Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

Significance Unless there are strong constraints, the probability of complex organs originating multiple times through similar trajectories should be vanishingly small. Here, we report that similar light-producing organs (photophores) evolved separately in two squid species, yet each organ expresses similar genes at comparable levels. Gene expression is so similar that overall expression levels alone can predict organ identity, even in separately evolved traits of squid species separated by tens of millions of years. The striking similarity of expression of hundreds of genes in distinct photophores indicates complex trait evolution may sometimes be more constrained and predictable than expected, either because of internal factors, like a limited array of suitable genetic building blocks, or external factors, like natural selection favoring an optimum. Despite contingency in life’s history, the similarity of evolutionarily convergent traits may represent predictable solutions to common conditions. However, the extent to which overall gene expression levels (transcriptomes) underlying convergent traits are themselves convergent remains largely unexplored. Here, we show strong statistical support for convergent evolutionary origins and massively parallel evolution of the entire transcriptomes in symbiotic bioluminescent organs (bacterial photophores) from two divergent squid species. The gene expression similarities are so strong that regression models of one species’ photophore can predict organ identity of a distantly related photophore from gene expression levels alone. Our results point to widespread parallel changes in gene expression evolution associated with convergent origins of complex organs. Therefore, predictable solutions may drive not only the evolution of novel, complex organs but also the evolution of overall gene expression levels that underlie them.
Multi-objective Uniform-diversity Genetic Algorithm (MUGA)

Optimization in engineering design has always been of great importance and interest particularly in solving complex real-world design problems. Basically, the optimization process is defined as finding a set of values for a vector of design variables so that it leads to an optimum value of an objective or cost function. In such single-objective optimization problems, there may or may not exist some constraint functions on the design variables and they are respectively referred to as constrained or unconstrained optimization problems. There are many calculus-based methods including gradient approaches to search for mostly local optimum solutions and these are well documented in (Arora, 1989; Rao, 1996). However, some basic difficulties in the gradient methods such as their strong dependence on the initial guess can cause them to find a local optimum rather than a global one. This has led to other heuristic optimization methods, particularly Genetic Algorithms (GAs) being used extensively during the last decade. Such nature-inspired evolutionary algorithms (Goldberg, 1989; Back et al., 1997) differ from other traditional calculus based techniques. The main difference is that GAs work with a population of candidate solutions, not a single point in search space. This helps significantly to avoid being trapped in local optima (Renner & Ekart, 2003) as long as the diversity of the population is well preserved. In multi-objective optimization problems, there are several objective or cost functions (a vector of objectives) to be optimized (minimized or maximized) simultaneously. These objectives often conflict with each other so that as one objective function improves, another deteriorates. Therefore, there is no single optimal solution that is best with respect to all the objective functions. Instead, there is a set of optimal solutions, well known as Pareto optimal solutions (Srinivas & Deb, 1994; Fonseca & Fleming, 1993; Coello Coello & Christiansen, 2000; Coello Coello & Van Veldhuizen, 2002), which distinguishes significantly the inherent natures between single-objective and multi-objective optimization problems. V. Pareto (1848-1923) was the French-Italian economist who first developed the concept of multiobjective optimization in economics (Pareto, 1896). The concept of a Pareto front in the space of objective functions in multi-objective optimization problems (MOPs) stands for a set of solutions that are non-dominated to each other but are superior to the rest of solutions in the search space. Evidently, changing the vector of design variables in such a Pareto optimal O pe n A cc es s D at ab as e w w w . ite ch on lin e. co m
Handbook of Learning and Approximate Dynamic Programming (IEEE Press Series on Computational Intelligence)

Foreword. 1. ADP: goals, opportunities and principles. Part I: Overview. 2. Reinforcement learning and its relationship to supervised learning. 3. Model-based adaptive critic designs. 4. Guidance in the use of adaptive critics for control. 5. Direct neural dynamic programming. 6. The linear programming approach to approximate dynamic programming. 7. Reinforcement learning in large, high-dimensional state spaces. 8. Hierarchical decision making. Part II: Technical advances. 9. Improved temporal difference methods with linear function approximation. 10. Approximate dynamic programming for high-dimensional resource allocation problems. 11. Hierarchical approaches to concurrency, multiagency, and partial observability. 12. Learning and optimization - from a system theoretic perspective. 13. Robust reinforcement learning using integral-quadratic constraints. 14. Supervised actor-critic reinforcement learning. 15. BPTT and DAC - a common framework for comparison. Part III: Applications. 16. Near-optimal control via reinforcement learning. 17. Multiobjective control problems by reinforcement learning. 18. Adaptive critic based neural network for control-constrained agile missile. 19. Applications of approximate dynamic programming in power systems control. 20. Robust reinforcement learning for heating, ventilation, and air conditioning control of buildings. 21. Helicopter flight control using direct neural dynamic programming. 22. Toward dynamic stochastic optimal power flow. 23. Control, optimization, security, and self-healing of benchmark power systems.
A fast wavelet algorithm for image deblurring

