Individual Site Level Research Articles

Patterns of pastoralism: Temporal and regional variation within the Indus Valley Civilisation

The archaeozoological study of the Indus Valley Civilisation, particularly in the last few decades, has resulted in a better understanding of human-animal interactions, providing information about species that have been commonly found at Indus Valley sites, both wild and domestic. This is also indicative of the nature of animal-based subsistence at these settlements and the interplay between humans, animals, and the environment. However, these studies have largely been conducted at the level of individual sites, and despite extensive analysis of excavated faunal materials, synthesis of faunal data across different developmental phases of this civilisation and its regions, has rarely taken place. As a result, there exists little understanding of broader animal utilisation patterns within the Indus Valley Civilisation and their relation to climate and landscape. This article produces a comparative analysis of domestic animal utilisation by combining and reanalysing faunal data from different regions of the Indus Valley Civilisation. Our analysis reveals extreme disparity in the spatial and temporal distribution of domesticated animals within this Civilisation. Of the different regions, the amount of data required for interpretation is only available from Haryana and Gujarat, and this largely pertains to the Mature Harappan period, with the Early and Late Harappan phases being grossly underrepresented. Although cattle, buffalo, goats, sheep, and pigs were the primary domesticates across regions, their distribution and economic importance varied and changed over time. This variation may indicate differentiated regional and temporal cultures and adaptations to climatic change.

Prediction of methylation status using WGS data of plasma cfDNA for multi-cancer early detection (MCED)

BackgroundCell-free DNA (cfDNA) contains a large amount of molecular information that can be used for multi-cancer early detection (MCED), including changes in epigenetic status of cfDNA, such as cfDNA fragmentation profile. The fragmentation of cfDNA is non-random and may be related to cfDNA methylation. This study provides clinical evidence for the feasibility of inferring cfDNA methylation levels based on cfDNA fragmentation patterns. We performed whole-genome bisulfite sequencing and whole-genome sequencing (WGS) on both healthy individuals and cancer patients. Using the information of whole-genome methylation levels, we investigated cytosine–phosphate–guanine (CpG) cleavage profile and validated the method of predicting the methylation level of individual CpG sites using WGS data.ResultsWe conducted CpG cleavage profile biomarker analysis on data from both healthy individuals and cancer patients. We obtained unique or shared potential biomarkers for each group and built models accordingly. The modeling results proved the feasibility to predict the methylation status of single CpG sites in cfDNA using cleavage profile model from WGS data.ConclusionBy combining cfDNA cleavage profile of CpG sites with machine learning algorithms, we have identified specific CpG cleavage profile as biomarkers to predict the methylation status of individual CpG sites. Therefore, methylation profile, a widely used epigenetic biomarker, can be obtained from a single WGS assay for MCED.

Comparative life-cycle sustainability assessment of centralized and decentralized remediation strategies at the city level

Remediation of contaminated soil at industrial sites has become a challenge and an opportunity for sustainable urban land use, considering the substantial secondary impacts resulting from remediation activities. The design of soil remediation strategies for multi-site remediation from a regional perspective is of great significance for cities with a large number of brownfields. Centralized and decentralized facilities have been studied in different environmental fields, yet limited research has focused on centralized soil remediation, specifically the treatment of contaminated soil from different sites through the construction of shared soil treatment facilities. This study proposes a framework for comparing centralized and decentralized strategies for contaminated soil remediation based on the integration of life-cycle sustainability assessment and multi-objective optimization. With Zhuzhou, an industrial city in China, serving as an example, results show that after optimization, the centralized scenario can reduce total environmental impacts by 25 %–41 %. In addition, the centralized scenario can reduce economic costs by 27 %–39 %, saving up to 176 million USD. The advantages of the centralized soil remediation strategy include: (1) increased use of soil washing, (2) reduced use of off-site disposal, and (3) reduced construction and efficient utilization of soil treatment facilities. In conclusion, the centralized strategy is relatively suitable for cities or areas with a large number of medium or small-sized contaminated sites. The built framework can quantitatively evaluate multiple sites soil remediation at both the city and individual site level, allowing for a straightforward and objective comparison with the optimal remediation design.

