of SEN1998: a conserved gene carried by the Enterobacteriaceae-associated ROD21-like family of genomic islands
Authors: Piña-Iturbe Alejandro , Hoppe-Elsholz Guillermo , Fernández Paulina A. , Santiviago Carlos A. , González Pablo A. , Bueno Susan M. 
Published: February 2022

AbstractGenomic islands (GIs) are horizontally transferred elements that shape bacterial genomes and contributes to the adaptation to different environments. Some GIs encode an integrase and a recombination directionality factor (RDF), which are the molecular GI-encoded machinery that promotes the island excision from the chromosome, the first step for the spread of GIs by horizontal transfer. Although less studied, this process can also play a role in the virulence of bacterial pathogens. While the excision of GIs is thought to be similar to that observed in bacteriophages, this mechanism has been only studied in a few families of islands. Here, we aimed to gain a better understanding of the factors involved in the excision of ROD21 a pathogenicity island of the food-borne pathogen Salmonella enterica serovar Enteritidis and the most studied member of the recently described Enterobacteriaceae-associated ROD21-like family of GIs. Using bioinformatic and experimental approaches, we characterized the conserved gene SEN1998, showing that it encodes a protein with the features of an RDF that binds to the regulatory regions involved in the excision of ROD21. While deletion or overexpression of SEN1998 did not alter the expression of the integrase-encoding gene SEN1970, a slight but significant trend was observed in the excision of the island. Surprisingly, we found that the expression of both genes, SEN1998 and SEN1970, were negatively correlated to the excision of ROD21 which showed a growth phase-dependent pattern. Our findings contribute to the growing body of knowledge regarding the excision of GIs, providing insights about ROD21 and the recently described EARL family of genomic islands.
Ferric citrate hydrate is associated with a reduced cost of drugs and a smaller change in red blood cell distribution width
Authors: Ito Kyoko , Yokoyama Keitaro , Nakayama Masaaki , Fukagawa Masafumi , Hirakata Hideki 
Published: February 2022

AbstractThe ASTRIO study was a randomised, multicentre, 24-week study that compared the effects of ferric citrate hydrate (FC) and non-iron-based phosphate binders (control) on anaemia management in haemodialysis (HD) patients receiving erythropoiesis-stimulating agents (ESAs). In that study, FC reduced the doses of ESAs and intravenous iron without affecting haemoglobin (Hb); however, the cost-effectiveness of FC was unclear. We retrospectively implemented a cost-effectiveness analysis comparing the incremental cost-effectiveness ratios (ICERs) in FC (n = 42) and control (n = 40) groups in patients with serum phosphate and Hb controlled within the ranges of 3.5–6.0 mg/dL and 10–12 g/dL, respectively. Costs included drug costs of phosphate binders, ESAs, and intravenous iron. Elevated red cell distribution width (RDW) has been reported to be associated with mortality in HD patients and was therefore used as an effectiveness index. The mean (95% confidence interval) differences in drug costs and RDW between the FC and control groups were US$ − 421.36 (− 778.94 to − 63.78, p = 0.02) and − 0.83% (− 1.61 to – 0.05, p = 0.04), respectively. ICER indicated a decrease of US$ 507.66 per 1% decrease in RDW. FC was more cost-effective than non-iron-based phosphate binders. Iron absorbed via FC could promote erythropoiesis and contribute to renal anaemia treatment.