Miracle-dz/UniFAR-FTUs huggingface dataset:
A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates

Ubiquitination of proteins is central to protein homeostasis and other cellular processes including DNA repair, vesicular transport, cell-division etc. The process of ubiquitination is conserved from yeast to humans and is carried out by the sequential action of three enzymes: E1, E2 and E3. There are an estimated >600 E3 ligases in humans that execute ubiquitination of specific target proteins in a spatio-temporal manner to elicit desired signaling effects. Here, we developed a ubiquitin-specific proximity-based labeling method to selectively biotinylate substrates of a given ubiquitin ligase. Our method exploits the proximity and the relative orientation of the E3-ligase catalytic domain with respect to ubiquitin observed in the enzymatic intermediate-state structures of E3-E2∼Ub. By fusing the biotin ligase BirA and an Avi-tag variant to the candidate E3 ligase and ubiquitin, respectively, we were able to specifically enrich bona fide substrates and potential new substrates of a ligase using a one-step streptavidin pulldown under denaturing conditions. As proof-of-principle, we applied our method, which we named Ub-POD, to the RING E3 ligase RAD18. RAD18 ubiquitinates DNA-sliding clamp PCNA upon UV-induced DNA damage. We identified PCNA and several other critical players in the DNA damage repair pathway in a single RAD18 Ub-POD experiment. We went on to validate DNA replicase POLE as a possible new substrate of RAD18. Through RAD18 Ub-POD, we were also able to pin down the cellular localization of RAD18-mediated ubiquitination to the damaged DNA nuclear puncta using streptavidin immunofluorescence. Furthermore, we applied Ub-POD to TRAF6, another RING ubiquitin ligase involved in NF-κB signaling and successfully identified known and potentially new TRAF6 substrates. Finally, we adapted our method to the U-box-type E3 ubiquitin ligase CHIP to demonstrate that we can identify substrates of two major classes of mammalian ubiquitin ligases. We anticipate that our method and principle could be widely adapted to all classes of ubiquitin ligases to identify substrates and localize the cellular site(s) of ubiquitination.
Economic Sociology: A Systematic Inquiry

The sociological study of economic activity has witnessed a significant resurgence. Recent texts have chronicled economic sociology's nineteenth-century origins while pointing to the importance of context and power in economic life, yet the field lacks a clear understanding of the role that concepts at different levels of abstraction play in its organization. Economic Sociology fills this critical gap by surveying the current state of the field while advancing a framework for further theoretical development. Alejandro Portes examines economic sociology's principal assumptions, key explanatory concepts, and selected research sites. He argues that economic activity is embedded in social and cultural relations, but also that power and the unintended consequences of rational purposive action must be factored in when seeking to explain or predict economic behavior. Drawing upon a wealth of examples, Portes identifies three strategic sites of research--the informal economy, ethnic enclaves, and transnational communities--and he eschews grand narratives in favor of mid-range theories that help us understand specific kinds of social action. The book shows how the meta-assumptions of economic sociology can be transformed, under certain conditions, into testable propositions, and puts forward a theoretical agenda aimed at moving the field out of its present impasse.
Current and potential distributions of Nassella neesiana (Chilean needle grass) in Australia and New Zealand.

Nassella neesiana (Trin. & Rupr.) Barkworth, var. neesiana (Chilean needle grass) is an invasive weed in Australia and New Zealand where it is the subject of management programmes to reduce its impacts (downgrading of wool, skins, hides and carcasses, reduced stock carrying capacity, reduced grassland biodiversity) and spread. Inferring the species’ climate preference from its distribution in its native range in South America using CLIMEX, we estimate that 180 and 15 million ha respectively are climatically suitable in Australia and New Zealand under current climate. We also estimate that 0.24 and 0.52% respectively of this suitable area has been invaded in Australia and New Zealand. These results imply that N. neesiana could become a much greater problem in both Australia and New Zealand and that management to limit its spread is justified.
Clustering Ensemble Selection Considering Quality and Diversity

