Miracle-dz/UniFAR-FTUs huggingface dataset:
Fetal alleles predisposing to metabolically favorable adiposity are associated with higher birth weight

Background Higher birth weight is associated with higher adult body mass index (BMI). If genetic variants can be identified with alleles that predispose to both greater fetal growth and to greater adult adiposity, such shared genetic effects might indicate biological processes important in the early patterning of adiposity. However, variants identified in genome-wide association studies of adult BMI have overall been only weakly associated with birth weight. Genetic variants have recently been identified where one allele is associated with higher adult body fat percentage, but lower risk of metabolic disease, likely due to a favourable body fat distribution. The effect of these adult metabolically favourable adiposity alleles on an individual’s own birth weight is unknown. Aim We aimed to test the effect on birth weight of a fetal genetic predisposition to higher metabolically favourable adult adiposity and to compare this with the effects of a fetal genetic predisposition to higher adult BMI. We also aimed to examine the effects of a genetic predisposition to higher metabolically favourable adult adiposity or BMI on other birth anthropometric traits (length, ponderal index, head circumference and skinfold thickness) and on cord-blood insulin, leptin and adiponectin. Methods We used published GWAS data from up to 406,063 individuals to estimate the fetal effects on birth weight of alleles that are robustly associated with higher metabolically favourable adult adiposity or BMI. We additionally used 9,350 mother-child pairs from four cohorts to test the effects of the same alleles on other birth anthropometric traits and cord-blood markers. In all analyses, we adjusted for potential confounding due to the maternal genotype. We used inverse-variance weighted meta-analyses to combine summary data across SNPs. Results Fetal genetic predisposition to higher metabolically favourable adult adiposity was associated with higher birth weight (10 grams (95% CI: 7 to 13) higher mean birth weight per 1 SD pooled “genetic score”). Fetal genetic predisposition to higher adult BMI was also associated with higher birth weight, but with a smaller magnitude of effect (4 grams (95% CI: 0 to 8) higher mean birth weight per 1 SD pooled “genetic score”) and with higher heterogeneity across SNPs. Effects on other birth anthropometric outcomes were consistent with the effect on birth weight but with wider confidence intervals. There was no strong evidence for an effect on cord-blood markers. Conclusions Some genetic variants previously linked to adult adiposity influence birth weight. Alleles that predispose to higher metabolically favourable adult adiposity collectively have a stronger effect on birth weight than those predisposing to higher BMI. This suggests that the early accumulation of a metabolically favourable fat distribution might underlie part of the observed association between higher birth weight and higher adult BMI. Larger samples are needed to clarify the effects on other birth anthropometric measures and cord-blood markers.
Reduction of neuronal activity mediated by blood-vessel regression in the brain

The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we reported that a substantial proportion of blood vessels in the adult brain sporadically occluded and regressed. Their regression proceeded through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels were found to be widespread in mouse, monkey and human brains. Both brief occlusions of the middle cerebral artery and lipopolysaccharide-mediated inflammation induced an increase of vessel regression. Blockage of leukocyte adhesion to endothelial cells alleviated LPS-induced vessel regression. We further revealed that blood vessel regression caused a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain.
Functional diversity of microboring Ostreobium algae isolated from corals

