Miracle-dz/UniFAR-FTUs huggingface dataset:
The gene regulatory system for specifying germ layers in early embryos of the simple chordate

The regulatory system of gene expression in ascidian 32-cell embryos is represented as Boolean functions. In animal embryos, gene regulatory networks control the dynamics of gene expression in cells and coordinate such dynamics among cells. In ascidian embryos, gene expression dynamics have been dissected at the single-cell resolution. Here, we revealed mathematical functions that represent the regulatory logics of all regulatory genes expressed at the 32-cell stage when the germ layers are largely specified. These functions collectively explain the entire mechanism by which gene expression dynamics are controlled coordinately in early embryos. We found that regulatory functions for genes expressed in each of the specific lineages contain a common core regulatory mechanism. Last, we showed that the expression of the regulatory genes became reproducible by calculation and controllable by experimental manipulations. Thus, these regulatory functions represent an architectural design for the germ layer specification of this chordate and provide a platform for simulations and experiments to understand the operating principles of gene regulatory networks.
Altered brain network centrality in patients with mild cognitive impairment: an fMRI study using a voxel-wise degree centrality approach

Purpose: Previous studies in patients with Alzheimer’s disease have shown amyloid beta accumulation in the brain and abnormal brain activity, with mild cognitive impairment (MCI) in early stages of the disease. The aim of the current study was to investigate functional connectivity in patients with MCI. Methods: We recruited 24 subjects in total, including 12 patients with MCI (6 men and 6 women) and 12 healthy controls (HCs) (6 men and 6 women), matched for age, gender, and lifestyle factors. All subjects underwent resting-state functional magnetic resonance imaging scans and voxel-wise degree centrality (DC) was used to evaluate alterations in the strength of brain network connectivity. Results: The DC value of the left inferior temporal gyrus was lower in MCI but significantly higher in the right fusiform gyrus and the left supplementary motor area, compared with HCs. The DC value in left inferior temporal gyrus correlated positively with disease duration and negatively with Mini-Mental State Examination. ROC curve analysis of brain regions showed acceptable specificity and accuracy of DC values between MCIs and HCs in the area under the curve (right fusiform gyrus, 0.955; left supplementary motor area, 0.992; left inferior temporal gyrus, 1.000). Conclusions: Abnormal functional connectivity in brain regions of patients with MCI may reflect the pathological process of Alzheimer’s disease development and could prove useful in clinical diagnosis and treatment.
Finding Neymar: The Role of Colour in the Detection and Discrimination of Football Kits

Association Football (hereafter football) is a fast-moving sport in which rapid decisions need to be made; where are other players, are they on my team? Two experiments investigated how kit variations affect the search of teammates. Experiment 1 confirmed that discriminability is slower when playing in crossed kits (e.g., red shirts-blue shorts vs. blue shirts-red shorts), versus uniform kits (e.g., all red vs. all blue). Experiment 2 found that there is significant confusion when both teams wear the same-coloured shorts. Based on these findings, we suggest changes to the Laws of the game concerning kit colours.
Genetic diversity and population structure of Cynara cardunculus L. in southern Portugal

Cynara cardunculus L. is a cardoon species native to the Mediterranean region, which is composed of three botanical taxa, each having distinct biological characteristics. The aim of this study was to examine wild populations of C. cardunculus established in Portugal, in order to determine their genetic diversity, geographic distribution, and population structure. Based on SSR markers, 121 individuals of C. cardunculus from 17 wild populations of the Portuguese Alentejo region were identified and analysed. Ten SSRs were found to be efficient markers in the genetic diversity analysis. The total number of alleles ranged from 9 to 17 per locus. The expected and observed means in heterozygosity, by population analysed, were 0.591 and 0.577, respectively. The wild population exhibited a high level of genetic diversity at the species level. The highest proportion of genetic variation was identified within a geographic group, while variation was lower among groups. Geographic areas having highest genetic diversity were identified in Alvito, Herdade da Abóboda, Herdade da Revilheira and Herdade de São Romão populations. Moreover, significant genetic differentiation existed between wild populations from North-Alentejo geographic locations (Arraiolos, Évora, Monte da Chaminé) and Centro Hortofrutícola, compared with other populations. This study reports genetic diversity among a representative number of wild populations and genotypes of C. cardunculus from Portugal. These results will provide valuable information towards future management of C. cardunculus germplasm.
Suppression of hypolimnetic methylmercury accumulation by liquid calcium nitrate amendment: redox dynamics and fate of nitrate

