bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in ultra-processed food consumption during the first Italian lockdown following the COVID-19 pandemic and major correlates: results from two population-based cohorts
Authors: Bonaccio Marialaura , Costanzo Simona , Ruggiero Emilia , Persichillo Mariarosaria , Esposito Simona , Olivieri Marco , Di Castelnuovo Augusto , Cerletti Chiara , Donati Maria Benedetta , de Gaetano Giovanni , Iacoviello Licia ,   for the Moli-LOCK Study Investigators
Published: March 2021

AbstractObjective:To evaluate changes in ultra-processed food (UPF) intake and its major correlates during the first Italian lockdown (9 March–3 May 2020).Design:Retrospective observational study.Setting:Italy.Participants:We analysed 2992 subjects (mean age 57·9 ± 15·3 years, 40·4 % men). Individual participant data were pooled from two retrospective cohorts: (1) The Moli-LOCK cohort consists of 1501 adults, a portion of the larger Moli-sani study (n 24 325; 2005–2010) who were administered a phone-based questionnaire to assess lifestyles and psychological factors during confinement and (2) the Analysis of Long Term Risk of Covid-19 Emergency is a web-based survey of 1491 individuals distributed throughout Italy who self-responded to the same questionnaire by using Google forms.UPF was defined according to NOVA classification based on degree of food processing. An UPF score was created by assigning 1 point to increased consumption, −1 to decreased and 0 point for unchanged intakes of nineteen food items, with higher values indicating an increase in UPF during confinement.Results:Overall, 37·5 % of the population reported some increase in UPF (UPF score ≥1). Adults were more likely to decrease UPF (multivariable regression coefficient β = −1·94; 95 % CI −2·72, −1·17 for individuals aged >75 years as compared with 18–39 years) as did individuals from southern Italian regions as compared with Northern inhabitants (β = −1·32; 95 % CI −1·80, −0·84), while UPF lowering associated with increased exercise (β = −0·90; 95 % CI −1·46, −0·35) and weight loss (β = −1·05; 95 % CI −1·51, −0·59) during confinement.Conclusions:During the first Italian lockdown, about 40 % of our population switched to unfavourable eating as reflected by increased UPF intake and this may have long-term effects for health.
A comparative study of the structural and mechanical properties of avian eggshells among hosts of obligate brood parasitic cowbirds (genusMolothrus)
Authors: López Analía V , Reboreda Juan C , Fiorini Vanina D , Gerschenson Lía N , Hauber Mark E 
Published: March 2021

AbstractObligate avian brood parasites depend on hosts for parental care, which in turn suffer fitness losses as a result of parasitism. Mechanisms by which brood parasitic cowbirds (Molothrus spp.) reduce host breeding success include the puncture (M. rufoaxillaris and M. bonariensis) or removal (M. ater) of the eggs of the host. Our working hypothesis is that the host eggs’ mechanical strength and their size and shape in species with higher frequency of parasitism covaries with the cowbird’s strategy to reduce host clutch size. Our results, obtained through phylogenetic analyses based on egg 2D geometric morphometry and eggshell mechanical and ultrastructural measurements, suggest that egg-puncturer behaviour has led to an increase in the strength of the host’s eggshell, which might make them more difficult to be pierced. We also characterized larger, more rounded and asymmetrical eggs in frequent hosts of M. ater, which might be more difficult to be removed. These interspecific host egg and shell traits were also positively affected by the frequency of parasitism, indicating that species-specific patterns of parasitic costs select for respective anti-parasitic defences in hosts.
Decolonizing the British Army: a preliminary response
Authors: King Anthony 
Published: March 2021

