Miracle-dz/UniFAR-FTUs huggingface dataset:
Birth Legacies and State Failure

We argue patterns of state failure are influenced by variation in how states emerged as independent political actors. In particular, states with positive birth legacies, those whose emergence required relatively high levels of capacity and legitimacy, should be less likely to experience state failure than countries that experienced less auspicious births. We assess this claim on the universe of states in the international system between 1950 and 2002 with multistate duration models that estimate the probabilities states transition into and out of periods of failure. We find that states with positive birth legacies are less likely to experience state failure and that this relationship is driven by states with positive birth legacies being able to more quickly transition from failure back to being functioning states. Our findings offer evidence that state failure is usefully thought of in the context of state-making processes and show that how states emerge as independent actors influences phenomena central to comparative and international politics.
Local-to-global extensions for GLn in non-zero characteristic: a characterization of γF(s, π, Sym2, ψ) and γF(s, π, ∧2, ψ)

Let F be a locally compact field of positive characteristic. In his thesis, the second author used the Langlands-Shahidi method to define γ-factors for the symmetric square and exterior square representations of the dual group of GL n (F). We prove here that such γ-factors are characterized by local properties - including a multiplicativity property with respect to parabolic induction - and their role in global functional equations for L-functions. For this, we prove that a given cuspidal representation of GL n (F) is the component at some place of a global automorphic representation, the ramification of which is controlled at other places. In fact, we use an equivalent result for l-adic Galois representations, due to O. Gabber and N. Katz, and transport it via the global Langlands correspondence proved by L. Lafforgue.
A Possible mechanism for generating a small positive cosmological constant

We argue that in the context of string theory a large number N of connected degenerate vacua that mix will lead to a ground state with much lower energy, essentially because of the standard level repulsion of quantum theory for the wavefunction of the Universe. We imagine a history where initial quantum fluctuations give an energy density $\sim m_{susy}^2m_{Pl}^2$, but the universe quickly cascades to an energy density $\sim m_{susy}^2m_{Pl}^2/N$. Then at various phase transitions there are large contributions to the energy density and rearrangement of levels, followed again by a rapid cascade to the ground state or near it. If this mechanism is correct, the ground state of the theory describing our world would be a superposition of a large number of connected string vacua,with shared superselection sets of properties such as three families etc. The observed value of the cosmological constant in terms of the Planck mass, the scale of supersymmetry breaking and the number of connected string vacua.
Chemical Compositions of Field and Globular Cluster RR Lyrae Stars. I. NGC 3201

We present a detailed spectroscopic analysis of horizontal branch stars in the globular cluster NGC 3201. We collected optical (4580–5330 Å), high-resolution (∼34,000), high signal-to-noise ratio (∼200) spectra for 11 RR Lyrae stars and one red horizontal branch star with the multifiber spectrograph M2FS with the 6.5 m Magellan telescope at the Las Campanas Observatory. From measured equivalent widths, we derived atmospheric parameters and abundance ratios for α (Mg, Ca, and Ti), iron-peak (Sc, Cr, Ni, and Zn), and s-process (Y) elements. We found that NGC 3201 is a homogeneous, monometallic ([Fe/H] = −1.47 ± 0.04), α-enhanced ([α/Fe] = 0.37 ± 0.04) cluster. The relative abundances of the iron-peak and s-process elements were found to be consistent with solar values. In comparison with other large stellar samples, NGC 3201 RR Lyraes have similar chemical enrichment histories as do those of other old (t ≥ 10 Gyr) Halo components (globular clusters; red giants; blue and red horizontal branch stars; and RR Lyraes). We also provided a new average radial velocity estimate for NGC 3201 by using a template velocity curve to overcome the limit of single-epoch measurements of variable stars: Vrad = 494 ± 2 km s−1 (σ = 8 km s−1).
Attention-Augmented Memory Network for Image Multi-Label Classification

The purpose of image multi-label classification is to predict all the object categories presented in an image. Some recent works exploit graph convolution network to capture the correlation between labels. Although promising results have been reported, these methods cannot learn salient object features in the images and ignore the correlation between channel feature maps. In addition, the current researches only learn the feature information within individual input image, but fail to mine the contextual information of various categories from the dataset to enhance the input feature representation. To address these issues, we propose an Attention-Augmented Memory Network (AAMN) model for the image multi-label classification task. Specifically, we first propose a novel categorical memory module to excavate the contextual information of various categories from the dataset to augment the current input feature. Secondly, we design a new channel-relation exploration module to capture the inter-channel relationship of features, so as to enhance the correlation between objects in the images. Thirdly, we develop a spatial-relation enhancement module to model second-order statistics of features and capture long-range dependencies between pixels in feature maps, so as to learn salient object features. Experimental results on standard benchmarks, including MS-COCO 2014, PASCAL VOC 2007, and VG-500, demonstrate the effectiveness and superiority of AAMN model, which outperforms current state-of-the-art methods.
GEAR: a graph edge attention routing algorithm solving combinatorial optimization problem with graph edge cost

