Genomic analyses of agronomic traits in tea plants and related Camellia species.

The genus Camellia contains three types of domesticates that meet various needs of ancient humans: the ornamental C. japonica, the edible oil-producing C. oleifera, and the beverage-purposed tea plant C. sinensis. The genomic drivers of the functional diversification of Camellia domesticates remain unknown. Here, we present the genomic variations of 625 Camellia accessions based on a new genome assembly of C. sinensis var. assamica ('YK10'), which consists of 15 pseudo-chromosomes with a total length of 3.35 Gb and a contig N50 of 816,948 bp. These accessions were mainly distributed in East Asia, South Asia, Southeast Asia, and Africa. We profiled the population and subpopulation structure in tea tree Camellia to find new evidence for the parallel domestication of C. sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS). We also identified candidate genes associated with traits differentiating CSA, CSS, oilseed Camellia, and ornamental Camellia cultivars. Our results provide a unique global view of the genetic diversification of Camellia domesticates and provide valuable resources for ongoing functional and molecular breeding research.

Genetic analyses of ancient tea trees provide insights into the breeding history and dissemination of Chinese Assam tea (Camellia sinensis var. assamica).

Chinese Assam tea (Camellia sinensis var. assamica) is an important tea crop with a long history of cultivation in Yunnan, China. Despite its potential value as a genetic resource, its genetic diversity and domestication/breeding history remain unclear. To address this issue, we genotyped 469 ancient tea plant trees representing 26 C. sinensis var. assamica populations, plus two of its wild relatives (six and three populations of C. taliensis and C. crassicolumna, respectively) using 16 nuclear microsatellite loci. Results showed that Chinese Assam tea has a relatively high, but comparatively lower gene diversity (HS = 0.638) than the wild relative C. crassicolumna (HS = 0.658). Clustering in STRUCTURE indicated that Chinese Assam tea and its two wild relatives formed distinct genetic groups, with considerable interspecific introgression. The Chinese Assam tea accessions clustered into three gene pools, corresponding well with their geographic distribution. However, NewHybrids analysis indicated that 68.48% of ancient Chinese Assam tea plants from Xishuangbanna were genetic intermediates between the Puer and Lincang gene pools. In addition, 10% of the ancient Chinese Assam tea individuals were found to be hybrids between Chinese Assam tea and C. taliensis. Our results suggest that Chinese Assam tea was domesticated separately in three gene pools (Puer, Lincang and Xishuangbanna) in the Mekong River valley and that the hybrids were subsequently selected during the domestication process. Although the domestication history of Chinese Assam tea in southwestern Yunnan remains complex, our results will help to identify valuable genetic resources that may be useful in future tea breeding programs.

An evaluation of the cost of human papilloma virus (HPV) vaccine delivery in Zambia.

BACKGROUND: Human papillomavirus (HPV) is a common sexually transmitted infection and the leading cause of cervical cancer. The HPV vaccine is a safe and effective way to prevent HPV infection. In Zambia, the vaccine is given during Child Health Week to girls aged 14 years who are in and out of school in two doses over two years. The focus of this evaluation was to establish the cost to administer a single dose of the vaccine as well as for full immunisation of two doses. METHODS: This work was part of a broader study on assessing HPV programme implementation in Zambia. For HPV costing aspect of the study, with a healthcare provider perspective and reference year of 2020, both top-down and micro-costing approaches were used for financial costing, depending on the cost data source, and economic costs were gathered as secondary data from Expanded Programme for Immunisation Costing and Financing Project (EPIC), except human resource costs which were gathered as primary data using existing Ministry of Health salary scales and reported time spent by different health cadres on activities related to HPV vaccination. Data was collected from eight districts in four provinces, mainly using a structured questionnaire, document reviews and key informant interviews with staff at national, provincial, district and health facility levels. Administrative coverage rates were obtained for each district. RESULTS: Findings show that schools made up 53.3% of vaccination sites, community outreach sites 30.9% and finally health facilities 15.8%. In terms of coverage for 2020, for the eight districts sampled, schools had the highest coverage at 96.0%. Community outreach sites were at 6.0% of the coverage and health facilities accounted for only 1.0% of the coverage. School based delivery had the lowest economic cost at USD13.2 per dose and USD 28.1 per fully immunised child (FIC). Overall financial costs for school based delivery were US$6.0 per dose and US$12.4 per FIC. Overall economic costs taking all delivery models into account were US$23.0 per dose and US$47.6 per FIC. The main financial cost drivers were microplanning, supplies, service delivery/outreach and vaccine co-financing; while the main economic cost drivers were human resources, building overhead and vehicles. Nurses, environmental health technicians and community-based volunteers spent the most time on HPV related vaccination activities compared to other cadres and represented the greatest human resource costs. CONCLUSIONS: The financial cost of HPV vaccination in Zambia aligns favourably with similar studies conducted in other countries. However, the economic costs appear significantly higher than those observed in most international studies. This discrepancy underscores the substantial strain placed on healthcare resources by the program, a burden that often remains obscured. While the vaccine costs are currently subsidized through the generous support of Gavi, the Vaccine Alliance, it's crucial to recognize that these expenses pose a considerable threat to long-term sustainability. Consequently, countries such as Zambia must proactively devise strategies to address this challenge.