Abstract
Following the death of George Floyd in Minneapolis on 25 May 2020, anti-racist protests occurred across America and Europe. As a result, public institutions in the UK have begun to re-examine their cultures and practices to ensure not only that they are non-discriminatory, but also that they are actively anti-racist. The Army will not be immune to this process. Indeed, senior commanders including the Chief of the Defence Staff have already embraced the ‘decolonizing’ programme. Since 2000, the Army has incorporated significant numbers of Black, Asian and minority ethnic (BAME) soldiers; just over 10 per cent of the Army is now BAME. This article examines the integration of minority soldiers over the last two decades in order to assess the prospects of ‘de-colonization’ in the Army today. Despite the apparent success of the Army's integration policy, this article identifies three obstacles which still obstruct minority integration and are likely to impede de-colonization. Firstly, the majority of the Army's BAME soldiers are not British citizens, but foreign and Commonwealth nationals. Secondly, the young age of the majority of British soldiers generates interactional dynamics in barracks and training which often accidentally excludes foreign minority soldiers. Thirdly, the military ideal of the British Army remains understandably Anglo-Saxon. This article considers the tensions inherent in the Army's multicultural project and lays out suggestions about how they might be overcome to pursue a de-colonizing agenda.
The alignment of interstellar dust grains: thermal flipping and the Davis–Greenstein mechanism
Authors: Weingartner Joseph C , Kolasi Erald , Woods Cameron 
Published: March 2021

ABSTRACT
Interstellar dust grains are non-spherical and, in some environments, partially aligned along the direction of the interstellar magnetic field. Numerous alignment theories have been proposed, all of which examine the grain rotational dynamics. In 1999, Lazarian & Draine introduced the important concept of thermal flipping, in which internal relaxation processes induce the grain body to flip while its angular momentum remains fixed. Through detailed numerical simulations, we study the role of thermal flipping on the grain dynamics during periods of relatively slow rotation, known as ‘crossovers’, for the special case of a spheroidal grain with a non-uniform mass distribution. Lazarian & Draine proposed that rapid flipping during a crossover would lead to ‘thermal trapping’, in which a systematic torque, fixed relative to the grain body, would time average to zero, delaying spin-up to larger rotational speeds. We find that the time-averaged systematic torque is not zero during the crossover and that thermal trapping is not prevalent. As an application, we examine whether the classic Davis–Greenstein alignment mechanism is viable, for grains residing in the cold neutral medium and lacking superparamagnetic inclusions. We find that Davis–Greenstein alignment is not hindered by thermal trapping, but argue that it is, nevertheless, too inefficient to yield the alignment of large grains responsible for optical and infrared starlight polarization. Davis–Greenstein alignment of small grains could potentially contribute to the observed ultraviolet polarization. The theoretical and computational tools developed here can also be applied to analyses of alignment via radiative torques and rotational disruption of grains.
Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines
Authors: Tablizo Francis A. , Kim Kenneth M. , Lapid Carlo M. , Castro Marc Jerrone R. , Yangzon Maria Sofia L. , Maralit Benedict A. , Ayes Marc Edsel C. , Cutiongco-de la Paz Eva Maria , De Guzman Alethea R. , Yap Jan Michael C. , Llames Jo-Hannah S. , Araiza Shiela Mae M. , Punayan Kris P. , Asin Irish Coleen A. , Tambaoan Candice Francheska B. , Chong Asia Louisa U. , Padilla Karol Sophia Agape R. , Cruz Rianna Patricia S. , Morado El King D. , Dizon Joshua Gregor A. , Hao Razel Nikka M. , Zamora Arianne A. , Pacial Devon Ray , Magalang Juan Antonio R. , Alejandria Marissa , Carlos Celia , Ong-Lim Anna , Salvaña Edsel Maurice , Wong John Q. , Montoya Jaime C. , Singh-Vergeire Maria Rosario , Saloma Cynthia P. 
Published: March 2021

ABSTRACTThe emergence of SARS-CoV-2 variants of concern such as the B.1.1.7, B.1.351 and the P.1 have prompted calls for governments worldwide to increase their genomic biosurveillance efforts. Globally, quarantine and outbreak management measures have been implemented to stem the introduction of these variants and to monitor any emerging variants of potential clinical significance domestically. Here, we describe the emergence of a new SARS-CoV-2 lineage, mainly from the Central Visayas region of the Philippines. This emergent variant is characterized by 13 lineage-defining mutations, including the co-occurrence of the E484K, N501Y, and P681H mutations at the spike protein region, as well as three additional radical amino acid replacements towards the C-terminal end of the said protein. A three-amino acid deletion at positions 141 to 143 (LGV141_143del) in the spike protein was likewise seen in a region preceding the 144Y deletion found in the B.1.1.7 variant. A single amino acid replacement, K2Q, at the N-terminus of ORF8 was also shared by all 33 samples sequenced. The mutation profile of this new virus variant warrants closer investigation due to its potential public health implications. The current distribution of this emergent variant in the Philippines and its transmission are being monitored and addressed by relevant public health agencies to stem its spread in nearby islands and regions in the country.
Quantitative estimates of deciduousness in woody species from a seasonally dry tropical forest are related to leaf functional traits and the timing of leaf flush
Authors: Chakrabarty Souparna , Sharma Sheetal , Ganguly Shatarupa , Jezeera Asmi , Mohanbabu Neha , Barua Deepak 
Published: March 2021

