Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotype‐environment interaction reveals varied developmental responses to unpredictable host phenology in a tropical insect

Understanding the genetic architecture of life history plasticity may inform resilience under environmental change, but relatively little is known for the inhabitants of unpredictable wet‐dry tropical environments. Here, I explore the quantitative genetics of juvenile growth and development relative to hostplant phenology in the butterfly Eurema hecabe. Wet season generations of this species breed explosively on leguminous annuals whereas dry season generations subsist at low density upon an alternative perennial host. The wet‐to‐dry season transition is temporally unpredictable and marked by widespread host defoliation, forcing a large cohort of stranded larvae to either pupate prematurely or prolong development in the hope of renewed foliage production. A split‐brood experiment demonstrated greater performance on high quality annual as opposed to perennial host foliage and a marked decline under the stressed conditions faced by stranded wet season larvae. Genetic variances for rates of growth and development were equivalent among high quality treatments but strikingly elevated under resource stress, and the associated cross‐environment genetic correlations were indistinguishable from zero. The results demonstrate genotype‐environment interaction involving both rank order and variance scale, thereby revealing genetic variance for norms of reaction that may reflect variable risk aversion given an unpredictable tropical host phenology.
Effects of Zinc in an Outdoor Freshwater Microcosm System

A long‐term exposure outdoor microcosm study was conducted to evaluate the effects of zinc (Zn) on zooplankton, phytoplankton, and periphyton in a freshwater system. Five Zn treatment concentrations (nominal: 8, 20, 40, 80, and 160 μg/L Zn) and an untreated control with 3 replicates each were used. Various physical and chemical characteristics of the microcosms and biological assessment endpoints (e.g., total abundance, group abundance, species richness, chlorophyll a, etc.) were measured to determine the effects of Zn over time. In general, physical and chemical characteristics (e.g., total dissolved solids, total suspended solids, dissolved oxygen, pH, dissolved organic carbon) of water fluctuated over time, but they were not significantly different within treatments and controls during the study. Zinc significantly affected the population dynamics and community structure of plankton. The effects occurred 7 d after initial treatment exposures began and continued to the end of the treatment phase, especially at the high treatment concentrations. Total and group abundance, species richness, the Shannon index, and chlorophyll a concentrations for high Zn treatment concentrations were significantly lower than the controls during the treatment phase. The no‐observed‐effect, lowest‐observed‐effect, and median effect concentrations were generally lower than the literature‐reported results from single‐species toxicity tests for fish and invertebrates, suggesting that plankton are more sensitive to Zn than planktivores. Although primary producers play an important role in the ecosystem, they have not been consistently incorporated into numerical environmental quality criteria for freshwater organisms, at least in the United States. The results of the present study are useful for development of environmental quality guidelines for freshwater ecosystems and ecological risk assessment. Environ Toxicol Chem 2021;40:2051–2070. © 2021 SETAC
Lipidic Cubic Phases as a Versatile Platform for the Rapid Detection of Biomarkers, Viruses, Bacteria, and Parasites

Rapid and affordable detection of analytes is critical in diagnostic technologies, but current methods are typically expensive and unsuitable for field detection. Lipidic cubic phases are optically isotropic, transparent lyotropic liquid crystals (LC), containing highly confined water nanochannels in‐between percolating lipid bilayers following defined space groups. Due to this nanoconfinement, the water in these systems provides a unique environment for chemical and enzymatic reactions. Here, it is shown that during the in meso peroxidase enzymatic reaction, the converted product crystallizes within the mesophase domains, generating a detectable birefringence signal and a new general assay principle is presented for the detection of an unprecedented vast class of analytes using such birefringence as sole optical output signal. By exploiting bienzymatic cascade reactions or introducing an enzyme‐linked immunosorbent assay based on birefringence (Birefringent‐ELISA), this approach is used for real‐time detection of exemplary analytes, such as glucose and cholesterol, model pathogenic microorganisms, Escherichia coli, and viruses such as Ebola and HIV. It is also shown how the same technology enables the rapid, naked‐eye screening of malaria infection via in meso detection of hemozoin crystallites. This new technology is general and readily adaptable to the rapid detection of virtually any type of analyte, such as disease biomarkers, viruses, bacteria, and parasites.
Viral determinants that drive Enterovirus-A71 fitness and virulence

