bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling of tuna around fish aggregating devices: the importance of ocean flow and prey
Authors: Nooteboom Peter D. , Scutt Phillips Joe , Kehl Christian , Nicol Simon , van Sebille Erik 
Published: September 2022

AbstractCatch and distribution of tuna in the ocean are typically investigated with ocean basin-scale models. Due to their large scale, such models must greatly simplify tuna behaviour occurring at a scale below ∼100 km, despite interactions at this level potentially being important to both catch and distribution of tuna. For example, the associative behaviour of tuna with man-made floating objects, that are deployed by fishers to improve their catch rates (Fish Aggregating Devices; FADs), are usually ignored or simplified. Here we present a model that can be used to investigate the influence of tuna dynamics below the ∼100 km scale on larger scales. It is an Agent-Based Model (ABM) of a hypothetical, tuna-like species, that includes their interactions with each other, free-floating FADs and prey. In this ABM, both tuna and FADs are represented by Lagrangian particles that are advected by an ocean flow field, with tuna also exhibiting active swimming based on internal states such as stomach fullness. We apply the ABM in multiple configurations of idealised flow and prey fields, alongside differing interaction strengths between agents. When tuna swimming behaviour is influenced equally by prey and FADs, we find that the model simulations compare well with observations at the ≲ 100 km scale. For instance, compared to observations, tuna particles have a similar stomach fullness when associated or non-associated to a FAD, tuna colonize at similar timescales at FADs after their deployment and tuna particles exhibit similar variations in continuous residence times. However, we find large differences in emergent dynamics such as residence and catch among different flow configurations, because the flow determines the time scale at which tuna encounter FADs. These findings are discussed in the context of directing future research, and an improved interpretation of tuna catch and other data for the sustainable management of these economically important species.
FGF21 protects against hepatic lipotoxicity and macrophage activation to attenuate fibrogenesis in nonalcoholic steatohepatitis
Authors: Liu Cong , Schönke Milena , Spoorenberg Borah , Lambooij Joost M. , van der Zande Hendrik J.P. , Zhou Enchen , Tushuizen Maarten E. , Andréasson Anne-Christine , Park Andrew , Oldham Stephanie , Uhrbom Martin , Ahlstedt Ingela , Ikeda Yasuhiro , Wallenius Kristina , Peng Xiao-Rong , Guigas Bruno , Boon Mariëtte R. , Wang Yanan , Rensen Patrick C.N. 
Published: September 2022

AbstractAnalogues of the hepatokine FGF21 are in clinical development for type 2 diabetes and nonalcoholic steatohepatitis (NASH) treatment. Although their glucose-lowering and insulin-sensitizing effects have been largely unraveled, the mechanisms by which they alleviate liver injury have only been scarcely addressed. Here, we aimed to unveil the mechanisms underlying the protective effects of FGF21 on NASH using APOE*3-Leiden.CETP mice, a well-established model for human-like metabolic diseases. Liver-specific FGF21 overexpression was achieved in mice, followed by administration of a high-fat high-cholesterol diet for 23 weeks. FGF21 prevented hepatic lipotoxicity, accompanied by activation of thermogenic tissues and attenuation of adipose tissue inflammation, improvement of hyperglycemia and hypertriglyceridemia, and upregulation of hepatic programs involved in fatty acid oxidation and cholesterol removal. Furthermore, FGF21 inhibited hepatic inflammation, as evidenced by reduced Kupffer cell (KC) activation, diminished monocyte infiltration and lowered accumulation of monocyte-derived macrophages. Moreover, FGF21 decreased lipid- and scar-associated macrophages, which correlated with less hepatic fibrosis as demonstrated by reduced collagen accumulation. Collectively, hepatic FGF21 overexpression limits hepatic lipotoxicity, inflammation and fibrogenesis. Mechanistically, FGF21 blocks hepatic lipid influx and accumulation through combined endocrine and autocrine signaling, respectively, which prevents KC activation and lowers the presence of lipid- and scar-associated macrophages to inhibit fibrogenesis.
RNASeq as a tool to understand dysregulation of potential biomarkers in HNSC
Authors: Mithu Ezhuthachan , Joshi Madhvi , Raval Ishan , Joshi Chaitanya , Dasgupta Anirban , Majumdar Sharmistha , Shah Siddharth A 
Published: September 2022