In combinatorial optimization problems, the traveling salesman problem (TSP) and the vehicle routing problem (VRP) have been widely used in many business scenarios such as transportation management and disaster response. However, conventional methods for these problems still have potential for improvement in terms of accuracy and scalability. Meanwhile, in practical business applications, issues such as routing and re-planning while considering real road conditions remain unsolved. In this paper, we propose a Graph Edge Attention Routing (GEAR) model that solves the above-mentioned problems in both academic research and real-world applications. Specifically, GEAR embeds the features of nodes (destinations to be visited) and edges (moving costs between each two nodes) through Graph Convolutional Networks (GCN). We then combine GCN features and Pointer Networks [1] to construct the policy network model of the GEAR and train it by minimizing the total edge cost through REINFORCE with baseline. Experimental results show that GEAR outperforms the conventional methods in both standard and large-scale combinatorial optimization problems. Additionally, GEAR also enables routes to be re-planned when impassable sections of roads appear, which commonly occurs in real-world business scenarios. Furthermore, by testing GEAR on an enterprise-level business dataset by using the commercial Map API to extract real distances between nodes, GEAR can achieve tour efficiency without real data being used to train it and proves its effectiveness and robustness in real-world combinatorial optimization applications.
Cell Mechanics From cytoskeletal dynamics to tissue-scale mechanical phenomena

This dissertation explores the mechanics of living cells, integrating the role of intracellular activity to capture the emergent mechanical behavior of cells. The topics covered in this dissertation fall into three broad categories : (a) intracellular mechanics, (b) interaction of cells with the extracellular matrix and (c) collective mechanics of multicellular colonies. In part (a) I propose theoretical models for motor-filament interactions in the cell cytoskeleton, which is the site for mechanical force generation in cells. The models predict in a unified manner how contractility, dynamic instabilities and mechanical waves arise in the cytoskeleton by tuning the activity of molecular motors. The results presented in (a) holds relevance to a variety of cellular systems that behave elastically at long time scales, such as muscle sarcomeres, actomyosin stress fibers, adherent cells. In part (b) I introduce a continuum mechanical model for cells adherent to two-dimensional extracellular matrix, and discuss how cells can sense mechanical and geometrical cues from its surrounding matrix. The model provides an important step towards a unified theoretical description of the dependence of traction forces on cell size, actomyosin activity, matrix depth and stiffness, strength of focal adhesions and makes experimentally testable predictions. In part (c) we combine experiment and theory to reveal how intercellular adhesions modulate forces transmitted to the extracellular matrix. We find that In the absence of cadherin-based adhesions, cells within a colony appear to act independently, whereas with strong cadherin-based adhesions, the cell colony behaves like a liquid droplet wetting the substrate underneath. This work defines the importance of intercellular adhesions in coordinating mechanical activity of cell monolayers and has implications for the mechanical regulation of tissues during development, homeostasis, and disease. Cell Mechanics From cytoskeletal dynamics to tissue-scale mechanical phenomena
High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS)

High-throughput transgenesis using synthetic DNA libraries is a powerful method for systematically exploring genetic function. Diverse synthesized libraries have been used for protein engineering, identification of protein-protein interactions, characterization of promoter libraries, developmental and evolutionary lineage tracking, and various other exploratory assays. However, the need for library transgenesis has effectively restricted these approaches to single-cell models. Here we present Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS), a simple yet powerful approach to large-scale transgenesis that overcomes typical limitations encountered in multicellular systems. TARDIS splits the transgenesis process into a two-step process: creation of individuals carrying experimentally introduced sequence libraries, followed by inducible extraction and integration of individual sequences/library components from the larger library cassette into engineered genomic sites. Thus, transformation of a single individual, followed by lineage expansion and functional transgenesis, gives rise to thousands of genetically unique transgenic individuals. We demonstrate the power of this system using engineered, split selectable TARDIS sites in Caenorhabditis elegans to generate (1) a large set of individually barcoded lineages and (2) transcriptional reporter lines from pre-defined promoter libraries. We find that this approach increases transformation yields up to approximately 1000-fold over current single-step methods. While we demonstrate the utility of TARDIS using C. elegans, in principle the process is adaptable to any system where experimentally generated genomic loci landing pads and diverse, heritable DNA elements can be generated.
The splicing switch of SLK controls tumor progression 1 partially via different associations with occludin 2