Information clustering means classifying information or partitioning some samples in clusters such that samples inside each cluster have maximum similarity to each other and maximum distance from other clusters. As clustering is unsupervised, selecting a specific algorithm for clustering of an unknown set may fail. As a consequence of problem complexity and deficiencies in basic clustering methods, most of studies have focused on ensemble clustering methods in recent years. Diversity in initial results is one of the most important factors which may affect final quality of the results. Moreover, the quality of primary results affects the quality of final results. Both factors have been investigated in recent studies on clustering. Here, a new framework is proposed which is used for improving clustering efficiency and it is based on use of a subset of initial clusters. Selection of this subset plays a significant role in performance of the scheme. The subset is selected using two intelligent methods. The main idea in these methods is utilizing stable clusters through intelligent search algorithms. Two stability factors are utilized for cluster evaluation. One of these two stability factors is based on mutual information and the other one is based on Fisher measure. Finally, the selected clusters are added using several final combining methods. Practical results of several standard data sets demonstrate that the proposed method may improve combination clustering method significantly.
Comparison of quantum dot lasers with and without tunnel-injection quantum well

A comparison between QD lasers with and without tunnel-injection QW designs was performed. In both cases, six layers of a QD or TI-QD design were grown by molecular beam epitaxy equipped with group-V valved cracker cells. The InAs QDs are embedded in InAlGaAs barriers lattice matched to InP. The TI-QW consists of InGaAs separated by a thin InAlGaAs tunnel barrier. The lasers were processed into broad area and ridge waveguide lasers. Both laser designs exhibited high modal gain values in the range of 10-15 cm−1 per dot layer. The static and dynamic device properties of the different QD laser designs were measured and compared against each other.
Productivity growth and international capital flows in an integrated world

The financial globalization for the past decades witnesses the global imbalance phenomenon on which the deficit current accounts by some large advanced economics are continuously financed by some developing economies with the high output growth rates and the scarce capital stocks. On the theoretical ground, the Neo-Classical growth model implies that one economy with scarcity of capital would have a high marginal product of capital and a high autarky interest rate therefore, at the integration with the free mobile capital, that country would experience the net total capital inflows so that the domestic interest rate equals that to the rest of world’s rate (Lucas 1990). Furthermore, one economy growing faster than the rest of the world would also have a higher investment demand and should experience the inflows of net total capitals (Gourinchas and Jeanne 2015). The global imbalances are the result of the heterogeneity in the patterns of savings and investments across countries. Indeed, one country experiences an inflow of capital if its saving is less that its investment: that country borrows from the rest of the world to finance the excess investment demand. Similarly, one country would lend to the rest of the world if its saving is higher than its investment. The thesis would employ the productivity growth to shed the refresh lights on this heterogeneity across countries. [. ]
Multi-Region Ensemble Convolutional Neural Networks for High-Accuracy Age Estimation

In real life, when telling a person’s age from his/her face, we tend to look at his/her whole face first and then focus on certain important regions like eyes. After that we will focus on each particular facial feature individually like the nose or the mouth so that we can decide the age of the person. Similarly, in this paper, we propose a new framework for age estimation, which is based on human face sub-regions. Each sub-network in our framework takes the input of two images each from human facial region. One of them is the global face, and the other is a vital sub-region. Then, we combine the predictions from different sub-regions based on a majority voting method. We call our framework Multi-Region Network Prediction Ensemble (MRNPE) and evaluate our approach using two popular public datasets: MORPH Album II and Cross Age Celebrity Dataset (CACD). Experiments show that our method outperforms the existing state-of-the-art age estimation methods by a significant margin. The Mean Absolute Errors (MAE) of age estimation are dropped from 3.03 to 2.73 years on the MORPH Album II and 4.79 to 4.40 years on the CACD.
Numerical modeling of present-day stress field and deformation pattern in Anatolia