We present a nonlinear fully adaptive wavelet algorithm which can recover a blurred image (n? n) observed in white noise with O(n 2 (logn) 2 ) steps. Our method exploits both the natural representation of the convolution operator in the Fourier domain and the typical characterisation of Besov classes in the wavelet domain. A particular feature of our method includes "cycle-spinning" band-limited wavelet approximations over all circulant shifts. The speed and the accuracy of the algorithm is illustrated with numerical examples of image deblurring. All figures presented in this paper are reproducible using the WaveD software package.
Student Content Engagement as a Construct for the Measurement of Effective Classroom Instruction and Teacher Knowledge

® INTRODUCTION The effort to link statistically student achievement to measures of teaching or teachers has proven very difficult. Analysts generally agree that the impacts of effective teachers on student 1 The problem for analysts has been in identifying the characteristics of high quality teaching or teachers. Analysts have been able to estimate the size of the impact of teacher quality, through methods that isolate the impact of having one teacher compared with another teacher. But they have been less successful in isolating what it is about higher quality teachers or instruction that produces these effects. A stumbling block in the effort to identify key aspects of teachers and teaching has been the lack of adequate measures of potentially important characteristics of teaching and teachers (see for reviews of measures of instruction Burstein et al. In the absence of appropriate measures analysts are left using whatever measures are available to them and labeling the measures as proxies for potentially important characteristics of teaching or teachers. It is not surprising, then, that analysts have struggled to link characteristics of teachers or teaching to student achievement. Much of the analysis of extant survey measures of instruction has focused on reliability and validity (including generalizability) issues associated with asking teachers to self-report on something as complex and sensitive as instruction (see, for instance, Lanahan, Scotchmer, & McLaughlin, 2004). Less attention has been devoted to concerns about what actually are important things on which to survey teachers. Important work remains in mapping out for survey designers the topics that warrant investigation. Although the research is thin on what is important about teaching and teachers, there have been many decades of basic research on how people learn and there is accumulating research on appropriate instructional methods for specific subject matter. In this paper, we present a framework that divides characteristics of teaching and teachers into four categories representing elements that research on learning suggests need to be in place in order for students to learn. The framework is intended for use in helping to develop and organize 1 The impact of good teaching over one school year may be relatively small, but the cumulative effect could be large. A 1 standard deviation difference in teacher quality is likely to produce an impact on students on the order of 0.1 standard deviation of the distribution of all students' test scores on a given subject This effect …
Forces for Good: The Six Practices of High-Impact Nonprofits

Foreword. Preface. Acknowledgments. The Authors. Introduction. 1. Forces for Good. 2. Advocate and Serve. 3. Make Markets Work. 4. Inspire Evangelists. 5. Nurture Nonprofit Networks. 6. Master the Art of Adaptation. 7. Share Leadership. 8. Sustaining Impact. 9. Putting It into Practice. Appendix A: Research Methodology. Appendix B: Field Experts. Appendix C: Case Study Research Guidelines and Questions. Appendix D: Key Stakeholders Interview List. Appendix E: Organization Profiles. Endnotes. Additional Resources. Index.
Structure and Mechanism of Mouse Cyclase-associated Protein (CAP1) in Regulating Actin Dynamics*

