Miracle-dz/UniFAR-FTUs huggingface dataset:
Barcodes and area-preserving homeomorphisms

In this paper we use the theory of barcodes as a new tool for studying dynamics of area-preserving homeomorphisms. We will show that the barcode of a Hamiltonian diffeomorphism of a surface depends continuously on the diffeomorphism, and furthermore define barcodes for Hamiltonian homeomorphisms. Our main dynamical application concerns the notion of {\it weak conjugacy}, an equivalence relation which arises naturally in connection to $C^0$ continuous conjugacy invariants of Hamiltonian homeomorphisms. We show that for a large class of Hamiltonian homeomorphisms with a finite number of fixed points, the number of fixed points, counted with multiplicity, is a weak conjugacy invariant. The proof relies, in addition to the theory of barcodes, on techniques from surface dynamics such as Le Calvez's theory of transverse foliations. In our exposition of barcodes and persistence modules, we present a proof of the Isometry Theorem which incorporates Barannikov's theory of simple Morse complexes.
From nonlocal to local Cahn-Hilliard equation

In this paper we prove the convergence of a nonlocal version of the Cahn-Hilliard equation to its local counterpart as the nonlocal convolution kernel approximates a Dirac delta in a periodic boundary conditions setting. It is worth mentioning that $\Gamma$-convergence for the energy functionals associated to the equations is unknown. This convergence result strongly relies on the dynamics of the problem. More precisely, the $H^{-1}$-gradient flow structure of the equation allows to deduce uniform $H^1$ estimates for solutions of the nonlocal Cahn-Hilliard equation and, together with a Poincar\'e type inequality by Ponce, provides the compactness argument that allows to prove the convergence result.
Reconstruction and Convergence in Quantum K-Theory via Difference Equations

We give a new reconstruction method of big quantum $K$-ring based on the $q$-difference module structure in quantum $K$-theory. The $q$-difference structure yields commuting linear operators $A_{i,\rm com}$ on the $K$-group as many as the Picard number of the target manifold. The genus-zero quantum $K$-theory can be reconstructed from the $q$-difference structure at the origin $t=0$ if the $K$-group is generated by a single element under the actions of $A_{i,\rm com}$. This method allows us to prove the convergence of the big quantum $K$-rings of certain manifolds, including the projective spaces and the complete flag manifold $\operatorname{Fl}_3$.
Discrimination of non-nestmate early brood in ants: behavioural and chemical analyses

Brood is critically important in social insect colonies. It carries the colony’s fitness through delivering future reproductive adults as well as workers that will increase the colony’s workforce. Adoption of non-nestmate brood can increase the colony workforce but entails the risk of rearing unrelated sexuals or social parasites. Thus, theory would predict that ant workers will evolve the ability to discriminate between nestmate and alien brood using the chemical cues displayed at the brood’s surface. This appears especially true for eggs and first instar (L1) larvae, which require more resources before becoming adult workers compared to older brood. However, the chemical signature of ant early brood stages and its recognition by workers remains understudied. To fill this gap, we investigated the chemical basis of early brood nestmate and cross-species recognition in six ant species. We also tested the discrimination behaviour of workers in brood retrieval trials. We observed species-level cues and discrimination against hetero-specific brood. We also found that eggs and most L1 larvae displayed a colony signature. However, only some species discriminated against non-nestmate early brood. Interestingly, these species belong to genera subject to brood parasitism. We hypothesize that non-nestmate brood discrimination could arise from species adaptations against brood parasitism.
Cell wall thickness has phylogenetically consistent effects on photosynthetic nitrogen-use efficiency of terrestrial plants: a meta-analysis

