Miracle-dz/UniFAR-FTUs huggingface dataset:
Oo-site: A dashboard to visualize gene expression during Drosophila oogenesis reveals meiotic entry is regulated post-transcriptionally

Determining how stem cell differentiation is controlled has important implications for understanding the etiology of degenerative disease and designing regenerative therapies. In vivo analyses of stem cell model systems have revealed regulatory paradigms for stem cell self-renewal and differentiation. The germarium of the female Drosophila gonad, which houses both germline and somatic stem cells, is one such model system. Bulk mRNA sequencing (RNA-seq), single-cell (sc) RNA-seq, and bulk translation efficiency of mRNAs are available for stem cells and their differentiating progeny within the Drosophila germarium. However, visualizing those data is hampered by the lack of a tool to spatially map gene expression and translational data in the germarium. Here, we have developed Oo-site (https://www.ranganlab.com/Oo-site), a tool for visualizing bulk RNA-seq, scRNA-seq, and translational efficiency data during different stages of germline differentiation, that makes these data accessible to non-bioinformaticians. Using this tool, we recapitulated previously reported expression patterns of developmentally regulated genes and discovered that meiotic genes, such as those that regulate the synaptonemal complex, are regulated at the level of translation.
Repair of mismatched templates during Rad51-dependent Break-Induced Replication

Using budding yeast, we have studied Rad51-dependent break-induced replication (BIR), where the invading 3’ end of a site-specific double-strand break (DSB) and a donor template share 108 bp of homology that can be easily altered. When every 10th base is mismatched between donor and recipient, BIR is 44% efficient compared to fully homologous sequences; but BIR still occurs about 10% when every 6th base is mismatched. Here we explore the tolerance of mismatches in more detail, by examining donor templates that each carry 10 mismatches, but where they are clustered with spacings of every 6th bp. These different arrangements of uneven mismatch distribution were in general less efficient in recombination as templates with evenly distributed mismatches. A donor with all 10 mismatches clustered every 6th base at the 3’ invading end of the DSB was not impaired compared to the case where mismatches were clustered at the 5’ end. These data suggest that the efficiency of strand invasion is principally dictated by thermodynamic considerations, i.e., by the total number of base pairs that can be formed; but sequence-specific factors are also important. Mismatches in the donor template are incorporated into the BIR product in a strongly polar fashion up to ~40 nucleotides from the 3’ end. Mismatch incorporation depends on the 3’ → 5’ proofreading exonuclease activity of DNA polymerase δ, with little contribution from Msh2/Mlh1 mismatch repair proteins. Surprisingly, the probability of a mismatch 27 nt from the 3’ end being replaced by donor sequence was the same whether the preceding 26 nucleotides were mismatched every 6th base or fully homologous. These data suggest that DNA polymerase δ “chews back” the 3’ end of the invading strand without any mismatch-dependent cues from the strand invasion structure. Author Summary DNA double-strand breaks (DSBs) are the most lethal forms of DNA damage and inaccurate repair of these breaks presents a serious threat to genomic integrity and cell viability. Break-induced replication (BIR) is a homologous recombination pathway that results in a nonreciprocal translocation of chromosome ends. We used budding yeast Saccharomyces cerevisiae to investigate Rad51-mediated BIR, where the invading 3’ end of the DSB and a donor template share 108 bp of homology. We examined the tolerance of differently distributed mismatches on a homologous donor template and found that BIR efficiency was the same whether the mismatches were clustered at the 3’ invading end or at the 5’ end. We confirmed that mismatches are incorporated into the BIR product in a strongly polar fashion as far as about 40 nucleotides from the 3’ end. We conclude that the proofreading activity of DNA polymerase δ “chews back” the 3’ end of the invading strand even when the sequences removed have no mismatches for the first 26 nucleotides. These observations enrich our understanding of the details of Rad51-mediated strand invasion and provide insight into the mechanism of the 3’ to 5’ proofreading activity of DNA polymerase during homologous recombination.
Tension at intercellular junctions is necessary for accurate orientation of cell division in the epithelium plane

