Miracle-dz/UniFAR-FTUs huggingface dataset:
The NDH complex reveals a trade-off that constrains maximising photosynthesis in Arabidopsis thaliana

The Green Revolution has resulted in major improvements in crop productivity, but left photosynthesis largely unimproved. Despite ample variation of photosynthetic performance in crops and their wild relatives, the photosynthetic capacity of elite breeding lines remains well below its theoretical maximum. As yield is often the primary selective trait, current plant breeding approaches result in photosynthetic trade-offs that prevent positive selection for photosynthetic performance itself. Currently, genetic variation for photosynthetic performance is seldomly validated at the genetic level, and as a result these photosynthetic trade-offs remain poorly understood. Here we reveal the physiological nature of a photosynthetic trade-off caused by the NAD(P)H dehydrogenase (NDH) complex. The use of an Arabidopsis thaliana cybrid panel revealed how a natural allele of the chloroplastic gene NAD(P)H-QUINONE OXIDOREDUCTASE SUBUNIT 6 - a subunit of the NDH complex - results in a faster recovery of photosystem II efficiency after a transition from high to low irradiances. This improvement is due to a reduction in NDH activity. Under low-light conditions this reduction in NDH activity has a neutral effect on biomass, while under highly fluctuating light conditions, including high irradiances, more NDH activity is favoured. This shows that while allelic variation in one gene can have beneficial effects on one aspect of photosynthesis, it can, depending on environmental conditions, have negative effects on other aspects of photosynthesis. As environmental conditions are hardly ever stable in agricultural systems, understanding photosynthetic trade-offs allows us to explore shifting photosynthetic performance closer to the theoretical maximum.
Exact zero modes in closed systems of interacting fermions

We show that for closed finite sized systems with an odd number of real fermionic modes, even in the presence of interactions, there are always at least two fermionic operators that commute with the Hamiltonian.There is a zero mode corresponding to the fermion parity operator, as shown by Akhmerov, as well as additional linearly independent zero modes, one of which is 1) the one that is continuously connected to the Majorana mode solution in the non-interacting limit, and 2) less prone to decoherence when the system is opened to contact with an infinite bath. We also show that in the idealized situation where there are two or more well separated zero modes each associated with a finite number of fermions at a localized vortex, these modes have non-Abelian Ising statistics under braiding. Furthermore the algebra of the zero mode operators makes them useful for fermionic quantum computation.
Role of multiple pericentromeric repeats on heterochromatin assembly

Although the length and constituting sequences for pericentromeric repeats are highly variable across eukaryotes, the presence of multiple pericentromeric repeats is one of the conserved features of the eukaryotic chromosomes. Pericentromeric heterochromatin is often misregulated in human diseases, with the expansion of pericentromeric repeats in human solid cancers. In this article, we have developed a mathematical model of the RNAi-dependent methylation of H3K9 in the pericentromeric region of fission yeast. Our model, which takes copy number as an explicit parameter, predicts that the pericentromere is silenced only if there are many copies of repeats. It becomes bistable or desilenced if the copy number of repeats is reduced. This suggests that the copy number of pericentromeric repeats alone can determine the fate of heterochromatin silencing in fission yeast. Through sensitivity analysis, we identified parameters that favor bistability and desilencing. Stochastic simulation shows that faster cell division and noise favor the desilenced state. These results show the unexpected role of pericentromeric repeat copy number in gene silencing and elucidate how the copy number of silenced genomic regions may impact genome stability. Author Summary Pericentromeric repeats vary in length and sequences, but their presence is a conserved feature of eukaryotes. This suggests that the repetitive nature of pericentromeric sequences is an evolutionarily conserved feature of centromeres, which is under selective pressure. Here we developed a quantitative model for gene silencing at the fission yeast pericentromeric repeats. Our model is one of the first models which incorporates the copy number of pericentromeric repeats and predicts that the number of repeats can solely govern the dynamics of pericentromeric gene silencing. Our results suggest that the repeat copy number is a dynamic parameter for gene silencing, and copy-number-dependent silencing is an effective machinery to repress the repetitive part of the genome.
Thermal phenotypic plasticity of pre- and post-copulatory male harm buffers sexual conflict in wild Drosophila melanogaster