The present-day stress field in the Earth's crust is important and provides insights into mechanisms that drive plate motions. In this study, an elastic plane stress finite elemenl modeling incorporating realistic rock parameters have been used to calculate the stress field, displacement field and deformation of the plate interactions in Anatolia. Modeled stress data for the African-Arabian-Anatolian plate interactions with fixed Eurasian platform cOIl'elate well with observed stress indicator from the world stress map (WSM) and focal mechanism of earthquakes; while displacement field agree qualitatively well with GPS vectors and sense of motion indicated by focal mechanisms for large crustal earthquakes (M>6) and plate motion models. Modeling result shows the direction of maximum horizontal compressive stress ( 0'Hmax) toward the direction of absolute motion of these plates. Large perturbations in O'Hmax orientations are shown to occur in and around tectonic boundaries between those plates. It is observed that, although the African plate acts mostly as indenter, which transmits the collisional motion from tbe Arabian plate to the Anatolian plate, in the current situation the far-field stress probably from the Hellenic subduction is needed to satisfy the present-day stress field in Anatolia. 5
One-to-many Reconstruction of 3D Geometry of cultural Artifacts using a synthetically trained Generative Model

Estimating the 3D shape of an object using a single image is a difficult problem. Modern approaches achieve good results for general objects, based on real photographs, but worse results on less expressive representations such as historic sketches. Our automated approach generates a variety of detailed 3D representation from a single sketch, depicting a medieval statue, and can be guided by multi-modal inputs, such as text prompts. It relies solely on synthetic data for training, making it adoptable even in cases of only small numbers of training examples. Our solution allows domain experts such as a curators to interactively reconstruct potential appearances of lost artifacts.
and Compounds

to k * p = 1.1 ⋅ 10 −4 µm 2 /s for W 0.66 Ta 0.34 B 2−z as well as k l = 2.6 ⋅ 10 −5 µm/s for TaB 2−z , underlined by decreasing scale thicknesses ranging from 1170 nm (WB 2−z ), over 610 nm (W 0.66 Ta 0.34 B 2−z ) to 320 nm (TaB 2−z ) after 10 min at 700 °C. Dense and adherent scales exhibit an increased tantalum content (columnar oxides), which suppresses the volatile character of tungsten-rich as well as boron oxides, hence being a key-factor for enhanced oxidation resistance. Thus, adding Ta (in the range of x = 0.2–0.3) to α -structured WB 2−z does not only positively influence the ductile character and thermal stability but also drastically increases the oxidation resistance. © 2020 The Author(s). Published by Elsevier B.V. CC_BY_4. 0
Sliver-Free Three Dimensional Delaunay Mesh Generation

A key step in the finite element method is to generate well-shaped meshes in 3D. A mesh is well-shaped if every tetrahedron element has a small aspect ratio. It is an old outstanding problem to generate well-shaped Delaunay meshes in three or more dimensions. Existing algorithms do not completely solve this problem, primarily because they can not eliminate all slivers. A sliver is a tetrahedron whose vertices are almost coplanar and whose circumradius is not much larger than its shortest edge length. We present two new algorithms to generate sliver-free Delaunay meshes. The first algorithm locally moves the vertices of an almost-good mesh, whose tetrahedra have small circumradius to shortest edge length ratio. We show that the Delaunay triangulation of the perturbed mesh vertices is still almost good. Furthermore, most slivers disappear after a mild perturbation of the mesh vertices. The remaining slivers migrate to the boundary where they can be peeled off or can be treated with boundary enforcement heuristics. The second algorithm adds points to generate well-shaped meshes. It is based on the following observations. Any tetrahedron will disappear from the Delaunay triangulation if a point is added inside the circumsphere of the tetrahedron. Among the tetrahedra created by inserting this new point there could be tetrahedra with large radius-edge ratios, or slivers, or both. However, the new point is incident to every new tetrahedron. We first eliminate tetrahedra with large radius-edge ratios. We then select the point that avoids creating any small slivers when inserting point inside the circumsphere of slivers. We show that the algorithm will not introduce short edges to the Delaunay triangulation. A simple volume argument implies that the algorithm terminates and generates a well-shaped Delaunay mesh. The generated mesh has a good grading. The number of mesh elements is within a small constant factor of any almost-good mesh for that given domain. We also describe some variations of this refinement-based algorithm. In particular, we show that inserting points near sinks instead of circumcenters of bad tetrahedra also generates sliver-free Delaunay meshes.
Techniques for the Interactive Development of Numerical Linear Algebra Libraries for Scientific Computation

