bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host body size, not host population size, predicts genome-wide effective population size of parasites
Authors: Doña Jorge , Johnson Kevin P 
Published: June 2023

Abstract
The effective population size (Ne) of an organism is expected to be generally proportional to the total number of individuals in a population. In parasites, we might expect the effective population size to be proportional to host population size and host body size, because both are expected to increase the number of parasite individuals. However, among other factors, parasite populations are sometimes so extremely subdivided that high levels of inbreeding may distort these predicted relationships. Here, we used whole-genome sequence data from dove parasites (71 feather louse species of the genus Columbicola) and phylogenetic comparative methods to study the relationship between parasite effective population size and host population size and body size. We found that parasite effective population size is largely explained by host body size but not host population size. These results suggest the potential local population size (infrapopulation or deme size) is more predictive of the long-term effective population size of parasites than is the total number of potential parasite infrapopulations (i.e., host individuals).
Rapidly evolved traits enable new conservation tools: perspectives from the cane toad invasion of Australia
Authors: Shine Richard , Baeckens Simon 
Published: June 2023

AbstractNatural populations can show rapid adaptive responses to intense (human-mediated) environmental change. The potential for exploiting rapidly evolved traits for conservation management has been often discussed but rarely implemented. Capitalizing on a well-studied biological invasion, we here explore the idea that rapid phenotypic change in the invaders, their pathogens, and the native biota provide opportunities for managers to control invader abundance and buffer adverse impacts on native wildlife. Intensive studies of the invasion of tropical Australia by cane toads (Rhinella marina) have identified newly evolved vulnerabilities that we could exploit for toad control; and newly evolved resilience of native wildlife that we could exploit for impact reduction. For example, distinctive phenotypes of toads at the expanding range edge enhance dispersal rate but reduce reproductive output, intraspecific competitive ability, and immunocompetence; and the evolution of larval cannibalism creates opportunities not only for species-specific trapping of toad tadpoles, but also could be exploited (when allied to emerging CRISPR-Cas9 techniques) to intensify intraspecific conflict in invasive toads. That is, we could use the invasive species to control their own populations. This case study illustrates the potential of detailed basic research to identify novel approaches for conservation.
The application of Melissa officinalis L. essential oil nanoemulsions protects sea bass (Lateolabrax japonicus) against myofibrillar protein and lipid oxidation during refrigeration
Authors: Xie Yao , Yu Huijie , Zhao Xin , Bian Chuhan , Cheng Hao , Mei Jun , Xie Jing 
Published: June 2023

Abstract

Objectives
The nutrient rich sea bass is prone to oxidation of lipid and protein during refrigeration.

Materials and Methods
The research was to investigate the effect of different concentrations of Melissa officinalis L. essential oil (MOEO) nanoemulsions on myofibrillar protein (MP) and lipid oxidation in sea bass (Lateolabrax japonicus) during refrigeration at 4 °C.

Results
The results of thiobarbituric acid reactive substances and mitochondrial membrane potential showed that carboxymethyl chitosan/locust bean gum active coating solutions incorporating 2% MOEO nanoemulsions (C/L-2M) was the most effective in inhibiting lipid oxidation that occurred in sea bass under attack by reactive oxygen species. Low-field nuclear magnetic resonance results showed that C/L-2M maximally slowed the conversion of bound water to free water during storage. The oxidation of lipids and MP disrupted the secondary and tertiary conformations of MP and accelerated protein aggregation and degradation.

Conclusions
C/L-2M slowed the oxidation of lipids and proteins by inhibiting the oxidation of reactive oxygen species. C/L-2M is a very promising preservative emulsion for the preservation of sea bass.
Expanding on Our Knowledge of Ecdysozoan Genomes: A Contiguous Assembly of the Meiofaunal Priapulan Tubiluchus corallicola
Authors: Lord Arianna , Cunha Tauana J , de Medeiros Bruno A S , Sato Shoyo , Khost Danielle E , Sackton Timothy B , Giribet Gonzalo 
Published: June 2023