Background: Mechanistic and structural conservation between evolutionarily distant Srv2/CAP homologs has remained unclear. Results: Mouse CAP1 forms hexameric structures that autonomously bind F-actin, enhance cofilin-mediated severing, and catalyze nucleotide exchange on actin. Conclusion: Yeast and mouse CAP share similar structures and functions. Significance: The role of CAP in actin regulation is remarkably well conserved. Srv2/CAP is a conserved actin-binding protein with important roles in driving cellular actin dynamics in diverse animal, fungal, and plant species. However, there have been conflicting reports about whether the activities of Srv2/CAP are conserved, particularly between yeast and mammalian homologs. Yeast Srv2 has two distinct functions in actin turnover: its hexameric N-terminal-half enhances cofilin-mediated severing of filaments, while its C-terminal-half catalyzes dissociation of cofilin from ADP-actin monomers and stimulates nucleotide exchange. Here, we dissected the structure and function of mouse CAP1 to better understand its mechanistic relationship to yeast Srv2. Although CAP1 has a shorter N-terminal oligomerization sequence compared with Srv2, we find that the N-terminal-half of CAP1 (N-CAP1) forms hexameric structures with six protrusions, similar to N-Srv2. Further, N-CAP1 autonomously binds to F-actin and decorates the sides and ends of filaments, altering F-actin structure and enhancing cofilin-mediated severing. These activities depend on conserved surface residues on the helical-folded domain. Moreover, N-CAP1 enhances yeast cofilin-mediated severing, and conversely, yeast N-Srv2 enhances human cofilin-mediated severing, highlighting the mechanistic conservation between yeast and mammals. Further, we demonstrate that the C-terminal actin-binding β-sheet domain of CAP1 is sufficient to catalyze nucleotide-exchange of ADP-actin monomers, while in the presence of cofilin this activity additionally requires the WH2 domain. Thus, the structures, activities, and mechanisms of mouse and yeast Srv2/CAP homologs are remarkably well conserved, suggesting that the same activities and mechanisms underlie many of the diverse actin-based functions ascribed to Srv2/CAP homologs in different organisms.
On the limited interchangeability of rule of law measures

During the latest decade, empirical research on the causes and consequences of the rule of law has expanded and, in the process, become extremely influential. However, we show that a number of widely used indices of the rule of law are not interchangeable. This lack of interchangeability is reflected in the fact that they are based on different defining attributes, to some extent cover distinct empirical scopes, do not correlate highly with each other, and support different explanatory factors. Until a consensus has been established with respect to the conceptualization of the rule of law, scholars are thus not free to opt for the measure that fits their data requirements best regarding spatial and/or temporal scope. Instead, they must carefully assess the content validity vis-à-vis their stipulated definition of the rule of law. Given the amount of money and time poured into the rule of law agenda, the problems identified reflect the lack of maturity of ‘good governance’ research.
CR2+ Marginal Zone B Cell Production of Pathogenic Natural Antibodies Is C3 Independent

Intestinal ischemia-reperfusion (IR)–induced damage requires complement receptor 2 (CR2) for generation of the appropriate natural Ab repertoire. Pathogenic Abs recognize neoantigens on the ischemic tissue, activate complement, and induce intestinal damage. Because C3 cleavage products act as ligands for CR2, we hypothesized that CR2hi marginal zone B cells (MZBs) require C3 for generation of the pathogenic Abs. To explore the ability of splenic CR2+ B cells to generate the damaging Ab repertoire, we adoptively transferred either MZBs or follicular B cells (FOBs) from C57BL/6 or Cr2−/− mice into Rag-1−/− mice. Adoptive transfer of wild type CR2hi MZBs but not CR2lo FOBs induced significant damage, C3 deposition, and inflammation in response to IR. In contrast, similarly treated Rag-1−/− mice reconstituted with either Cr2−/− MZB/B1 B cells (B1Bs) or FOBs lacked significant intestinal damage and displayed limited complement activation. To determine whether C3 cleavage products are critical in CR2-dependent Ab production, we evaluated the ability of the natural Ab repertoire of C3−/− mice to induce damage in response to IR. Infusion of C3−/− serum into Cr2−/− mice restored IR-induced tissue damage. Furthermore, Rag-1−/− mice sustained significant damage after infusion of Abs from C3−/− but not Cr2−/− mice. Finally, adoptive transfer of MZBs from C3−/− mice into Rag-1−/− mice resulted in significant tissue damage and inflammation. These data indicate that CR2 expression on MZBs is sufficient to induce the appropriate Abs required for IR-induced tissue damage and that C3 is not critical for generation of the pathogenic Abs.
Adoption and impact of index-insurance and credit for smallholder farmers in developing countries: A systematic review