AbstractWith its rising fatality rates, oral cancer is one of the most concerning public health issues. To reduce disease-related mortality and morbidity, advancements in screening and detection are critical. Finding specific biomarkers is one of the most successful approaches for screening, diagnosing, and staging this dreadful disease. In this study differentially expressed genes associated with oral cancer were analyzed using RNASeq to find the potential biomarkers. Functional enrichment of upregulated genes found that 253 genes were present in the plasma membrane. Three clusters were formed using KMean Clustering from the PPI networks, and highly connected hub genes were identified from each cluster. Eventually, expression and survival analyses of hub genes were performed using The Cancer Genome Atlas (TCGA) database targeting Head and Neck Squamous Cell Carcinoma. Among those genes, expression levels of eight genes SLC2A1, ITGA6, LAMC2, COL1A2, COL1A1, TNC, THY1, and CD276 have significantly changed in Head and Neck Squamous cell carcinoma. There are reports that suggest these genes were significantly dysregulated in Oral Squamous cell carcinoma and can be explored further as potential biomarkers for margin clearance.
Genetic drift promotes and recombination hinders speciation on holey fitness landscapes
Authors: Kalirad Ata , Burch Christina L. , Azevedo Ricardo B. R. 
Published: September 2022

AbstractDobzhansky and Muller proposed a general mechanism through which microevolution, the substitution of alleles within populations, can cause the evolution of reproductive isolation between populations and, therefore, macroevolution. As allopatric populations diverge, many combinations of alleles differing between them have not been tested by natural selection and may thus be incompatible. Such genetic incompatibilities often cause low fitness in hybrids between species. Furthermore, the number of incompatibilities grows with the genetic distance between diverging populations. However, what determines the rate and pattern of accumulation of incompatibilities remains unclear. We investigate this question by simulating evolution on holey fitness landscapes on which genetic incompatibilities can be identified unambiguously. We find that genetic incompatibilities accumulate more slowly among genetically robust populations and identify two determinants of the accumulation rate: recombination rate and population size. In large populations with abundant genetic variation, recombination selects for increased genetic robustness and, consequently, incompatibilities accumulate more slowly. In small populations, genetic drift interferes with this process and promotes the accumulation of genetic incompatibilities. Our results suggest a novel mechanism by which genetic drift promotes and recombination hinders speciation.Author summaryAs geographically isolated populations evolve, genetic incompatibilities accumulate between them. Eventually, these incompatibilities may cause the populations to become different species. What determines how quickly species are formed in this way remains unclear. We investigate this question using computer simulations and find that genetic incompatibilities accumulate more slowly among populations with individuals that are robust to genetic perturbations. We identify two factors that influence the accumulation rate via their effects on genetic robustness: the size of the populations and how much recombination takes place in them. Small populations with rare recombination accumulate incompatibilities more quickly.
Affinity-matured homotypic interactions induce spectrum of PfCSP-antibody structures that influence protection from malaria infection
Authors: Martin Gregory M. , Torres Jonathan L. , Pholcharee Tossapol , Oyen David , Flores-Garcia Yevel , Gibson Grace , Moskovitz Re’em , Beutler Nathan , Jung Diana D. , Copps Jeffrey , Lee Wen-Hsin , Gonzalez-Paez Gonzalo , Emerling Daniel , MacGill Randall S. , Locke Emily , King C. Richter , Zavala Fidel , Wilson Ian A. , Ward Andrew B. 
Published: September 2022

SummaryThe generation of high-quality antibody responses to PfCSP, the primary surface antigen ofPlasmodium falciparumsporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by theIGHV3-33germline gene, which is among the most prevalent and potent antibody families induced in the anti-CSP immune response and targets the NANP repeat region. Cryo-EM reveals a remarkable spectrum of helical Fab-CSP structures stabilized by homotypic interactions between tightly packed Fabs, many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to CSP and in protection fromP. falciparummalaria infection. These data emphasize the importance of anti-homotypic affinity maturation in the frequent selection ofIGHV3-33antibodies, advance our understanding of the mechanism(s) of antibody-mediated protection, and inform next generation CSP vaccine design.
Theoretical design of a space bioprocessing system to produce recombinant proteins
Authors: Soundararajan Mathangi , Paddock Matthew B. , Dougherty Michael , Jones Harry W. , Hogan John A. , Donovan Frances M. , Galazka Jonathan M. , Settles A. Mark 
Published: September 2022