COVID-19 Vaccination Rates and Predictors of Uptake Among Adults With Coronary Heart Disease: Insight From the 2022 National Health Interview Survey.

INTRODUCTION: COVID-19 has become a burden to all nations across the globe, and vaccination currently remains the most effective means of fighting the SARS-COV-2 pandemic. From the time of approval and subsequent distribution of the various COVID-19 vaccines, nearly 72.3% (5.5 billion) of the globe's population have been vaccinated, leaving slightly more than a quarter of the globe's population at risk. With the approval and availability of booster vaccine dosages to individuals with chronic conditions, including coronary heart disease (CHD), it is vital to comprehend the factors underlying the uptake of COVID-19 vaccination in such subgroups. Further, the American Heart Association recommends vaccination against COVID-19 in populations with coronary heart disease (CHD). This is because they are more likely to experience severe outcomes due to COVID-19 infection. This study assesses the uptake of COVID-19 vaccines as well as predictors of its uptake. METHODS: Using the 2022 survey data from the National Health Interview Survey (NHIS), 1,708 adults ≥ 40 years with CHD who responded yes/no to whether they had received the vaccine were identified. A Pearson's chi-square test was used to ascertain differences among those who had received the vaccine and those who had not. A logistic regression (multivariate regression) was used to evaluate predictors of COVID-19 vaccination. RESULTS: About 1,491/1,708 (86.8%) adults ≥ 40 years reported being vaccinated against COVID-19. Among them, 1,065/1,491 (68.4%) had received more than two vaccination doses. The predictors of COVID-19 vaccination were older age (odds ratio (OR): 2.01 (95% confidence interval (CI): 1.40-2.89), p < 0.001), ratio of family income to poverty threshold of 1 and above (OR: 2.40 (95% CI: 1.58-3.64), p < 0.001), having a college degree (OR: 3.09 (95% CI: 1.85-5.14), p < 0.001), and being insured (OR: 3.26 (95% CI: 1.03-10.26), p = 0.044). CONCLUSION: The findings of the study have indicated that 68.4% of adults 40 years and above with CHD have been vaccinated against COVID-19 and have received more than two doses of vaccines. More than half have followed recommendations and have received booster doses of the vaccine. Old age (above 40 years) and a higher socioeconomic class are associated with being more likely to follow COVID-19 vaccination guidelines. Despite the higher vaccination rate of 68.4% in the adults with heart diseases group, strategies for improving booster vaccine awareness alongside accessibility are needed to enhance additional dosage uptake, protect them against novel COVID-19 variants, and ensure the development of sustained immunity.

Phase 3 efficacy and safety trial of proposed liraglutide biosimilar for reduction of glycosylated hemoglobin (HbA1c) in patients with Type 2 diabetes mellitus.

Liraglutide is indicated for glycaemic control in adults with Type 2 diabetes mellitus (T2DM) as an adjunct to diet and exercise. A proposed biosimilar of liraglutide (Levim Liraglutide) was investigated for efficacy & safety in a phase 3 study against the originator reference liraglutide (Victoza®) manufactured by Novo Nordisk A/S, Denmark. Patients aged 18-65 years of age with glycosylated hemoglobin (HbA1c) between 7 and 10 %, among other criteria, were included in the study. Patients were randomized 1:1 to receive daily doses of either Levim liraglutide or reference liraglutide for 24 weeks. The least square mean (standard error, SE) for the primary efficacy endpoint of reduction in HbA1c% at Week 24 was -1.09 (0.15)% for Levim liraglutide group and -1.04 (0.14)% for reference liraglutide. The upper bound of the confidence interval for treatment difference was less than the non-inferiority margin of 0.4 % at one-sided alpha of 0.025 (P-value = 0.0003). The secondary endpoints for proportion of patients achieving reduction in HbA1c, glycaemic level and weight, changes in cardiovascular parameters and the overall safety profiles of the study drugs were comparable. Levim liraglutide demonstrated non-inferior efficacy and similar safety to reference liraglutide and may be an option in treatment of T2DM (CTRI.nic.in, no. CTRI/2022/02/040261).