Abstract Anoxia, specifically sulfate (SO42−) reduction, in the hypolimnia of stratified lakes is a prerequisite for monomethylmercury (HgCH3+) formation in sediments and subsequent efflux into the water column. A whole-lake pilot project used liquid calcium nitrate (LCN) to suppress formation of HgCH3+ by raising hypolimnetic redox in a dimictic, mesotrophic lake in Minnesota. A nearby lake of similar morphology and trophic status served as a reference. In the experimental lake, the HgCH3+ concentration at the onset of LCN application was 0.34 ng/L and 0.30 ng/L at the point of nitrate (NO3−) depletion. The NO3− concentration peaked at 17.7 mg/L (as ion) 16 days after application and declined to 0.5 mg/L at day 64. A principal NO3− sink was anaerobic oxidation of sulfidic compounds, but dissimilatory NO3− reduction to ammonium (NH4+) may also have been a major sink. SO42− at the time of the LCN dose was 0.99 mg/L and rose to 4.0 mg/L at the point of NO3− depletion (<0.5 mg/L). Thereafter, NO3−-induced SO42− enrichment of the hypolimnion induced HgCH3+ to increase to 1.09 ng/L by SO42− reduction. In both lakes, we observed strong redox functional relationships in the hypolimnia with unambiguous breakpoints (thresholds) for SO42− reduction and sediment efflux of iron, manganese, orthophosphate, NH4+, and HgCH3+. Study results suggest that LCN application be done in frequent, small doses with redox monitoring to prevent SO42− reduction until turnover. This method would minimize downstream NO3− loading at turnover while avoiding inadvertent SO42− enrichment that can boost HgCH3+ production in SO42− limited lakes.
Synthesis of silicon oxide nanowires by the GJ EBP CVD method using different diluent gases

Nanowires of silicon oxide SiOx (x ≤ 2) were synthesized from a mixture of monosilane and hydrogen (helium, argon) by gas‐jet electron beam plasma chemical vapor deposition (GJ EBP CVD) method with simultaneous supply of oxygen into the vacuum chamber. The synthesis was performed on monocrystalline silicon and glass substrates coated with micron‐sized particles of a tin catalyst. In particular, aligned arrays of nanowire bundles (microropes) were synthesized from a mixture of monosilane and hydrogen (argon). A bundle of amorphous silicon oxide nanowires, each of which is about 15 nm in diameter, grows from a catalyst particle. The growth rate of the microropes is about 25 nm s−1 at a synthesis temperature of 320–330 °C. The morphology of the nanostructures was investigated by transmission and scanning electron microscopy, their composition by X‐ray energy dispersive spectroscopy and optical properties by photoluminescence spectroscopy. The synthesis was carried out using the well‐known vapor–liquid–solid (VLS) mechanism. A model is proposed for the synthesis of the nanostructures by the above method, including the formation of aligned bundles of nanowires (microropes) due to nonuniform heating of the catalyst particle by directed plasma flow. The obtained nanostructures have intense photoluminescence in the visible region of the spectrum at room temperature.
Comparative Efficacy of Atezolizumab plus Bevacizumab and Other Treatment Options for Patients with Unresectable Hepatocellular Carcinoma: A Network Meta-Analysis