Leaf photosynthetic nitrogen-use efficiency (PNUE) diversified significantly among C3 species. However, morpho-physiological mechanisms and interrelationships forming PNUE remain unclear on the evolutionary time scale. In this study, we compiled a novel extensive matrix of morpho-anatomical and physiological traits of leaf in 679 C3 species ranging from bryophytes to angiosperms to understand the intricacy of interrelationships underlying the variations in PNUE. We found that LMA, mesophyll cell wall thickness (Tcwm), Rubisco N allocation fraction (PR), and mesophyll conductance (gm) together interpreted 83% of variations in PNUE, with PR and gm accounting for 65% of those variations. However, the PR effects were species-dependent on gm; that is, the contribution of PR on PNUE was extensively significant in high-gm species in comparison to low-gm species. Standard major analysis (SMA) and path analysis suggested a weak correlation between PNUE and LMA, whereas the SMA correlation for PNUE–Tcwm was strong. The PR was inversely proportional to Tcwm, which was similar to the relationship between gm and Tcwm (p-value < 0.01), so that the internal CO2 drawdown from intercellular airspace to carboxylaton sites was relatively conservative over a wide range of Tcwm. Collectively, the coordination of changes in PR and gm connecting Tcwm suggested the complex physiological mechanisms mediated by Tcwm modulating PNUE across contrasting plant groups.
Snell envelope with path dependent multiplicative optimality criteria

We analyze the Snell envelope with path dependent multiplicative optimality criteria. Especially for this case, we propose a variation of the Snell envelope backward recursion which allows to extend some classical approxima- tion schemes to the multiplicatively path dependent case. In this framework, we propose an importance sampling particle approximation scheme based on a specific change of measure, designed to concentrate the computational effort in regions pointed out by the criteria. This new algorithm is theoritically studied. We provide non asymptotic convergence estimates and prove that the resulting estimator is high biased.
On the content of polynomials over semirings and its applications

In this paper, we prove that Dedekind–Mertens lemma holds only for those semimodules whose subsemimodules are subtractive. We introduce Gaussian semirings and prove that bounded distributive lattices are Gaussian semirings. Then we introduce weak Gaussian semirings and prove that a semiring is weak Gaussian if and only if each prime ideal of this semiring is subtractive. We also define content semialgebras as a generalization of polynomial semirings and content algebras and show that in content extensions for semirings, minimal primes extend to minimal primes and discuss zero-divisors of a content semialgebra over a semiring who has Property ([Formula: see text]) or whose set of zero-divisors is a finite union of prime ideals. We also discuss formal power series semirings and show that under suitable conditions, they are good examples of weak content semialgebras.
The molecular genetic landscape of human brain size variation

Human brain size increases dynamically through early development, peaks in adolescence, and varies up to two-fold among adults. Although previous studies have elucidated changes in brain size across evolution, development, traits, and diseases, the molecular underpinnings of interindividual variation in brain size remain unknown. Here, we leverage postmortem brain RNA sequencing and estimates of brain weight (BW) in 2,531 individuals across three independent datasets, to identify 928 genes that show genome-wide significant associations with either higher or lower BW (BW+, BW-, respectively). These BW gene sets showed distinct neurodevelopmental trajectories and spatial patterns that mapped onto developmental, functional and cellular axes of brain organization. Expression differences among evolutionarily conserved BW genes were predictive of interspecies differences in brain size, and functional annotation of BW genes revealed enrichment for neurogenesis and cell-cell communication. Genome-wide, transcriptome-wide, and phenome-wide association analyses of in vivo neuroimaging phenotypes confirmed that the genetic regulation of BW-transcripts influences cortical surface area and volume, as well as behavioral traits related to brain function and disease. Cumulatively, our study represents a major step towards the goal of delineating the causal mechanisms of human brain size variation in health and disease.
Nongeneric J–holomorphic curves and singular inflation

This paper investigates the geometry of a symplectic 4‐manifold . M;! / relative to a J‐holomorphic normal crossing divisor S . Extending work by Biran, we give conditions under which a homology class A2H2.MIZ/ with nontrivial Gromov invariant has an embedded J‐holomorphic representative for some S ‐compatible J . This holds for example if the class A can be represented by an embedded sphere, or if the components of S are spheres with self-intersection 2. We also show that inflation relative to S is always possible, a result that allows one to calculate the relative symplectic cone. It also has important applications to various embedding problems, for example of ellipsoids or Lagrangian submanifolds. 53D35
Controls of spatial grain size and environmental variables on observed beta diversity of molluscan assemblage at a regional scale