Human diet in Lithuania during the Late Roman and Migration periods ( ca. 200–700 AD) based on stable carbon and nitrogen isotope data

In this study, 71 human individuals were subjected to stable carbon (δ13C) and nitrogen (δ15N) isotope analysis of bone collagen samples for the purpose of determining human dietary patterns in Lithuania during the Late Roman and Migration periods. More specifically, based on the isotopic data, the aim was to determine and evaluate any potential dietary differences between individuals on the basis of their sex, age, social status and place of residence during the periods in question. The results of this study suggest that there were isotopically clearly distinguishable dietary differences between individuals from different parts/regions of Lithuania. Also, statistically significant dietary differences (on the basis of δ15N values) between males and females were observed (although, when making the same sex-based isotopic comparisons at an individual site level, the same result was observed only among those from Marvelė cemetery). However, no statistically significant isotopic differences were detected between different social or age groups. Overall, these results give us one of the first glimpses into the types of dietary habits practiced by people in various parts of Lithuania during the Roman and Migration periods, which could also serve as a good starting point for future investigations into other dietary aspects in the territories and periods in question that still remain unknown.

Restoration of linear disturbances from oil-and-gas exploration in boreal landscapes: How can network models help?

In western Canada, decades of oil-and-gas exploration have fragmented boreal landscapes with a dense network of linear forest disturbances (seismic lines). These seismic lines are implicated in the decline in wildlife populations that are adapted to function in unfragmented forest landscapes. In particular, anthropogenic disturbances have led to a decline of woodland caribou populations due to increasing predator access to core caribou habitat. Restoration of seismic lines aims to reduce the landscape fragmentation and stop the decline of caribou populations. However, planning restoration in complex landscapes can be challenging because it must account for a multitude of diverse aspects.To assist with restoration planning, we present a spatial network optimization approach that selects restoration locations in a fragmented landscape while addressing key environmental and logistical constraints. We applied the model to develop restoration scenarios in the Redrock-Prairie Creek caribou range in northwestern Alberta, Canada, which includes a combination of caribou habitat and active oil-and-gas and timber extraction areas.Our study applies network optimization at two distinct scales to address both the broad-scale restoration policy planning and project-level constraints at the level of individual forest sites. We first delineated a contiguous set of coarse-scale regions where restoration is most cost-effective and used this solution to solve a fine-scale network optimization model that addresses environmental and logistical planning constraints at the level of forest patches. Our two-tiered approach helps address the challenges of fine-scale spatial optimization of restoration activities. An additional coarse-scale optimization step finds a feasible starting solution for the fine-scale restoration problem, which serves to reduce the time to find an optimal solution. The added coarse-scale spatial constraints also make the fine-scale restoration solution align with the coarse-scale landscape features, which helps address the broad-scale restoration policies. The approach is generalizable and applicable to assist restoration planning in other regions fragmented by oil-and-gas activities.

Evaluating the Regional Differences in Pediatric Injury Patterns During the COVID-19 Pandemic

IntroductionReports of pediatric injury patterns during the COVID-19 pandemic are conflicting and lack the granularity to explore differences across regions. We hypothesized there would be considerable variation in injury patterns across pediatric trauma centers in the United States. Materials and methodsA multicenter, retrospective study evaluating patients <18 y old with traumatic injuries meeting National Trauma Data Bank criteria was performed. Patients injured after stay-at-home orders through September 2020 (“COVID” cohort) were compared to “Historical” controls from an averaged period of equivalent dates in 2016–2019. Differences in injury type, intent, and mechanism were explored at the site level. Results47,385 pediatric trauma patients were included. Overall trauma volume increased during the COVID cohort compared to the Historical (COVID 7068 patients versus Historical 5891 patients); however, some sites demonstrated a decrease in overall trauma of 25% while others had an increase of over 33%. Bicycle injuries increased at every site, with a range in percent change from 24% to 135% increase. Although the greatest net increase was due to blunt injuries, there was a greater relative increase in penetrating injuries at 7/9 sites, with a range in percent change from a 110% increase to a 69% decrease. ConclusionsThere was considerable discrepancy in pediatric injury patterns at the individual site level, perhaps suggesting a variable impact of the specific sociopolitical climate and pandemic policies of each catchment area. Investigation of the unique response of the community during times of stress at pediatric trauma centers is warranted to be better prepared for future environmental stressors.