Strong sexual selection frequently leads to sexual conflict and ensuing male harm, whereby males increase their reproductive success at the expense of harming females. Male harm is a widespread evolutionary phenomenon with a strong bearing on population viability. Thus, understanding how it unfolds in the wild is a current priority. Here, we sampled a wild Drosophila melanogaster population and studied male harm across the normal range of temperatures under which it reproduces optimally in nature by comparing female lifetime reproductive success and underlying male harm mechanisms under monogamy (i.e., low male competition/harm) vs. polyandry (i.e., high male competition/harm). While females had equal lifetime reproductive success across temperatures under monogamy, polyandry resulted in a maximum decrease of female fitness at 24°C (35%), reducing its impact at both 20°C (22%), and 28°C (10%). Furthermore, female fitness components and pre- (i.e., harassment) and post-copulatory (i.e., ejaculate toxicity) mechanisms of male harm were asymmetrically affected by temperature. At 20°C, male harassment of females was reduced, and polyandry accelerated female actuarial ageing. In contrast, the effect of mating on female receptivity (a component of ejaculate toxicity) was affected at 28°C, where the mating costs for females decreased and polyandry mostly resulted in accelerated reproductive ageing. We thus show that, across a natural thermal range, sexual conflict processes and their effects on female fitness components are plastic and complex. As a result, the net effect of male harm on overall population viability is likely to be lower than previously surmised. We discuss how such plasticity may affect selection, adaptation and, ultimately, evolutionary rescue under a warming climate.
Optimizing the Benefits of Mental Practice on Motor Acquisition and Consolidation with Moderate-Intensity Exercise

The optimization of mental practice (MP) protocols matters for sport and motor rehabilitation. In this study, we were interested in the benefits of moderate-intensity exercise in MP, given its positive effects on the acquisition and consolidation of motor skills induced by physical practice (PP). Four experimental groups were tested: i) physical practice without exercise (PP-Rest), ii) mental practice without exercise (MP-Rest), iii) mental practice preceded by Exercise (Exe-MP), and iv) mental practice followed by Exercise (MP-Exe). We hypothesized that exercise before MP would further increase speed and accuracy at a finger-sequence task measured right after MP (potentiation of motor acquisition), whereas exercise after MP would further increase speed and accuracy the day after MP (promotion of motor consolidation). Motor performance (movement speed and accuracy) was measured during a sequential finger tapping task before (Pre-Test), immediately after (Post-Test 0h, acquisition), and one day after practice (Post-Test 24h, consolidation). Results suggest that exercise before MP did not additionally improve motor acquisition in comparison to the MP-Rest group (both for accuracy and speed, p’s>0.05). Interestingly, moderate-intensity exercise after MP further increased performance during motor consolidation (speed, p=0.051; accuracy, p=0.028), at the level of the PP-Rest group. This novel finding represents a promising advance in the optimization of mental practice protocols in sport-related and rehabilitation settings.
Fluoxetine degrades luminance perceptual thresholds while enhancing motivation and reward sensitivity

Selective serotonin reuptake inhibitors (SSRIs) increase serotonin activity in the brain. While they are mostly known for their antidepressant properties, they have been shown to improve visual functions in amblyopia and impact cognitive functions ranging from attention to motivation and sensitivity to reward. Yet, a clear understanding of the specific action of serotonin to each of bottom-up sensory and top-down cognitive control components and their interaction is still missing. To address this question, we characterize, in two adult macaques, the behavioral effects of fluoxetine, a specific SSRI, on visual perception under varying bottom-up (luminosity, distractors) and top-down (uncertainty, reward biases) constraints while they are performing three different visual tasks. We first manipulate target luminosity in a visual detection task, and we show that fluoxetine degrades luminance perceptual thresholds. We then use a target detection task in the presence of spatial distractors, and we show that under fluoxetine, monkeys display both more liberal responses as well as a degraded perceptual spatial resolution. In a last target selection task, involving free choice in the presence of reward biases, we show that monkeys display an increased sensitivity to reward outcome under fluoxetine. In addition, we report that monkeys produce, under fluoxetine, more trials and less aborts, increased pupil size, shorter blink durations, as well as task-dependent changes in reaction times. Overall, while low level vision appears to be degraded by fluoxetine, performance in the visual tasks are maintained under fluoxetine due to enhanced top-down control based on task outcome and reward maximization.
Genericity of weak-mixing measures on geometrically finite manifolds