Beta diversity, which quantifies the compositional variation among communities, is one of the fundamental partitions of biodiversity and is associated with abiotic and biotic drivers. Unveiling these drivers is essential for understanding various ecological processes in past and recent faunal communities. Although the quantification of measures of beta diversity has improved over the years, the potential dependence of beta diversity on methodological choices are relatively understudied. Here, we investigate the effect of the variable scale of sampling on different measures of beta diversity at a regional scale. The west coast of India bordering the eastern margin of the Arabian sea, presents a coastal stretch of approximately 6100km from 8–21°N. We used marine bivalve distribution data, consisting of live occurrence data from literature reports and abundance data from death assemblages collected from localities representing latitude bins. We tested if the observed variation in beta diversity is explained by variable sampling scales due to differences in bin sizes and unequal coastline length. We developed a null model to generate a beta diversity pattern with an increase in spatial scale of sampling by increasing the spatial grain size along the 14 latitude bins progressively. Our null model demonstrates that for the both live and dead dataset, the total beta diversity measured by Bray-Curtis, Whittaker and Sorenson indices decreases with increasing sampling scale. The species replacement (turnover) evaluated by Simpson index decreases and the species loss (nestedness) measured by Sorenson index increases with increasing sampling scale. A comparison between the simulated and observed beta diversity distribution using K-S test demonstrated that the observed pattern of beta diversity is significantly different from the pattern generated from the null model in both live and death assemblages. This implies that sampling alone does not generate the spatial variation in beta diversity in this region. The results show that environmental parameters such as salinity, productivity, and cyclones play a significant role in shaping the regional beta diversity along the west coast. Our study provides an approach for evaluating the effect of variable sampling scale on comparing regional beta diversity. It also highlights the importance of spatial standardization while inferring about processes driving spatial diversity changes.
Covariant affine integral quantization(s)

Covariant affine integral quantization of the half-plane is studied and applied to the motion of a particle on the half-line. We examine the consequences of different quantizer operators built from weight functions on the half-plane. To illustrate the procedure, we examine two particular choices of the weight function, yielding thermal density operators and affine inversion, respectively. The former gives rise to a temperature-dependent probability distribution on the half-plane whereas the latter yields the usual canonical quantization and a quasi-probability distribution (affine Wigner function) which is real, marginal in both momentum p and position q.
Attractor and synchronization for a complex network of reaction-diffusion systems of FitzHugh-Nagumo type

We focus on the long time behavior of complex networks of reaction-diffusion (RD) systems. We prove the existence of the global attractor and a $L^{\infty}$-bound for a network of $n$ RD systems with $d$ variables each. This allows us to prove the identical synchronization for general class of networks and establish the existence of a coupling strength threshold value that ensures such a synchronization. Then, we apply these results to some particular networks with different structures (i.e. different topologies) and perform numerical simulations. We found out theoretical and numerical heuristic laws for the minimal strengh coupling needed for synchronization relatively to the number of nodes and the network topology, and discuss the link between spatial dimension and synchronization.
Invigoration Improved Quality and Storability of True Seed of Shallot ( Allium ascalonicum L.)