Background: Most phase 3 clinical trials of systemic therapy for first-line unresectable hepatocellular carcinoma (HCC) have failed, with the exception of SHARP, REFLECT, and IMbrave150. We conducted indirect comparisons of therapies evaluated for first-line HCC treatment. Summary: We conducted a systematic review and meta-analysis of treatments for adults with locally advanced or metastatic unresectable HCC and no prior systemic treatment, including atezolizumab plus bevacizumab, sorafenib, lenvatinib, nivolumab, selective internal radiotherapy (SIRT), transarterial chemoembolization, and placebo or best supportive care. Randomized controlled trials published from January 1, 2007, to March 12, 2020, were retrieved from MEDLINE and Embase. Qualitative assessment of heterogeneity evaluated study designs, populations, and outcomes. Indirect comparisons used generalized linear models with random effects within a Bayesian framework and informative priors. We calculated relative efficacy estimates with 95% credible intervals (CrIs) and Bayesian posterior probability estimates of atezolizumab-bevacizumab being superior to other treatments. Nine clinical studies with a total of 3,897 participants were identified from 8,783 records and used to build the all-trials evidence network. Indirect comparisons suggested an improved overall survival (OS) with atezolizumab-bevacizumab versus lenvatinib (odds ratio, 0.63 [95% CrI 0.39–1.04]; with 97% Bayesian posterior probability of being superior), nivolumab (0.68 [95% CrI 0.41–1.14]; 94%), sorafenib (0.59 [95% CrI 0.39–0.87]; 99%), SIRT (0.51 [95% CrI 0.32–0.82]; 100%), or placebo/best supportive care (0.40 [95% CrI 0.25–0.64]; 100%). Key Messages: Within the context of indirect comparisons, analyses of OS favored atezolizumab-bevacizumab versus other treatment options for patients with locally advanced or metastatic unresectable HCC.
Using large-scale experiments and machine learning to discover theories of human decision-making

Discovering better theories Theories of human decision-making have proliferated in recent years. However, these theories are often difficult to distinguish from each other and offer limited improvement in accounting for patterns in decision-making over earlier theories. Peterson et al. leverage machine learning to evaluate classical decision theories, increase their predictive power, and generate new theories of decision-making (see the Perspective by Bhatia and He). This method has implications for theory generation in other domains. Science, abe2629, this issue p. 1209; see also abi7668, p. 1150 A machine learning approach suggests that people make decisions in a way that violates the assumptions of classic decision-making theories. Predicting and understanding how people make decisions has been a long-standing goal in many fields, with quantitative models of human decision-making informing research in both the social sciences and engineering. We show how progress toward this goal can be accelerated by using large datasets to power machine-learning algorithms that are constrained to produce interpretable psychological theories. Conducting the largest experiment on risky choice to date and analyzing the results using gradient-based optimization of differentiable decision theories implemented through artificial neural networks, we were able to recapitulate historical discoveries, establish that there is room to improve on existing theories, and discover a new, more accurate model of human decision-making in a form that preserves the insights from centuries of research.
Effect of moisture sorption hysteresis on thermodynamic properties of two millet varieties