ABSTRACT Hand, Foot and Mouth Disease (HFMD) is usually a self-limiting, mild childhood disease that is caused mainly by Coxsackie virus A16 (CVA16) and Enterovirus A71 (EV-A71), both members of the Picornaviridae family. However, recurring HFMD outbreaks and epidemics due to EV-A71 infection in the Western Pacific region, and the propensity of EV-A71 strains to cause severe neurological complications have made this neurotropic virus a serious public health concern in afflicted countries. High mutation rate leading to viral quasispecies combined with frequent intra- and inter-typic recombination events amongst co-circulating EV-A71 strains have contributed to the great diversity and fast evolution of EV-A71 genomes, making impossible any accurate prediction of the next epidemic strain. Comparative genome sequence analyses and mutagenesis approaches have led to the identification of a number of viral determinants involved in EV-A71 fitness and virulence. These viral determinants include amino acid residues located in the structural proteins of the virus, affecting attachment to the host cell surface, receptor binding, and uncoating events. Critical residues in non-structural proteins have also been identified, including 2C, 3A, 3C proteases and the RNA-dependent RNA polymerase. Finally, mutations altering key secondary structures in the 5’ untranslated region were also found to influence EV-A71 fitness and virulence. While our current understanding of EV-A71 pathogenesis remains fragmented, these studies may help in the rational design of effective treatments and broadly protective vaccine candidates.
What do the public really know about dementia and its risk factors?

Dementia has become a major public health concern globally. With no cure available and strong evidence for modifiable risk factors, it is imperative that the public are knowledgeable about dementia and to reduce their risk. The aim of this study was to measure the knowledge of dementia and its risk factors in the Australian public, as well as the number and type of information sources used. An online survey promoted through various social media platforms was completed by 596 Australian adults aged 18–78 years (59% aged 18–44 years; 78% female). Eighty-eight percent of respondents were able to recognise dementia from a vignette, more so from a moderate than from a mild symptom vignette. Only 19% of respondents had a good understanding of dementia, that is describing impairment in both cognition and function. Ninety-five percent of respondents recognised that genetics and old age contributed to a person getting dementia. However, respondents had poor knowledge of empirically supported modifiable risk factors, with most viewed as likely contributors to dementia at chance levels (50%) or below. Respondents reported using informal information sources more often than formal information sources to learn about dementia. The public appear to be able to recognise the symptoms of dementia but lack understanding of how dementia impacts both a person’s cognitive functioning and ability to perform everyday tasks. Furthermore, the public remain largely unaware of empirically supported modifiable risk factors that contribute to the development of dementia. It is imperative that the public are educated on how to access and evaluate dementia-related information sources in order to increase their knowledge and understanding of dementia.
Anthropometric study as a predictor of anterior cruciate ligament sizes in Asian Indonesian population