The development of high-performance numerical algorithms and their effective use in application codes is an iterative process involving the refinement of the algorithms and their implementations that continues during the lifetime of the algorithm. Knowledge and expertise from the areas of numerical analysis, computer software, compilers, machine architecture, and applications are required during the development. To improve this process, the FALCON environment was developed to combine the analysis techniques from restructuring compilers with the algebraic techniques from numerical analysis. In this thesis, interactive techniques that were developed to extend the FALCON environment are described. These techniques allow the developer to improve the analysis of the algorithm, to restructure the algorithm using transformation patterns, to utilize additional information about structures within the data, and to control the generation of the target code. The experimental results show that the codes generated by the interactive techniques have better performance than those generated automatically. In addition, the environment was extended to support the generation of C++ code. When the C++ code generated by FALCON is compared to the code generated by other MATLAB translators, the C++ code is typically faster. However, when compared against the Fortran~90 code generated by FALCON, the C++ code is usually slower.
Observation of juvenile Stichopus vastus in Pohnpei Lagoon, Federated States of Micronesia

From: Jeff Kinch, Principal, National Fisheries College, Papua New Guinea [jkinch@fisheries.gov. pg] Species: Stichopus vastus Note: During visits to coastal and island communities as part of an evaluation of sponge and coral farming in Pohnpei, large numbers of juvenile Stichopus vastus were sighted on the northeastern side of Pohnpei Lagoon adjacent to Pharewm Island. All of the juveniles were located on shallow seagrass beds with soft sandy substrate in around 1 m of water (flood tide). Date observed: 2 March 2011 (~ 10.30 am) Reference: Byrne M. , Rowe F. and Uthicke S. 2010. Molecular taxonomy, phylogeny and evolution in the family Stichopodidae (Aspidochirotida: Holothuroidea) based on COI and 16S mitochondrial DNA. Molecular Phylogenetics and Evolution 56(3):1068–1081.
Sensible Heating over the Tibetan Plateau Linked to the Onset of Asian Monsoon

Abstract Land surface heating of the Tibetan Plateau partment finally removed snow accumulation as the pre(TP) plays an important role in the Asian Monsoon sysdictor of monsoon intensity in the 1960s after a long petem. In this study, the interannual variability of the sensiriod of poor snow-rainfall correspondence (Fasullo, ble heat flux over the TP and its connection with the 2004). summer monsoon intensity and onset date was examined Although there is no apparent relationship with the In-based on the newly released land “reanalysis” data, prodian monsoon, the thermal forcing due to anomalous duced by NASA Global Land Data Assimilation System. snow cover over the TP is still believed to exert an influ-Although correlation analyses don't show a significant ence on summer rainfall over East Asia (EA). As EA is relevance to the summer monsoon intensity, the interanlocated in the downstream region of the Tibetan Plateau nual anomalies in sensible heating near the south flank of (TP), snow cover anomalies over the TP could exert a the TP indicate a weak reversal in the relationship with stronger thermal forcing on the East Asian Summer the onset date of the West Pacific East Asian monsoon. A Monsoon (EASM). Chen and Yan (1979, 1981) first diagnostic study shows that above (below) normal sensifound that positive snow depth anomalies over the Tible heating over the south flake of the TP will lead to betan Plateau in boreal winter are accompanied with rapid (slow) warming of the upper air column over the TP above normal May-June rainfall in southern China (Huaand early (later) reversal of (overturn) the meridional nan). Other observational studies (Chen et al., 2000; Wu temperature gradient and the vertical wind shear. This will and Qian, 2003), however, suggested a negative correla-further lead to an earlier (later) onset of the Asian Monsoon.
Forests and people: the role of forest production in frontier farming systems in eastern Amazonia

