bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drastic shift in flowering phenology of F1 hybrids causing rapid reproductive isolation in Imperata cylindrica in Japan
Authors: Nomura Yasuyuki , Shimono Yoshiko , Mizuno Nobuyuki , Miyoshi Ikuya , Iwakami Satoshi , Sato Kazuhiro , Tominaga Tohru 
Published: April 2022

Abstract

Hybridization is a major source of phenotypic variation and a driving force for evolution. Although novel hybrid traits can often disrupt adaptive relationships between the parental phenotypes and their environments, how new hybrid traits disrupt local adaptation remains unclear. Here, we report how a new phenotype of hybrids between two Imperata cylindrica ecotypes contributes to rapid reproductive isolation from their parents and affects hybrid fitness.

We analysed 350 accessions of I. cylindrica collected from the 1980s to the 2010s throughout Japan to explore the genetic population structure of the hybrids. We surveyed the flowering periods, seed set, and germination of two ecotypes and their hybrids in both natural habitats and common gardens.

Genetic analyses of population structure revealed that the hybrid populations consisted of only F1 individuals, without advanced generation hybrids. The flowering phenology of the F1 plants was delayed until autumn, 5–6 months later than the parental ecotypes. The drastic shift in flowering phenology prevents F1s from backcrossing. In addition, it changes their seed dispersal time to winter. Germination is inhibited by low temperatures, and the seeds likely decay before the next spring, resulting in the absence of an F2 generation. We identified the environmental mismatch of the F1 population as a specific mechanism for the maintenance of an only F1 population.

Synthesis. We have demonstrated that this flowering phenology mismatch promotes reproductive isolation between the parents and F1s and affects various temporal components of the hybrids, resulting in a unique hybrid population consisting only of F1s. This system sheds light on the importance of hybrid traits in driving rapid reproductive isolation.
Intermediate dispersal hypothesis of species diversity: New insights
Authors: Yamaguchi Ryo 
Published: April 2022

AbstractThe origin and patterns of species diversity are fundamental themes in ecology and evolutionary biology. Insular systems play an important role in biogeography, and the species richness within an insular system has classically been considered as determined by the balance between the rate of speciation plus net migration and the rate of species extinction. A recent wave of studies integrating comprehensive phenotypic, phylogenetic, and environmental data is accumulating additional macroevolutionary insights at unprecedented scales. In this review, I summarize and discuss the hypothesis that intermediate dispersal ability leads to clades with high species diversity by recurrent speciation events (referred to as the intermediate dispersal hypothesis, IDH). Although some recent empirical and theoretical studies have supported the IDH, further integration of other ecological and evolutionary concepts spanning different timescales is needed to resolve long‐standing debates about the non‐linear relationship between diversification and organismal dispersal ability. This paper presents a framework for future studies that intend to test the IDH; I organize the factors that should be taken into account, including the indices for quantifying dispersal ability and species diversification, and methods of taxon sampling. The IDH requires more attention and could be used to unveil the diversity of extant species and how dispersal ability affects rates of speciation and extinction.
Early experience of the quality improvement award program in federally funded health centers
Authors: Jin Janel L. , Bolton Joshua , Nocon Robert S. , Huang Elbert S. , Hoang Hank , Sripipatana Alek , Chin Marshall H. 
Published: April 2022

AbstractObjectivesTo describe the Health Resources and Services Administration's Quality Improvement Award (QIA) program, award patterns, and early lessons learned.Study Setting1413 health centers were eligible for QIA from 2014 to 2018.Study DesignWe assessed cumulative QIA funding earned and modified funding excluding payments for per‐patient bonuses, electronic health record (EHR) use, patient‐centered medical home (PCMH) accreditation, and health information technology. We compared health centers on rural/urban location, PCMH accreditation, EHR reporting, and size.Data CollectionOrganizational and quality measures are reported in the Uniform Data System, QIA program data.Principal FindingsAverage cumulative funding was higher for health centers that were not rural (USD 380,387 [± USD 233,467] vs. USD 303,526 [± USD 164,272]), had PCMH accreditation (USD 401,675 [± USD 218,246] vs. USD 250,784 [± USD 144,404]), used their EHR for quality reporting (USD 374,214 (± USD 222,866) vs. USD 331,150 (± USD 198,689)), and were large (USD 435,473 (± USD 238,193) vs. USD 270,681 (± USD 114,484) an USD 231,917 (± USD 97,847) for small and medium centers, respectively). There were similar patterns, with smaller differences, for average modified payments.ConclusionsQIA is an important feasible initiative to introduce value‐based payment principles to health centers. Early lessons for program design include announcing award criteria in advance and focusing on a smaller number of priority targets.
snpfiltr: An R package for interactive and reproducible SNP filtering
Authors: DeRaad Devon A. 
Published: April 2022

