bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome organisation and evolution of a eukaryotic nicotinate co-inducible pathway
Authors: Bokor Eszter , Flipphi Michel , Kocsubé Sándor , Ámon Judit , Vágvölgyi Csaba , Scazzocchio Claudio , Hamari Zsuzsanna 
Published: April 2021

AbstractInAspergillus nidulansa regulon including 11hxngenes (hxnS, T, R, P, Y, Z, X, W, V, MandN) is inducible by a nicotinate metabolic derivative, repressible by ammonium and under stringent control of the nitrogen-state sensitive GATA factor AreA and the specific transcription factor HxnR. This is the first report in a eukaryote of the genomic organisation of a possibly complete pathway of nicotinate utilisation. InA. nidulansthe regulon is organised in three distinct clusters, this organisation is variable in theAscomycota. In somePezizomycotinaspecies all the 11 genes map in a single cluster, in other in two clusters. This variable organisation sheds light on cluster evolution. Instances of gene duplication, followed by, or simultaneous with, integration in the cluster; partial or total cluster loss; horizontal gene transfer of several genes, including an example of whole cluster re-acquisition inAspergillusof sectionFlaviwere detected, together with the incorporation in some clusters of genes not found in theA. nidulansco-regulated regulon, which underlie both the plasticity and the reticulate character of metabolic cluster evolution. This study provides a comprehensive phylogeny of six members of the cluster across representatives of allAscomycotaclasses.
DNMT3A-dependent DNA methylation is required for spermatogonial stem cells to commit to spermatogenesis
Authors: Dura Mathilde , Teissandier Aurélie , Armand Mélanie , Barau Joan , Bonneville Lorraine , Weber Michael , Baudrin Laura G. , Lameiras Sonia , Bourc’his Deborah 
Published: April 2021

AbstractDNA methylation plays a critical role in spermatogenesis, as evidenced by the male sterility of DNA methyltransferase (DNMT) mutant mice. Here, we report a striking division of labor in the establishment of the methylation landscape of male germ cells and its functions in spermatogenesis: while DNMT3C is essential for preventing retrotransposons from interfering with meiosis, DNMT3A broadly methylates the genome—at the exception of DNMT3C-dependent retrotransposons—and controls spermatogonial stem cell (SSC) plasticity. By reconstructing developmental trajectories through single-cell RNA-seq and by profiling chromatin states, we found thatDnmt3Amutant SSCs can only self-renew and no longer differentiate due to spurious enhancer activation that enforces an irreversible stem cell gene program. We therefore provide a novel function for DNA methylation in male fertility: the epigenetic programming of SSC commitment to differentiation and to life-long spermatogenesis supply.
Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila
Authors: Das Souradip , Caballero Madison , Kolesnikova Tatyana , Zhimulev Igor , Koren Amnon , Nordman Jared 
Published: April 2021

AbstractRegulation of DNA replication and copy number are necessary to promote genome stability and maintain cell and tissue function. DNA replication is regulated temporally in a process known as replication timing (RT). Rif1 is key regulator of RT and has a critical function in copy number control in polyploid cells. In a previous study (Munden et al., 2018), we demonstrated that Rif1 functions with SUUR to inhibit replication fork progression and promote underreplication (UR) of specific genomic regions. How Rif1-dependent control of RT factors into its ability to promote UR is unknown. By applying a computational approach to measure RT in Drosophila polyploid cells, we show that SUUR and Rif1 have differential roles in controlling UR and RT. Our findings reveal that Rif1 functions both upstream and downstream of SUUR to promote UR. Our work provides new mechanistic insight into the process of UR and its links to RT.
Differential learning by native versus invasive predators to avoid distasteful cleaning mutualists
Authors: Tuttle Lillian J. , Lamb Robert W. , Stringer Allison L. 
Published: April 2021

Abstract

Cleaning symbioses on coral reefs are mutually beneficial interactions between two individuals, in which a ‘cleaner’ removes and eats parasites from the surface of a ‘client’ fish. A suite of behavioural and morphological traits of cleaners signal cooperation with co‐evolved species, thus protecting the cleaner from being eaten by otherwise predatory clients. However, it is unclear whether cooperation between cleaners and predatory clients is innate or learned, and therefore whether an introduced predator might consume, cooperate with or alter the behaviour of cleaners.