Objectives: To evaluate whether anthropometric data can predict anterior cruciate ligament (ACL) sizes on magneti resonance imaging (MRI) in Asian population. Background: Reconstruction of ACL has been performed over a decade ago. Recently, more individualized ACL reconstruction is performed taking account of each patient’s ACL characteristics. However, there has been limited study regarding ACL sizes in Asian Indonesian population. This study aimed to evaluate the role of anthropometric data in ACL sizes using MRI in Asian Indonesian population. Study Design: Retrospective Study. Method: A series of 531 knees from 420 patients with knee pain and intact ACL confirmed by MRI study. Length, width and inclination angle of ACL were measured using a T2-weighted sagittal MRI 3.0 Tesla Magnetom Skyra. Height, weight, body mass index (BMI) and age were recorded. Multiple regression analysis was used to determine relationship between the anthropometric data and size of ACL measurements. Result: ACL length and width were significantly different between male and female, consecutively. Mean ACL length was 35.36 ± 3.63 mm, male was significantly longer (36.59 ± 3.24 mm) compared to female (32.77 ± 2.99 mm), p < 0.0001. Mean ACL width was 10.23 ± 1.84 mm, male was significantly wider (10.85 ± 1.59 mm) compared to female (8.93 ± 1.64 mm), p < 0.0001. The mean ACL inclination angle was 47.75° ± 3.07° (range 40.17°–57.12°). The strongest correlation for ACL length was height and weight (r = 0.437; r = 0.341 consecutively, p < 0.0001). Females had stronger correlation compared to males for ACL length (R2 = 0.489 vs R2 = 0.418). ACL width showed weak correlation with anthropometric data. The following regression analysis equation was obtained for ACL length: ACL length = 60.697 − 0.11*age + 0.461*weight (kg) − 16.522*height (meter) − 1.093*BMI (R2 = 0.539; p < 0.0001). Conclusion: Anthropometric data can be utilized as a predictor of ACL length in Asian Indonesian population. The ACL length in Asian Indonesian population is shorter than that in Western population study.
Nutrient supplementation among pregnant women in China: an observational study

Abstract Objective: To clarify nutrient supplementation usage and primary source of information among pregnant women in China. Design: This cross-sectional study used information on nutrient supplementation and primary source of information collected via face-to-face interviews. Data on the usage of folic acid, Ca/vitamin D, Fe, vitamins, DHA and other dietary supplements were collected. Primary source of information was categorised as family/relatives, friends/co-workers, the Internet, books/magazines, television/radio, doctors, other people and oneself. Setting: Maternal and Child Health Hospital in Chengdu, China. Participants: One thousand eighty-one Chinese pregnant women aged ≥20 years with singleton pregnancies. Results: In all three trimesters of pregnancy, usage was highest and most stable for folic acid (81·7 %), followed by vitamins (vitamin A, B-group vitamins, vitamin C and multivitamins; 75·0 %), whereas Ca/vitamin D (51·4 %) and Fe (18·1 %) usage was low, potentially indicating a deficiency risk. All supplementation usage percentages increased with pregnancy duration (P < 0·05). Notably, approximately 10 % of the pregnant women in our study did not use any nutrient supplementation, and this was especially common in early pregnancy. More than 50 % of the women reported getting information on nutrient supplementation from family members, and about 30 % reported getting this information from doctors. Conclusions: Among pregnant women in China, awareness about nutrient supplementation increases as the pregnancy progresses, but some types of nutrient supplementation (such as Ca/vitamin D and Fe) remain at low levels. It is necessary to pay more attention to the health education of pregnant women in China, and the influence of family members should be emphasised.
Good general health and lack of family history influence the underestimation of cardiovascular risk: a cross-sectional study.

AIMS Underestimation of cardiovascular risk may interfere with prevention of cardiovascular diseases (CVDs). We investigate whether general health and family history of myocardial infarction (MI) are associated with underestimation of perceived cardiovascular risk, and if the participants' calculated risk modifies that association. METHODS AND RESULTS The analysis sample consisted of 526 individuals, 50-64 years old, from a population-based cohort study. Information on general health (poor/fairly good, good, and very good/excellent), family history of MI, and self-perceived risk relative to others of similar age and sex were collected though a web-based survey. Participants were categorized into underestimation (n = 162, 31%), accurate estimation (n = 222, 42%), and overestimation (n = 142, 27%) of cardiovascular risk by comparing calculated Systematic Coronary Risk Estimation (SCORE) with self-perceived risk. Adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for underestimation vs. accurate estimation of cardiovascular risk were computed using logistic regression (n = 384). Very good general health (OR 2.60, 95% CI 1.10-6.16) and lack of family history (OR 2.27, 95% CI 1.24-4.18) were associated with underestimation of cardiovascular risk. The associations were modified by the participants' calculated risk level; the association was stronger for high-risk individuals; without family history OR 22.57 (95% CI 6.17-82.54); with very good/excellent health OR 15.78 (95% CI 3.73-66.87). CONCLUSION A good general health and the lack of family CVD history can obscure the presence of other risk factors and lead to underestimation of cardiovascular risk, especially for high-risk individuals. It is, therefore, crucial to address the fact that the development of CV disease may be silent and multifactorial.
A local dielectric constant model for solvation free energies which accounts for solute polarizability