Dynamic propagation of mode III cracks in a Lattice Boltzmann method for solids

This work presents concepts and algorithms for the simulation of dynamic fractures with a Lattice Boltzmann method (LBM) for linear elastic solids. This LBM has been presented previously and solves the wave equation, which is interpreted as the governing equation for antiplane shear deformation. Besides the steady growth of a crack at a prescribed crack velocity, a fracture criterion based on stress intensity factors has been implemented. This is the first time that crack propagation with a mechanically relevant criterion is regarded in the context of LBMs. Numerical results are examined to validate the proposed method. The concepts of crack propagation introduced here are not limited to mode III cracks or the simplified deformation assumption of antiplane shear. By introducing a rather simple processing step into the existing LBM at the level of individual lattice sites, the overall performance of the LBM is maintained. Our findings underline the validity of the LBM as a numerical tool to simulate solids in general as well as dynamic fractures in particular.

Antigingivitis efficacy of a sodium bicarbonate toothpaste: Pooled analysis.

The objective of this study was to investigate the antigingivitis and antiplaque treatment effect of a toothpaste containing 67% w/w sodium bicarbonate, at the individual tooth site, tooth region and whole mouth (overall) level, by way of a pooled analysis of data from similarly designed clinical trials. Six randomized controlled GSKCH clinical trials, 12-24 weeks in duration, were selected based on pre-specified criteria which included access to patient level data, pre-treatment dental prophylaxis, >20 bleeding sites and mild-moderate gingivitis at screening and use of 67% sodium bicarbonate toothpaste and non-sodium bicarbonate (regular) toothpaste (negative control) for ≥4 weeks. Efficacy outcomes comprised plaque index (TPI), modified gingival index (MGI) and gingival bleeding (bleeding index (BI), number of bleeding sites (BS)). Treatment comparisons were made using ANCOVA for whole mouth (overall) scores and by tooth site region (facial overall, lingual overall; margin/body overall, facial margin/body, lingual margin/body; papillae/interproximal overall, facial papillae/interproximal, lingual papillae/interproximal). Pooled data for BI, MGI, and TPI at individual tooth sites was plotted as a mouthmap to summarize treatment response (change from baseline) by tooth site, at the 24-week timepoint. For all measures, whole mouth and for all tooth regions at all post-treatment timepoints, significant (p < 0.001) differences in favour of the 67% sodium bicarbonate toothpaste compared with control were observed. At the 24-week timepoint, facial regions demonstrated greater improvements than lingual regions, with the greatest between treatment improvement seen for the facial-papillae regions for bleeding (BS/BI), facial-margin regions for MGI and facial-body regions for TPI. All individual tooth sites demonstrated numerically greater reductions from baseline for the 67% sodium bicarbonate toothpaste than the control toothpaste following 24 weeks use, with the greatest improvements (change from baseline) seen for posterior and papillae tooth sites for bleeding, margin tooth sites for MGI and body tooth sites for TPI. This pooled analysis of patient level-data, limited to GSKCH long-term gingivitis clinical studies, demonstrates that twice daily use of a 67% sodium bicarbonate toothpaste effectively removes plaque from all tooth sites, and results in clinically significant improvements in measures of gingival health, overall and for all the tooth regions investigated, compared with a non-sodium bicarbonate (regular) toothpaste following 24 weeks twice daily use.

