bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylation dynamics of sperm cell lineage development in tomato
Authors: Lu Yunlong , Song Yunyun , Liu Lingtong , Wang Tai 
Published: November 2020

SUMMARYDuring the sexual reproduction of higher plants, DNA methylation and transcription are broadly changed to reshape a microspore into two sperm cells (SCs) and a vegetative cell (VC). However, when and how the DNA methylation of SCs is established remains not fully understood. Here we investigate the DNA methylation (5 mC) dynamics of SC lineage and the VC in tomato using whole‐genome bisulfite sequencing. We find the asymmetric division of the microspore gives its two daughter cells differential methylome. Compared with the generative cell (GC), the VC is hypomethylated at CG sites while hypermethylated at CHG and CHH sites, with the majority of differentially methylation regions targeted to transposable elements (TEs). SCs have a nearly identical DNA methylome to the GC, suggesting that the methylation landscape in SCs may be pre‐established following the asymmetric division or inherited from the GC. The random forest classifier for predicting gene and TE expression shows that methylation within the gene body is a more powerful predictor for gene expression. Among all tested samples, gene and TE expression in the microspore may be more predictable by DNA methylation. Our results depict an intact DNA methylome landscape of SC lineage in higher plants, and reveal that the impact of DNA methylation on transcription is variant in different cell types.
A chromosome‐scale genome assembly of European hazel (Corylus avellana L.) reveals targets for crop improvement
Authors: Lucas Stuart J. , Kahraman Kadriye , Avşar Bihter , Buggs Richard J.A. , Bilge Ipek 
Published: November 2020

SummaryThe European hazelnut (Corylus avellana L.) is a tree crop of economic importance worldwide, but especially for northern Turkey, where the majority of production takes place. Hazelnut production is currently challenged by environmental stresses, such as a recent outbreak of severe powdery mildew disease; furthermore, allergy to hazelnuts is an increasing health concern in some regions. In order to provide a foundation for using the available hazelnut genetic resources for crop improvement, we produced a fully assembled genome sequence and annotation for a hazelnut species, from C. avellana cv. ‘Tombul’, one of the most important Turkish varieties. A hybrid sequencing strategy, combining short reads, long reads and proximity ligation methods, enabled us to resolve heterozygous regions and produce a high‐quality 370‐Mb assembly that agrees closely with cytogenetic studies and genetic maps of the 11 C. avellana chromosomes, and covers 97.8% of the estimated genome size. The genome includes 27 270 high‐confidence protein‐coding genes, over 20 000 of which were functionally annotated based on homology with known plant proteins. We focused particularly on gene families encoding hazelnut allergens, and the Mildew resistance Locus O (MLO) proteins that are an important susceptibility factor for powdery mildew. The complete assembly enabled us to differentiate between members of these families and to identify homologues that may be important in mildew disease and hazelnut allergy. These findings provide examples of how the genome can be used to guide research and to develop effective strategies for crop improvement in C. avellana.
Whole‐genome assembly and resequencing reveal genomic imprint and key genes of rapid domestication in narrow‐leafed lupin
Authors: Wang Penghao , Zhou Gaofeng , Jian Jianbo , Yang Huaan , Renshaw Daniel , Aubert Matthew K. , Clements Jonathan , He Tianhua , Sweetingham Mark , Li Chengdao 
Published: November 2020

SummaryShifting from a livestock‐based protein diet to a plant‐based protein diet has been proposed as an essential requirement to maintain global food sustainability, which requires the increased production of protein‐rich crops for direct human consumption. Meanwhile, the lack of sufficient genetic diversity in crop varieties is an increasing concern for sustainable food supplies. Countering this concern requires a clear understanding of the domestication process and dynamics. Narrow‐leafed lupin (Lupinus angustifolius L.) has experienced rapid domestication and has become a new legume crop over the past century, with the potential to provide protein‐rich seeds. Here, using long‐read whole‐genome sequencing, we assembled the third‐generation reference genome for the narrow‐leafed lupin cultivar Tanjil, comprising 20 chromosomes with a total genome size of 615.8 Mb and contig N50 = 5.65 Mb. We characterized the original mutation and putative biological pathway resulting in low seed alkaloid level that initiated the recent domestication of narrow‐leafed lupin. We identified a 1133‐bp insertion in the cis‐regulatory region of a putative gene that may be associated with reduced pod shattering (lentus). A comparative analysis of genomic diversity in cultivars and wild types identified an apparent domestication bottleneck, as precisely predicted by the original model of the bottleneck effect on genetic variability in populations. Our results identify the key domestication genetic loci and provide direct genomic evidence for a domestication bottleneck, and open up the possibility of knowledge‐driven de novo domestication of wild plants as an avenue to broaden crop plant diversity to enhance food security and sustainable low‐carbon emission agriculture.
Long‐distance stress and developmental signals associated with abscisic acid signaling in environmental responses
Authors: Yoshida Takuya , Fernie Alisdair R. , Shinozaki Kazuo , Takahashi Fuminori 
Published: November 2020