AbstractHere, I describe the R package snpfiltr and demonstrate its functionality as the backbone of a customizable, reproducible single nucleotide polymorphism (SNP) filtering pipeline implemented exclusively via the widely adopted R programming language. SNPfiltR extends existing SNP filtering functionalities by automating the visualization of key parameters such as sequencing depth, quality, and missing data proportion, allowing users to visually optimize and implement filtering thresholds within a single, cohesive work session. All SNPfiltR functions require vcfr objects as input, which can be easily generated by reading a SNP data set stored in standard variant call format (vcf) into an R working environment using the function read.vcfR() from the R package vcfr. Performance and accuracy benchmarking reveal that for moderately sized SNP data sets (up to 50 M genotypes, plus associated quality information), SNPfiltR performs filtering with comparable accuracy and efficiency to current state of the art command‐line‐based programs. These results indicate that for most reduced‐representation genomic data sets, SNPfiltR is an ideal choice for investigating, visualizing, and filtering SNPs as part of a user friendly bioinformatic pipeline. The snpfiltr package can be downloaded from CRAN with the command install.packages(“snpfiltr”), and the current development version is available from GitHub at: (github.com/DevonDeRaad/SNPfiltR). Thorough documentation for SNPfiltR, including multiple comprehensive vignettes detailing realistic use‐cases, is available at the website: devonderaad.github.io/SNPfiltR/.
Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA
Authors: Suchan Tomasz , Chauvey Lorelei , Poullet Marine , Tonasso‐Calvière Laure , Schiavinato Stéphanie , Clavel Pierre , Clavel Benoit , Lepetz Sébastien , Seguin‐Orlando Andaine , Orlando Ludovic 
Published: April 2022

AbstractAncient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post‐mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER‐treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st–17th century CE), including horses, donkeys and their first‐generation mule hybrids. We found that USER‐treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on‐target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey‐specific and horse‐specific alleles in mule capture sequence data, due to the combined effects of USER‐treatment, probe sets and reference bias. Our work demonstrates that while USER‐treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.
China engages the Global South: From Bandung to the Belt and Road Initiative
Authors: Liu Hong 
Published: April 2022

AbstractThis article addresses China’s engagement with the Global South regarding the transnational transfer of knowledge and policy. It argues that China’s active participation in the Bandung Conference constituted historical capital in legitimating its (leadership) role in the Global South and as an alternative modernity. The past decade has witnessed the growing importance of the Global South for China. Apart from a geopolitical motive, China’s expanding economic ties with the developing world serve as an overarching framework facilitating transnational knowledge transfer, with the centrality of development reinforced by an institutionalization drive. The essay concludes that China’s engagement with the Global South in the context of the Belt and Road Initiative has been shaped by the complex logics of domestic political economy and changing global geopolitics, not all of which are within China’s control. A stakeholder‐centric approach, therefore, will be beneficial to all countries concerned.
Let's teach Kibot: Discovering discussion patterns between student groups and two conversational agent designs
Authors: Nguyen Ha 
Published: April 2022

AbstractConversational agents can deepen reasoning and encourage students to build on others' knowledge in collaborative learning. Embedding agents in group work, however, presents challenges where groups may ignore the agents, and this calls for designs where students perceive agents as learning partners. This study examines group interactions with two text‐based agents (ie, chatbots) that posed as an expert and a less knowledgeable peer in a high school marine biology lesson. Student messages (N = 1764) from 18 groups (52 students ages 14–15) received codes for reasoning, building on prior ideas, and responsiveness to the agents. Results indicate no differences between agents in how often each discussion move occurred. Interestingly, sequential pattern mining suggests that the less‐knowledgeable‐peer agent prompted groups to show questioning and building on others' ideas, similar to how students may act as peer tutors to the agent. Meanwhile, sequences with the expert agent resembled student‐teacher exchange, where groups responded to the agent's nudges and then provided reasoning. Findings illustrate the affordances of embedding humanized features in technology designs to promote discussion.
Practitioner notesWhat is already known about this topic

Conversational agents can facilitate group discussions, but can get abused or ignored by student groups.
To engage students, agent designs can simulate the characteristics of familiar classroom figures, such as peers or teachers.
There are limited explorations of how student groups adapt their interactions to different agent designs in collaborative settings.
What the paper adds