Hypermethylation of tumor suppressor lncRNA MEF2C-AS1 frequently happened in patients at all stages of colorectal carcinogenesis

BackgroundThe novel long noncoding RNA MEF2C-AS1 has been identified to play suppressor roles during tumorigenesis. DNA methylation has a regulatory effect on gene expression in cancer initiation and progression. However, the methylation status of MEF2C-AS1 and its role in colorectal cancer (CRC) development remain unclear.MethodsThe expression and methylation levels of MEF2C-AS1 were systematically analyzed among 31 cancers with available qualified data in GEPIA and UCSC Xena databases. Then, the MEF2C-AS1 methylation status was firstly examined among 12 CRCs by Illumina Infinium MethylationEPIC BeadChip in in-house step 1 and further quantified among 48 CRCs by the MassARRAY method in in-house step 2. Subsequently, its methylation and expression levels were quantified among 81 non-advanced adenomas (NAAs), 81 advanced adenomas (AAs), and 286 CRCs using the MassARRAY method, and among 34 NAAs, 45 AAs, and 75 CRCs by qRT-PCR, in in-house step 3, respectively. The effect of MEF2C-AS1 methylation on CRC survival was analyzed by the Kaplan–Meier method. Additionally, in vitro cell proliferation, migration and invasion assays, and bioinformatics analysis were performed to explore the role of MEF2C-AS1 in colorectal carcinogenesis.ResultsLower expression and higher methylation of MEF2C-AS1 were found in CRC by online databases. In the comparisons of lesion tissues with adjacent normal tissues, MEF2C-AS1 hypermethylation of each individual site and mean level was found among CRC patients in in-house step 1 and step 2, more meaningfully, among NAA patients, AA patients, and CRC patients at all stages during colorectal carcinogenesis in in-house step 3 (all p < 0.05). Further comparisons demonstrated significant differences between CRC and NAA (p = 0.025), AA and NAA (p = 0.020). Moreover, MEF2C-AS1 hypermethylation was associated with poorer disease-specific survival of CRC patients (p = 0.044). In addition, hypermethylation and lower expression of MEF2C-AS1 were verified in RKO cells, and the MEF2C-AS1 overexpression significantly suppressed RKO cell proliferation, migration, and invasion.ConclusionsThe findings reveal that MEF2C-AS1 hypermethylation might be an early driven event during colorectal carcinogenesis. It might serve as a promising prognostic biomarker for CRC survival. Our study also indicates the potential tumor-suppressing role of MEF2C-AS1 in CRC.

Grasshoppers exhibit asynchrony and spatial non-stationarity in response to the El Niño/Southern and Pacific Decadal Oscillations

Grasshoppers are preeminent herbivores and perhaps the most significant rangeland pests in the United States (US). Despite the important ecosystem functions they provide, grasshopper populations often obtain densities that cause significant economic harm to grazing operations and agricultural production. Although numerous studies conducted at the level of individual field sites have examined potential mechanisms contributing to grasshopper population “boom and bust” cycles, there has yet to be a large, regional scaled analysis that quantified grasshopper variation across the Western US as a whole. While taking steps to account for data collection biases, mediating effects, and variable confounding, we assessed the influence of Pacific Ocean sea surface temperature oscillations on a 40-year record of grasshopper density in the Western US. Central to our analysis was employing spatially varying coefficients to model time and location-specific variation in grasshopper response to climate. Our results quantitatively demonstrated interannual changes in grasshopper density to be indirectly effected by seasonal El Niño/Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO) variability and to exhibit spatial asynchrony and non-stationarity such that the relative influence of climate on grasshopper density varied through time and across geographic space. Our model is the first to incorporate climate indices as spatially varying coefficients for assessment of a terrestrial species and represents a critical step towards understanding causal drivers of regional grasshopper density.

The precedence effect in spatial hearing manifests in cortical neural population responses