We explored the role of learning in cleaning symbioses by comparing the interactions of native cleaner fishes with both naïve and experienced, non‐native and native fish predators. In so doing, we tested the vulnerability of the predominant cleaners on Atlantic coral reefs, cleaning gobies (Elacatinus spp.), to the recent introduction of a generalist predator, the Indo‐Pacific red lionfish (Pterois volitans).

Naïve juveniles of both invasive (P. volitans) and native predators (Cephalopholis spp. groupers) initially attacked cleaning gobies and hyperventilated from a putative toxin on the gobies' skin during laboratory experiments. After one to five such encounters, invasive lionfish often approached the cleaner closely, then turned away without striking. Consistent with learned avoidance, invasive lionfish rarely interacted with cleaning gobies in the wild, either antagonistically or cooperatively, and did not affect gobies' abundance. Native predators showed little evidence of learning during early encounters; they repeatedly attacked the cleaner during laboratory experiments and hyperventilated less violently than did lionfish. However, consistent with learned cooperation, native predators rarely antagonised and were frequently cleaned by gobies in the wild.

We demonstrated that rapid, learned avoidance protects a distasteful cleaning mutualist from an invasive predator. The behavioural plasticity of this invader likely contributes to its success across its invaded range. Additionally, our results suggest that the cleaner's chemical defence most likely evolved as a way to deter predation and reinforce cooperation with naïve individuals of native species.
Fine‐scale plant defence variability increases top‐down control of an herbivore
Authors: Paul Ryan L. , Pearse Ian S. , Ode Paul J. 
Published: April 2021

Abstract

Herbivore populations are regulated by a combination of plant defences and natural enemies. While plant defence can suppress herbivore populations, these defences can also adversely affect natural enemies, thereby releasing herbivores from top‐down control.

Over their life spans, herbivores and their natural enemies may experience substantial variation in plant defence. Recent studies have demonstrated that individual herbivores feeding on diets containing variable concentrations of plant toxins suffer substantially reduced fitness compared to herbivores feeding on a constant toxin concentration, even when both groups of herbivores experience equivalent means. However, the impacts of defence variability on natural enemies and top‐down control of herbivores are unknown.

Using artificial diets, we independently manipulated the mean concentration and variation of a plant toxin experienced by individual Trichoplusia ni caterpillars and its parasitoid Copidosoma floridanum. Additionally, by combining the performance of individual caterpillars on different constant diet concentrations of toxin, we were able to estimate the effect of toxin variability between herbivores using nonlinear averaging.

Increases in the mean toxin concentration in the diet of parasitized T. ni hosts decreased the fitness of C. floridanum, while variance in individual diets did not impact parasitoid fitness, even though both mean and variance decreased the fitness of T. ni caterpillars. Increased variability in encountered plant defences suppressed individual herbivore fitness with no perceptible cost to top‐down control. At the population level, however, increased variability between individual herbivore diets decreased the success of parasitoids relative to herbivores, thus reducing the strength of top‐down control.

Our study highlights the importance of defence variability at different scales in regulating herbivore performance. Variability in plant defence has the potential to reduce herbivore populations through a combination of bottom‐up and top‐down effects, but only at small spatial scales experienced by individual herbivores.

A free Plain Language Summary can be found within the Supporting Information of this article.
Thermal evolution ameliorates the long‐term plastic effects of warming, temperature fluctuations and heat waves on predator–prey interaction strength
Authors: Wang Ying‐Jie , Sentis Arnaud , Tüzün Nedim , Stoks Robby 
Published: April 2021

Abstract

How thermal evolution may affect trophic interactions and its implications for trophic system stability remains unstudied. To advance insights in how global warming shapes trophic interactions, we need to consider besides increases in mean temperatures, also daily thermal fluctuations (DTF) and heat waves (HW), and how their effects are modulated by thermal evolution.