The filamentous chlorophyte Ostreobium sp. dominates shallow marine carbonate microboring communities, and is one of the major agents of reef bioerosion. While its large genetic diversity has emerged, its physiology remains little known, with unexplored relationship between genotypes and phenotypes (endolithic versus free-living growth forms). Here, we isolated 9 strains affiliated to 2 lineages of Ostreobium (>8% sequence divergence of the plastid gene rbcL), one of which was assigned to the family Odoaceae, from the fast-growing coral host Pocillopora acuta Lamarck 1816. Free-living isolates maintained their bioerosive potential, colonizing pre-bleached coral carbonate skeletons. We compared phenotypes, highlighting shifts in pigment and fatty acid compositions, carbon to nitrogen ratios and stable isotope compositions (δ13C and δ15N). Our data show a pattern of higher chlorophyll b and lower arachidonic acid (20:4ω6) content in endolithic versus free-living Ostreobium. Photosynthetic carbon fixation and nitrate uptake, quantified via 8h pulse-labeling with 13C-bicarbonate and 15N-nitrate, showed lower isotopic enrichment in endolithic compared to free-living filaments. Our results highlight the functional plasticity of Ostreobium phenotypes. The isotope tracer approach opens the way to further study the biogeochemical cycling and trophic ecology of these cryptic algae at coral holobiont and reef scales.
Impact of sleep fragmentation, heart failure, and their combination, on the gut microbiome

Heart failure (HF) is a common condition associated with a high rate of hospitalizations and adverse outcomes. HF is characterized by impairments of the cardiac ventricular filling and/or ejection of blood capacity. Sleep fragmentation (SF) involves a series of short sleep interruptions that lead to fatigue and contribute to cognitive impairments and dementia. Both conditions are known to be associated with increased inflammation and dysbiosis of the gut microbiota. In the present study, male mice were distributed into four groups, and subjected for four weeks to either HF, SF, both HF and SF, or left unperturbed as controls. We used 16S metabarcoding to assess fecal microbiome composition before and after the experiments. Evidence for distinct alterations in several bacterial groups and an overall decrease in alpha diversity emerged in HF and SF treatment groups. Combined HF and SF conditions, however, showed no synergism, and observed changes were not always additive, suggesting that some of the individual effects of either HF or SF cancel each other out when applied concomitantly. IMPORTANCE The study demonstrates the potential of the gut microbiome as a source of molecular markers for the diagnosis, prevention, and treatment of both heart failure and sleep fragmentation conditions in isolation. Our results provide the first evidence of an antagonistic effect of the presence of both conditions in the gut microbiome dysbiosis, showing an attenuation of the alterations that are observed when considering them separately.
Effects of novel feed additives on performance, carcass traits and E. coli, aerobic bacteria and yeast counts in broilers Einfluss neuer Futterzusatzstoffe auf Leistung, Schlachtkörpermerkmale und Besiedelung des Verdauungstraktes mit E. coli, aeroben Bakterien und Hefen bei Broilern

Antibiotics are natural metabolites produced by bacteria. The use of antibiotics as feed additive is hazardous due to cross-resistance and to multiple resistances of pathogens (SCHWARZ et al., 2001). In the last few years frequent outbreaks of resistant bacterial strains in field settings occured and claims regarding the hazard of multiple resistance to antibiotics used in human medicine increased. These events have led the European Union to ban the use of most of these additives in poultry feeds. For this reason, many studies have recently been undertaken investigating the use of promising yet novel natural feed-additives (organic acids, probiotics, prebiotics, plant extracts, enzymes and essential oils). Probiotics are a live culture of microorganisms designed to manipulate and maintain a beneficial microbial population in the gut of the host organism. Lactobacillus, a common probiotic, has an immuno-stimulatory action, which increases phagocytic activity and production of immunoglobins in the blood. These microorganisms improve the intestinal microbial balance by growing and multiplying and competitively excluding undesirable bacteria (O’KEEFE, 2005). Prebiotics are nondigestible carbohydrates that assist an animal by selectively stimulating the growth and-or activity of beneficial, native bacterial species resident in the gastrointestinal tract and by stimulating immune function. Some prebiotics provide binding sites for pathogenic bacteria that are then flushed out of the digestive tract with the faeces while others promote the growth of beneficial bacteria by acting as a food source (MCCANN et al., 2006). Herbs, spices and various plant extracts have received increased attention as possible replacements for antibiotic growth promoters. Essential oils are derived mainly from spices and herbs and their purified compounds have been shown to have antimicrobial properties in vitro (FALEIRO et al., 2003). Natural antimicrobial compounds include carvacrol, tymol, limonene and cineole are present in the essential oil fraction of oregano (ULTEE et al., 2002). Their antimicrobial mode of action consists of interactions with
SARS-CoV-2 ribosomal frameshifting pseudoknot: Improved secondary structure prediction and detection of inter-viral structural similarity