A model for treating solute polarizability in solvation processes is presented. The model, which requires little computation compared to atomic detail simulations, is based on a classical electrostatic treatment, whereby the solute polarizability is represented by local dielectric constants (LDC) rather than the usual point inducible dipoles. Point inducible dipoles and local dielectric constants are shown to be formally equivalent ways of representing solute polarizability for a simple spherical, point dipolar solute. For more realistic solute representations, however, there are some advantages to the local dielectric model
Escherichia coli O121 outbreak associated with raw milk Gouda-like cheese in British Columbia, Canada, 2018.

Background In 2018, a Shiga toxin-producing Escherichia coli O121 outbreak that affected seven individuals was associated with raw milk Gouda-like cheese produced in British Columbia, Canada. Objectives To describe the E. coli O121 outbreak investigation and recommend greater control measures for raw milk Gouda-like cheese. Methods Cases of E. coli O121 were identified through laboratory testing results and epidemiologic surveillance data. The cases were interviewed on exposures of interest, which were analyzed against Foodbook Report values for British Columbia. Environmental inspection of the dairy plant and the cheese products was conducted to ascertain a source of contamination. Whole genome multi-locus sequence typing (wgMLST) was performed on all positive E. coli O121 clinical and food isolates at the provincial laboratory. Results Four out of the seven cases consumed the same raw milk Gouda-like cheese between August and October 2018. The implicated cheese was aged longer than the required minimum of 60 days, and no production deficiencies were noted. One sample of the implicated cheese tested positive for E. coli O121. The seven clinical isolates and one cheese isolate matched by wgMLST within 6.5 alleles. Conclusion Raw milk Gouda and Gouda-like cheese has been implicated in three previous Shiga toxin-producing E. coli outbreaks in North America. It was recommended product labelling to increase consumer awareness and thermization of milk to decrease the risk of illness associated with raw milk Gouda and Gouda-like cheese.
The role of extracellular DNA in the formation, architecture, stability, and treatment of bacterial biofilms

Advances in biotechnology to treat and cure human disease have markedly improved human health and the development of modern societies. However, substantial challenges remain to overcome innate biological factors that thwart the activity and efficacy of pharmaceutical therapeutics. Until recently, the importance of extracellular DNA (eDNA) in biofilms was overlooked. New data reveal its extensive role in biofilm formation, adhesion, and structural integrity. Different approaches to target eDNA as anti‐biofilm therapies have been proposed, but eDNA and the corresponding biofilm barriers are still difficult to disrupt. Therefore, more creative approaches to eradicate biofilms are needed. The production of eDNA often originates with the genetic material of bacterial cells through cell lysis. However, genomic DNA and eDNA are not necessarily structurally or compositionally identical. Variations are noteworthy because they dictate important interactions within the biofilm. Interactions between eDNA and biofilm components may as well be exploited as alternative anti‐biofilm strategies. In this review, we discuss recent developments in eDNA research, emphasizing potential ways to disrupt biofilms. This review also highlights proteins, exopolysaccharides, and other molecules interacting with eDNA that can serve as anti‐biofilm therapeutic targets. Overall, the array of diverse interactions with eDNA is important in biofilm structure, architecture, and stability.
Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album)