Using a common‐garden approach, we tested how each thermal factor affected predator metabolic rate and functional response parameters, and used these responses to predict long‐term predator–prey interaction strength between larvae of the damselfly Ischnura elegans and the water flea Daphnia magna. Using high‐ and low‐latitude predator populations with the latter being exposed to higher mean temperatures, higher DTF and more frequent HW, we assessed the potential impact of thermal evolution at the high latitude using a space‐for‐time substitution.

In line with thermal adaptation, growth rates were faster and handling times shorter in low‐latitude compared to high‐latitude larvae at 24°C while the opposite was true at 20°C. Warming weakened the long‐term interaction strength, except for the high‐latitude trophic system at DTF and HW where plastic responses therefore may not stabilize the high‐latitude system. This extends the emerging insight that temperature variation may make ectotherms more vulnerable to warming. The contributions of metabolic rate, search rate and handling time in shaping thermal effects on interaction strength differed between latitudes. A key finding was that thermal evolution may further weaken the long‐term interaction strength of the high‐latitude trophic system under increases in mean temperatures, even at DTF and potentially also at HW.

Our results underscore the importance of daily thermal fluctuations and heat waves in shaping predator–prey interactions, and may suggest an overall stabilizing contribution of predator thermal evolution ameliorating thermal plastic effects on food web stability.

A free Plain Language Summary can be found within the Supporting Information of this article.
Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles
Authors: Bunse Carina , Koch Hanna , Breider Sven , Simon Meinhard , Wietz Matthias 
Published: April 2021

SummaryPolysaccharide particles are important substrates and microhabitats for marine bacteria. However, substrate‐specific bacterial dynamics in mixtures of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed. Here, we studied the composition, functional diversity and gene expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Amplicon, metagenome and metatranscriptome sequencing revealed that communities on alginate and pectin particles significantly differed from their free‐living counterparts. Unexpectedly, microbial dynamics on alginate and pectin particles were similar, with predominance of amplicon sequence variants (ASVs) from Tenacibaculum, Colwellia, Psychrobium and Psychromonas. Corresponding metagenome‐assembled genomes (MAGs) expressed diverse alginate lyases, several colocalized in polysaccharide utilization loci. Only a single, low‐abundant MAG showed elevated transcript abundances of pectin‐degrading enzymes. One specific Glaciecola ASV dominated the free‐living fraction, possibly persisting on particle‐derived oligomers through different glycoside hydrolases. Elevated ammonium uptake and metabolism signified nitrogen as an important factor for degrading carbon‐rich particles, whereas elevated methylcitrate and glyoxylate cycles suggested nutrient limitation in surrounding waters. The bacterial preference for alginate, whereas pectin primarily served as colonization scaffold, illuminates substrate‐driven dynamics within mixed polysaccharide pools. These insights expand our understanding of bacterial niche specialization and the biological carbon pump in macroalgae‐rich habitats.
Grammatical Encoding of Discourse Structure: A Case Study of The Arabic Discourse Particle Tara
Authors: Jarrah Marwan , Harb Mustafa 
Published: April 2021

AbstractThis study shows that the discourse particle tara in Jordanian Arabic identifies whether its utterance presents new or given information. In other words, there exists a relation between the presence of this particle (i.e. its position) and the type of information packaging of its utterance. When tara appears utterance‐initially, the accompanying utterance is presented as being in sentence focus (i.e. as all‐new). By contrast, when tara appears utterance‐finally, the accompanying utterance is presented as all‐given, and the hearer in such cases is instructed to pay attention to the content of the utterance which he/she should be previously aware of, from the speaker’s perspective. Additionally, this paper shows that tara can be used as a topic marker when it appears utterance‐internally. In such cases, tara is preceded by the element(s) expressing Referential Topic(s) (RTop) which convey the shared and anaphoric information with respect to the interlocutors’ mental state and previous discourse.
Five‐year impact of Medicare Part D coverage gap reform on drug expenditures and utilization
Authors: Park Joohyun , Look Kevin A. 
Published: April 2021