Application of reversible thermodynamic principles to gain fundamental understanding of food–water interactions in foods has met with limited success due to the presence of moisture sorption hysteresis which is a manifestation of irreversibility. This study was aimed at understanding the nature and extent of influence of hysteresis on thermodynamic properties of two millet varieties namely EX-BORNO and SOSAT C88. Moisture sorption data (adsorption and desorption) in the water activity and temperature ranges of 0.07 – 0.98 and 30°C – 70°C, respectively were used. Ratio of latent heat of moisture sorption to the latent heat of pure water was determined using Clausius-Clapeyron equation. Effect of moisture content on ratio of latent heat of sorption to latent heat of pure water was determined using Gallaher model. Net integral enthalpy was determined at constant spreading pressure with monolayer moisture contents calculated using Brunauer-Emmett-Teller (BET) and Guggenheim-Anderson-de Boer (GAB) models. Spreading pressure was determined using an analytical procedure. Gibbs equation was used to evaluate net integral entropy. Net isosteric heat of sorption and differential entropy were evaluated and used to investigate the enthalpy‐entropy compensation theory. Latent heat of moisture sorption in the two millet varieties decreased with increase in moisture content and approached latent heat of pure water at a ‘free water’ point of between 32% and 42% moisture content (d.b.) in adsorption and desorption, respectively. Desorption latent heat of moisture was higher than the adsorption values and the difference decreased with increase in moisture content. Monolayer moisture content decreased with increase in temperature, with the GAB being higher than the BET values. Desorption monolayer moisture was higher than that of adsorption. Spreading pressure increased with increase in water activity, with adsorption isotherm being higher than that of desorption and temperature having no significant effect. Net integral enthalpy decreased with increase in moisture content with effect of hysteresis being more marked in EX-BORNO than in SOSAT C88. Net integral entropy decreased with increase in moisture content to minimum values and thereafter, maintained sinusoidal trend with adsorption curve lagging behind desorption and varnishing at 18% and 16% (db) moisture content in EX-BORNO and SOSAT C88 respectively. Net isosteric heat of sorption and differential entropy decreased with increase in moisture content with effect of hysteresis being more pronounced in EX-BORNO. Moisture sorption process in the grains was found to be enthalpy driven with differential enthalpy varying linearly with differential entropy. Inequality in isokinetic and harmonic mean temperatures confirmed the enthalpy‐entropy compensation theory. Hysteresis was found to have effect on the isokinetic temperature, causing the values of desorption isokinetic temperature to be higher than the adsorption values.
Changes in the Volatile Compounds of Artemisia princeps var. orientalis Essential Oils During Storage

The compositional changes of wormwood (Artemisia princeps var. orientalis) essential oils were studied under 4 different storage conditions i.e., being exposed to air at 20 and 40℃. Sixty-four volatile compounds consisting of 24 terpene hydrocarbons, 18 alcohols, 11 ketones, 6 esters, 1 aldehyde, 2 hydrocarbons, and 2 oxides were identified on the basis of their mass spectra characteristics and retention indices in original wormwood essential oils. Identified compounds constituted 80.53% of the total peak area. Borneol (12.13%) was the most abundant compound, followed by α-thujone (8.66%), T-cadinol (6.67%), and 1,8-cineole (6.21%) in original wormwood essential oils. Under the condition of 40℃ of temperature with the cap being opened for 3 min everyday respectively during 6 months of storage, the total amount of functional groups in essential oil determined by peak area percent were decreased by 79.45%, at most. The total level of monoterpene hydrocarbons decreased markedly in the aerobic condition and high temperatures. Whereas the total level of esters increased significantly. Wormwood essential oils were stored in experimental conditions, with the changes in the volatile compounds of essential oils being accelerated by high temperatures and contact with the atmosphere.
Direct numerical simulation of roughness-induced transition controlled by two-dimensional wall blowing

Abstract Discrete roughness-induced transition in Mach $2.25$ flow controlled by two-dimensional wall blowing is studied using direct numerical simulation. Spectral analysis and flow freezing operations reveal that the main source of unsteadiness in the case without blowing is the separated shear layer/counter-rotating vortex system: the shear layer is bent by the vortex pair, and this interaction induces disturbance growth at the shear layer. With the existence of weak wall blowing, the transition is delayed. Flow visualization demonstrates that upstream-positioned blowing achieves this by lifting the inflow boundary layer and decreasing the roughness Reynolds number. In contrast, downstream-positioned blowing takes effect by weakening the counter-rotating vortex pair and inhibiting the interaction. Vorticity transportation analysis suggests that this result is accomplished by increasing dissipation for streamwise vorticity and converting some of it into spanwise vorticity. In cases with strong wall blowing, the control effect is reversed, as wall blowing with enough strength can induce unsteadiness and promote transition. In upstream-positioned strong blowing cases, a new unstable mode is observed in spectral results throughout the near-roughness region, and further analysis indicates that this mode originating from the separation zone upstream of the blowing is the key factor for transition. With regard to downstream-positioned strong blowing cases, a very low-frequency mode is generated from the separation bubble between the roughness element and the blowing, but it only provides an initial disturbance for the transition process. The transition that occurs downstream is due to the distortion of the boundary layer in the wake.
Parallel and non-parallel divergence within polymorphic populations of brook stickleback, Culaea inconstans (Actinopterygii: Gasterosteidae)

