Miracle-dz/UniFAR-FTUs huggingface dataset:
A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis

Abstract Background Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis. Findings To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ∼17–kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ∼656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ∼70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ∼99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules. Conclusions Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.
Return of Menstruation among Exclusive Breastfeeding Women in Southwest Nigeria

Background: Women experience variations in postpartum amenorrhea, the length of which depends on the type of breastfeeding and women’s physiology. We conducted the present Study to assess the perception and pattern of resumption of menstruation, and identify the determinants of resumption of menstruation and proportion at risk of unplanned pregnancy among exclusive breastfeeding women. Methods: Study employed sequential explanatory mixed method research design and was conducted between September and November, 2019. We collected the quantitative data using a semi-structured questionnaire from 497 exclusive breastfeeding women selected through a two-stage sampling technique in Southwest Nigeria. In addition, Focus Group Discussion guide was utilized to conduct qualitative study. The quantitative data were analyzed with SPSS version 22 using appropriate statistic, and the level of significance was p Results: Our result revealed that 43.4% of women whose postpartum period begins in less than eight weeks were amenorrheic, 65.6% of women whose postpartum period occurs between the 8th and 16th week were also amenorrheic, 85.8% of women whose postpartum period begins between 17th and 24th week remained amenorrheic. 76% of the women studied relied on Lactational Amenorrhea for contraception. Age (P=0.001, OR=0.24, CI=0.10-0.50), parity (P=0.04, OR=0.55, CI=0.31-0.79), and postpartum length (P=0.002, OR=0.23, CI=0.18-0.75) remained significant determinants of the return of menstruation. Conclusion: A significant proportion of women studied perceived themselves to be at no risk of unplanned pregnancy which may ultimately influence timely postpartum contraceptive uptake. Advocacy should therefore focus on addressing effective contraception among this group of women
A functional variant in SLC1A3 influences ADHD risk by disrupting a hsa‐miR‐3171 binding site: A two‐stage association study

Attention‐deficit hyperactivity disorder (ADHD) is one of the most common neuropsychiatric disorders in children and adolescents with high heritability. Evidence is accumulating that SLC1A3 may play a role in ADHD etiology. Therefore, a two‐stage case‐control study was conducted on 752 cases and 774 controls to explore the role of SLC1A3 in ADHD. Bioinformatic annotations and functional experiments were applied to reveal the potential biological mechanisms. Finally, SLC1A3 rs1049522 showed significant association with ADHD risk in two stages with CA genotype vs AA genotype, odds ratio (OR) = 0.694 (95% confidence interval, CI = 0.570‐0.844) and dominant model, OR = 0.749 (95% CI = 0.621‐0.904) in the combined stage. Besides, rs1049522 was found to be related to ADHD hyperactive/impulsive symptom, and rs1049522‐C showed increased SLC1A3 mRNA expression in the cerebellar cortex. Dual‐luciferase reporter assay further indicated that rs1049522‐C allele enhanced SLC1A3 expression by disrupting the hsa‐miR‐3171 binding site. In conclusion, SLC1A3 variant rs1049522 was implicated in ADHD susceptibility in a Chinese Han population probably by enhancing the SLC1A3 expression in a miRNA‐mediated manner.
How Does Crossing Roads with Friends Impact Risk Taking in Young Adolescents and Adults?

OBJECTIVE The goal of this investigation was to examine how crossing roads with a friend versus alone affects gap decisions and movement timing in young adolescents and adults. METHODS Ninety-six 12-year-olds and adults physically crossed a single lane of continuous traffic in an immersive pedestrian simulator. Participants completed 30 crossings either with a friend or alone. Participants were instructed to cross the road without being hit by a car, but friend pairs were not instructed to cross together. RESULTS Pairs of adolescent friends exhibited riskier road-crossing behavior than pairs of adult friends. For gaps crossed together, adult pairs were more discriminating in their gap choices than adult solo crossers, crossing fewer of the smaller gaps and more of the larger gaps. This pattern did not hold for 12-year-old pairs compared to 12-year-old solo crossers. To compensate for their less discriminating gap choices, pairs of 12-year-olds adjusted their movement timing by entering and crossing the road more quickly. For gaps crossed separately, both adult and 12-year-old first crossers chose smaller gaps than second crossers. Unlike adults, 12-year-old first crossers were significantly less discriminating in their gap choices than 12-year-old second crossers. CONCLUSIONS Compared to adults, young adolescents took riskier gaps in traffic when crossing virtual roads with a friend than when crossing alone. Given that young adolescents often cross roads together in everyday life, peer influences may pose a significant risk to road safety in early adolescence.
International Association of Athletics Federations Consensus Statement 2019: Nutrition for Athletics.