Maraba region, a pioneer frontier in Eastern Brazilian Amazonia, is an example of the immense diversity of Amazonia region, which should be understand in order to establish adequate development strategies. The six Maraba localities, focus of this study, show a diversity of social and ecological situations that shape what is possible to do in relation to farming and gathering activities. The forest is very important to colonist farmers living there. They recognise and use a wide range of plant and animal species (respectively 142 and 39 were listed) which provide them food, fuel, raw materials, medicinal plants and represent a source of income. Forest activities are more important to poor families, for whom it represents up to 58% of gross income. Even though, they have been replacing forests by more profitable in short term and less risk land uses, as cattle ranching. One of the problems to increase the forest contribution to farms economy is that markets for forest products are very restrict and experiences with commercialisation in the region do not provide the necessary assurance for farmers to invest more in extractivism. The search for alternatives to decrease forest conversion should recognise that colonist livelihoods encompass diversified strategies, where forest is just one component. These alternatives can be more easily found and tested if farmers can discuss their problems in order to identify possible solutions. Research institutions have an important and challenging role to play to help farmers in this process.
Type Passion, Family Life, and Government Support: Explaining the Success of MSME Women Entrepreneurs

In the Sukmajaya sub-district, Depok, most of the MSMEs (771 out of 2,835) are in the culinary field. However, the Covid-19 pandemic has made it challenging for them to sell their products. Therefore, digital marketing is crucial for MSMEs to thrive in this changing market, as customers now prefer to buy digitally. To investigate the impact of SOSTAC digital marketing planning on marketing performance through competitive advantage, this study uses a quantitative descriptive method with SmartPLS 3.0 tool. The researchers collected primary data from 125 culinary MSMEs in the Sukmajaya sub-district through questionnaires and analyzed the data using descriptive and inferential analysis and hypothesis testing. The study found that SOSTAC digital marketing planning has a positive and significant impact on competitive advantage, which, in turn, has a positive and significant impact on marketing performance. Furthermore, the indirect relationship between SOSTAC Digital Marketing Planning and marketing performance through competitive advantage was more significant than the direct relationship. Therefore, MSMEs must prioritize creating a competitive advantage if they want to achieve good marketing performance with SOSTAC Digital Marketing Planning.
Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing neurons

The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identified several examples of such a regulation in developing neurons. However, the systems-level effects of AS-NMD in this context are poorly understood. We developed an R package, factR2, which offers a comprehensive suite of AS-NMD analysis functions. Using this tool, we conducted a longitudinal analysis of gene expression in pluripotent stem cells undergoing induced neuronal differentiation. Our analysis uncovered hundreds of AS-NMD events with significant potential to regulate gene expression. Notably, this regulation was significantly overrepresented in specific functional groups of developmentally downregulated genes. Particularly strong association with gene downregulation was detected for alternative cassette exons stimulating NMD (NS-CEs) upon their inclusion into mature mRNA. By combining bioinformatics analyses with CRISPR/Cas9 genome editing and other experimental approaches we show that NS-CEs regulated by the RNA-binding protein PTBP1 dampen the expression of their genes in developing neurons. We also provide evidence that the NS-CE activity is temporally coordinated with NMD-independent gene repression mechanisms. Our study provides an accessible workflow for the discovery and prioritization of AS-NMD targets. It further argues that the AS-NMD pathway plays a widespread role in developing neurons by facilitating the downregulation of functionally related non-neuronal genes.