Abstract
Genomic data for priapulans are limited to a single species, restricting broad comparative analyses and thorough interrogation of questions spanning phylogenomics, ecdysozoan physiology, and development. To help fill this void, we present here a high-quality priapulan genome for the meiofaunal species Tubiluchus corallicola. Our assembly combines Nanopore and Illumina sequencing technologies and makes use of a whole-genome amplification, to generate enough DNA to sequence this small meiofaunal species. We generated a moderately contiguous assembly (2,547 scaffolds), with a high level of completeness (metazoan BUSCOs n = 954, single-copy complete = 89.6%, duplicated = 3.9%, fragmented = 3.5%, and missing = 3.0%). We then screened the genome for homologs of the Halloween genes, key genes implicated in the ecdysis (molting) pathway of arthropods, recovering a putative homolog of shadow. The presence of a shadow ortholog in two priapulan genomes suggests that the Halloween genes may not have evolved in a stepwise manner in Panarthropoda, as previously thought, but may have a deeper origin at the base of Ecdysozoa.
Genome of the Lord Howe Island Stick Insect Reveals a Highly Conserved Phasmid X Chromosome
Authors: Stuart Oliver P , Cleave Rohan , Magrath Michael J L , Mikheyev Alexander S 
Published: June 2023

Abstract
We present a chromosome-scale genome assembly for Dryococelus australis, a critically endangered Australian phasmid. The assembly, constructed with Pacific Biosciences continuous long reads and chromatin conformation capture (Omni-C) data, is 3.42 Gb in length with a scaffold N50 of 262.27 Mb and L50 of 5. Over 99% of the assembly is contained in 17 major scaffolds, which corresponds to the species’ karyotype. The assembly contains 96.3% of insect Benchmarking Unique Single Copy Ortholog genes in single copy. A custom repeat library identified 63.29% of the genome covered by repetitive elements; most were not identifiable based on similarity to sequences in existing databases. A total of 33,793 putative protein-coding genes were annotated. Despite the high contiguity and single-copy Benchmarking Unique Single Copy Ortholog content of the assembly, over 1 Gb of the flow-cytometry-estimated genome size is not represented, likely due to the large and repetitive nature of the genome. We identified the X chromosome with a coverage-based analysis and searched for homologs of genes known to be X-linked across the genus Timema. We found 59% of these genes on the putative X chromosome, indicating strong conservation of X-chromosomal content across 120 million years of phasmid evolution.
De Novo Structural Variations of Escherichia coli Detected by Nanopore Long-Read Sequencing
Authors: Zhou Xia , Pan Jiao , Wang Yaohai , Lynch Michael , Long Hongan , Zhang Yu 
Published: June 2023

Abstract
Spontaneous mutations power evolution, whereas large-scale structural variations (SVs) remain poorly studied, primarily because of the lack of long-read sequencing techniques and powerful analytical tools. Here, we explore the SVs of Escherichia coli by running 67 wild-type (WT) and 37 mismatch repair (MMR)–deficient (ΔmutS) mutation accumulation lines, each experiencing more than 4,000 cell divisions, by applying Nanopore long-read sequencing and Illumina PE150 sequencing and verifying the results by Sanger sequencing. In addition to precisely repeating previous mutation rates of base-pair substitutions and insertion and deletion (indel) mutation rates, we do find significant improvement in insertion and deletion detection using long-read sequencing. The long-read sequencing and corresponding software can particularly detect bacterial SVs in both simulated and real data sets with high accuracy. These lead to SV rates of 2.77 × 10−4 (WT) and 5.26 × 10−4 (MMR-deficient) per cell division per genome, which is comparable with previous reports. This study provides the SV rates of E. coli by applying long-read sequencing and SV detection programs, revealing a broader and more accurate picture of spontaneous mutations in bacteria.
Discovery of Paralogous GnRH and Corazonin Signaling Systems in an Invertebrate Chordate
Authors: Yañez Guerra Luis Alfonso , Zandawala Meet 
Published: June 2023