AbstractSpace-based biomanufacturing has the potential to improve the sustainability of deep space exploration. To advance biomanufacturing, bioprocessing systems need to be developed for space applications. Here, commercial technologies were assessed to design space bioprocessing systems to supply a liquid amine carbon dioxide scrubber with active carbonic anhydrase produced recombinantly. Design workflows encompassed biomass dewatering of 1 L Escherichia coli cultures through to recombinant protein purification. Equivalent system mass (ESM) analyses had limited utility for selecting specific technologies. Instead, bioprocessing system designs focused on minimizing complexity and enabling system versatility. Three designs that differed in biomass dewatering and protein purification approaches had nearly equivalent ESM of 357-522 kg eq. Values from the system complexity metric (SCM), technology readiness level (TRL), and degree of crew assistance metric identified a simpler, less costly, and easier to operate design for automated biomass dewatering, cell lysis, and protein affinity purification.
Three-dimensional chromatin re-organization during muscle stem cell aging
Authors: Yang Benjamin A. , Larouche Jacqueline A. , Sabin Kaitlyn M. , Fraczek Paula M. , Parker Stephen C. J. , Aguilar Carlos A. 
Published: September 2022

AbstractAge-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world’s population continues to increase. A critical contributor to sarcopenia is the loss in the number and function of muscle stem cells, which maintain tissue homeostasis and regenerate damage. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA
Authors: Kwun Min Jung , Ion Alexandru V. , Cheng Hsueh-Chien , D’Aeth Joshua C. , Dougan Sam , Oggioni Marco R. , Goulding David A. , Bentley Stephen D. , Croucher Nicholas J. 
Published: September 2022

AbstractThe respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 100 immunologically-distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mucoid serotype 3 has persisted despite its inclusion in PCV13. This capsule type is predominantly associated with a single globally-disseminated strain, GPSC12 (CC180), which was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage ϕOXC141. Prior to the introduction of PCV13, this clade’s composition shifted towards a ϕOXC141-negative subpopulation in a systematically-sampled UK collection. In the post-PCV era, more rapidly-recombining non-Clade I isolates, also ϕOXC141-negative, have risen in prevalence. The low in vitro transformation efficiency of a Clade I isolate could not be fully explained by the ∼100-fold reduction attributable to the serotype 3 capsule. Accordingly, prophage ϕOXC141 was found to modify csRNA3, a non-coding RNA that inhibits the induction of transformation. This alteration was identified in ∼30% of all pneumococci, and was particularly common in the unusually-clonal serotype 1 GPSC2 strain. RNA-seq and quantitative reverse transcriptase PCR data demonstrated the altered csRNA3 was more effective at inhibiting production of the competence stimulating peptide pheromone. This interference with the quorum sensing needed to induce competence lowered the rate of spontaneous transformation, reducing the risk of the prophage being deleted by homologous recombination. Hence the selfish prophage-driven alteration of a regulatory RNA limits cell-cell communication and horizontal gene transfer, complicating the interpretation of post-vaccine population dynamics.
RNA degradation heavily impacts mRNA co-expression
Authors: Blay Óscar García , Verhagen Pieter , Martin Benjamin , Hansen Maike M.K. 
Published: September 2022

SUMMARYCo-expression of genes measured with single-cell RNA sequencing is extensively utilized to understand the principles of gene regulation within and across cell types and species. It is assumed that the presence of correlation in gene expression values at the single-cell level demonstrates the existence of common regulatory mechanisms. However, the regulatory mechanisms that should lead to observed co-expression at an mRNA level often remain unexplored. Here we investigate the relationship between processes upstream and downstream of transcription (i.e., promoter architecture and coordination, DNA contact frequencies and mRNA degradation) and pairwise gene expression correlations at an mRNA level. We identify that differences in mRNA degradation (i.e., half-life) is a pivotal source of single-cell correlations in mRNA levels independently of the presence of common regulatory mechanisms. These findings reinforce the necessity of including post-transcriptional regulation mechanisms in the analysis of gene expression in mammalian cells.
Nanoparticle-mediated Targeting of the Fusion Gene RUNX1/ETO in t(8;21)-positive Acute Myeloid Leukaemia
Authors: Issa Hasan , Swart Laura , Rasouli Milad , Ashtiani Minoo , Nakjang Sirintra , Jyotsana Nidhi , Schuschel Konstantin , Heuser Michael , Blair Helen , Heidenreich Olaf 
Published: September 2022