A Multiplex PCR System of Novel Microsatellite Loci for Population Genetic Application in Walnuts.

Multiplex polymerase chain reaction (PCR) of microsatellite loci allows for simultaneous amplification of two or more pairs of primers in a single PCR reaction; hence, it is cost and time effective. However, very few attempts have been reported in non-model species. In this study, by combining a genome-based de novo development and cross-species application approach, a multiplex PCR system comprising 5 PCR reactions of 33 microsatellites consisting of 26 novel genomic and 7 literature-sourced loci was tested for polymorphisms, cross-species transferability, and the ability to assess genetic diversity and population structure of three walnut species (Juglans spp.). We found that the genome-based approach is more efficient than other methods. An allelic ladder was developed for each locus to enhance consistent genotyping among laboratories. The population genetic analysis results showed that all 33 loci were successfully transferred across the three species, showing high polymorphism and a strong genetic structure. Hence, the multiplex PCR system is highly applicable in walnut species. Furthermore, we propose an efficient pipeline to characterize and genotype polymorphic microsatellite loci. The novel toolbox developed here will aid future ecology and evolution studies in walnut and could serve as a model for other plant species.

Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021.

Non-pharmaceutical interventions minimize social contacts, hence the spread of respiratory pathogens such as influenza and SARS-CoV-2. Globally, there is a paucity of social contact data from the workforce. In this study, we quantified two-day contact patterns among USA employees. Contacts were defined as face-to-face conversations, involving physical touch or proximity to another individual and were collected using electronic self-kept diaries. Data were collected over 4 rounds from 2020 to 2021 during the COVID-19 pandemic. Mean (standard deviation) contacts reported by 1456 participants were 2.5 (2.5), 8.2 (7.1), 9.2 (7.1) and 10.1 (9.5) across round 1 (April-June 2020), 2 (November 2020-January 2021), 3 (June-August 2021), and 4 (November-December 2021), respectively. Between round 1 and 2, we report a 3-fold increase in the mean number of contacts reported per participant with no major increases from round 2-4. We then modeled SARS-CoV-2 transmission at home, work, and community settings. The model revealed reduced relative transmission in all settings in round 1. Subsequently, transmission increased at home and in the community but remained exceptionally low in work settings. To accurately parameterize models of infection transmission and control, we need empirical social contact data that capture human mixing behavior across time.

Social contact patterns among employees in U.S. long-term care facilities during the COVID-19 pandemic, December 2020 to June 2021.

OBJECTIVE: We measured contact patterns using social contact diaries for 157 U.S. long-term care facility employees from December 2020 - June 2021. These data are crucial for analyzing mathematical transmission models and for informing healthcare setting infection control policy. RESULTS: The median number of daily contacts was 10 (IQR 8-11). Household contacts were more likely partially masked than fully masked, more likely to involve physical contact, and longer in duration compared to facility contacts.

Genetic imprints of grafting in wild iron walnut populations in southwestern China.

BACKGROUND: Anthropogenic activities are causing unprecedented loss of genetic diversity in many species. However, the effects on genetic diversity from large-scale grafting onto wild plants of crop species are largely undetermined. Iron walnut (Juglans sigillata Dode) is a deciduous nut tree crop endemic to southwestern China with a long history of cultivation. Due to the rapid expansion of the walnut industry, many natural populations are now being replaced by cultivars grafted onto wild rootstocks. However, little is known about the potential genetic consequences of such action on natural populations. RESULTS: We sampled the scion and the rootstock from each of 149 grafted individuals within nine wild populations of J. sigillata from Yunnan Province which is the center of walnut diversity and cultivation in China, and examined their genetic diversity and population structure using 31 microsatellite loci. Scions had lower genetic diversity than rootstocks, and this pattern was repeated in seven of the nine examined populations. Among those seven populations, AMOVA and clustering analyses showed a clear genetic separation between all rootstocks and all scions. However, the two remaining populations, both from northern Yunnan, showed genetic similarity between scions and rootstocks, possibly indicating that wild populations here are derived from feralized local cultivars. Moreover, our data indicated probable crop-to-wild gene flow between scions and rootstocks, across all populations. CONCLUSIONS: Our results indicate that large-scale grafting has been causing genetic diversity erosion and genetic structure breakdown in the wild material of J. sigillata within Yunnan. To mitigate these effects, we caution against the overuse of grafting in wild populations of iron walnut and other crop species and recommend the preservation of natural genotypes through in situ  and ex situ conservation.