Let $M$ be a manifold with pinched negative sectional curvature. We show that when $M$ is geometrically finite and the geodesic flow on $T^1 M$ is topologically mixing then the set of mixing invariant measures is dense in the set $\mathscr{M}^1(T^1M)$ of invariant probability measures. This implies that the set of weak-mixing measures which are invariant by the geodesic flow is a dense $G_{\delta}$ subset of $\mathscr{M}^1(T^1 M)$. We also show how to extend these results to manifolds with cusps or with constant negative curvature.
A sharp Adams inequality in dimension four and its extremal functions

Let $\Omega$ be a smooth oriented bounded domain in $\mathbb R^4$, $H_0^2(\Omega)$ be the Sobolev space, and $\lambda_1(\Omega)= \inf \{\|\Delta u\|_2^2 : u\in H_0^2(\Omega), \|u\|_2 =1\}$ be the first eigenvalue of the bi-Laplacian operator $\Delta^2$ on $\Omega$. For $\alpha \in [0,\lambda_1(\Omega))$, we define $\|u\|_{2,\alpha}^2 = \|\Delta u\|_2^2 - \alpha \|u\|_2^2$, for $u \in H_0^2(\Omega)$. In this paper, we will prove the following inequality \[ \sup_{u\in H_0^2(\Omega),\, \|u\|_{2,\alpha} \leq 1} \int_{\Omega} e^{32 \pi^2 u(x)^2} dx < \infty. \] This strengthens a recent result of Lu and Yang \cite{LuYang}. We also show that there exists a function $u^*\in H_0^2(\Omega)\cap C^4(\overline{\Omega})$ such that $\|u^*\|_{2,\alpha} =1$ and the supremum above is attained by $u^*$. Our proofs are based on the blow-up analysis method.
Semi-Lagrangian schemes for linear and fully non-linear Hamilton-Jacobi-Bellman equations

We consider the numerical solution of Hamilton-Jacobi-Bellman equations arising in stochastic control theory. We introduce a class of monotone approximation schemes relying on monotone interpolation. These schemes converge under very weak assumptions, including the case of arbitrary degenerate diffusions. Besides providing a unifying framework that includes several known first order accurate schemes, stability and convergence results are given, along with two different robust error estimates. Finally, the method is applied to a super-replication problem from finance.
Physiological determinant of health and disease in executive health check-up

: Background: Early detection of the disease in its latent phase through executive health checkup facilitates timely therapeutic interventions, thereby significantly reducing the associated morbidity, mortality and economic burden. Objectives: To evaluate the physiological determinants of health and disease in executive health checkup. Methods: In this hospital-based, cross-sectional study, a total of 768 individuals aged >20 years, irrespective of their gender, reporting for an executive health check-up were included. Demographic parameters, radiological examinations and psychological wellbeing score were evaluated and compared. Data were analyzed using statistical software R version 3.6. 3. Results: The study consisted of 768 patients (515 males and 253 females) and majority of them were aged >40 years, almost 75%. No significant difference was found between demographic variables and mean psychological wellbeing scores, environmental mastery and personal growth ( P >0.05). A significant association was found between age and findings of ECT and TMT ( P =0.001), between gender and findings of TMT ( P =0.01). No positive relation was found between sub-categories of demographic variables with respect to psychological wellbeing. A significant difference was found only between different classes of socioeconomic status with respect to self-acceptance and purpose in life ( P =0.08). Conclusion: Age and gender associated abnormal ECG and TMT findings are common physiological determinants found in this study. Executive checkups are integral to health promotion, especially in the current scenario of silent killer diseases; preventive health services reduce eventual demand for medical care, thus, enhancing the economic efficiency.
Gravity as a constrained BF theory: Noether charges and Immirzi parameter