AbstractLeaf phenology based classification of woody species into discrete evergreen and deciduous categories is widely used in ecology, but these categories hide important variation in leaf phenological behaviour. Few studies have examined the continuous nature of deciduousness and our understanding of variation in quantitative estimates of leaf shedding behaviour and the causes and consequences of this is limited. In this study we monitored leaf phenology in 75 woody species from a seasonally dry tropical forest to quantify three quantitative measures of deciduousness, namely: maximum canopy loss, duration of deciduousness, and average canopy loss. Based on proposed drought tolerance and drought avoidance strategies of evergreen and deciduous species, respectively, we tested whether the quantitative measures of deciduousness were related to leaf functional traits. Additionally, to understand the functional consequences of variation in deciduousness we examined relationships with the timing of leaf flushing and senescing. We found wide and continuous variation in quantitative measures of deciduousness in these coexisting species. Variation in deciduousness was related to leaf function traits, and the timing of leaf flushing. Along a continuous axis ranging from evergreen to deciduous species, increasing deciduousness was associated with more acquisitive leaf functional traits, with lower leaf mass per area and leaf dry matter content, and greater leaf nitrogen content. These results indicate that the continuous nature of deciduousness is an important component of resource acquisition strategies in woody species from seasonally dry forests.
Organelle genome assembly uncovers the dynamic genome reorganization and cytoplasmic male sterility associated genes in tomato
Authors: Kuwabara Kosuke , Harada Issei , Matsuzawa Yuma , Ariizumi Tohru , Shirasawa Kenta 
Published: March 2021

AbstractTo identify cytoplasmic male sterility (CMS)-associated genes in tomato, we determined the genome sequences of mitochondria and chloroplasts in three CMS tomato lines derived from independent asymmetric cell fusions, their nuclear and cytoplasmic donors, and male fertile weedy cultivated tomato and wild relatives. The structures of the CMS mitochondrial genomes were highly divergent from those of the nuclear and cytoplasmic donors, and genes of the donors were mixed up in these genomes. On the other hand, the structures of CMS chloroplast genomes were moderately conserved across the donors, but CMS chloroplast genes were unexpectedly likely derived from the nuclear donors. Comparative analysis of the structures and contents of organelle genes and transcriptome analysis identified three genes that were uniquely present in the CMS lines, but not in the donor or fertile lines. RNA sequencing analysis indicated that these three genes transcriptionally expressed in anther, two of which were also expressed in pollen. They could be potential candidates for CMS-associated genes. This study suggests that organelle reorganization mechanisms after cell fusion events differ between mitochondria and chloroplasts, and provides insight into the development of new F1 hybrid breeding programs employing the CMS system in tomato.
The analysis of epigenomic evolution
Authors: Sahm Arne , Koch Philipp , Horvath Steve , Hoffmann Steve 
Published: March 2021

AbstractWhile the investigation of the epigenome becomes increasingly important, still little is known about the long-term evolution of epigenetic marks and systematic investigation strategies are still withstanding. Here, we systematically demonstrate the transfer of classic phylogenetic methods such as maximum likelihood based on substitution models, parsimony, and distance-based to interval-scaled epigenetic data (available atGithub). Using a great apes blood data set, we demonstrate that DNA methylation is evolutionarily conserved at the level of individual CpGs in promotors, enhancers and genic regions. Our analysis also reveals that this epigenomic conservation is significantly correlated with its transcription factor binding density. Binding sites for transcription factors involved in neuron differentiation and components of AP-1 evolve at a significantly higher rate at methylation than at nucleotide level. Moreover, our models suggest an accelerated epigenomic evolution at binding sites of BRCA1, CBX2, and factors of the polycomb repressor 2 complex in humans. For most genomic regions, the methylation-based reconstruction of phylogenetic trees is at par with sequence-based reconstruction. Most strikingly, phylogenetic reconstruction using methylation rates in enhancer regions was ineffective independently of the chosen model. We identify a set of phylogenetically uninformative CpG sites enriching in enhancers controlling immune-related genes.
Accounting for B cell behaviour and sampling bias yields a superior predictor of anti-PD-L1 response in bladder cancer
Authors: Dyugay I.A. , Lukyanov D.K. , Turchaninova M.A. , Zaretsky A.R. , Khalmurzaev O. , Matveev V.B. , Shugay M. , Shelyakin P.V. , Chudakov D.M. 
Published: March 2021