BackgroundTo localize sound sources accurately in a reverberant environment, human binaural hearing strongly favors analyzing the initial wave front of sounds. Behavioral studies of this “precedence effect” have so far largely been confined to human subjects, limiting the scope of complementary physiological approaches. Similarly, physiological studies have mostly looked at neural responses in the inferior colliculus, the main relay point between the inner ear and the auditory cortex, or used modeling of cochlear auditory transduction in an attempt to identify likely underlying mechanisms. Studies capable of providing a direct comparison of neural coding and behavioral measures of sound localization under the precedence effect are lacking.ResultsWe adapted a “temporal weighting function” paradigm previously developed to quantify the precedence effect in human for use in laboratory rats. The animals learned to lateralize click trains in which each click in the train had a different interaural time difference. Computing the “perceptual weight” of each click in the train revealed a strong onset bias, very similar to that reported for humans. Follow-on electrocorticographic recording experiments revealed that onset weighting of interaural time differences is a robust feature of the cortical population response, but interestingly, it often fails to manifest at individual cortical recording sites.ConclusionWhile previous studies suggested that the precedence effect may be caused by early processing mechanisms in the cochlea or inhibitory circuitry in the brainstem and midbrain, our results indicate that the precedence effect is not fully developed at the level of individual recording sites in the auditory cortex, but robust and consistent precedence effects are observable only in the auditory cortex at the level of cortical population responses. This indicates that the precedence effect emerges at later cortical processing stages and is a significantly “higher order” feature than has hitherto been assumed.

Parallel functional assessment of m6A sites in human endodermal differentiation with base editor screens

N6-methyladenosine (m6A) plays important role in lineage specifications of embryonic stem cells. However, it is still difficult to systematically dissect the specific m6A sites that are essential for early lineage differentiation. Here, we develop an adenine base editor-based strategy to systematically identify functional m6A sites that control lineage decisions of human embryonic stem cells. We design 7999 sgRNAs targeting 6048 m6A sites to screen for m6A sites that act as either boosters or barriers to definitive endoderm specification of human embryonic stem cells. We identify 78 sgRNAs enriched in the non-definitive endoderm cells and 137 sgRNAs enriched in the definitive endoderm cells. We successfully validate two definitive endoderm promoting m6A sites on SOX2 and SDHAF1 as well as a definitive endoderm inhibiting m6A site on ADM. Our study provides a functional screening of m6A sites and paves the way for functional studies of m6A at individual m6A site level.

Who’s afraid of the big, bad predator? Contrasting effects of apex predator presence on the behaviour of a mesopredator

Context Mesopredators experience top down pressure from apex predators, which may lead to behavioural changes such as spatial avoidance to reduce both interference and exploitative competition. However, apex predators may also facilitate mesopredators through the provision of carrion, so mesopredators should respond flexibly to the presence of apex predators. Aims We aimed to investigate the drivers of black-backed jackal (Canis mesomelas) space use and detection in areas with and without lions (Panthera leo). We predicted that jackal detection and space use will be greater if apex predators facilitate rather than suppress them. Additionally, we predicted that in the absence of lions, the relative abundance of small ungulate species may become important drivers of space use and detection, because jackals can switch from scavenging to hunting. Comparatively, in the presence of lions, larger ungulate species will become important drivers of space use and detection as these species become accessible to jackals through scavenging. Methods We used camera-trapping surveys, a single-species, single-season occupancy modelling approach, and the assessment of activity patterns to explore how apex predators influence the presence and probability of use of different sites in the Eastern Cape province of South Africa. Key results Apex predators both positively and negatively affected the detection of jackals, indicating that these mesopredators show behavioural flexibility at the individual site level. There was high overlap between jackal activity patterns in the presence and absence of lions; however, at one site with lions, jackal activity did not peak at night as observed at other sites. Conclusions Our results indicate that jackals demonstrate behavioural flexibility in the presence and absence of apex predators. Importantly, our results show that apex predators can both facilitate and suppress mesopredators, and that their behavioural responses are dependent on site-specific factors. Implications Our findings highlight that sympatric predator behaviours should be based on site-specific behaviours instead of the general patterns observed in more temperate systems.

Evaluating Completeness of Discrete Data on Physical Functioning for Children With Cerebral Palsy in a Pediatric Rehabilitation Learning Health System.