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the COVID-19 pandemic; a pandemic of a scale that has not been seen in the modern era. Despite over 29 million reported cases and over 900, 000 deaths worldwide as of September 2020, herd immunity and widespread vaccination efforts by many experts are expected to be insufficient in addressing this crisis for the foreseeable future. Thus, there is an urgent need for treatments that can lessen the effects of SARS-CoV-2 in patients who become seriously affected. Many viruses including HIV, the common cold, SARS-CoV and SARS-CoV-2 use a unique mechanism known as −1 programmed ribosomal frameshifting (−1 PRF) to successfully replicate and infect cells in the human host. SARS-CoV (the coronavirus responsible for SARS) and SARS-CoV-2 possess a unique RNA structure, a three-stemmed pseudoknot, that stimulates −1 PRF. Recent experiments identified that small molecules can be introduced as antiviral agents to bind with the pseudoknot and disrupt its stimulation of −1 PRF. If successfully developed, small molecule therapy that targets −1 PRF in SARS-CoV-2 is an excellent strategy to improve patients’ prognoses. Crucial to developing these successful therapies is modeling the structure of the SARS-CoV-2 −1 PRF pseudoknot. Following a structural alignment approach, we identify similarities in the −1 PRF pseudoknots of the novel coronavirus SARS-CoV-2, the original SARS-CoV, as well as a third coronavirus: MERS-CoV, the coronavirus responsible for Middle East Respiratory Syndrome (MERS). In addition, we provide a better understanding of the SARS-CoV-2 −1 PRF pseudoknot by comprehensively investigating the structural landscape using a hierarchical folding approach. Since understanding the impact of mutations is vital to long-term success of treatments that are based on predicted RNA functional structures, we provide insight on SARS-CoV-2 −1 PRF pseudoknot sequence mutations and their effect on the resulting structure and its function.
When conflicts get heated, so does the planet: social-climate dynamics under inequality

Climate dynamics are inextricably linked to processes in social systems that are highly unequal. This suggests a need for coupled social-climate models that capture pervasive real-world asymmetries in the population distribution of the consequences of anthropogenic climate change and climate (in)action. Here we develop a simple social-climate model with group structure to investigate how anthropogenic climate change and population heterogeneity co-evolve. We find that greater homophily and resource inequality cause an increase in the global peak temperature anomaly by as much as 0.7°C. Also, climate change can structure human populations by driving opinion polarization. Finally, climate mitigation achieved by reducing the cost of mitigation measures paid by individuals tends to be contingent upon socio-economic conditions, whereas policies that achieve communication between different strata of society show climate mitigation benefits across a broad socio-economic regime. We conclude that advancing climate change mitigation efforts can benefit from a social-climate systems perspective.
Complete Logarithmic Sobolev inequality via Ricci curvature bounded below II

We study the “geometric Ricci curvature lower bound”, introduced previously by Junge, Li and LaRacuente, for a variety of examples including group von Neumann algebras, free orthogonal quantum groups [Formula: see text], [Formula: see text]-deformed Gaussian algebras and quantum tori. In particular, we show that Laplace operator on [Formula: see text] admits a factorization through the Laplace–Beltrami operator on the classical orthogonal group, which establishes the first connection between these two operators. Based on a non-negative curvature condition, we obtain the completely bounded version of the modified log-Sobolev inequalities for the corresponding quantum Markov semigroups on the examples mentioned above. We also prove that the “geometric Ricci curvature lower bound” is stable under tensor products and amalgamated free products. As an application, we obtain a sharp Ricci curvature lower bound for word-length semigroups on free group factors.
Overt and covert prosody are reflected in neurophysiological responses previously attributed to grammatical processing