Seed invigoration is a pre-planting seed treatment by balancing the seed water potential and stimulating their metabolic activities so that the seeds germinate simultaneously. In this study, invigoration treatments were applied to improve the quality of the true seeds of shallots (TSS) that had started to deteriorate. Invigoration increases the moisture content of the seeds so the seeds need to be re-dried to extend their storability. The aims of the study were to determine the best invigoration treatment and the drying method to maintain the benefit of invigoration, and to prolong TSS storability after invigoration and drying. This research was conducted at the Laboratory of Seed Quality Testing, IPB University, Indonesia, and consisted of three experiments, i.e., invigoration of deteriorating TSS to improve their viability and vigor, drying after invigoration to extend seed storability, and seed storability after invigoration and drying treatments. The first experiment was arranged in completely randomized design with one-factor (invigoration solutions), i.e. control, medium containing 3% KNO 3 , 50 ppm GA 3 , 0.5 % ZnSO 4 or -10 bar PEG6000. The second experiment was conducted using a two-factor completely randomized design, drying temperature (20˚C, 30˚C, and 40˚C), and drying duration (8 hours, 16 hours, 32 hours, and 48 hours). The third experiment was arranged in a nested design with two factors. The first factor was a seed storage condition, i.e., ambient temperature, air-conditioned room, and refrigerator. The second factor was seed packages, i.e., aluminum foil and polypropylene plastic. Non-invigorated seeds were used as control. The studies were conducted on two shallot varieties separately, “Trisula” and “Lokananta”, except in the third experiment which only used “Lokananta”. The results showed that invigoration in 3 % KNO 3 and 50 ppm GA 3 effectively improved the vigor of deteriorating TSS . Drying the seeds at 40˚C for 8 hours was the most effective method to reduce seed moisture content without reducing the benefit of invigoration. Storing the invigorated TSS in an air-conditioned room with aluminum foil packaging, or in a refrigerator with aluminum foil or plastic packaging until 14 weeks maintained the benefit of invigoration. The quality of the invigorated TSS was maintained until 14 weeks in an air-conditioned room with aluminum foil packaging, or in a refrigerator with aluminum.
NBER WORKING PAPER SERIES MEASURING VALUATION OF LIQUIDITY WITH PENALIZED WITHDRAWALS

We propose using penalized withdrawals from retirement savings accounts, identified from U.S. tax records, as a revealed-preference tool to characterize households' valuation of liquidity. A simple dynamic model formalizes the notion that the prevalence of withdrawals can be used to characterize American households' valuation of liquidity over time and space. We find pervasive evidence of high valuation of liquidity, hence that shocks are imperfectly insured. Declines in households' income lead to sudden, large, and persistent jumps in the probability of penalized withdrawals. Both local economic conditions and persistent household characteristics play an important role, with the average valuation of liquidity being higher in financially underdeveloped areas as well as in black communities which are plausibly marginalized from the credit market. Finally, applying our tool to the Great Recession, we find that more affected areas saw larger increases in penalized withdrawals, plausibly driven by tightening of local credit conditions. Our analysis offers a new tool to study the valuation of liquidity and our results point to sizable welfare gains from social insurance policies targeted at both households and locations over time. David Coyne Department of the Treasury 1500 Pennsylvania Ave NW, MT1222A Washington, DC 20220 david.coyne@treasury.gov Itzik Fadlon Department of Economics University of California, San Diego 9500 Gilman Drive, #0508 La Jolla, CA 92093 and NBER fadlon@ucsd.edu Tommaso Porzio Columbia Business School 3022 Broadway Uris Hall 824 New York, NY 10027 and NBER tommaso.porzio@columbia.edu
Patched Multi-Key Partitioning for Robust Query Performance

Data partitioning is the key for parallel query processing in modern analytical database systems. Choosing the right partitioning key for a given dataset is a difficult task and crucial for query performance. Real world data warehouses contain a large amount of tables connected in complex schemes resulting in an over-whelming amount of partition key candidates. In this paper, we present the approach of patched multi-key partitioning, allowing to define multiple partition keys simultaneously without data replication. The key idea is to map the relational table partitioning problem to a graph partition problem in order to use existing graph partitioning algorithms to find connectivity components in the data and maintain exceptions (patches) to the partitioning separately. We show that patched multi-key partitioning offer opportunities for achieving robust query performance, i.e. reaching reasonably good performance for many queries instead of optimal performance for only a few queries.
Global topology of hyperbolic components: Cantor circle case

We prove that in the moduli space Md of degree d⩾2 rational maps, any hyperbolic component in the disconnectedness locus and of Cantor circle type is a finite quotient of R4d−4−n×Tn , where n is determined by dynamics. The proof uses some ideas from Riemann surface theory (Abel's Theorem), dynamical system and algebraic topology.
WIDER Working Paper 2022/120 Domestic revenue mobilization and informality Challenges and opportunities for sub-Saharan Africa