The purpose of this study was to determine the extent that physical function discrete data elements (DDE) documented in electronic health records (EHR) are complete within pediatric rehabilitation settings. A descriptive analysis on completeness of EHR-based DDEs detailing physical functioning for children with cerebral palsy was conducted. Data from an existing pediatric rehabilitation research learning health system data network, consisting of EHR data from 20 care sites in a pediatric specialty health care system, were leveraged. Completeness was calculated for unique data elements, unique outpatient visits, and unique outpatient records. Completeness of physical function DDEs was low across 5766 outpatient records (10.5%, approximately 2 DDEs documented). The DDE for Gross Motor Function Classification System level was available for 21% (n = 3746) outpatient visits and 38% of patient records. Ambulation level was the most frequently documented DDE. Intercept only mixed effects models demonstrated that 21.4% and 45% of the variance in completeness for DDEs and the Gross Motor Function Classification System, respectively, across unique patient records could be attributed to factors at the individual care site level. Values of physical function DDEs are missing in designated fields of the EHR infrastructure for pediatric rehabilitation providers. Although completeness appears limited for these DDEs, our observations indicate that data are not missing at random and may be influenced by system-level standards in clinical documentation practices between providers and factors specific to individual care sites. The extent of missing data has significant implications for pediatric rehabilitation quality measurement. More research is needed to understand why discrete data are missing in EHRs and to further elucidate the professional and system-level factors that influence completeness and missingness. Completeness of DDEs reported in this study is limited and presents a significant opportunity to improve documentation and standards to optimize EHR data for learning health system research and quality measurement in pediatric rehabilitation settings.

RELATIONSHIP OF PRECIPITATION AND HABITAT TO THE SPATIAL AND TEMPORAL ABUNDANCE OF AEDES ATLANTICUS AND AEDES INFIRMATUS IN ST. JOHNS COUNTY, FLORIDA

The purpose of this study was to perform descriptive and inferential analyses to better understand the presence of the abundant mosquito species Aedes atlanticus and Aedes infirmatus in St. Johns County, northeastern Florida. Historical surveillance data (2010-2019) obtained from Anastasia Mosquito Control District of St. Johns County, St. Augustine, FL, was organized to graph temporal mosquito abundance trends and inverse distance weighted (IDW) interpolation was used to map spatial distribution patterns of mosquitoes. Precipitation and habitat composition were investigated as spatiotemporal predictors of mosquito abundance using Pearson’s correlation statistics. There were considerable and inconsistent fluctuations in the population abundance of Ae. atlanticus and Ae. infirmatus across and within individual surveillance seasons during the last decade. Precipitation was significantly associated with total county-wide mosquito population counts by season (Ae. atlanticus, R = 0.810, p = 0.005; Ae. infirmatus, R = 0.850, p = 0.002), while the association with weekly mosquito population trends was inconsistently significant across species, lag time, and years. The proportion of surrounding land covered by upland forest, water, and agriculture was associated with species abundance at the spatial level of individual trap sites. Overall, the results identify that Ae. atlanticus and Ae. infirmatus share a spatiotemporal relationship and are similarly impacted by rainfall and habitat type. Findings of the study might help to inform improved surveillance by integrating IDW estimation maps with current district resources and improved knowledge of species’ ecology.

Mid-Holocene coastline reconstruction from geomorphological sea level indicators in the Tràng An World Heritage Site, Northern Vietnam

In this paper we present a high resolution palaeo coastline model for the isolated limestone massif of Tràng An, Ninh Bình province, Vietnam. The archaeological and palaeoecological record here comprise rich archives of human activity set within a landscape that was cyclically transformed between inland and archipelagic states under the influence of past sea level changes. These records have become informative proxies in the study of current sea level rise. Well-preserved notches along the vertical limestone cliffs within the study property reveal several phases of prolonged stable sea levels that likely pertain to the Mid-Holocene marine transgression 8 ka BP to 4 ka BP and allow for detailed coastline reconstructions for parts of the Red River Delta (RRD). The resulting coastline model facilitates a closer look at past human responses to landscape and environmental changes at local and individual site-level, which improves our understanding of past human adaptations to climate-change induced sea level rise. These data also stand to inform current coastal vulnerability assessments and climate change response models.