Illustrations of the utilities of diversifying agent designs in collaborative learning.
Insights into the unique interaction patterns that student groups displayed to different designs, such as questioning and building on others' ideas with a less‐knowledgeable‐peer agent.
Implications for practice and/or policy

Embedding signs of humanness in classroom facilitation and technology design can foster responsiveness among users.
Pedagogy can consider adaptive designs to promote interaction sequences that contribute to learning (eg, questioning, expanding on prior ideas) at opportune moments.
Late recurrence of lymphoid malignancies after initial treatment for Hodgkin lymphoma – A study from the Danish Lymphoma Registry
Authors: Andersen Maja Dam , Hamilton‐Dutoit Stephen , Modvig Lena , Vase Maja , Christiansen Ilse , Christensen Jacob Haaber , Dahl‐Sørensen Rasmus Bo , Stoltenberg Danny , Kamper Peter , d'Amore Francesco 
Published: April 2022

SummaryWe analysed a large cohort of Hodgkin lymphoma (HL) patients in order to characterize: (1) the pattern of late recurrence of lymphoid malignancies (LR) after initial treatment for HL over a 35‐year period; (2) the clinicopathological parameters influencing the risk of LR; and (3) the outcome of patients experiencing LR. We reviewed data of 3350 HL patients diagnosed in Denmark between 1982 and 2018 and registered in the Danish National Lymphoma Registry (LYFO). LR was defined as a recurrence of lymphoid malignancy at least five years after initial diagnosis. LR occurred in 58 patients, with a cumulative incidence at 10, 15 and 20 years of 2.7%, 4.0% and 5.4% respectively. LR was more frequently observed in patients with nodular lymphocyte‐predominant HL (NLPHL) [hazard ratio (HR) 4.5; 95% confidence interval (CI): 2.4–8.4, p < 0.001]. In classical HL (cHL) patients, older age and lymphocytopenia were risk factors for LR with HRs of 1.04 per additional year (95% CI: 1.02–1.06) and 5.6 (95% CI: 2.7–11.5) respectively. Mixed cellularity histological subtype was a risk factor for LR, but only in females, with a HR of 5.4 (95% CI: 1.4–20.4, p = 0.014). In contrast to what was observed in NLPHL, LR in cHL was associated with an almost threefold increased risk of death compared with patients in continuous complete remission. Approximately one fifth (22.4%) of patients with LR experienced a second relapse.
Narrow‐Band Screen‐Space Fluid Rendering
Authors: Oliveira Felipe , Paiva Afonso 
Published: April 2022

AbstractThis paper presents a novel and practical screen‐space liquid rendering for particle‐based fluids for real‐time applications. Our rendering pipeline performs particle filtering only in a narrow‐band around the boundary particles to provide a smooth liquid surface with volumetric rendering effects. We also introduce a novel boundary detection method allowing the user to select particle layers from the liquid interface. The proposed approach is simple, fast, memory‐efficient, easy to code and it can be adapted straightforwardly in the standard screen‐space rendering methods, even in GPU architectures. We show through a set of experiments how the prior screen‐space techniques can be benefited and improved by our approach.
Varieties of Ignorance: Mystery and the Unknown in Science and Religion
Authors: Davoodi Telli , Lombrozo Tania 
Published: April 2022

AbstractHow and why does the moon cause the tides? How and why does God answer prayers? For many, the answer to the former question is unknown; the answer to the latter question is a mystery. Across three studies testing a largely Christian sample within the United States (N= 2524), we investigate attitudes toward ignorance and inquiry as a window onto scientific versus religious belief. In Experiment 1, we find that science and religion are associated with different forms of ignorance: scientific ignorance is typically expressed as a personal unknown (“it's unknown to me”), whereas religious ignorance is expressed as a universal mystery (“it's a mystery”), with scientific unknowns additionally regarded as more viable and valuable targets for inquiry. In Experiment 2, we show that these forms of ignorance are differentially associated with epistemic goals and norms: expressing ignorance in the form of “unknown” (vs. “mystery”) more strongly signals epistemic values and achievements. Experiments 2 and 3 additionally show that ignorance is perceived to be a greater threat to science and scientific belief than to religion and religious belief. Together, these studies shed light on the psychological roles of scientific and religious belief in human cognition.
Suicide amongst transplant recipients: Trends and unique risk factors
Authors: Serpico Scott , Parsikia Afshin , Goodarzi Alireza , Manikath James Rosy , Koizumi Naoru , Ortiz Jorge 
Published: April 2022