Recent neurophysiological research suggests that slow cortical activity tracks hierarchical syntactic structure during online sentence processing (e.g., Ding, Melloni, Zhang, Tian, & Poeppel, 2016). Here we tested an alternative hypothesis: electrophysiological activity peaks at sentence constituent frequencies reflect cortical tracking of overt or covert (implicit) prosodic grouping. In three experiments, participants listened to series of sentences while electroencephalography (EEG) was recorded. First, prosodic cues in the sentence materials were neutralized. We found an EEG spectral power peak elicited at a frequency that only ‘tagged’ covert prosodic change, but not any major syntactic constituents. In the second experiment, participants listened to a series of sentences with overt prosodic grouping cues that either aligned or misaligned with the syntactic phrasing in the sentences (initial overt prosody trials). Immediately after each overt prosody trial, participants were presented with a second series of sentences (covert prosody trial) with all overt prosodic cues neutralized and asked to imagine the prosodic contour present in the previous, overt prosody trial. The EEG responses reflected an interactive relationship between syntactic processing and prosodic tracking at the frequencies of syntactic constituents (sentences and phrases): alignment of syntax and prosody boosted EEG responses, whereas their misalignment had an opposite effect. This was true for both overt and covert (imagined) prosody. We conclude that processing of both overt and covert prosody is reflected in the frequency tagged neural responses at sentence constituent frequencies, whereas identifying neural markers that are narrowly reflective of syntactic processing remains difficult and controversial.
Latency and amplitude of the stop-signal P3 event-related potential are related to inhibitory GABAa activity in primary motor cortex

By stopping actions even after their initiation, humans can adapt their ongoing behavior rapidly to changing environmental circumstances. The neural processes underlying the implementation of rapid action-stopping are still controversially discussed. In the early 1990s, a fronto-central P3 event-related potential (ERP) was identified in the human EEG response following stop-signals in the classic stop-signal task, accompanied by the proposal that this ERP reflects the “inhibitory” side of the purported horse-race underlying successful action-stopping. Later studies have lent support to this interpretation by finding that the amplitude and onset of the stop-signal P3 relate to both overt behavior and to movement-related EEG activity in ways predicted by the race model. However, such studies are limited by the ability of EEG to allow direct inferences about the presence (or absence) of true, physiologically inhibitory signaling at the neuronal level. To address this, we here present a cross-modal individual differences investigation of the relationship between the features stop-signal P3 ERP and GABAergic neurotransmission in primary motor cortex (M1, as measured by paired-pulse transcranial magnetic stimulation). Following recent work, we measured short-interval intracortical inhibition (SICI), a marker of inhibitory GABAa activity in M1, in a group of 41 human participants who also performed the stop-signal task while undergoing EEG recordings. In line with the P3-inhibition hypothesis, we found that subjects with stronger inhibitory GABA activity in M1 also showed both faster onsets and larger amplitudes of the stop-signal P3. This provides direct evidence linking the properties of this ERP to a true physiological index of motor system inhibition. We discuss these findings in the context of recent theoretical developments and empirical findings regarding the neural implementation of inhibitory control during action-stopping.
Identifying Barriers to Forage Innovation: Native Grasses and Producer Knowledge

Adoption of native warm-season grasses (NWSGs) in the tall fescue belt is limited despite studies documenting the potential contribution of these forages to profitable beef production. On the basis of two surveys conducted in Tennessee, a survey of beef producers and a survey of agricultural professionals, we evaluated perceptions of NWSG forages and how those perceptions could influence their adoption. Although agricultural professionals were more familiar with NWSGs than producers, both populations had limited knowledge regarding these forages, indicating that additional Extension education is needed. Our results provide useful guidance for developing NWSG forage educational programs for producers and agricultural professionals.
Knowledge Transfer in Modern Code Review