Sea-level rise enhances carbon accumulation in United States tidal wetlands

Sea-level rise enhances carbon accumulation in United States tidal wetlands

Workshop processes to generate stakeholder consensus about post-mining land uses: an Australian case study

A major challenge in post-mining land use planning is identifying areas of consensus among engaged stakeholders about major concerns and suitable post-mining land use and land management. This paper takes as an example, the Bowen Basin, a major coal-mining region in Australia where several mines are approaching closure stages but consensus on post-mining land use in this region is yet to be established. This paper examines the use of workshop processes to generate consensus among different stakeholder interests about priority issues and acceptable post-mining land use(s) in this region. Four decision-making workshops about post-mining land use were used in this study. Results show that facilitated group workshop processes involving diverse stakeholders could lead to a broad consensus about key options for future land uses at an individual site level; and also lead to the identification of the factors relevant to land-use decisions to be considered for each case study. These findings guide mining companies and government regulators about why and how to involve local and regional stakeholders in post-mining land-use decisions, and the extent to which group processes can lead to convergence of diverse interests.

Molecular Evolution and Developmental Expression of Melanin Pathway Genes in Lepidoptera

Pigmentation is involved in a wide array of biological functions across insect orders, including body patterning, thermoregulation, and immunity. The melanin pathway, in particular, has been characterized in several species. However, molecular evolution of the genes involved in this pathway is poorly explored. We traced the molecular evolution of six melanin pathway genes in 53 species of Lepidoptera covering butterflies and moths, and representing over 100 million years of diversification. We compared the rates of synonymous and nonsynonymous substitutions within and between these genes to study signatures of selection at the level of individual sites, genes, and branches of the gene tree. We found that molecular evolution of all six genes was governed by strong purifying selection. Yet, a number of sites showed signs of being under positive selection, including in the highly conserved domain regions of three genes. Further, we traced the expression of these genes across developmental stages, tissues, and sexes in the Papilio polytes butterfly using a developmental transcriptome dataset. We observed that the expression patterns of the genes in P. polytes largely reflected their known tissue-specific function in other species. The expression of sequentially acting genes in the melanin pathway was correlated. Interestingly, melanin pathway genes also showed a sexually dimorphic pattern of developmental heterochrony; i.e., females showed prominent upregulation of melanin pathway genes in pre-pupal stage compared to males, while males showed prominent upregulation in 9-day pupal wings compared to females. Our evolutionary and developmental analyses suggest that the vast diversity of wing patterning and pigmentation in Lepidoptera may have evolved despite largely constrained sequence evolution, with potential contribution from differential developmental expression of genes in a highly conserved pathway.

Increasing Capacity for Farm to Early Care and Education in Maryland and Washington: Study Protocol

Abstract Objectives Farm to early care and education (farm to ECE) incorporates local food purchasing; on-site gardens; and food, nutrition, and agriculture education into ECE settings to advance child health and well-being, engage families and communities, and enhance ECE quality. This project aims to advance capacity for farm to ECE training and implementation in Maryland and Washington by (1) measuring uptake and sustainability of farm to ECE activities at two demonstration sites; and (2) testing the feasibility of a train-the-trainer model, which includes training professionals who offer technical assistance to ECE providers to incorporate farm to ECE into existing training models. Methods For this demonstration study, researchers will work in partnership with each site to determine interests, needs, and capacity and develop a plan for integrating farm to ECE activities. Evaluation will consist of process and outcome components, including: (1) Semi-structured interviews with site administrators and educators to determine site needs and priorities (pre), progress and on-going needs (mid) and feedback on process, challenges, successes, and program sustainability (post); and (2) pre and post implementation assessment of ECE program quality (e.g., child nutrition, family engagement, learning environment). For the train-the-trainer model, researchers will utilize pre, post, and follow up surveys to assess changes in knowledge, attitudes, and self-efficacy regarding delivery and implementation of farm to ECE activities and participant uptake and implementation of training content. Results N/A. Conclusions Farm to ECE has the potential to promote healthier ECE environments and healthier community food systems. This project aims to examine impacts of expanding farm to ECE through state training and individual site level activities, with the goal of identifying best practices to support expansion of sustained and comprehensive farm to ECE initiatives. Funding Sources Bloomberg American Health Initiative Collaboration Awards; Lerner Center for Public Health Promotion, Johns Hopkins Bloomberg School of Public Health.