Abstract
Gonadotropin-releasing hormone (GnRH) is a key regulator of reproductive function in vertebrates. GnRH is related to the corazonin (CRZ) neuropeptide which influences metabolism and stress responses in insects. Recent evidence suggests that GnRH and CRZ are paralogous and arose by a gene duplication in a common ancestor of bilaterians. Here, we report the identification and complete characterization of the GnRH and CRZ signaling systems in the amphioxus Branchiostoma floridae. We have identified a novel GnRH peptide (YSYSYGFAP-NH2) that specifically activates two GnRH receptors and a CRZ peptide (FTYTHTW-NH2) that activates three CRZ receptors in B. floridae. The latter appear to be promiscuous, as two CRZ receptors can also be activated by GnRH in the physiological range. Hence, there is a potential for cross-talk between these closely related signaling systems. Discovery of both the GnRH and CRZ signaling systems in one of the closest living relatives of vertebrates provides a framework to discover their roles at the transition from invertebrates to vertebrates.
How flower development genes were identified using forward genetic screens in Arabidopsis thaliana
Authors: Smyth David R 
Published: June 2023

Abstract
In the later part of the 1980s, the time was ripe for identifying genes controlling flower development. In that pregenomic era, the easiest way to do this was to induce random mutations in seeds by chemical mutagens (or irradiation) and to screen thousands of plants for those with phenotypes specifically defective in floral morphogenesis. Here, we discuss the results of premolecular screens for flower development mutants in Arabidopsis thaliana, carried out at Caltech and Monash University, emphasizing the usefulness of saturation mutagenesis, multiple alleles to identify full loss-of-function, conclusions based on multiple mutant analyses, and from screens for enhancer and suppressor modifiers of original mutant phenotypes. One outcome was a series of mutants that led to the ABC floral organ identity model (AP1, AP2, AP3, PI, and AG). In addition, genes controlling flower meristem identity (AP1, CAL, and LFY), floral meristem size (CLV1 and CLV3), development of individual floral organ types (CRC, SPT, and PTL), and inflorescence meristem properties (TFL1, PIN1, and PID) were defined. These occurrences formed targets for cloning that eventually helped lead to an understanding of transcriptional control of the identity of floral organs and flower meristems, signaling within meristems, and the role of auxin in initiating floral organogenesis. These findings in Arabidopsis are now being applied to investigate how orthologous and paralogous genes act in other flowering plants, allowing us to wander in the fertile fields of evo-devo.
A dual, catalytic role for the fission yeast Ccr4-Not complex in gene silencing and heterochromatin spreading
Authors: Challal Drice , Menant Alexandra , Goksal Can , Leroy Estelle , Al-Sady Bassem , Rougemaille Mathieu 
Published: June 2023

Abstract
Heterochromatic gene silencing relies on combinatorial control by specific histone modifications, the occurrence of transcription, and/or RNA degradation. Once nucleated, heterochromatin propagates within defined chromosomal regions and is maintained throughout cell divisions to warrant proper genome expression and integrity. In the fission yeast Schizosaccharomyces pombe, the Ccr4-Not complex partakes in gene silencing, but its relative contribution to distinct heterochromatin domains and its role in nucleation versus spreading have remained elusive. Here, we unveil major functions for Ccr4-Not in silencing and heterochromatin spreading at the mating type locus and subtelomeres. Mutations of the catalytic subunits Caf1 or Mot2, involved in RNA deadenylation and protein ubiquitinylation, respectively, result in impaired propagation of H3K9me3 and massive accumulation of nucleation-distal heterochromatic transcripts. Both silencing and spreading defects are suppressed upon disruption of the heterochromatin antagonizing factor Epe1. Overall, our results position the Ccr4-Not complex as a critical, dual regulator of heterochromatic gene silencing and spreading.
Introduction: Material Cultures and Communities in the Holy Roman Empire
Authors: Hill Kat , Rublack Ulinka 
Published: June 2023

Abstract
This introduction outlines the key themes of this Special Issue, which responds to a need to formulate nuanced accounts of material cultures in relation to social life, religion and politics in the Holy Roman Empire. It approaches ‘the material’ through different themes in relation to sites of production, consumption and practices that created specific material regimes and communities throughout time. It also explores fundamental changes in the connection of materials, bodies and people.
Association of Neighborhood Deprivation and Depressive Symptoms With Epigenetic Age Acceleration: Evidence From the Canadian Longitudinal Study on Aging
Authors: Joshi Divya , van Lenthe Frank J , Huisman Martijn , Sund Erik R , Krokstad Steinar , Avendano Mauricio , Raina Parminder 
Published: June 2023