ABSTRACTTumor-infiltrating B cells and intratumorally-produced immunoglobulins (IG) play important roles in the tumor microenvironment and response to immunotherapy1–5. IgG antibodies produced by intratumoral B cells may drive antibody-dependent cellular cytotoxicity (ADCC) and enhance antigen presentation by dendritic cells6–8. Furthermore, B cells are efficient antigen-specific antigen presenters that can essentially modulate the behaviour of helper T cells9–11.Here we investigated the role of intratumoral IG isotype and clonality in bladder cancer. Our results show that the IgG1/IgA ratio offers a strong and independent prognostic indicator for theBasal squamousmolecular subtype and for the whole ImVigor210 cohort in anti-PD-L1 immunotherapy. Our findings also indicate that effector B cell functions, rather than clonally-produced antibodies, are involved in the antitumor response. High IgG1/IgA ratio was associated with relative abundance of cytotoxic genes and prominence of the IL-21/IL-21R axis suggesting importance of T cell/B cell interaction.We integrated the B, NK, and T cell components, employing immFocus-like normalization to account for the stochastic nature of tumor tissue sampling. Using a random forest model with nested cross-validation, we developed a tumor RNA-Seq-based predictor of anti-PD-L1 therapy response in muscle-invasive urothelial carcinoma. The resulting PRIMUS (PRedIctive MolecUlar Signature) predictor achieves superior sensitivity compared to PD-L1 expression scores or existing gene signatures, allowing for reliable identification of responders even within thedesertpatient subcohort analyzed as a hold out set.
Barcode Sequencing and a High-throughput Assay for Chronological Lifespan
Uncover Ageing-associated Genes in Fission Yeast
Authors: Romila Catalina A. , Townsend StJohn , Malecki Michal , Kamrad Stephan , Rodríguez-López María , Hillson Olivia , Cotobal Cristina , Ralser Markus , Bähler Jürg 
Published: March 2021

ABSTRACT
Ageing-related processes are largely conserved, with simple organisms
remaining the main platform to discover and dissect new ageing-associated genes.
Yeasts provide potent model systems to study cellular ageing owing their
amenability to systematic functional assays under controlled conditions. Even
with yeast cells, however, ageing assays can be laborious and
resource-intensive. Here we present improved experimental and computational
methods to study chronological lifespan in Schizosaccharomyces
pombe. We decoded the barcodes for 3206 mutants of the latest
gene-deletion library, enabling the parallel profiling of ∼700 additional
mutants compared to previous screens. We then applied a refined method of
barcode sequencing (Bar-seq), addressing technical and statistical issues raised
by persisting DNA in dead cells and sampling bottlenecks in aged cultures, to
screen for mutants showing altered lifespan during stationary phase. This screen
identified 341 long-lived mutants and 1246 short-lived mutants which point to
many previously unknown ageing-associated genes, including 51 conserved but
entirely uncharacterized genes. The ageing-associated genes showed coherent
enrichments in processes also associated with human ageing, particularly with
respect to ageing in non-proliferative brain cells. We also developed an
automated colony-forming unit assay for chronological lifespan to facilitate
medium- to high-throughput ageing studies by saving time and resources compared
to the traditional assay. Results from the Bar-seq screen showed good agreement
with this new assay, validating 33 genes not previously associated with cellular
ageing. This study provides an effective methodological platform and identifies
many new ageing-associated genes as a framework for analysing cellular ageing in
yeast and beyond.
Translational evidence for RRM2 as a prognostic biomarker and therapeutic target in Ewing sarcoma
Authors: Ohmura Shunya , Marchetto Aruna , Orth Martin F. , Li Jing , Jabar Susanne , Ranft Andreas , Vinca Endrit , Ceranski Katharina , Carreño-Gonzalez Martha J. , Romero-Pérez Laura , Wehweck Fabienne S. , Musa Julian , Bestvater Felix , Knott Maximilian M. L. , Hölting Tilman L. B. , Hartmann Wolfgang , Dirksen Uta , Kirchner Thomas , Cidre-Aranaz Florencia , Grünewald Thomas G. P. 
Published: March 2021