Learning to manipulate a whip with simple primitive actions - A simulation study.

This simulation study investigated whether a 4-degrees-of-freedom (DOF) arm could strike a target with a 50-DOF whip using a motion profile similar to discrete human movements. The interactive dynamics of the multi-joint arm was modeled as a constant joint-space mechanical impedance, with values derived from experimental measurement. Targets at various locations could be hit with a single maximally smooth motion in joint-space coordinates. The arm movements that hit the targets were identified with fewer than 250 iterations. The optimal actions were essentially planar arm motions in extrinsic task-space coordinates, predominantly oriented along the most compliant direction of both task-space and joint-space mechanical impedances. Of the optimal movement parameters, striking a target was most sensitive to movement duration. This result suggests that the elementary actions observed in human motor behavior may support efficient motor control in interaction with a dynamically complex object.

An Evaluation of the Cost of Human Papilloma Virus (HPV) Vaccine Delivery In Zambia.

Background: Human papillomavirus (HPV) is a common sexually transmitted infection and the leading cause of cervical cancer. The HPV vaccine is a safe and effective way to prevent HPV infection. In Zambia, the vaccine is given during Child Health to girls aged 14 years who are in and out of school in two doses over two years. The focus of this evaluation was to establish the cost to administer a single dose of the vaccine well as for full immunisation of two doses. Methods: For HPV costing, both top-down and micro-costing approaches were used, depending on the cost data source, and economic costs were gathered from Expanded Programme for Immunisation Costing and Financing Project (EPIC). Data was collected from eight districts in four provinces, mainly using a structured questionnaire, document reviews and key informant interviews with staff at national, district and provincial levels. Results: Findings show that schools made up 53.3% of vaccination sites, community outreach sites 30.9% and finally health facilities 15.8%. In terms of coverage for 2020, for the eight districts sampled, schools had the highest coverage at 96.0%. Community outreach sites were at 6.0% of the coverage and health facilities accounted for only 1.0% of the coverage. School based delivery had the lowest cost economic cost at USD13.2 per dose and USD 26.4 per fully immunised child (FIC). Overall financial costs were US$6.0 per dose and US$11.9 per fully immunised child. Overall economic costs taking all delivery models into account were US$23.0 per dose and US$46.0 per FIC. The main cost drivers were human resources, building overhead and vehicles, microplanning, supplies and service delivery/outreach. were the top cost drivers. Nurses, environmental health technicians and community-based volunteers were the most involved in HPV vaccination. Conclusions: Future planning in Zambia and other African countries conducting HPV vaccination needs to prioritise these cost drivers as well as possibly find strategies to minimise some costs. Although not a challenge now due to Gavi support, vaccine costs are a major threat to sustainability in the long run. Countries like Zambia must find strategies to mitigate against this.

Understanding the Challenges of Intensive Care Staff in Communicating With Patients and Patients' Families During the COVID-19 Crisis: A Qualitative Exploration.