SummaryFlowering plants consist of highly differentiated organs, including roots, leaves, shoots and flowers, which have specific roles: root system for water and nutrient uptake, leaves for photosynthesis and gas exchange and reproductive organs for seed production. The communication between organs through the vascular system, by which water, nutrient and signaling molecules are transported, is essential for coordinated growth and development of the whole plant, particularly under adverse conditions. Here, we highlight recent progress in understanding how signaling pathways of plant hormones are associated with long‐distance stress and developmental signals, with particular focus on environmental stress responses. In addition to the root‐to‐shoot peptide signal that induces abscisic acid accumulation in leaves under drought stress conditions, we summarize the diverse stress‐responsive peptide signals reported to date to play a role in environmental responses.
Histologic effects of MicroPulse™ transscleral cyclophotocoagulation in normal equine eyes
Authors: Foote Braidee C. , Smith Jodi D. , Allbaugh Rachel A. , Sebbag Lionel 
Published: November 2020

AbstractObjectiveDetermine the immediate post‐operative effects of MicroPulse™ transscleral cyclophotocoagulation (MP‐TSCPC) in healthy equine eyes.Animals studiedTen adult horses.MethodsMP‐TSCPC was performed on sedated horses in 12 eyes (4 groups) using the following parameters (power, duration, duty cycle): (1) 2000 mW, 180 seconds, 31.3%; (2) 3000 mW, 180 seconds, 31.3%; (3) 3000 mW, 270 seconds, 31.3%; and (4) 3000 mW, 270 seconds, 50%. Three additional eyes were left untreated (control). Eyes were monitored clinically until euthanasia (mean = 3 hours post‐procedure). Histologic sections were assessed with light microscopy and transmission electron microscopy (TEM).ResultsMP‐TSCPC was well tolerated by sedated horses. Adverse effects were only noted in Group 4: ocular hypertension (n = 3/3), conjunctival burns (3/3), aqueous flare (2/3), and a corneal erosion (1/3). Histologic scoring of Group 4 was statistically greater than other treated groups (1‐3) and control eyes (P ≤ .021). TEM showed subtle changes to the mitochondria and plasma membrane infoldings of the basilar surface of the nonpigmented epithelium in all treated eyes.ConclusionsMP‐TSCPC does not cause immediate post‐procedure adverse clinical effects or pronounced morphological changes to the ciliary body, except with the highest laser settings evaluated (power 3000 mW, duration 270 seconds, duty cycle 50%).
Toxoplasma gondiiinfection in Colombia with a review of hosts and their ecogeographic distribution
Authors: Pérez‐Grisales Luis Javier , Cruz‐Moncada Mariana , Peláez‐Sánchez Ronald , Díaz‐Nieto Juan Fernando 
Published: November 2020

AbstractToxoplasma gondiiis one of the most prevalent zoonotic protozoan parasites among warm‐blooded animal populations (humans included) around the world, causing multiple clinic manifestations including death in the most severe cases of infection. Due to the versatile life cycle ofT. gondiiand its diversity of potential hosts, there is a common perception that natural areas and wildlife are highly prevalent reservoirs for the parasite; however, information and reports of the parasite on wildlife populations in Colombia are scarce. Using PRC‐based detection analyses of the B1 gene, we evaluated the presence ofT. gondiiin 49 native small mammal species (10% of the mammal species of Colombia) from 4 different undisturbed natural habitats. Additionally, to understand the ecogeographical distribution of the parasite in Colombia, we developed a literature search of infection reports including information on the host species, density of records and occurrence patterns (using landcover and ecoregions) in natural, rural and urban areas. Our literature review showed a total of 8,103 reports ofT. gondiifor Colombia of which 86% were related to humans, and 14% to non‐human mammals and other categories, with just a single report associated to wildlife; additionally, 82% of all reports were associated to urban areas whereas only 18% to rural sites. Based on the negative results for the presence ofT. gondiiin our PCR‐based analyses and our literature search, we suggest thatT. gondiihas a synanthropic distribution in Colombia occurring in ecoregions as variable as the xeric scrubs in the northern lowlands and humid montane Andean forests, also we show a lack of information on the parasite relationship with wildlife, a concerning fact given that zoonoses are the leading mechanism for the emergence of infectious diseases.
Cancer risk in individuals with major birth defects: large Nordic population based case-control study among children, adolescents, and adults
Authors: Daltveit Dagrun Slettebø , Klungsøyr Kari , Engeland Anders , Ekbom Anders , Gissler Mika , Glimelius Ingrid , Grotmol Tom , Madanat-Harjuoja Laura , Ording Anne Gulbech , Sæther Solbjørg Makalani Myrtveit , Sørensen Henrik Toft , Troisi Rebecca , Bjørge Tone 
Published: December 2020