The International Association of Athletics Federations recognizes the importance of nutritional practices in optimizing an Athlete's well-being and performance. Although Athletics encompasses a diverse range of track-and-field events with different performance determinants, there are common goals around nutritional support for adaptation to training, optimal performance for key events, and reducing the risk of injury and illness. Periodized guidelines can be provided for the appropriate type, amount, and timing of intake of food and fluids to promote optimal health and performance across different scenarios of training and competition. Some Athletes are at risk of relative energy deficiency in sport arising from a mismatch between energy intake and exercise energy expenditure. Competition nutrition strategies may involve pre-event, within-event, and between-event eating to address requirements for carbohydrate and fluid replacement. Although a "food first" policy should underpin an Athlete's nutrition plan, there may be occasions for the judicious use of medical supplements to address nutrient deficiencies or sports foods that help the athlete to meet nutritional goals when it is impractical to eat food. Evidence-based supplements include caffeine, bicarbonate, beta-alanine, nitrate, and creatine; however, their value is specific to the characteristics of the event. Special considerations are needed for travel, challenging environments (e.g., heat and altitude); special populations (e.g., females, young and masters athletes); and restricted dietary choice (e.g., vegetarian). Ideally, each Athlete should develop a personalized, periodized, and practical nutrition plan via collaboration with their coach and accredited sports nutrition experts, to optimize their performance.
Assessment of Vitamin D Level in Patients with Recurrent Renal Calcium Stones

Background: a higher concentration of the active vitamin D metabolite colic calciferol 1,25-dihydroxyvitamin D3 is associated with increased urinary calcium excretion, which could lead to increase the risk of stone formation. Objectives: To assess vitamin D level in patients with recurrent renal calcium (Ca) stones. Patients and methods: This study was conducted in Urology Department at Menoufia University Hospital during the period from March 2018 to December 2019. 96 patients were included in this study divided into two groups. The first group (group 1) consisted of 76 patients with renal Ca stone and the second group (group 2) consisted of 20 cases without renal stone. Patients who were included in this study seeking for treatment of recurrent renal stone that proved to be Ca stone by CT KUB or stone analysis. Results: there was no statistically significant difference between the two groups regarding vitamin D level, there was no statistically significant difference between different types of calcium stone in relation to vitamin D levels (P= 0.981). There was no statistically significant correlation between vitamin D levels with age (P=0.300), Hounsfield unites of stone (P=0.650) or serum creatinine (P=0.690). Conclusion: There was no statistically significant difference between studied groups regarding vitamin D level. Further studies are needed to determine whether there is any untoward consequence of a concomitant rise in intestinal absorption and urinary excretion of calcium associated with vit D supplementation in idiopathic stone formers.
Human SARS CoV‐2 spike protein mutations

The human spike protein sequences from Asia, Africa, Europe, North America, South America, and Oceania were analyzed by comparing with the reference severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) protein sequence from Wuhan‐Hu‐1, China. Out of 10333 spike protein sequences analyzed, 8155 proteins comprised one or more mutations. A total of 9654 mutations were observed that correspond to 400 distinct mutation sites. The receptor binding domain (RBD) which is involved in the interactions with human angiotensin‐converting enzyme‐2 (ACE‐2) receptor and causes infection leading to the COVID‐19 disease comprised 44 mutations that included residues within 3.2 Å interacting distance from the ACE‐2 receptor. The mutations observed in the spike proteins are discussed in the context of their distribution according to the geographical locations, mutation sites, mutation types, distribution of the number of mutations at the mutation sites and mutations at the glycosylation sites. The density of mutations in different regions of the spike protein sequence and location of the mutations in protein three‐dimensional structure corresponding to the RBD are discussed. The mutations identified in the present work are important considerations for antibody, vaccine, and drug development.
Rigidity percolation and geometric information in floppy origami