Background Coronavirus disease 2019 (COVID-19) isolation protocols in India restricted family members of COVID-19 patients from visiting them in hospitals and in intensive care units, especially during the peak of the pandemic. This along with the elaborate personal protective equipment (PPE) created challenges for intensivists and nurses in COVID ICUs in effectively communicating with patients and patients' families, especially in shared decision-making processes. Methods This article is the outcome of a qualitative study using in-depth one-on-one interviews with 10 intensivists and four intensive care nurses in two teaching hospitals in Bengaluru, South India. Each participant, purposively selected till data saturation was reached, had spent extensive periods of time in a COVID ICU during both COVID-19 waves in 2020 and 2021. A framework of descriptive phenomenology led to the design of the study in which varied experiences and insights of participants were captured using an interview guide to understand their lived reality. The interviews were conducted online or in person between July 2021 and October 2021 and were audio recorded and transcribed verbatim. Coding of transcripts using the NVivo 12 (Burlington, MA: QSR International Pty Ltd) software helped with the thematic analysis. This was guided by interpretive phenomenological methods that derived meaning from participants' life experiences. Results Four themes involving challenges in effective communication in the COVID ICU emerged as follows: physical barriers, emotional and mental stressors, infrastructural challenges, and ethical and moral dilemmas. Sub-themes included personal protective equipment as a barrier, reduced energy levels, and isolation of family from patients under the domain of physical challenges; fears of the unknown, handling death of patients in isolation, and the frustrations of families were challenges under the emotional and mental domain. Infrastructural/systemic challenges included poor connectivity and insufficient mobile phones, and the absence of rules to handle interruptions. Privacy breaches, taking consent over the phone, end-of-life discussions, and medico-legal risks emerged as the subthemes under the domain of ethical and moral challenges. A mobile phone communication policy specifying usage times and operating methods, a mandatory communication and counseling training module for intensivists and intensive care nurses, and a set of protocols for highly restrictive, intensive care units in pandemic situations were recommendations and lessons learned. Conclusions The lack of face-to-face interactions was a serious barrier to communication between ICU staff and patients and their caregivers. It had a bearing on trust levels and had emotional and ethical consequences for healthcare teams to handle. Opportunities for self-care, venting of anxiety and distress, and opportunities to celebrate and reward special efforts and cooperation between consultants, residents, nurses, and technicians in stressful environments like a pandemic ICU were important to sustain empathy and keep care and communication humane.

Genetic analysis of walnut cultivars from southwest China: Implications for germplasm improvement.

Walnuts are highly valued for their rich nutritional profile and wide medicinal applications. This demand has led to the intensification of breeding activities in major walnut production areas such as southwest China, in order to develop more superior cultivars. With the increasing number of cultivars, accurate identification becomes fundamental to selecting the right cultivar for grafting, industrial processing or development of new cultivars. To ensure proper identification of cultivars and understand the genetic structure of wild and cultivated material, we genotyped 362 cultivated and wild individuals of walnut trees from southwest China (with two additional populations from Xinjiang, plus three cultivars from Canada, France and Belgium) using 36 polymorphic microsatellite loci. We found relatively low indices of genetic diversity (H O = 0.570, H E = 0.404, N A = 2.345) as well as a high level of clonality (>85% of cultivars), indicating reliance on genetically narrow sources of parental material for breeding. Our STRUCTURE and PCoA analyses generally delineated the two species, though considerable levels of introgression were also evident. More significantly, we detected a distinct genetic group of cultivated Juglans sigillata, which mainly comprised individuals of the popular 'Yangbidapao' landrace. Finally, a core set of 18 SSR loci was selected, which was capable of identifying 32 cultivars. In a nutshell, our results call for more utilization of genetically disparate material, including wild walnut trees, as parental sources to breed for more cultivars. The data reported herein will significantly contribute towards the genetic improvement and conservation of the walnut germplasm in southwest China.

Evaluating the functionality and effectiveness of ZITAG and related expanded programme on immunisation technical committees in Zambia.

The Zambia Immunisation Technical Advisory Group (ZITAG) was established in 2016 as an advisory body to provide evidence-based recommendations on vaccine policy. As part of the Gave Full Country Evaluation, we evaluated the functionality and effectiveness of ZITAG and related EPI committees through an online stakeholder survey of Interagnecy Coordinating Committee (ICC), ZITAG and Extended programme on Immunisation Technical Working Group (EPI-TWG) members, document review and key informant interviews. The survey was sent out via SurveyMonkey between May and July 2020 to 69 members of ZITAG, ICC or the EPI TWG. A total of 52 individuals responded (75%). Eight key informant interviews were also carried out at the national and global level in September 2020 to elaborate further on some of the quantitative findings and for triangulation. Findingsrevealed that the EPI committees were reasonably functional and effective entities, each with its unique role, though some overlaps occurred. Functionality was shown by having a broad membership with wide expertise and long-serving members; sub-committees existed and meetings were occurring regularly. Leadership and coordination structures also existed and were largely felt to be working well. Funding challenges however persisted, in particular for ZITAG operations and functionality of its subcommittees. Effectiveness and value addition fo the committees to the EPI was illustrated through decision-making processes and evidence use as well as relatively good country ownership in terms of commitment, legitimacy, capacity and accountability. Full independence and ownership may however be compromised by funding challenges. Recent changes to ICC terms of reference and focus beyond immunisation side-lined the EPI and weakened the linkage between ICC and ZITAG with many ZITAG recommendations not having been followed through by ICC as the ultimate endorsing entity.