AbstractObjectiveTo estimate the impact of the Medicare Part D coverage gap reform under the Affordable Care Act (ACA) on the utilization of and expenditures for prescription drugs within the first five years of the policy's implementation.Data Sources2008‐2015 Medicare Current Beneficiary Survey (MCBS).Study DesignWe used a difference‐in‐differences approach to estimate the year‐by‐year changes in prescription drug use and expenditures before (2006‐2010) and after (2011‐2015) the ACA’s Part D coverage gap reform between Part D beneficiaries not receiving the Low‐Income Subsidy (LIS) and those receiving the LIS.Data CollectionThe study sample included Part D beneficiaries (a) aged 65 years or older; (b) not disabled or having end‐stage renal disease; (c) continuously enrolled in a Part D plan (d) having at least one prescription fill in a given year. Survey‐reported and administrative Part D events data in the MCBS were used for the analyses.Principal FindingsAfter the ACA reform, annual out‐of‐pocket drug spending significantly decreased by $88 (P < .01) among non‐LIS beneficiaries compared to LIS beneficiaries, with growing decreases over time (average decreases of $41 in 2011, $49 in 2012, $105 in 2013, and $135 in 2015, P < .01 or <.05). Changes in out‐of‐pocket costs were largely driven by significant decreases among brand‐name drugs (overall decrease of $106, P < .01). Despite significantly reduced out‐of‐pocket spending, there were no significant changes in the overall number of 30‐day drug fills and total drug spending; however, changes in the use of brand‐name and generic drugs were seen after the ACA (increase of 1.9 fills for brand‐name drugs and decrease of 2.3 fills for generic drug in 2015, P < .05).ConclusionsThe ACA coverage gap reform has helped to reduce the out‐of‐pocket drug cost burden for beneficiaries, although it had no noticeable impact on drug use or total drug spending.
Gender disparity in bipolar disorder diagnosis in the United States: A retrospective analysis of the 2005–2017 MarketScan Commercial Claims database
Authors: Liu Guodong , Kong Lan , Baweja Ritika , Ba Djibril , Saunders Erika F. H. 
Published: April 2021

AbstractObjectiveTo examine gender disparities in the diagnosis of bipolar disorder (BD) within a privately insured population in the United States and investigate potential contributing factors for these gender differences.MethodsThis retrospective cohort study utilized 2005–2017 claims data from the MarketScan® Commercial Claims and Encounters database. The study cohort included subjects, aged 10–64 years, who had a minimum of 1‐year continuous insurance coverage and no record of a BD diagnosis before cohort entry. We examined the gender difference in BD diagnosis rate, overall and by subgroups. We then used Cox regression models to evaluate the gender effect on time to first BD diagnosis, and the potential moderators of gender effect.ResultsThe study cohort consisted of 97,193,443 subjects; 0.45% of subjects were diagnosed with BDs after cohort entry with males having a lower diagnosis rate than females (0.36% vs. 0.54%). The Cox regression analysis indicated that males were less likely to be diagnosed with BDs (unadjusted Hazard Ratio, HR [95% CI]: 0.69 [0.68–0.69]) and gender difference remained significant after adjusting for demographics, comorbidity and healthcare utilizations (adjusted HR [95% CI]: 0.77 [0.76–0.77]). Gender disparity was consistently strong among most age groups, but varied in other demographic subgroups.ConclusionsEven though the prevalence of BDs is approximately equal between genders in the general population, our study found a much lower diagnosis rate in men compared to women for a privately insured U.S. population. Future studies aimed at identifying and understanding the barriers to diagnosis of BDs in men are warranted.
Investigating the role of self‐control beliefs in predicting exercise behaviour: A longitudinal study
Authors: Kaushal Navin , Bérubé Béatrice , Hagger Martin S. , Bherer Louis 
Published: April 2021