Significance Origami structures are a particularly interesting class of thin-sheet–based mechanical metamaterials that rely on folds for their morphology and mechanical properties. Here, we study how excess folds in a simple origami pattern control the rigidity of the structure. Furthermore, we show that the onset of geometrical cooperativity in the system allows for information storage in a scale-free manner. Understanding how mechanical rigidity and geometric information can be simultaneously controlled in folded sheets has implications for structures on a range of scales, from graphene to architecture. Origami structures with a large number of excess folds are capable of storing distinguishable geometric states that are energetically equivalent. As the number of excess folds is reduced, the system has fewer equivalent states and can eventually become rigid. We quantify this transition from a floppy to a rigid state as a function of the presence of folding constraints in a classic origami tessellation, Miura-ori. We show that in a fully triangulated Miura-ori that is maximally floppy, adding constraints via the elimination of diagonal folds in the quads decreases the number of degrees of freedom in the system, first linearly and then nonlinearly. In the nonlinear regime, mechanical cooperativity sets in via a redundancy in the assignment of constraints, and the degrees of freedom depend on constraint density in a scale-invariant manner. A percolation transition in the redundancy in the constraints as a function of constraint density suggests how excess folds in an origami structure can be used to store geometric information in a scale-invariant way.
Effect of prebiotic and synbiotic supplementation in diet on growth performance, small intestinal morphology, stress, and bacterial population under high stocking density condition of broiler chickens.

The current study investigated the effect of prebiotic mannan-oligosaccharide (MOS) and synbiotic (MOS mixed with Bacillus subtilis and Bacillus licheniformis) on growth performance and bacterial population under high stocking density (HSD) conditions in broilers. A total of 605 one-day-old male Arbor Acres broiler chickens were randomly assigned to 4 treatments: normal stocking density (NSD; 30 kg/m2 fed basal diets), HSD (40 kg/m2 fed basal diets), HSD chickens fed 0.1% prebiotic (HSDp), and HSD fed 0.1% synbiotic (HSDs). At 35 D of age, the body weight of HSD and HSDp were poorer than NSD group (P < 0.01), whereas the feed conversion ratio (FCR) of the HSDs) group was better than the NSD group (P < 0.01). The HSDp and HSDs groups improved FCR (P < 0.01) and has cheaper feed cost per gain compared to the HSD group. Moreover, the body weight of HSDs group was heavier than the HSDp group (P < 0.05). The level of corticosterone and the heterophil to lymphocyte ratio were highest in the HSD group, whereas these indexes were reduced in both HSDp and HSDs groups (P < 0.05). Duodenal, jejunal, and ileal villus heights were shortest in the HSD group (P < 0.01), and the lowest ileal segment goblet cell counts were also observed in this group (P < 0.05). The HSDp and HSDs groups improved the morphology of gastrointestinal (GI) tract (P < 0.05). The Lactobacillus sp. and Clostridium sp. count in the GI tract of HSD group were low (P < 0.01), whereas Escherichia coli was high (P < 0.01), and Salmonella spp. in jejunum and cecum were detectable when compared with NSD group. Conversely, Bacillus sp. , Lactobacillus sp. , and Clostridium sp. in HSDp and HSDs groups were increased, and E. coli was reduced in the HSDs group (P < 0.01). Therefore, it is clear that stress from HSD negatively affected growth performance, gut morphology, and microbial population, whereas the supplementation of prebiotic or synbiotic can mitigate the effect of stress and microbial dysbiosis in gut of broiler chickens under HSD condition. Comparatively, under this condition, using synbiotic appears to have more beneficial effects than using the prebiotic.
Coevolutionary dynamics shape the structure of bacteria‐phage infection networks

Coevolution—reciprocal evolutionary change among interacting species driven by natural selection—is thought to be an important force in shaping biodiversity. This ongoing process takes place within tangled networks of species interactions. In microbial communities, evolutionary change between hosts and parasites occurs at the same time scale as ecological change. Yet, we still lack experimental evidence of the role of coevolution in driving changes in the structure of such species interaction networks. Filling this gap is important because network structure influences community persistence through indirect effects. Here, we quantified experimentally to what extent coevolutionary dynamics lead to contrasting patterns in the architecture of bacteria–phage infection networks. Specifically, we look at the tendency of these networks to be organized in a nested pattern by which the more specialist phages tend to infect only a proper subset of those bacteria infected by the most generalist phages. We found that interactions between coevolving bacteria and phages become less nested over time under fluctuating dynamics, and more nested under arms race dynamics. Moreover, when coevolution results in high average infectivity, phages and bacteria differ more from each other over time under arms race dynamics than under fluctuating dynamics. The tradeoff between the fitness benefits of evolving resistance/infectivity traits and the costs of maintaining them might explain these differences in network structure. Our study shows that the interaction pattern between bacteria and phages at the community level depends on the way coevolution unfolds.
Probiotics in the next-generation sequencing era