Genetic Diversity and Structure of Persian Walnut (Juglans regia L.) in Pakistan: Implications for Conservation.

Persian (Common) walnut (Juglans regia L.) is a famous fruit tree species valued for its nutritious nuts and high-quality wood. Although walnut is widely distributed and plays an important role in the economy and culture of Pakistan, the genetic diversity and structure of its populations in the country remains poorly understood. Therefore, using 31 nuclear microsatellites, we assessed the genetic diversity and population structure of 12 walnut populations sampled across Pakistan. We also implemented the geostatistical IDW technique in ArcGIS to reveal "hotspots" of genetic diversity. Generally, the studied populations registered relatively low indices of genetic diversity (NA = 3.839, HO = 0.558, UHE = 0.580), and eight populations had positive inbreeding coefficient (FIS) values. Low among-population differentiation was indicated by AMOVA, pairwise FST and DC. STRUCTURE, PCoA and neighbor joining (NJ) analysis revealed a general lack of clear clustering in the populations except that one population in Upper Dir was clearly genetically distinct from the rest. Furthermore, the Mantel test showed no correlation between the geographic and genetic distance (r = 0.14, p = 0.22), while barrier analysis suggested three statistically significant genetic barriers. Finally, the spatial interpolation results indicated that populations in Ziarat, Kashmir, Dir, Swat, Chitral, and upper Dir had high intrapopulation genetic diversity, suggesting the need to conserve populations in those areas. The results from this study will be important for future breeding improvement and conservation of walnuts in Pakistan.

School Meal Programs in Africa: Regional Results From the 2019 Global Survey of School Meal Programs.

Introduction: School meal programs operate throughout Africa, serving as a social safety net and aiming to improve children's nutrition, influence their dietary choices, and strengthen the agrifood economy through local procurement. Despite their rapid expansion in the past decade, there has been no systematic effort to comprehensively document school feeding activities across the continent. Methods: Detailed information on school feeding activities in each country was captured in the Global Survey of School Meal Programs©, which launched in 2019. An invitation to participate was extended to each government, which appointed a national-level respondent to gather information on every large-scale school meal program in the country. Results: Forty-one countries in Africa (38 in sub-Saharan Africa) responded to the survey in 2019 with information on 68 large-scale programs that together reached 60.1 million children. Across these countries, the aggregate school feeding budget was USD 1.3 billion. Diversity in school meal programs is evident across regions, country income levels, and levels of national commitment. Coverage rates tended to be highest in southern Africa, in countries with school feeding as a line item in the national budget, and in countries with the greatest domestic share of the school feeding budget. Diversity in the school menu tended to be greatest in programs that sourced food through domestic purchase rather than relying on foreign in-kind donations. To address micronutrient malnutrition, about two-thirds of the programs served fortified foods, and one-quarter included micronutrient supplements. Even as rates of overweight/obesity are rising among African school children, just 10% of school meal programs identified its prevention as an objective. Conclusion: The extent to which school meal programs in Africa are supported with domestic funding reflects a dramatic shift in favor of national ownership and domestic food procurement. At the same time, programs have grappled with inadequate and unpredictable budgets and challenges related to supply chains and logistics-impediments that need to be addressed if these programs are to achieve their objectives. Overall, the survey results underscore the important position of school meal programs within African food systems and their potential (if well-designed) to sustainably improve food security, child health, and nutrition.

Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae).

Urticeae s.l., a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data-CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions-for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110-112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.

Determinants of Genetic Structure in a Highly Heterogeneous Landscape in Southwest China.