ABSTRACTPurposeEwing sarcoma (EwS) is a highly aggressive bone- or soft tissue-associated malignancy mostly affecting children, adolescents, and young adults. Although multimodal therapies have strongly improved patients’ overall survival over the past decades, the development of prognostic biomarkers for risk-based patient stratification and more effective therapies with less adverse effects is stagnating. Thus, new personalized medicine approaches are urgently required.Experimental designGene expression data of EwS and normal tissues were crossed with survival data to identify highly overexpressed, prognostically relevant, and actionable potential targets. RNA-interference and dose-response assays as well as tissue-microarray analyses were carried out to explore the functional role and druggability of a prominent candidate genein vitroandin vivo, and to validate its suitability as a prognostic biomarker.ResultsEmploying a multilayered screening approach, we discover ribonucleotide reductase regulatory subunit M2 (RRM2) as a promising therapeutic target and prognostic biomarker in EwS. Through analysis of two independent EwS patient cohorts, we show that RRM2 mRNA and protein overexpression is associated with an aggressive clinical phenotype and poor patients’ overall survival. In agreement,RRM2silencing as well as pharmacological inhibition by the specific inhibitor triapine (3-AP) significantly reduces EwS growthin vitroandin vivo. Furthermore, we present evidence that pharmacological RRM2 inhibition by triapine can overcome chemoresistance against doxorubicin or gemcitabine, and synergize with cell cycle checkpoint inhibitors (CHEK1 or WEE1).ConclusionsBased on the aggressive phenotype mediated by and the druggability of RRM2 our results provide a translational rationale for exploiting RRM2 as a novel therapeutic target in EwS and prompt further clinical investigations.
Differential levels of IFNα subtypes in autoimmunity and viral infection
Authors: Bondet Vincent , Rodero Mathieu P , Posseme Céline , Bost Pierre , Decalf Jérémie , Haljasmägi Liis , Bekaddour Nassima , Rice Gillian , Upasani Vinit , Herbeuval Jean-Philippe , Reynolds John A , Briggs Tracy A , Bruce Ian N , Mauri Claudia , Isenberg David , Menon Madhvi , Hunt David , Schwikowski Benno , Mariette Xavier , Pol Stanislas , Rozenberg Flore , Cantaert Tineke , Gottenberg J Eric , Kisand Kai , Duffy Darragh 
Published: March 2021

AbstractType I interferons are essential for host response to viral infections, while dysregulation of their response can result in autoinflammation or autoimmunity. Among IFNα (alpha) responses, 13 subtypes exist that signal through the same receptor, but have been reported to have different effector functions. However, the lack of available tools for discriminating these closely related subtypes, in particular at the protein level, has restricted the study of their differential roles in disease. We developed a digital ELISA with specificity and high sensitivity for the IFNα2 subtype. Application of this assay, in parallel with our previously described pan-IFNα assay, allowed us to study different IFNα protein responses following cellular stimulation and in diverse patient cohorts. We observed different ratios of IFNα protein responses between viral infection and autoimmune patients. This analysis also revealed a small percentage of autoimmune patients with high IFNα2 protein measurements but low pan-IFNα measurements. Correlation with an ISG score and functional activity showed that in this small sub group of patients, IFNα2 protein measurements did not reflect its biological activity. This unusual phenotype was partly explained by the presence of anti-IFNα auto-antibodies in a subset of autoimmune patients. This study reports ultrasensitive assays for the study of IFNα proteins in patient samples and highlights the insights that can be obtained from the use of multiple phenotypic readouts in translational and clinical studies.