ABSTRACT Technological developments, including massively parallel DNA sequencing, gnotobiotics, metabolomics, RNA sequencing and culturomics, have markedly propelled the field of microbiome research in recent years. These methodologies can be harnessed to improve our in-depth mechanistic understanding of basic concepts related to consumption of probiotics, including their rules of engagement with the indigenous microbiome and impacts on the human host. We have recently demonstrated that even during probiotic supplementation, resident gut bacteria in a subset of individuals resist the mucosal presence of probiotic strains, limiting their modulatory effect on the microbiome and on the host gut transcriptional landscape. Resistance is partly alleviated by antibiotics treatment, which enables probiotics to interact with the host at the gut mucosal interface, although rather than promoting reconstitution of the indigenous microbiome and of the host transcriptional profile, they inhibit these components from returning to their naïve pre-antibiotic configurations. In this commentary, we discuss our findings in the context of previous and recent works, and suggest that incorporating the state-of-the-art methods currently utilized in microbiome research into the field of probiotics may lead to improved understanding of their mechanisms of activity, as well as their efficacy and long-term safety.
Single-Cell Membrane Potential Fluctuations Evince Network Scale-Freeness and Quasicriticality

What information single neurons receive about general neural circuit activity is a fundamental question for neuroscience. Somatic membrane potential (Vm) fluctuations are driven by the convergence of synaptic inputs from a diverse cross-section of upstream neurons. Furthermore, neural activity is often scale-free, implying that some measurements should be the same, whether taken at large or small scales. Together, convergence and scale-freeness support the hypothesis that single Vm recordings carry useful information about high-dimensional cortical activity. Conveniently, the theory of “critical branching networks” (one purported explanation for scale-freeness) provides testable predictions about scale-free measurements that are readily applied to Vm fluctuations. To investigate, we obtained whole-cell current-clamp recordings of pyramidal neurons in visual cortex of turtles with unknown genders. We isolated fluctuations in Vm below the firing threshold and analyzed them by adapting the definition of “neuronal avalanches” (i.e., spurts of population spiking). The Vm fluctuations which we analyzed were scale-free and consistent with critical branching. These findings recapitulated results from large-scale cortical population data obtained separately in complementary experiments using microelectrode arrays described previously (Shew et al., 2015). Simultaneously recorded single-unit local field potential did not provide a good match, demonstrating the specific utility of Vm. Modeling shows that estimation of dynamical network properties from neuronal inputs is most accurate when networks are structured as critical branching networks. In conclusion, these findings extend evidence of critical phenomena while also establishing subthreshold pyramidal neuron Vm fluctuations as an informative gauge of high-dimensional cortical population activity. SIGNIFICANCE STATEMENT The relationship between membrane potential (Vm) dynamics of single neurons and population dynamics is indispensable to understanding cortical circuits. Just as important to the biophysics of computation are emergent properties such as scale-freeness, where critical branching networks offer insight. This report makes progress on both fronts by comparing statistics from single-neuron whole-cell recordings with population statistics obtained with microelectrode arrays. Not only are fluctuations of somatic Vm scale-free, they match fluctuations of population activity. Thus, our results demonstrate appropriation of the brain's own subsampling method (convergence of synaptic inputs) while extending the range of fundamental evidence for critical phenomena in neural systems from the previously observed mesoscale (fMRI, LFP, population spiking) to the microscale, namely, Vm fluctuations.
Aggressive Tax Avoiders: U.S. Multinationals Shifting Domestic Earnings to Zero

We investigate whether U.S. multinational corporations shift income overseas to the point of recording domestic pretax earnings around zero. We label firms with near-zero domestic earnings "Small" firms, and present evidence that Small captures targeted income shifting that minimizes worldwide and domestic current taxes. Because shifting essentially all income out of the U.S. represents a very aggressive form of international tax planning, Small firms represent an important margin for understanding the income shifting of U.S. MNCs. We find that firms facing tax incentives to shift income and firms with greater income shifting ability are more likely to report near-zero domestic earnings. In addition, investors value the earnings of Small firms higher than that of other U.S. multinational firms, conditional on overall profitability, suggesting that, on average, investors hold a positive view of income shifting to the point of recording domestic earnings around zero.