Knowledge transfer is one of the main goals of modern code review, as shown by several studies that surveyed and interviewed developers. While knowledge transfer is a clear expectation of the code review process, there are no analytical studies using data mined from software repositories to assess the effectiveness of code review in “training” developers and improve their skills over time. We present a mining-based study investigating how and whether the code review process helps developers to improve their contributions to open source projects over time. We analyze 32,062 peer-reviewed pull requests (PRs) made across 4,981 GitHub repositories by 728 developers who created their GitHub account in 2015. We assume that PRs performed in the past by a developer $D$ that have been subject to a code review process have “transferred knowledge” to D. Then, we verify if over time (i.e., when more and more reviewed PRs are made by D), the quality of the contributions made by $D$ to open source projects increases (as assessed by proxies we defined, such as the acceptance of PRs, or the polarity of the sentiment in the review comments left for the submitted PRs). With the above measures, we were unable to capture the positive impact played by the code review process on the quality of developers' contributions. This might be due to several factors, including the choices we made in our experimental design.Additional investigations are needed to confirm or contradict such a negative result.
Seasonal growth stimulation of sub-temperate estuarine phytoplankton to nitrogen and phosphorus: An outdoor microcosm experiment

A study of nutrient limitation of phytoplankton biomass production with emphasis on nitrate-nitrogen (NO3−) and ortho-phosphate-phosphorus (PO43−) was conducted in Perdido Bay, Alabama-Florida. The experimental design employed 18-1 outdoor microcosms operated in a static renewal mode. Phytoplankton growth responses (i.e., growth stimulation) measured as chlorophyll a (chl a) fell into three principal categories: primary P stimulation occurred mostly during the cooler months at the upper bay (tidal brackish) and mid bay (lower mesohaline) stations; a total of 12 out of 36 experiments; primary N stimulation occurred mostly during the warmer months primarily at the mid-bay station and infrequently at the upper and lower bay stations (upper mesohaline); a total of 7 out of 36 experiments; and N+P costimulation occurred primarily during the warmer months in the upper bay and mid bay and during both warmer and cooler months of the lower bay; a total of 17 out of 36 experiments. Primary P stimulation was generally associated with high ratios of dissolved inorganic nitrogen (DIN) to dissolved inorganic phosphate (DIP) (ratio range: 18 to 288). Conversely, primary N stimulation was associated with decreasing DIN:DIP ratios (range 8–46). Redfield ratios of particulate organic N (PON) to particulate organic P (POP) often indicated N limitation (i.e., values often less than 10). PON:chl a ratios often indicated N sufficiency, but three occasions were noted where PON:POP and PON:chl a ratios were not congruent. It is difficult to reconcile the inorganic and organic N and P ratios with the relatively low DIP and DIN concentrations. The phytoplankton assemblage appeared not to be strongly nutrient-limited but, given a nutrient increase, responded differentially to N and P, both seasonally and along the longitudinal salinity gradient. Grazing pressure in concert with nutrient limitation was advanced as an hypothesis to explain N+P co-limitation.
The Risks of the Blockchain A Review on Current Vulnerabilities and Attacks

Although the ﬁrst hype of blockchains is over, subject matter experts are still convinced, that this technology has potential to enable more groundbreaking innovations in multiple business domains. However, to develop the full potential of this emerging technology, it is necessary to consider and address the associated risks. This survey aims at supporting researchers and practitioners to design, implement and improve their blockchain security and resilience by providing a concise overview on the subject. In this article, we describe 24 risks, which we structured into the four domains “Blockchain Structure Vulnerabilities”, “Attacks on the Consensus Mechanism”, “Application Oriented Attacks” and “Attacks on the Peer-to-Peer System”. For each entry, we outline a precise description of the vulnerability or attack, the complexity and its prerequisites.