AbstractIntroductionThere are higher rates of depression and suicidal ideation among those with chronic diseases, including end‐stage renal disease, diabetes mellitus and liver disease. Suicide is the tenth leading cause of death worldwide and is more prevalent among transplant recipients. Although transplantation has the potential to improve quality of life, many transplant recipients commit suicide each year. The extent to which sex, race, age, type of insurance coverage, time on waitlist, comorbidities, immunosuppressive regimen and graft loss contribute to suicide risk in this population remains understudied.MethodsWe queried UNOS data collected between 1990 and 2019 to determine what risk factors contribute to suicide in the transplant population. Suicide mortality rate was calculated by determining the fraction of organ recipients who died by suicide since 1990 and was expressed as deaths per 100 000. Two groups (suicide and all other cause mortality) were compared via univariate and multivariate statistical analysis. Time to graft loss was estimated using a Kaplan Meier Product Limit method. A propensity score analysis was performed to match patients who committed suicide to those who did not, allowing us to balance the relatively small sample of size of the suicide cohort with the larger all other cause mortality group to minimize the effect of confounding variables. We estimated years of organ life lost using the restricted mean. Statistical significance was defined by p < .05.ResultsThe data included 135 432 transplant deaths in total; the majority were kidney recipients—82 305 (61%). We determined suicide rates of .28%, .31%, and .44% for kidney, liver and pancreas, respectively, with an overall rate of .3%. Across all three organs the most significant risk factor was male sex. Non‐Hispanic whites were also at elevated risk (OR = 2.16, p < .003). In the liver and kidney transplant groups, the odds of committing suicide were reduced by 4% with advancing age. The odds of taking one's own life was inversely related to BMI in the kidney and pancreas groups. We observed a doubling of suicide rates from .3% in 2014 to .6% in 2018. There were no other statistically significant correlations.ConclusionSuicide is more prevalent among transplant recipients than in the general population. White males in particular are most at risk. The highest rate of suicide was in pancreas recipients. Advancing age and increasing BMI conferred some protective effect. There were no significant associations between suicide incidence and glucocorticoid use, type of insurance coverage, time on waitlist or graft loss. The phenomenon has become more prevalent in recent years.
The origins of cognitive flexibility in chimpanzees
Authors: Cantwell Averill , Buckholtz Joshua W. , Atencia Rebeca , Rosati Alexandra G. 
Published: April 2022

AbstractCognitive flexibility is a core component of executive function, a suite of cognitive capacities that enables individuals to update their behavior in dynamic environments. Human executive functions are proposed to be enhanced compared to other species, but this inference is based primarily on neuroanatomical studies. To address this, we examined the nature and origins of cognitive flexibility in chimpanzees, our closest living relatives. Across three studies, we examined different components of cognitive flexibility using reversal learning tasks where individuals first learned one contingency and then had to shift responses when contingencies flipped. In Study 1, we tested n = 82 chimpanzees ranging from juvenility to adulthood on a spatial reversal task, to characterize the development of basic shifting skills. In Study 2, we tested how n = 24 chimpanzees use spatial versus arbitrary perceptual information to shift, a proposed difference between human and nonhuman cognition. In Study 3, we tested n = 40 chimpanzees on a probabilistic reversal task. We found an extended developmental trajectory for basic shifting and shifting in response to probabilistic feedback—chimpanzees did not reach mature performance until late in ontogeny. Additionally, females were faster to shift than males were. We also found that chimpanzees were much more successful when using spatial versus perceptual cues, and highly perseverative when faced with probabilistic versus consistent outcomes. These results identify both core features of chimpanzee cognitive flexibility that are shared with humans, as well as constraints on chimpanzee cognitive flexibility that may represent evolutionary changes in human cognitive development.
Visual context processing and its development in gamers and non‐gamers
Authors: Kütük Bahtım , Aslan Aslı , Aytemur Ali 
Published: April 2022

AbstractVisual context processing was investigated in both action video game players and nonplayers using the Ebbinghaus illusion task (N = 312, 39.4% female) in a cross‐sectional study design. When presented in context, players showed markedly poorer target size discrimination accuracy compared with nonplayers in the 6‐, 7‐, 8‐, and 9‐years old age groups, but this difference was reduced in 10‐years old group and diminished in adults. When presented in isolation (no‐context), the two groups displayed similar performance in all age groups. Furthermore, nonplayers (linear) and players (bell curve) showed profoundly different age‐related differences in context processing. These findings provide evidence that players might have enhanced perceptual bias to process visual context in the transition from early childhood to early adolescence, and the differences between the two groups start at early ages and continue with distinct developmental profiles.