The direction in which a cell divides is set by the orientation of its mitotic spindle and is important for determining cell fate, controlling tissue shape and maintaining tissue architecture. Division perpendicular to the plane of the substrate can promote tissue stratification during development or wound healing, but also metastasis when orientation is aberrant. Much is known about the molecular mechanisms involved in setting the spindle orientation. However, less is known about the contribution of mechanical factors, such as tissue tension, in ensuring spindle orientation in the plane of the epithelium, despite epithelia being continuously subjected to mechanical stresses. Here, we used suspended epithelial monolayers devoid of extracellular matrix and subjected to varying levels of tissue tension to study the orientation of division relative to the tissue plane. We found that decreasing tissue tension by compressing the monolayers or by inhibiting myosin contractility leads to a higher frequency of out-of-plane divisions. Reciprocally, accurate in-plane division can be restored by increasing tissue tension by increasing cell contractility or by tissue stretching. By considering the full three-dimensional geometry of the epithelium, we show that spindles are sensitive to tissue tension, independently of cell shape, through its impact on the tension at subcellular surfaces. Overall, our data suggest that accurate spindle orientation in the plane of the epithelium necessitates the presence of a sufficiently large tension at intercellular junctions. Significance statement In growing epithelia, divisions are typically oriented in the plane of the tissue to drive expansion. In some organs, divisions are then re-oriented so that they occur perpendicular to the epithelium plane to drive tissue stratification and cell differentiation. When uncontrolled, this switch in orientation can lead to defects in tissue organisation and, in cancer, likely contribute to metastasis. While much is known about the molecular mechanisms controlling mitotic spindle orientation, less is known about the role of mechanical factors. Here we use mechanical and chemical perturbations to show that mechanics plays a role in controlling the plane of division. Overall, our data suggest that the orientation of spindles in the epithelium plane requires sufficient tension across intercellular junctions.
Chapter IV: The Organizational Context of School Systems and the Functions of Staff Development

On a day-to-day basis it is sometimes difficult for teachers, building administrators, and those who study life within schools to see that events occurring outside the context of school buildings have any relevance for them or the problems they confront. Indeed, among teachers and building administrators, there is a tendency to disparage those who occupy positions outside the school as "useless bureaucrats" who use up valued resources that would be better spent for instructional purposes. Furthermore, there is a tendency among practitioners to view whatever impact these outsiders have as largely negative--interrupting routine operations in schools for needless meetings, "snoopervising," and so on. If, however, one takes a larger view of the problems of schools and classrooms and if one thinks of careers as well as jobs, biographies as well as personalities, and trends as well as events, the meaning of what happens in classrooms and corridors cannot be properly understood without reference to the system-level context in which schools and classrooms exist. For example, in some schools it would be difficult to understand the relationship between younger teachers and older teachers without taking into account how school system policy relating to reductions in force is shaping those relationships. Furthermore, one cannot properly understand school system policy relating to reductions in force without understanding how teacher organizations
Chapter III: Stages of Linking School and Nonschool Learning Environments

Our society has labored to create an educational system compatible with our noblest aspirations as a free and just society. This effort has been played out historically in cons.iderably varied ways; each locality has developed in its own way just as each era has called for its own responses to changes in the larger social system. The reaffirmation of civil rights for women, people of color, and handicapped citizens, along with the emphasis on b~lingual and multicultural education, responds to the current emphasis on the recognition, respect, and support for the individuality of every person. What has emerged is a tradition of pluralism in schooling and education, characterizedby local community control, committed to the twin goals of quality and equality, and struggling with a diversity of means to achieve those goals. Such efforts reflect the process of modernization. In this process, the public, through governmental structures, establishes policies geared to changing trends and times, while leaders and professionals in all fields have the obligation to put advances in knowledge into practice. Transformations in the socioeconomic nature of the larger Society now mandate modernization of our scholastic and educational pro 7 cesses in both school and nonschool settings. The distinction between schooling and education is, therefore, important. The former relates to activities concerning schools while the latter refers to the total community context, relating all of the learning environments in which and through which people progress. This chapter provides a historical overview of four stages in the
Research on Education Reform: Lessons on the Implementation of Policy

Education reform was the major state policy activity of the 1980s. Beginning in the early years of the decade and continuing with new momentum following the publication of A Nation at Risk1 and other reform reports, states increased their standards for student performance, revised their systems of teacher certification, improved teacher compensation, and enhanced accountability mechanisms. Virtually every state made new policy in these areas and state aid to education increased on the average about 21 percent in real terms between 1983 and 1987.2 In our study of the shaping and implementation of these reforms, we are acquiring a new understanding of the policy process. The paths taken by these reforms are not entirely consistent with the histories of other educational changes. They differ from what we would expect from past research on policy enactment and implementation. In this article, we report initial findings about the reform process and effects in Arizona, California, Florida, Georgia, Minnesota, and Pennsylvania, where we interviewed state and local policymakers and educators in twenty-four districts and fifty-nine schools.3 These interviews, which took place between April 1986 and June 1987, constitute the first phase of a fiveyear study of the reforms. We compare our findings about the reform process and local implementation to what we expected from past research in policy implementation and suggest a new model for the implementation of state re-
In vitro evolution of uracil glycosylase towards DnaKJ and GroEL binding evolves different misfolded states