Aberrant RNA splicing is significantly associated with tumorigenesis and cancer progression. From a pan-cancer transcriptome analysis, we discovered 19 a critical cancer-associated splicing event at exon 13 of SLK that encodes a 20 fragment of 31 amino acids in its coiled-coil domain. We found that alternative 21 skipping of this exon produces a long and short isoform (SLK-L and SLK-S). 22 The splicing is dramatically shifted towards SLK-L across thirteen common 23 cancer types. The two SLK isoforms have distinct functions in controlling cancer 24 development. SLK-L is essential for cancer development while SLK-S leads to 25 cancer repression. Mechanistically, the splicing factor Rbfox2 was identified to 26 specifically bind intron 12 of SLK and inhibit the inclusion of exon 13. Moreover, 27 different SLK isoforms exhibited distinct affinities in binding to the tight junction 28 protein occludin. SLK-L bounds less occludin compared with SLK-S, which may 29 dysregulate the function of tight junctions and disrupt the structural integrity of 30 cells. Finally, we used antisense oligonucleotides to inhibit the inclusion of SLK 31 exon 13, resulting in significant suppression of cancer growth and migration. 32 Collectively, this study uncovered biological consequences and underlying 33 mechanisms for one of the most mis-spliced genes in cancer, shedding light on new cancer therapy via splicing manipulation.
The three waves: Rethinking the structure of the first Upper Paleolithic in Western Eurasia

The Neronian is a lithic tradition recognized in the Middle Rhône Valley of Mediterranean France now directly linked to Homo sapiens and securely dated to 54,000 years ago (ka), pushing back the arrival of modern humans in Europe by 10 ka. This incursion of modern humans into Neandertal territory and the relationships evoked between the Neronian and the Levantine Initial Upper Paleolithic (IUP) question the validity of concepts that define the first H. sapiens migrations and the very nature of the first Upper Paleolithic in western Eurasia. Direct comparative analyses between lithic technology from Grotte Mandrin and East Mediterranean archeological sequences, especially Ksar Akil, suggest that the three key phases of the earliest Levantine Upper Paleolithic have very precise technical and chronological counterparts in Western Europe, recognized from the Rhône Valley to Franco-Cantabria. These trans-Mediterranean technical connections suggest three distinct waves of H. sapiens expansion into Europe between 55-42 ka. These elements support an original thesis on the origin, structure, and evolution of the first moments of the Upper Paleolithic in Europe tracing parallel archaeological changes in the East Mediterranean region and Europe.
Variability and Impact of Musculoskeletal Modeling Parameters for the Human Elbow

Musculoskeletal modeling has significant potential as a translational and clinical research tool for examining neuromuscular injuries and disorders. However its adoption has been limited due, in part, to the difficulty of measuring the subject-specific physiological measures that define model parameters. These measurements may require substantial time and expensive methods, such as MRI, to determine the parameters of a model and thus ensure its accuracy. We used a Monte Carlo simulation to examine the impact of parameter variability on the ill-defined, inverse approximation of muscle activity. We first amalgamated previously published measurements of the physiological characteristics of the upper/lower arm and the biceps/triceps muscles. We then used the observed distributions of these measurements to set physiologically plausible boundaries on uniform distributions and then generated perturbed parameter sets. We computed the root mean squared error (RMSE) between muscle activity patterns generated by the perturbed model parameters to those generated by the original parameters. Regression models were fit to the RMSE of the approximated muscle activity patterns to determine the sensitivity of the simulation results to variation in each parameter. We found that variation in parameters associated with muscle physiology had the most effect on RMSE, suggesting that these parameters may require subject-specific scaling, whereas parameters associated with skeletal bodies had less effect, and might be safely approximated by their population means.
A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat

Zymoseptoria tritici is the fungal pathogen responsible for Septoria tritici blotch on wheat. Disease outcome in this pathosystem is partly determined by isolate-specific resistance, where wheat resistance genes recognize specific fungal factors triggering an immune response. Despite the large number of known wheat resistance genes, fungal molecular determinants involved in such cultivar-specific resistance remain largely unknown. We identified the avirulence factor AvrStb9 using association mapping and functional validation approaches. Pathotyping AvrStb9 transgenic strains on Stb9 cultivars, near isogenic lines and wheat mapping populations, showed that AvrStb9 interacts with Stb9 resistance gene, triggering an immune response. AvrStb9 encodes an unusually large avirulence gene with a predicted secretion signal and a protease domain. It belongs to a S41 protease family conserved across different filamentous fungi in the Ascomycota class and may constitute a core effector. AvrStb9 is also conserved among a global Z. tritici population and carries multiple amino acid substitutions caused by strong positive diversifying selection. These results demonstrate the contribution of an ‘atypical’ conserved effector protein to fungal avirulence and the role of sequence diversification in the escape of host recognition, adding to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation. Author Summary Fungal avirulence (Avr) genes are involved in gene-for-gene relationships with host resistance genes. Avr genes may at the same time target host defenses to allow infection and be recognized by a host resistance gene triggering a defense response. The fungus Zymoseptoria tritici causes Septoria tritici blotch, a major disease of wheat worldwide. Z. tritici populations rapidly adapt to selection pressures such as host resistance, leading to resistance breakdown. We report the identification of the avirulence gene AvrStb9 based on genetic mapping, sequence polymorphisms and allele swapping. AvrStb9 is involved in the interaction with Stb9 resistance gene following the gene-for-gene model, and its recognition hinders disease symptoms in hosts carrying the corresponding resistance gene. Unlike other known Z. tritici Avr effectors, AvrStb9 encodes for an unusually large Avr protein with a predicted protease S41 domain conserved among diverse ascomycete lineages. We also highlight several gene mutations likely involved in escaping Stb9-mediated recognition.
Different genetic architectures of complex traits and 1 their relevance to polygenic score performance

19 Complex traits differ in their genetic architectures, and these differences can affect polygenic 20 score performance. Examining 177 complex traits from the UK Biobank, we first identified pairs 21 of traits that have trait-associated SNPs in shared genomic regions. We then compared and 22 contrasted three aspects of genetic architecture (SNP heritability, trait-specific recombination 23 rates, and a novel metric of polygenicity) with three aspects of polygenic score performance 24 (correlations between predicted and actual trait values, portability of genetic predictions, and 25 divergence across populations). Although highly heritable traits tended to be easier to predict, 26 heritability was largely uninformative with respect to the portability of genetic predictions. By 27 contrast, there was a positive relationship between trait-specific recombination rates and the 28 portability of genetic predictions. Analyzing 100kb bins, we used Gini coefficients to quantify the 29 extent that SNP heritability is unequally distributed across the genome. Polygenic score 30 performance was largely independent of Gini – traits with more Mendelian architectures need not 31 be easier to predict. By contrast, Gini coefficients were negatively correlated with the prevalence 32 of binary traits. We also found that binary traits were more difficult to predict than quantitative 33 traits. Interestingly, lifestyle and psychological traits tend to have low heritability, low Gini 34 coefficients, as well as poor predictability and portability across populations. Because of this, our 35 results caution against the application of polygenic scores to traits like general happiness, alcohol 36 frequency, and average income, especially when polygenic scores are applied to individuals who 37 have an ancestry that differs from the original source population. 38
Population Genomic Evidence of Adaptive Response during the Invasion History of Plasmodium falciparum in the Americas

Plasmodium falciparum, the most virulent agent of human malaria, spread from Africa to all continents following the out-of-Africa human migrations. During the transatlantic slave trade between the 16th and 19th centuries, it was introduced twice independently to the Americas where it adapted to new environmental conditions (new human populations and mosquito species). Here, we analyzed the genome-wide polymorphisms of 2,635 isolates across the current P. falciparum distribution range in Africa, Asia, Oceania, and the Americas to investigate its genetic structure, invasion history, and selective pressures associated with its adaptation to the American environment. We confirmed that American populations originated from Africa with at least two independent introductions that led to two genetically distinct clusters, one in the North (Haiti and Columbia) and one in the South (French Guiana and Brazil), and the admixed Peruvian group. Genome scans revealed recent and more ancient signals of positive selection in the American populations. Particularly, we detected positive selection signals in genes involved in interactions with host (human and mosquito) cells and in genes involved in resistance to malaria drugs in both clusters. We found that some genes were under selection in both clusters. Analyses suggested that for five genes, adaptive introgression between clusters or selection on standing variation was at the origin of this repeated evolution. This study provides new genetic evidence on P. falciparum colonization history and on its local adaptation in the Americas.