We derive and analyze Noether charges associated with the diffeomorphism invariance for the constrained SO(2,3) BF theory. This result generalizes the Wald approach to the case of the first order gravity with a negative cosmological constant, the Holst modification, and topological terms (Nieh-Yan, Euler, and Pontryagin). We show that differentiability of the action is automatically implemented by the structure of the constrained BF model. Finally, we calculate the AdS-Schwarzschild black hole entropy from the Noether charge and we find that it does not depend on the Immirzi parameter.
Exploring Students’ Entry Profiles: English Proficiency Level, Affective Variables, and Academic Performance in a Chilean English Teacher Education Program 1

Having valuable information about newly enrolled university students in the form of entry profiles is key to addressing their academic needs as they advance through their educational trajectories. In Chile, this is acknowledged by Law 20903, which mandates that all tertiary-level pedagogy programs implement a diagnostic assessment at the beginning of the studies. This, in order to even out students’ academic level and establish supportive measures for those who obtain low results. Aiming to enrich the entry profile of a group of Chilean English language teaching (TEFL) undergraduates, this research explores how factors such as English proficiency level, class attendance, and motivation influence their academic performance during the first semester of their university studies. Through the analysis of quantitative sources of data, the results suggest that class attendance and scores on an institutional English entry test provide valuable information about students’ performance but do not fully explain their academic success. Qualitative data from teacher interviews suggest that profiling students also involves looking into factors such as motivation. Findings should spark reflection on the need for more detailed entry profiles and comprehensive diagnostic assessments that transcend the assessment of English skills and linguistic knowledge in order to ensure better learning trajectories for university students.
Isoperimetric problems for a nonlocal perimeter of Minkowski type

Abstract We show a quantitative version of the isoperimetric inequality for a non local perimeter of Minkowski type. We also apply this result to study isoperimetric problems with repulsive interaction terms, under volume and convexity constraints.We prove existence of minimizers, and we describe their shape as the volume tends to zero or to infinity.
Non-manifest symmetries in quantum field theory

Non-manifest symmetries are an important feature of quantum field theories, and yet their characteristics are not fully understood. In particular, the construction of the charge operators associated with these symmetries is ambiguous. In this paper we adopt a rigorous axiomatic approach in order to address this issue. It turns out that charge operators of non-manifest symmetries are not unique, and that although this does not affect their property as generators of the corresponding symmetry transformations, additional physical input is required in order to determine how they act on states. Applying these results to the examples of spacetime translation and Lorentz symmetry, it follows that the assumption of the uniqueness of the vacuum state is sufficient to uniquely specify the charges associated with these symmetries. In the case of supersymmetry though, there exists no such physical requirement, and therefore the supersymmetric charge is not uniquely defined.
Orbital period determinations for four SMC Be/X-ray binaries

We present an optical and X-ray study of four Be/X-ray binaries located in the Small Magellanic Cloud (SMC). OGLE I-band data of up to 11 years of semicontinuous monitoring has been analysed for SMC X-2, SXP172 and SXP202B, providing both a measurement of the orbital period (P orb = 18.62, 68.90 and 229.9 d for the pulsars, respectively) and a detailed optical orbital profile for each pulsar. For SXP 172 this has allowed a direct comparison of the optical and X-ray emission seen through regular RXTE monitoring, revealing that the X-ray outbursts precede the optical by around 7 d. Recent X-ray studies by XMM-Newton have identified a new source in the vicinity of SXP15.3 raising doubt on the identification of the optical counterpart to this X-ray pulsar. Here we present a discussion of the observations that led to the proposal of the original counterpart and a detailed optical analysis of the counterpart to the new X-ray source, identifying a 21.7 d periodicity in the OGLE I-band data. The optical characteristics of this star are consistent with that of a SMC Be/X-ray binary. However, this star was rejected as the counterpart to SXP15.3 in previous studies due to the lack of Hα emission.
A note on semilinear fractional elliptic equation: analysis and discretization