Abstract

Background
Neighborhood deprivation and depression have been linked to epigenetic age acceleration. The next-generation epigenetic clocks including the DNA methylation (DNAm) GrimAge, and PhenoAge have incorporated clinical biomarkers of physiological dysregulation by selecting cytosine–phosphate–guanine sites that are associated with risk factors for disease, and have shown improved accuracy in predicting morbidity and time-to-mortality compared to the first-generation clocks. The aim of this study is to examine the association between neighborhood deprivation and DNAm GrimAge and PhenoAge acceleration in adults, and assess interaction with depressive symptoms.

Methods
The Canadian Longitudinal Study on Aging recruited 51 338 participants aged 45–85 years across provinces in Canada. This cross-sectional analysis is based on a subsample of 1 445 participants at baseline (2011–2015) for whom epigenetic data were available. Epigenetic age acceleration (years) was assessed using the DNAm GrimAge and PhenoAge, and measured as residuals from regression of the biological age on chronological age.

Results
A greater neighborhood material and/or social deprivation compared to lower deprivation (b = 0.66; 95% confidence interval [CI] = 0.21, 1.12) and depressive symptoms scores (b = 0.07; 95% CI = 0.01, 0.13) were associated with higher DNAm GrimAge acceleration. The regression estimates for these associations were higher but not statistically significant when epigenetic age acceleration was estimated using DNAm PhenoAge. There was no evidence of a statistical interaction between neighborhood deprivation and depressive symptoms.

Conclusions
Depressive symptoms and neighborhood deprivation are independently associated with premature biological aging. Policies that improve neighborhood environments and address depression in older age may contribute to healthy aging among older adults living in predominantly urban areas.
Historical and Cross-Country Differences in Life Satisfaction Across Retirement in Germany and Switzerland From 2000 to 2019
Authors: Henning Georg , Baumann Isabel , Huxhold Oliver 
Published: June 2023

AbstractObjectivesRecent trends, such as changes in pension systems or cohort differences in individual resources, have altered the face of retirement transitions. Little is known about how these trends have affected older people’s life satisfaction around retirement age in the past decades. In this study, we investigated how levels and changes in life satisfaction before and after retirement changed over historical time in Germany and Switzerland.MethodsWe used longitudinal data from the German Socioeconomic Panel Study and the Swiss Household Panel (SHP) from 2000 to 2019. Level, preretirement change, and short- and long-term change in life satisfaction (0–10) after retirement were predicted by year of retirement (2001–2019) in a multigroup piecewise growth curve model.ResultsWe found improvements in levels of life satisfaction and preretirement changes in life satisfaction with historical time in both countries. Furthermore, we found that unlike in Switzerland, short-time changes in life satisfaction across retirement improved over historical time in Germany.DiscussionOur findings imply that life satisfaction trajectories around retirement age have improved over the last 20 years. These findings may be explained by general improvements in the health and psychosocial functioning of older people. More research is needed to show for whom these improvements are stronger or weaker and if they will be maintained in a changing retirement landscape.
Educational Disparities in Hypertension Prevalence and Blood Pressure Percentiles in the Health and Retirement Study
Authors: Zacher Meghan 
Published: June 2023

Abstract

Objectives
Hypertension and uncontrolled high blood pressure (BP) are more prevalent among less-educated older adults than those with more schooling. However, these dichotomous indicators may fail to fully characterize educational disparities in BP, a continuous measure that predicts morbidity and mortality across much of its range. This study therefore focuses on the distribution of BP, assessing educational disparities across BP percentiles in addition to disparities in hypertension and uncontrolled BP.

Methods
Data are from the 2014–2016 Health and Retirement Study, a nationally representative survey of older U.S. adults (n = 14,498, ages 51–89). To examine associations between education, hypertension, and uncontrolled BP, I estimate linear probability models. To assess relationships between education and BP, I fit linear and unconditional quantile regression models.