Abstract The comma butterfly (Polygonia c-album, Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.
Reference Values for Ventricular Volumes and Pulmonary Artery Dimensions in Pediatric Patients with Transposition of the Great Arteries After Arterial Switch Operation

Pulmonary artery (PA) anatomy in patients with transposition of the great arteries (TGA) after arterial switch operation (ASO) with Lecompte manoeuvre is different compared to healthy subjects, and stenoses of the PA are common. Magnetic resonance imaging (MRI) is an excellent imaging modality to assess PA anatomy in TGA patients. However, disease‐specific reference values for PA size are scarce.
Modeling multi-species RNA modification through multi-task curriculum learning

Abstract N6-methyladenosine (m6A) is the most pervasive modification in eukaryotic mRNAs. Numerous biological processes are regulated by this critical post-transcriptional mark, such as gene expression, RNA stability, RNA structure and translation. Recently, various experimental techniques and computational methods have been developed to characterize the transcriptome-wide landscapes of m6A modification for understanding its underlying mechanisms and functions in mRNA regulation. However, the experimental techniques are generally costly and time-consuming, while the existing computational models are usually designed only for m6A site prediction in a single-species and have significant limitations in accuracy, interpretability and generalizability. Here, we propose a highly interpretable computational framework, called MASS, based on a multi-task curriculum learning strategy to capture m6A features across multiple species simultaneously. Extensive computational experiments demonstrate the superior performances of MASS when compared to the state-of-the-art prediction methods. Furthermore, the contextual sequence features of m6A captured by MASS can be explained by the known critical binding motifs of the related RNA-binding proteins, which also help elucidate the similarity and difference among m6A features across species. In addition, based on the predicted m6A profiles, we further delineate the relationships between m6A and various properties of gene regulation, including gene expression, RNA stability, translation, RNA structure and histone modification. In summary, MASS may serve as a useful tool for characterizing m6A modification and studying its regulatory code. The source code of MASS can be downloaded from https://github.com/mlcb-thu/MASS.
Tipping the scale: the role of a national nutritional supplementation programme for pregnant mothers in reducing low birth weight and neonatal mortality in India

Abstract With over 1·3 million Anganwadi centres (AWC) (meaning ‘courtyard shelter’), the Indian government runs a nationwide intervention providing nutrition supplement to pregnant mothers to improve the health of their children. Using two successive rounds of the nationally representative cross-sectional National Family Health Survey data (collected during 2005–2006 and 2015–2016) of India, we assessed whether nutrition supplements given to pregnant mothers through AWC were associated with select child health indicators – extremely low birth weight (ELBW), very low birth weight (VLBW), low birth weight (LBW) and neonatal mortality (death during day 0–27) stratified by death during day 0–1, day 2–6 and day 7–27. A total of 148 019 children and 205 593 children were eligible for analysing birth weight and neonatal mortality, respectively. OR with 95% CI, estimated from multivariate logistic regression models, suggest that receipt of nutrition supplements was associated with decreased risk of VLBW (OR: 0·73, 95% CI 0·63, 0·83, P < 0·001), LBW (OR: 0·92, 95% CI 0·88, 0·96, P < 0·001), but not ELBW (OR: 0·80, 95% CI 0·56, 1·15, P = 0·226). Women who always received nutrition supplements during their pregnancy saw lower risk of death of their neonates (OR: 0·67, 95% CI 0·61, 0·73, P < 0·001), including death on day 0–1 (OR: 0·66, 95% CI 0·58, 0·74, P < 0·001), day 2–6 (OR: 0·69, 95% CI 0·58, 0·82, P < 0·001) and day 7–27 (OR: 0·68, 95% CI 0·53, 0·87, P = 0·002). Therefore, nutritional supplementation to pregnant mothers appears to be helpful in deterring various stages of neonatal mortality, VLBW and LBW, though it might not be effective in mitigating ELBW. Findings were discussed considering possible limitations of the study.