Studying parallel evolution allows us to draw conclusions about the repeatability of adaptive evolution. Whereas populations likely experience similar selective pressures in similar environments, it is not clear if this will always result in parallel divergence of ecologically relevant traits. Our study investigates the extent of parallelism associated with the evolution of pelvic spine reduction in brook stickleback populations. We find that populations with parallel divergence in pelvic spine morphology do not exhibit parallel divergence in head and body morphology but do exhibit parallel divergence in diet. In addition, we compare these patterns associated with pelvic reduction in brook stickleback to well-studied patterns of divergence between spined and unspined threespine stickleback. Whereas spine reduction is associated with littoral habitats and a benthic diet in threespine stickleback, spine reduction in brook stickleback is associated with a planktonic diet. Hence, we find that pelvic spine divergence is associated with largely non-parallel ecological consequences across species.
Bayesian Mapping of the Striatal Microcircuit Reveals Robust Asymmetries in the Probabilities and Distances of Connections

The striatum's complex microcircuit is made by connections within and between its D1- and D2-receptor expressing projection neurons and at least five species of interneuron. Precise knowledge of this circuit is likely essential to understanding striatum's functional roles and its dysfunction in a wide range of movement and cognitive disorders. We introduce here a Bayesian approach to mapping neuron connectivity using intracellular recording data, which lets us simultaneously evaluate the probability of connection between neuron types, the strength of evidence for it, and its dependence on distance. Using it to synthesize a complete map of the mouse striatum, we find strong evidence for two asymmetries: a selective asymmetry of projection neuron connections, with D2 neurons connecting twice as densely to other projection neurons than do D1 neurons, but neither subtype preferentially connecting to another; and a length-scale asymmetry, with interneuron connection probabilities remaining non-negligible at more than twice the distance of projection neuron connections. We further show that our Bayesian approach can evaluate evidence for wiring changes, using data from the developing striatum and a mouse model of Huntington's disease. By quantifying the uncertainty in our knowledge of the microcircuit, our approach reveals a wide range of potential striatal wiring diagrams consistent with current data. SIGNIFICANCE STATEMENT To properly understand a neuronal circuit's function, it is important to have an accurate picture of the rate of connection between individual neurons and how this rate changes with the distance separating pairs of neurons. We present a Bayesian method for extracting this information from experimental data and apply it to the mouse striatum, a subcortical structure involved in learning and decision-making, which is made up of a variety of different projection neurons and interneurons. Our resulting statistical map reveals not just the most robust estimates of the probability of connection between neuron types, but also the strength of evidence for them, and their dependence on distance.
Gut bacterial aggregates as living gels

The spatial organization of gut microbiota influences both microbial abundances and host-microbe interactions, but the underlying rules relating bacterial dynamics to large-scale structure remain unclear. To this end we studied experimentally and theoretically the formation of three-dimensional bacterial clusters, a key parameter controlling susceptibility to intestinal transport and access to the epithelium. Inspired by models of structure formation in soft materials, we sought to understand how the distribution of gut bacterial cluster sizes emerges from bacterial-scale kinetics. Analyzing imaging-derived data on cluster sizes for eight different bacterial strains in the larval zebrafish gut, we find a common family of size distributions that decay approximately as power laws with exponents close to −2, becoming shallower for large clusters in a strain-dependent manner. We show that this type of distribution arises naturally from a Yule-Simons-type process in which bacteria grow within clusters and can escape from them, coupled to an aggregation process that tends to condense the system toward a single massive cluster, reminiscent of gel formation. Together, these results point to the existence of general, biophysical principles governing the spatial organization of the gut microbiome that may be useful for inferring fast-timescale dynamics that are experimentally inaccessible.