Natural evolution is driven by random mutations that improve fitness. In vitro evolution mimics this process, however, on a short time scale and is driven by specific outcomes, such as binding to a high-affinity bait. Here, we used directed in vitro evolution to determine how DnaKJ and GroEL change the sequence and structure space of the E. coli protein Uracil glycosylase (eUNG). Using yeast surface display, we generated a random library of eUNG and selected it for binding to chaperones GroEL or DnaK+DnaJ+ATP (DnaKJ). We found that these chaperones select and enrich for mutations causing eUNG to misfold. Evolution in the presence of either chaperone thus resulted in the accumulation of mutations in buried and conserved positions, with a tendency to increase the positive charge. However, GroEL was selected for more exposed and less structured proteins that were highly sensitive to protease cleavage, while DnaKJ was selected for partially structured misfolded species with a tendency to refold, making them less sensitive to proteases. In a more general context, our results show that ATP-fueled chaperones can purge promiscuous misfolded protein mutants from the system, thereby avoiding their potentially detrimental effects, such as forming wrong interactions with native proteins or form aggregates, compromising cellular function.
Agrupamento de Sistemas Orientados a Objetos com Metaheurísticas Evolutivas

Several Software Engineering problems presenting high complexity and combinatorial possibilities and can be modeled as optimization problems. This paper proposes an evolutionary metaheuristic to solve a problem of clustering object-oriented information systems. The algorithms may use two versions of contructor procedures, a local search and path relinking. The computational results showed that the use of these algorithms is an efficient way to solve this problem, in which procedures achieve quality solutions in a reduced runtime. Resumo. Diversos Problemas da Engenharia de Software, por possuírem elevadas complexidade e possibilidades combinatórias, podem ser modelados como problemas de otimização. Este trabalho apresenta uma proposta para a clusterização de sistemas orientados a objetos mediante a utilização de algoritmos evolutivos. Os algoritmos propostos podem utilizar duas versões de procedimentos construtivos, uma busca local e reconexão de caminhos. Os resultados computacionais mostraram que a utilização dos algoritmos propostos é uma alternativa eficiente para a resolução deste problema de clusterização, em que procedimentos alcançam soluções de qualidade em um reduzido tempo de execução. 1. Introdução Diversos Problemas da Engenharia de Software (ES), por possuírem elevadas complexidade e possibilidades combinatórias, podem ser modelados como problemas de otimização (PO). As resoluções desses problemas sugerem algoritmos metaheurísticos, uma vez que métodos exaustivos podem ser ineficientes. A modelagem de problemas de ES em PO deu origem a uma nova e promissora área de pesquisa, denominada Searchbased Software Engineering (SBSE), que aborda temas da ES como: Engenharia de Requisitos, Teste, Manutenção e Estimativas de Software, Planejamento de Projeto, Otimização de Código-Fonte dentre outros (Freitas et al. 2009). Um dos maiores desafios encontrados por uma equipe de desenvolvimento de sistemas é realizar manutenções em softwares complexos, principalmente em sistemas que não possuem documentação ou ela não é suficiente (Doval et al. 1999). Nesse contexto, o presente trabalho propõe algoritmos metaheurísticos para a resolução de um problema de clusterização de sistemas de informação orientados a objetos. Tal problema consiste na Modularização do Software, baseada em sua VII Simpósio Brasileiro de Sistemas de Informação
Conversas sobre serviços públicos

CNPq Abstract. Many discussions enforce the need to encourage involvement and participation of Society in public issues. It is argued that the use of conversations on public services encourages closer ties between Society and Government. This paper presents a tool to support discussion and sharing of information about the provision process of public service. It enables that the information obtained can be used to understand the discussion and for identification of improvements in
Multilevel Polar-Coded Modulation: Performance Analysis and Code Construction

Multilevel polar-coded modulation with multistage decoding is a capacity-achieving coded modulation scheme. In this paper, we propose a general formulation for analyzing the performance of multilevel polar-coded modulation and then derive the error probability upper bounds. The analysis explicitly reveals the effect of the modulation scheme on the performance of component polar codes. Based on the derived upper bounds, we also propose two construction methods for multilevel polar-coded modulation. Compared with conventional methods, such as density evolution and Gaussian approximation which involve complicated recursive calculations, the proposed methods have a linear computational complexity. Simulation results also show that the proposed construction methods can achieve comparable performance to existing methods under SC decoding, and even better performance under SC list decoding.
A Riemannian Augmented Lagrangian Method for the Optimal Power Flow Problem in Radial Distribution Networks

The Second Order Cone Programming (SOCP) relaxation of the branch flow model has been widely applied to solve the Optimal Power Flow (OPF) problem in radial distribution networks. However, the SOCP relaxation does not guarantee solution exactness, unless several conditions are met, thereby occasionally yielding solutions that are not physically feasible. In this paper, we exploit the geometrical properties of the branch flow equations and formulate the OPF problem as a Riemannian optimization problem with inequality constraints. We present a Riemannian Augmented Lagrangian Method consisting of smooth Riemannian optimization subproblems, which ensures the physical feasibility of the solution. Computational experiments on several distribution networks provide encouraging results in terms of solution quality and speed.
VesselXnet - A lightweight and efficient encoder-decoder based model for Retinal Vessel Segmentation