AbstractObjectiveTo examine associations between birth defects and cancer from birth into adulthood.DesignPopulation based nested case-control study.SettingNationwide health registries in Denmark, Finland, Norway, and Sweden.Participants62 295 cancer cases (0-46 years) and 724 542 frequency matched controls (matched on country and birth year), born between 1967 and 2014.Main outcome measuresRelative risk of cancer in relation to major birth defects, estimated as odds ratios with 99% confidence intervals from logistic regression models.ResultsAltogether, 3.5% (2160/62 295) of cases and 2.2% (15 826/724 542) of controls were born with major birth defects. The odds ratio of cancer for people with major birth defects compared with those without was 1.74 (99% confidence interval 1.63 to 1.84). For individuals with non-chromosomal birth defects, the odds ratio of cancer was 1.54 (1.44 to 1.64); for those with chromosomal anomalies, the odds ratio was 5.53 (4.67 to 6.54). Many structural birth defects were associated with later cancer in the same organ system or anatomical location, such as defects of the eye, nervous system, and urinary organs. The odds ratio of cancer increased with number of defects and decreased with age, for both non-chromosomal and chromosomal anomalies. The odds ratio of cancer in people with any non-chromosomal birth defect was lower in adults (≥20 years: 1.21, 1.09 to 1.33) than in adolescents (15-19 years: 1.58, 1.31 to 1.90) and children (0-14 years: 2.03, 1.85 to 2.23). The relative overall cancer risk among adults with chromosomal anomalies was markedly reduced from 11.3 (9.35 to 13.8) in children to 1.50 (1.01 to 2.24). Among adults, skeletal dysplasia (odds ratio 3.54, 1.54 to 8.15), nervous system defects (1.76, 1.16 to 2.65), chromosomal anomalies (1.50, 1.01 to 2.24), genital organs defects (1.43, 1.14 to 1.78), and congenital heart defects (1.28, 1.02 to 1.59) were associated with overall cancer risk.ConclusionsThe increased risk of cancer in individuals with birth defects persisted into adulthood, both for non-chromosomal and chromosomal anomalies. Further studies on the molecular mechanisms involved are warranted.
Global health education in UK medical schools: a review of undergraduate university curricula
Authors: Matthews Natasha Roya , Davies Bethan , Ward Helen 
Published: December 2020

IntroductionIn recognition of our increasingly globalised world, global health is now a required component of the medical school curriculum in the UK. We review the current provision of global health education (GHE) in UK medical schools to identify gaps in compulsory teaching.MethodsWe conducted a review of the literature to inform a two-part electronic survey of global health compulsory teaching, optional teaching and pre-elective training. Surveys were sent to all 33 UK medical schools for completion by the faculty lead on global health and the nominated final year student representative.ResultsSurveys were returned by 29 (88%) medical school faculty and 15 (45%) medical student representatives; 24 (83%) faculty and 10 (67%) students reported including GHE in the core curriculum; however, there was wide variation in the learning outcomes covered. On average 75% of faculty and 82% of students reported covering recommended global health themes ‘global burden of disease’, ‘socioeconomic and environmental determinants of health’, ‘human rights and ethics’, and ‘cultural diversity and health’, while only 48% of faculty and 33% of students reported teaching on ‘health systems’ and ‘global health governance’. Almost all institutions offered optional global health programmes and most offered some form of pre-elective training, although content and delivery were variable.ConclusionOver the last decade, the inclusion of global health in the core curriculum of UK medical schools has increased dramatically. Yet, despite interest among students, significant gaps are apparent in current GHE. Governing bodies in medical education should establish a comprehensive national strategy to help improve access to fundamental GHE for all medical students.
Surgical site infection after gastrointestinal surgery in children: an international, multicentre, prospective cohort study
Authors:   GlobalSurg Collaborative
Published: December 2020