: Effective domestic revenue mobilization has gained renewed urgency, especially in the light of the need to recover from the COVID-19 pandemic. In taxation debates, the ‘informal sectors’ have hitherto been assumed to be a part of the problem and implicitly mistaken for lucrative tax bases. First, I critically interrogate current conceptualizations of informality to highlight how the informality that materially affects revenue mobilization goes beyond the hitherto narrow focus on the visible informal sectors. I then demonstrate that informality is only one among many factors negatively associated with tax revenue mobilization in sub-Saharan Africa. I also maintain that better scores on government quality and technology adoption in government systems can play a role in mitigating informality, but a limited one because deeper structural factors sustain informality. I argue for a re-articulation of the concept of informality when it is included in revenue mobilization research, including frank discussions on perennial measurement and data quality issues. Simultaneity in policy strategies is necessary, given that informality is multifaceted. It seems more appropriate to prioritize the securing of livelihoods and the building of local fiscal contracts, including on a quid-pro-quo basis, than tax surveillance, especially given that those who operate in shadow economies tend to be outside national safety nets.
UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS GRADUAÇÃO EM ONCOLOGIA CLÍNICA, CÉLULAS TRONCO

PLAÇA, Jessica Rodrigues. Evaluation of molecular profiles and microenvironments in B-cell lymphomas. 2022. Tese (Doutorado em Ciências) – Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, 2022. B-cell lymphoma comprises a heterogeneous group of malignancies that arise from a specific developmental stage of B-cells and shape of their microenvironment as depicted by the distinct morphological features. Several studies have shown biologically meaningful subgroups, which often coincides with either good or bad response to therapy. However, most of these studies have not been validated in independent cohorts and for several B-cell lymphoma subtypes available data are scarce. Thus, the aim of this project was to identify the genes associated with specific lymphoma signatures (either tumor related or microenvironment), characterize their expression profiles, and associate these profiles with biological functions and clinical outcomes. We characterized an in-depth gene expression pattern of two groups of B-cell lymphomas. The first was the classical Hodgkin lymphoma which has highly abundant CD4+ T cells in the vicinity of tumor cells are considered essential for tumor cell survival but are ill-defined. Although they are activated, they consistently lack expression of activation marker CD26. We compared sorted CD4+CD26and CD4+CD26+ T cells lymph node cell suspensions by RNA sequencing. This revealed that CD4+CD26T cells are antigen experienced. This can be explained by the expression of exhaustion associated transcription factors TOX and TOX2, immune checkpoints PDCD1 and CD200, and chemokine CXCL13, which were amongst the 100 significantly enriched genes in comparison with the CD4+CD26+ T cells. This population is likely a main contributor to the very high response rates to immune checkpoint inhibitors in cHL. The second group was diffuse large B-cell lymphoma which multiple gene expression profiles have been identified but besides the cell of origin (COO) classifier, no signatures have been reproduced in independent studies or evaluated for capturing distinct aspects of DLBCL biology. So, we reproduced 4 signatures in 175 samples of the HOVON-84 trial on a panel of 117 genes using the NanoString platform. The four gene signatures capture the COO, MYC activity, B-cell receptor signaling,
Performance MIDI-to-score conversion by neural beat tracking

Rhythm quantisation is an essential part of converting performance MIDI recordings into musical scores. Previous works on rhythm quantisation are limited to the use of probabilistic or statistical methods. In this paper, we propose a MIDI-to-score quantisation method using a convolutional-recurrent neural network (CRNN) trained on MIDI note sequences to predict whether notes are on beats. Then, we expand the CRNN model to predict the quantised times for all beat and non-beat notes. Further-more, we enable the model to predict the key signatures, time signatures, and hand parts of all notes. Our proposed performance MIDI-to-score system achieves significantly better performance compared to commercial software evaluated on the MV2H metric. We release the tool-box for converting performance MIDI into MIDI scores at: https://github.com/cheriell/PM2S .