In this paper we study existence, regularity, and approximation of solution to a fractional semilinear elliptic equation of order $s \in (0,1)$. We identify minimal conditions on the nonlinear term and the source which leads to existence of weak solutions and uniform $L^\infty$-bound on the solutions. Next we realize the fractional Laplacian as a Dirichlet-to-Neumann map via the Caffarelli-Silvestre extension. We introduce a first-degree tensor product finite elements space to approximate the truncated problem. We derive a priori error estimates and conclude with an illustrative numerical example.
The fundamental plane relation of early-type galaxies: environmental dependence

Using a sample of 70 793 early-type galaxies from SDSS DR7, we study the environmental dependence of the fundamental plane relation. With the help of the galaxy group catalog based on SDSS DR7, we calculate the fundamental planes in different dark matter halo mass bins for both central and satellite galaxies. We find the environmental dependence of the fundamental plane coefficients is similar in the g, r, i and z bands. The environmental dependence for central and satellite galaxies is significantly different. Although the fundamental plane coefficients for centrals vary systematically with the halo mass, those of satellites are similar in different halo mass bins. The discrepancy between centrals and satellites is significant in small halos, but negligible in the largest halo mass bins. These results remain the same when we only keep red galaxies, or galaxies with b/a > 0.6, or galaxies in a specific radius range in the sample. After the correction for the sky background, the results are still similar. We suggest that the different environmental effects of the halo mass on centrals and satellites may arise from their different quenching processes.
Clearing price distributions in call auctions

We propose a model for price formation in financial markets based on the clearing of a standard call auction with random orders, and verify its validity for prediction of the daily closing price distribution statistically. The model considers random buy and sell orders, placed employing demand- and supply-side valuation distributions; an equilibrium equation then leads to a distribution for clearing price and transacted volume. Bid and ask volumes are left as free parameters, permitting possibly heavy-tailed or very skewed order flow conditions. In highly liquid auctions, the clearing price distribution converges to an asymptotically normal central limit, with mean and variance in terms of supply/demand-valuation distributions and order flow imbalance. By means of simulations, we illustrate the influence of variations in order flow and valuation distributions on price/volume, noting a distinction between high- and low-volume auction price variance. To verify the validity of the model statistically, we predict a year's worth of daily closing price distributions for five constituents of the Eurostoxx 50 index; Kolmogorov–Smirnov statistics and QQ-plots demonstrate with ample statistical significance that the model predicts closing price distributions accurately, and compares favourably with alternative methods of prediction.
On the structure of join tensors with applications to tensor eigenvalue problems

We investigate the structure of join tensors, which may be regarded as the multivariable extension of lattice-theoretic join matrices. Explicit formulae for a polyadic decomposition (i.e., a linear combination of rank-1 tensors) and a tensor-train decomposition of join tensors are derived on general join semilattices. We discuss conditions under which the obtained decompositions are optimal in rank, and examine numerically the storage complexity of the obtained decompositions for a class of LCM tensors as a special case of join tensors. In addition, we investigate numerically the sharpness of a theoretical upper bound on the tensor eigenvalues of LCM tensors.
A new proof of the sharpness of the phase transition for Bernoulli percolation on $\mathbb Z^d$

We provide a new proof of the sharpness of the phase transition for nearest-neighbour Bernoulli percolation. More precisely, we show that - for $p<p_c$, the probability that the origin is connected by an open path to distance $n$ decays exponentially fast in $n$. - for $p>p_c$, the probability that the origin belongs to an infinite cluster satisfies the mean-field lower bound $\theta(p)\ge\tfrac{p-p_c}{p(1-p_c)}$. This note presents the argument of \cite{DumTas15}, which is valid for long-range Bernoulli percolation (and for the Ising model) on arbitrary transitive graphs in the simpler framework of nearest-neighbour Bernoulli percolation on $\mathbb Z^d$.