IntroductionSurgical site infection (SSI) is one of the most common healthcare-associated infections (HAIs). However, there is a lack of data available about SSI in children worldwide, especially from low-income and middle-income countries. This study aimed to estimate the incidence of SSI in children and associations between SSI and morbidity across human development settings.MethodsA multicentre, international, prospective, validated cohort study of children aged under 16 years undergoing clean-contaminated, contaminated or dirty gastrointestinal surgery. Any hospital in the world providing paediatric surgery was eligible to contribute data between January and July 2016. The primary outcome was the incidence of SSI by 30 days. Relationships between explanatory variables and SSI were examined using multilevel logistic regression. Countries were stratified into high development, middle development and low development groups using the United Nations Human Development Index (HDI).ResultsOf 1159 children across 181 hospitals in 51 countries, 523 (45·1%) children were from high HDI, 397 (34·2%) from middle HDI and 239 (20·6%) from low HDI countries. The 30-day SSI rate was 6.3% (33/523) in high HDI, 12·8% (51/397) in middle HDI and 24·7% (59/239) in low HDI countries. SSI was associated with higher incidence of 30-day mortality, intervention, organ-space infection and other HAIs, with the highest rates seen in low HDI countries. Median length of stay in patients who had an SSI was longer (7.0 days), compared with 3.0 days in patients who did not have an SSI. Use of laparoscopy was associated with significantly lower SSI rates, even after accounting for HDI.ConclusionThe odds of SSI in children is nearly four times greater in low HDI compared with high HDI countries. Policies to reduce SSI should be prioritised as part of the wider global agenda.
Intimate partner violence, contextual factors and under-5 mortality: a multilevel analysis of cross-sectional surveys from 20 Sub-Saharan African countries
Authors: Yaya Sanni , Anjorin Seun Stephen , Adedini Sunday A 
Published: December 2020

BackgroundUnder-5 mortality remains a public health concern in low-income and middle-income countries. Africa contributes about one-fifth of the burden of global under-5 mortality; intimate partner violence (IPV) and polygyny, which are highly prevalent on the continent, have been linked to under-5 mortality at the individual level. This study examined the relationship between IPV and polygyny as contextual factors and the experience of under-5 mortality among women in Sub-Saharan Africa (SSA).MethodsWe used data from the Demographic and Health Surveys (DHS) of 20 African countries with available data between 2010 and 2018 as of April 2020. We defined the experience of under-5 mortality as a woman’s loss of at least one child before their fifth birthday. The DHS primary sampling unit was used to define contextual factors. The study involved a multilevel logistic regression analysis of 227 121 women of childbearing age (15–49).ResultsA quarter (24.5%) of women have lost at least one child under 5 years old, more than two-thirds (40.1%) have experienced at least one form of IPV, and about two-thirds of women were in polygynous union. Our multilevel logistic regression showed that parity, polygynous union and experience of IPV were strongly associated with women’s experience of under-5 mortality. The results showed that 39.9% and 19.2% of variances in odds of a woman losing a child before their fifth birthday are attributable to community-level and country-level factors, respectively. Contextual prevalence of IPV, polygynous union and gender equity attenuate the strength of associations observed at the individual level. The interaction between contextual prevalence of polygyny and IPV exacerbates the risk of under-5 mortality. Women in SSA countries with higher Human Development Index were less likely to experience under-5 mortality.ConclusionThis study established that beyond individual-level effects, contextual prevalence of IPV and polygyny and their interactions shape women’s experience of under-5 mortality in Africa. In designing policies and interventions to address under-5 mortality, contextual factors, especially those linked to culturally laden social norms and practices, must be considered to ensure effectiveness and sustainable impact.
Weekly iron–folic acid supplements containing 2.8 mg folic acid are associated with a lower risk of neural tube defects than the current practice of 0.4 mg: a randomised controlled trial in Malaysia
Authors: Samson Kaitlyn L I , Loh Su Peng , Lee Siew Siew , Sulistyoningrum Dian C , Khor Geok Lin , Shariff Zalilah Binti Mohd , Ismai Irmi Zarina , Yelland Lisa N , Leemaqz Shalem , Makrides Maria , Hutcheon Jennifer A , Roche Marion L , Karakochuk Crystal D , Green Timothy J 
Published: December 2020