Results
Less-educated older adults are not only more likely to have hypertension and uncontrolled BP than those with more schooling, they also have higher systolic BP across nearly the entire BP distribution. Educational disparities in systolic BP increase in magnitude across BP percentiles and are largest at the highest levels of BP. This pattern is observed for those with and without diagnosed hypertension, is robust to early-life confounders, and is only partially explained by socioeconomic and health-related circumstances in adulthood.

Discussion
Among older U.S. adults, the distribution of BP is compressed at lower, healthier levels for those with more education, and skewed toward the highest, most harmful levels among those with less education. Educational inequities in hypertension awareness and treatment efficacy may underlie these patterns. Implications for fundamental cause theory are discussed.
Surface wave dispersion curve inversion using mixture density networks
Authors: Keil Sabrina , Wassermann Joachim 
Published: June 2023

SUMMARYIn many seismological, environmental and engineering applications a detailed S-wave velocity model of the shallow subsurface is required. This is generally achieved by the inversion of surface wave dispersion curves using various inversion methods. The classical inversion approaches suffer from several shortcomings, such as inaccurate solutions due to local minima or large computation times in case of a wide parameter space. A number of machine learning (ML) approaches have been suggested to tackle these problems, which however do not provide probabilistic solutions and/or constrain layer number and layer thickness to a fixed value. In this study, we develop a novel neural network (NN) approach in order to characterize the shallow velocity structure from Love and Rayleigh wave dispersion curves. The novelty of our method lies in the simultaneous estimation of layer numbers, layer depth and a complete probability distribution of the S-wave velocity structure. This is achieved by a two-step ML approach, where (1) a regular NN classifies the number of layers within the upper 100 m of the subsurface and (2) a mixture density network outputs the depth estimates together with a fully probabilistic solution of the S-wave velocity structure. We show the advantages of our ML approach compared to a conventional neighbourhood inversion and a Markov chain Monte Carlo algorithm. Our ML approach is then applied to dispersion curves extracted from recorded noise data in Munich, Germany. The resulting velocity profile is in accordance with lithologic information at the site, which highlights the potential of our approach.
Strengthening routine data reporting in private hospitals in Lagos, Nigeria
Authors: Ohiri Kelechi , Makinde Olasunmbo , Ogundeji Yewande , Mobisson Nneka , Oludipe Modupe 
Published: June 2023

Abstract
The availability of routine health information is critical for effective health planning, especially in resource-limited countries. Nigeria adopted the web-based District Health Information System (DHIS) to harmonize the collection, analysis and storage of data for informed decision-making. However, only 44% of all private hospitals in Lagos State reported to the DHIS despite constituting 90% of all health facilities in the state. To bridge this gap, this study implemented targeted interventions. This paper describes (1) the implemented interventions, (2) the effects of the interventions on data reporting on DHIS during the intervention period and (3) the evaluation of data reporting on DHIS after the intervention period in select private hospitals in Lagos State. A five-pronged intervention was implemented in 55 private hospitals (intervention hospitals), which entailed stakeholder engagement, on-the-job training, in-facility mentoring and the provision of data tools and job aids, to improve data reporting on DHIS from 2014 to 2017. A controlled before-and-after study design was employed to assess the effectiveness of the implemented interventions. A comparable cohort of 55 non-intervention private hospitals was selected, and data were extracted from both groups. Data analysis was conducted using paired and independent t-tests to assess the effect and measure the difference between both groups of hospitals, respectively. An average increase of 65.28% (P &lt; 0.01) in reporting rate and 50.31% (P &lt; 0.01) in the timeliness of reporting on DHIS was seen among intervention hospitals. Similarly, the difference between intervention and non-intervention hospitals post-intervention was significantly different for both data reporting (mean difference = −22.38, P &lt; 0.01) and timeliness (mean difference = −18.81, P &lt; 0.01), respectively. Furthermore, a sustained improvement in data reporting and timeliness of reporting on DHIS was observed among intervention hospitals 24 months after interventions. Thus, implementing targeted interventions can strengthen routine data reporting for better performance and informed decision-making.