AbstractA hallmark of acute myeloid leukaemias (AMLs) are chromosomal rearrangements that give rise to novel leukaemia-specific fusion genes. Most of these fusion genes are both initiating and driving events in AML and therefore constitute ideal therapeutic targets but are challenging to target by conventional drug development. siRNAs are frequently used for the specific suppression of fusion gene expression but require special formulations for efficient in vivo delivery. Here we describe the use of siRNA-loaded lipid nanoparticles for the specific therapeutic targeting of the leukaemic fusion gene RUNX1/ETO. Transient knockdown of RUNX1/ETO reduces its binding to its target genes and alters the binding of RUNX1 and its co-factor CBFβ. Transcriptomic changes in vivo were associated with substantially increased median survival of a t(8;21)-AML mouse model. Importantly, transient knockdown in vivo causes long-lasting inhibition of leukaemic proliferation and clonogenicity, induction of myeloid differentiation and a markedly impaired re-engraftment potential in vivo. These data strongly suggest that temporary inhibition of RUNX1/ETO results in long-term restriction of leukaemic self-renewal. Our results provide proof for the feasibility of targeting RUNX1/ETO in a pre-clinical setting and support the further development of siRNA-LNPs for the treatment of fusion gene-driven malignancies.
Activating words without language: Beta and theta oscillations reflect lexical access and control processes during verbal and non-verbal object recognition tasks
Authors: Branzi Francesca M. , Martin Clara D. , Biau Emmanuel 
Published: September 2022

AbstractThe intention to name an object modulates neural responses during object recognition tasks. However, the nature of this modulation is still unclear. We established whether a core operation in language, i.e., lexical access, can be observed even when the task does not require language (size-judgment task), and whether response selection in verbalversusnon-verbal semantic tasks relies on similar neuronal processes. We measured and compared neuronal oscillatory activities and behavioural responses to the same set of pictures of meaningful objects, while the type of task participants had to perform (picture-namingversussize-judgment) and the type of stimuli to measure lexical access (cognateversusnon-cognate) were manipulated. Despite activation of words was facilitated when the task required explicit word-retrieval (picture-naming task), lexical access occurred even without the intention to name the object (non-verbal size-judgment task). Activation of words and response selection were accompanied by beta (25-35 Hz) desynchronisation and theta (3-7 Hz) synchronisation, respectively. These effects were observed in both picture-naming and size-judgment tasks, suggesting that words became activated via similar mechanisms, irrespective of whether the task involves language explicitly. This finding has important implications to understand the link between core linguistic operations and performance in verbal and non-verbal semantic tasks.
Evolution of new variants of SARS-COV-2 during the pandemic: mutation limited or selection limited?
Authors: Bajpai Srashti , Watve Milind 
Published: September 2022

AbstractThe recent pandemic caused by SARS-Cov-2 has witnessed an evolving succession of variants of the virus. While the phenomenon of invasion by immunity evading variants is known for other viruses such as influenza, the dynamics of the ecological and evolutionary process in the succession is little known. Since during the Covid-19 pandemic, large scale epidemiological data were collected and made available in the public domain, it is possible to seek answers to a number of evolutionary questions, which will also have public health implications. We list multiple alternative hypotheses about the origin and invasion of the variants and evaluate them in the light of epidemiological data. Our analysis shows that invasion by novel variants is selection limited and not mutation limited. Further novel variants are not the necessary and sufficient causes of the repeated waves during the pandemic. Rather there is substantial overlap between the conditions leading to a wave and those favoring selection of a partial immune evading variant. This is likely to lead to an association between invasion by new variant and the rise of a new wave. But the association is not sufficiently strong and does not support a causal role of the new variant. The dynamics of interaction between epidemiological processes and selection on viral variants have many public health implications that can guide future policies for effective control of infectious epidemics.
The greater the incentives, the better the effect? Interactive moderating effects on the relationship between green motivation and green creativity
Authors: Liu Jingyan , Liu Jiaman 
Published: September 2022

Purpose
This study aims to address the gap in hospitality and tourism (H&T) research concerning green creativity (GC) and seeks to identify the ways in which the interaction between spiritual incentives (SI) and material incentives (MI) affects the relationships among green intrinsic motivation (GIM), green extrinsic motivation (GEM) and GC.

Design/methodology/approach
In accordance with the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines, this paper examines studies related to GC in the H&T industry and analyses them using content analysis and critical analysis.

Findings
By integrating self-determination theory and the componential theory of creativity, this study enhances the understanding of the interactive moderating role played by SI and MI in the relationship between green motivation and GC. When the level of SI is high and the level of MI is low, GIM has the strongest positive impact on GC. When the levels of MI and SI are both high, GEM has the strongest positive effect on GC.

Practical implications
In practical terms, “high SI-low MI” is the optimal combination for achieving high GC and promoting sustainable long-term green-oriented incentives.

Originality/value
To the best of the authors’ knowledge, this paper represents the first investigation of the interactive moderating effects of SI and MI on the relationships among GIM, GEM and GC, thus enriching the research on the factors influencing green motivation and GC. In addition, this paper proposes a better decision-making basis for organizations facing a green-oriented incentive situation, according to which “high SI-low MI” can facilitate the achievement of high GC at a low cost.