IntroductionWeekly iron–folic acid (IFA) supplements are recommended for all menstruating women in countries where anaemia prevalence is >20%. Anaemia caused by folate deficiency is low worldwide, and the need to include folic acid is in question. Including folic acid might reduce the risk of a neural tube defect (NTD) should a woman become pregnant. Most weekly supplements contain 0.4 mg folic acid; however, WHO recommends 2.8 mg because it is seven times the daily dose effective in reducing NTDs. There is a reluctance to switch to supplements containing 2.8 mg of folic acid because of a lack of evidence that this dose would prevent NTDs. Our aim was to investigate the effect of two doses of folic acid, compared with placebo, on red blood cell (RBC) folate, a biomarker of NTD risk.MethodsWe conducted a three-arm double-blind efficacy trial in Malaysia. Non-pregnant women (n=331) were randomised to receive 60 mg iron and either 0, 0.4, or 2.8 mg folic acid once weekly for 16 weeks.ResultsAt 16 weeks, women receiving 0.4 mg and 2.8 mg folic acid per week had a higher mean RBC folate than those receiving 0 mg (mean difference (95% CI) 84 (54 to 113) and 355 (316 to 394) nmol/L, respectively). Women receiving 2.8 mg folic acid had a 271 (234 to 309) nmol/L greater mean RBC folate than those receiving 0.4 mg. Moreover, women in the 2.8 mg group were seven times (RR 7.3, 95% CI 3.9 to 13.7; p<0.0001) more likely to achieve an RBC folate >748 nmol/L, a concentration associated with a low risk of NTD, compared with the 0.4 mg group.ConclusionWeekly IFA supplements containing 2.8 mg folic acid increases RBC folate more than those containing 0.4 mg. Increased availability and access to the 2.8 mg formulation is needed.Trail registration numberThis trial is registered with the Australian New Zealand Clinical Trial Registry (ACTRN12619000818134).
Development of a high-throughput SARS-CoV-2 antibody testing pathway using dried blood spot specimens
Authors: Moat Stuart J , Zelek Wioleta M , Carne Emily , Ponsford Mark J , Bramhall Kathryn , Jones Sara , El-Shanawany Tariq , Wise Matt P , Thomas Annette , George Chloe , Fegan Christopher , Steven Rachael , Webb Russell , Weeks Ian , Morgan B Paul , Jolles Stephen 
Published: December 2020

Background Serological assays for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have roles in seroepidemiology, convalescent plasma-testing, antibody durability and vaccine studies. Currently, SARS-CoV-2 serology is performed using serum/plasma collected by venepuncture. Dried blood spot (DBS) testing offers significant advantages as it is minimally invasive, avoids venepuncture with specimens being mailed to the laboratory. Methods A pathway utilizing a newborn screening laboratory infrastructure was developed using an enzyme-linked immunosorbent assay to detect IgG antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein in DBS specimens. Paired plasma and DBS specimens from SARS-CoV-2 antibody-positive and -negative subjects and polymerase chain reaction positive subjects were tested. DBS specimen stability, effect of blood volume and punch location were also evaluated. Results DBS specimens from antibody-negative ( n = 85) and -positive ( n = 35) subjects and polymerase chain reaction positive subjects ( n = 11) had a mean (SD; range) optical density (OD) of 0.14 (0.046; 0.03–0.27), 0.98 (0.41; 0.31–1.64) and 1.12 (0.37; 0.49–1.54), respectively. An action value OD >0.28 correctly assigned all cases. The weighted Deming regression for comparison of the DBS and the plasma assay yielded: y = 0.004041 + 1.005 x, r = 0.991, Sy/ x 0.171, n = 82. Extraction efficiency of antibodies from DBS specimens was >99%. DBS specimens were stable for at least 28 days at ambient room temperature and humidity. Conclusions SARS-CoV-2 IgG receptor-binding domain antibodies can be reliably detected in DBS specimens. DBS serological testing offers lower costs than either point of care or serum/plasma assays that require patient travel, phlebotomy and hospital/clinic resources; the development of a DBS assay may be particularly important for resource poor settings.