One of the contemporary issues present in medical image segmentation is the segmentation of the Retinal blood vessels. This is because many diseases can be accurately identified from the vascular structure of the retina and hence can be treated early and diagnosed thoroughly. Manual segmentation is hectic, cumbersome, time consuming and also error-prone. Hence there is a need for automatic vessel segmentation which can be a better technological advancement in the medical field. Some of the segmentation methods which were proposed previously have problems of low segmentation accuracy, incomplete segmentation and a large model size. With the progress of deep learning and convolutional neural networks several U-net based architectures were extensively used for this task which offered reliable segmentation results. In this paper, we proposed a light weight U-net based architecture which provides comparable accuracy with much less total parameters.
Inner Approximations of the Positive-Semidefinite Cone via Grassmannian Packings

We investigate the problem of finding inner approximations of positive semidefinite (PSD) cones. We develop a novel decomposition framework of the PSD cone by means of conical combinations of smaller dimensional sub-cones. We show that many inner approximation techniques could be summarized within this framework, including the set of (scaled) diagonally dominant matrices, Factor-width k matrices, and Chordal Sparse matrices. Furthermore, we provide a more flexible family of inner approximations of the PSD cone, where we aim to arrange the sub-cones so that they are maximally separated from each other. In doing so, these approximations tend to occupy large fractions of the volume of the PSD cone. The proposed approach is connected to a classical packing problem in Riemannian Geometry. Precisely, we show that the problem of finding maximally distant sub-cones in an ambient PSD cone is equivalent to the problem of packing sub-spaces in a Grassmannian Manifold. We further leverage existing computational method for constructing packings in Grassmannian manifolds to build tighter approximations of the PSD cone. Numerical experiments show how the proposed framework can balance between accuracy and computational complexity, to efficiently solve positive-semidefinite programs.
Model Predictive Interaction Control for Force Closure Grasping

In this paper, an MPC-based interaction control method for force closure grasping of rigid objects with an anthropomorphic hand is presented. The approach combines the trajectory planning problem of the finger joint positions according to a given object motion with the explicit incorporation of force and kinematic constraints. To this end, the finger forces are predicted by means of a linear-elastic interaction model as well as the dynamic object forces to consider grasping-based constraints on control level. The force closure friction cone condition, the minimal and maximal finger forces and hand-based kinematic limitations are handled as inequality constraints within the optimization problem. The method is evaluated in simulation as well as in experiments on an anthropomorphic hand.
Adaptive Control of Coupled Hyperbolic PDEs with Piecewise-Constant Inputs and Identification

We present an event-triggered state-feedback boundary control scheme with a, likewise, event-triggered batch least-squares parameter identification for a 2×2 hyperbolic PDE-ODE system, where two coefficients of the in-domain couplings between two transport PDEs, and the system parameter of a scalar ODE are unknown. The triggering condition is designed based on evaluating both the actuation deviation caused by the difference between the plant states and their sampled values, and the growth of the plant norm. When either condition is met, the piecewise-constant control input and parameter estimates are updated simultaneously. In the closed-loop system, the following results are obtained: 1) the absence of a Zeno phenomenon; 2) finite-time exact identification of the unknown parameters from all but a measure zero set of initial conditions; 3) exponential regulation of the plant states to zero. In the numerical simulation, the design is verified in an application of axial vibration control of a mining cable elevator, where the damping coefficients of the cable and the cage are unknown.
Hosting Capacity Enhancement Through IoT-based Active Power Curtailment of PV Generation

Due to the high cost of installing large thermal power plants and the resulting emissions from such plants, consumers were encouraged to install rooftop photovoltaic systems. Yet, challenges of integrating solar power into the distribution networks are restraining the amount of allowed generation from rooftop PV systems. Grid operators (GO) started to even limit rooftop PV systems installation capacity toa maximum of their respective load peak value. This paper presents an IoT-based hosting capacity enhancement techniqueby active power curtailment of the power generated from the PV systems at prosumers. Where the IoT establishes a communication channel between the Grid Operator (GO) and all prosumers using the Internet-of-Asset (IoA) architecture. Measurement signals of the Low Voltage (LV) network, solar irradiation, and temperature are necessary for the control technique to generate the reference control voltage for the solar inverter to produce the curtailed PV generation. Theeffect of load and irradiation variation is studied in the presence of the MPPT control, and the GO control, this term isused to describe GO's signal to curtail PV generation. The system has been modeled and simulated via the MATLAB/Simulink® software package. The results validate the effectiveness of this enhancement technique in keeping the overvoltage levels below limits.