Intra-specific genetic diversity is a fundamental component of biodiversity, and is key to species adaptation and persistence. However, significant knowledge gaps still exist in our understanding of the patterns of genetic diversity and their key determinants. Most previous investigations mainly utilized single-species and/or a limited number of explanatory variables; so here we mapped the patterns of plastid genetic diversity within 15 plant species, and explored the key determinants shaping these patterns using a wide range of variables. Population-level cpDNA sequence data for 15 plant species from the Longitudinal Range Gorge Region (LRGR), southwest China, were retrieved from literature and used to estimate haplotype diversity (H D) and population pairwise genetic differentiation (F ST) indices. Genetic diversity and divergence landscape surfaces were then generated based on the H D and F ST, respectively, to clarify the patterns of genetic structure in the region. Subsequently, we analyzed the relationships between plastid genetic diversity and 16 explanatory variables (classified as anthropogenic, climatic, and topographic). We found that the highest genetic diversity occurred in the Yulong Mountain region, with a significant proportion (~74.81%) of the high diversity land area being located outside of protected areas. The highest genetic divergence was observed approximately along the 25°N latitudinal line, with notable peaks in the western and eastern edges of the LRGR. Genetic diversity (H D) was weakly but significantly positively correlated with both Latitude (lat) and Annual Mean Wet Day Frequency (wet), yet significantly negatively correlated with all of Longitude (long), Annual Mean Cloud Cover Percent (cld), Annual Mean Anthropogenic Flux (ahf), and Human Footprint Index (hfp). A combination of climatic, topographic, and anthropogenic factors explained a significant proportion (78%) of genetic variation, with topographic factors (lat and long) being the best predictors. Our analysis identified areas of high genetic diversity (genetic diversity "hotspots") and divergence in the region, and these should be prioritized for conservation. This study contributes to a better understanding of the features that shape the distribution of plastid genetic diversity in the LRGR and thus would inform conservation management efforts in this species-rich, but vulnerable region.

The Role of C-Reactive Protein as a Triage Tool for Pulmonary Tuberculosis in Children.

BACKGROUND: C-reactive protein (CRP) has shown promise as a triage tool for pulmonary tuberculosis (TB) in adults living with the human immunodeficiency virus. We performed the first assessment of CRP for TB triage in children. METHODS: Symptomatic children less than 15 years old were prospectively enrolled in Kampala, Uganda. We completed a standard TB evaluation and measured CRP using a point-of-care assay. We determined the sensitivity and specificity of CRP to identify pulmonary TB in children using 10 mg/L and 5 mg/L cut-off points and generated a receiver operating characteristic (ROC) curve to determine alternative cut-offs that could approach the target accuracy for a triage test (≥90% sensitivity and ≥70% specificity). RESULTS: We included 332 children (median age 3 years old, interquartile range [IQR]: 1-6). The median CRP level was low at 3.0 mg/L (IQR: 2.5-26.6) but was higher in children with Confirmed TB than in children with Unlikely TB (9.5 mg/L vs. 2.9 mg/L, P-value = .03). At a 10 mg/L cut-off, CRP sensitivity was 50.0% (95% confidence interval [CI], 37.0-63.0) among Confirmed TB cases and specificity was 63.3% (95% CI, 54.7-71.3) among children with Unlikely TB. Sensitivity increased to 56.5% (95% CI, 43.3-69.0) at the 5 mg/L cut-off, but specificity decreased to 54.0% (95% CI, 45.3-62.4). The area under the ROC curve was 0.59 (95% CI, 0.51-0.67), and the highest sensitivity achieved was 66.1% at a specificity of 46.8%. CONCLUSIONS: CRP levels were low in children with pulmonary TB, and CRP was unable to achieve the accuracy targets for a TB triage test.

Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021.

Non-pharmaceutical interventions minimize social contacts, hence the spread of SARS-CoV-2. We quantified two-day contact patterns among USA employees from 2020-2021 during the COVID-19 pandemic. Contacts were defined as face-to-face conversations, involving physical touch or proximity to another individual and were collected using electronic diaries. Mean (standard deviation) contacts reported by 1,456 participants were 2.5 (2.5), 8.2 (7.1), 9.2 (7.1) and 10.1 (9.5) across round 1 (April-June 2020), 2 (November 2020-January 2021), 3 (June-August 2021), and 4 (November-December 2021), respectively. Between round 1 and 2, we report a 3-fold increase in the mean number of contacts reported per participant with no major increases from round 2-4. We modeled SARS-CoV-2 transmission at home, work, and community. The model revealed reduced relative transmission in all settings in round 1. Subsequently, transmission increased at home and in the community but remained very low in work settings. Contact data are important to parameterize models of infection transmission and control. Teaser: Changes in social contact patterns shape disease dynamics at workplaces in the USA.