BackgroundEngaging in exercise behaviour regularly requires a repeated investment of resources to reap the health benefits. An individual’s self‐control resources, when performing a behaviour can be perceived as being recharged or depleted. The investigation on how self‐control beliefs resources predict exercise behaviour is very limited in the literature. The purpose of this study was to understand how self‐control beliefs predict exercise behaviour across time in a physical activity model.MethodsParticipants (N = 161) were a sample of adults recruited across twelve gyms and recreation centres in a large city. Participants completed surveys across five months. Data were analysed using a multilevel structural equation model with participants (level 2) nested within time (level 1).ResultsBehaviour was found to be a function of intention, habit, and planning. Specifically, planning moderated the intention‐behaviour relationship, where those who scored higher on planning engaged in more exercise. Self‐control beliefs functioned as a proximal predictor of autonomous motivation and predicted habit, and intention when accounting for total effects.ConclusionsSelf‐control beliefs played a pivotal role in supporting recognized exercise determinants. Exercise‐focussed interventions that help participants strengthen their beliefs as recharging and reduce depletion beliefs could be beneficial for promoting regular exercise.
Curious Objects: How Visual Complexity Guides Attention and Engagement
Authors: Sun Zekun , Firestone Chaz 
Published: April 2021

AbstractSome things look more complex than others. For example, a crenulate and richly organized leaf may seem more complex than a plain stone. What is the nature of this experience—and why do we have it in the first place? Here, we explore how object complexity serves as an efficiently extracted visual signal that the object merits further exploration. We algorithmically generated a library of geometric shapes and determined their complexity by computing the cumulative surprisal of their internal skeletons—essentially quantifying the “amount of information” within each shape—and then used this approach to ask new questions about the perception of complexity. Experiments 1–3 asked what kind of mental process extracts visual complexity: a slow, deliberate, reflective process (as when we decide that an object is expensive or popular) or a fast, effortless, and automatic process (as when we see that an object is big or blue)? We placed simple and complex objects in visual search arrays and discovered that complex objects were easier to find among simple distractors than simple objects are among complex distractors—a classic search asymmetry indicating that complexity is prioritized in visual processing. Next, we explored the function of complexity: Why do we represent object complexity in the first place? Experiments 4–5 asked subjects to study serially presented objects in a self‐paced manner (for a later memory test); subjects dwelled longer on complex objects than simple objects—even when object shape was completely task‐irrelevant—suggesting a connection between visual complexity and exploratory engagement. Finally, Experiment 6 connected these implicit measures of complexity to explicit judgments. Collectively, these findings suggest that visual complexity is extracted efficiently and automatically, and even arouses a kind of “perceptual curiosity” about objects that encourages subsequent attentional engagement.
Counterexample Search in Diagram‐Based Geometric Reasoning
Authors: Hamami Yacin , Mumma John , Amalric Marie 
Published: April 2021

AbstractTopological relations such as inside, outside, or intersection are ubiquitous to our spatial thinking. Here, we examined how people reason deductively with topological relations between points, lines, and circles in geometric diagrams. We hypothesized in particular that a counterexample search generally underlies this type of reasoning. We first verified that educated adults without specific math training were able to produce correct diagrammatic representations contained in the premisses of an inference. Our first experiment then revealed that subjects who correctly judged an inference as invalid almost always produced a counterexample to support their answer. Noticeably, even if the counterexample always bore a certain level of similarity to the initial diagram, we observed that an object was more likely to be varied between the two drawings if it was present in the conclusion of the inference. Experiments 2 and 3 then directly probed counterexample search. While participants were asked to evaluate a conclusion on the basis of a given diagram and some premisses, we modulated the difficulty of reaching a counterexample from the diagram. Our results indicate that both decreasing the counterexample density and increasing the counterexample distance impaired reasoning performance. Taken together, our results suggest that a search procedure for counterexamples, which proceeds object‐wise, could underlie diagram‐based geometric reasoning. Transposing points, lines, and circles to our spatial environment, the present study may ultimately provide insights on how humans reason about topological relations between positions, paths, and regions.