Purpose – The purpose of this paper is to review the most recent scientific literature on the determinants explaining the demand for index-insurance, the impact of index-insurance and the existing links between insurance and credit. In this meta-analysis, the authors identify key discoveries on the potential of index-insurance in enhancing credit supply for smallholders and thus farm productivity. Design/methodology/approach – Following a systematic literature search in Scopus and Web of Science, relevant empirical articles were identified by using the following criteria search algorithm: “insurance” and (“weather” or “micro” or “area? based” or “rain*” or “livestock” or “index”), and ((“empiric*” or “experiment” or “trial” or “RCT” or “impact”) or (“credit” or “loan*” or “debt” or “finance”)). The authors identified 1,133 related papers, 110 of which were selected as closely matching the study criteria. After removing duplicates and analysing each document, 45 papers were included in the current analysis.
Manliness and Masculinities in Nineteenth-Century Britain: Essays on Gender, Family and Empire

Book synopsis: "Manliness and Masculinities "presents an innovative series of studies in the cultural and social history of nineteenth-century Britain. The book documents the rapid emergence of a new and increasingly important field, and takes forward the definition of this new field. John Tosh addresses the big issues of theory and periodisation, exploring the relationship between masculinity and patriarchy, and between men's public role and their emotional and domestic lives. These insights inform his sensitive treatment of the history of the Victorian family. In the final section of the book John Tosh re-examines some of the major themes of British imperial history, arguing that the empire needs to be seen as a specifically male enterprise answering to masculine aspirations and insecurities. The history of masculinity does not deal with a neglected group. It potentially modifies our view of every field of history in which men are the principal subject-matter ? most of written history. History is still predominantly about men, and this book shows what a difference it makes to our understanding of history to put their masculinity under scrutiny. This book is essential reading for students, teachers and researchers in the history of the family and of the British Empire, as well as Gender Studies.
An Overview of the Use of Precision Population Medicine in Cancer Care: First of a Series

Advances in science and technology in the past century and a half have helped improve disease management, prevention, and early diagnosis and better health maintenance. These have led to a longer life expectancy in most developed and middle-income countries. However, resource- and infrastructure-scarce countries and populations have not enjoyed these benefits. Furthermore, in every society, including in developed nations, the lag time from new advances, either in the laboratory or from clinical trials, to using those findings in day-to-day medical practice often takes many years and sometimes close to or longer than a decade. A similar trend is seen in the application of “precision medicine” (PM) in terms of improving population health (PH). One of the reasons for such lack of application of precision medicine in population health is the misunderstanding of equating precision medicine with genomic medicine (GM) as if they are the same. Precision medicine needs to be recognized as encompassing genomic medicine in addition to other new developments such as big data analytics, electronic health records (EHR), telemedicine, and information communication technology. By leveraging these new developments together and applying well-tested epidemiological concepts, it can be posited that population/public health can be improved. In this paper, we take cancer as an example of the benefits of recognizing the potential of precision medicine in applying it to population/public health. Breast cancer and cervical cancer are taken as examples to demonstrate these hypotheses. There exists significant evidence already to show the importance of recognizing “precision population medicine” (PPM) in improving cancer outcomes not only in individual patients but also for its applications in early detection and cancer screening (especially in high-risk populations) and achieving those goals in a more cost-efficient manner that can reach resource- and infrastructure-scarce societies and populations. This is the first report of a series that will focus on individual cancer sites in the future.
Monitoring restoration and aboveground biomass in tropical peat swamp forests on Borneo using multi-sensoral remote sensing data

Tropische Walder bilden einen gigantischen Kohlenstoffspeicher und verursachen enorme Kohlenstoffemissionen durch Entwaldung und Walddegradierung, die jahrlichen ca. 6 – 17 % der globalen anthropogenen Kohlenstoffdioxidemissionen ausmachen. Besonders tropische, bewaldete Torfgebiete bilden einen zusatzlichen Kohlenstoffspeicher durch tiefe, unterirdische Torfvorkommen (bis zu 20 m). Das groste, bekannte Vorkommen tropischer Torfmoore befindet sich in Indonesien. Starke anthropogene Einflusse gefahrden diese Gebiete, hauptsachlich aufgrund von Holzeinschlag und grosflachigen Plantagen (uberwiegend fur Palmol), was eine Reduktion des Baumbestandes und eine Trockenlegung des Torfes zur Folge hat. Dies fuhrt zu einer hohen Anfalligkeit fur Feuer, welches ublicherweise dazu genutzt wird, bewaldete Flachen zu roden. Dadurch wurde Indonesien zu einem der grosten globalen Treibhausgasemittenten und ruckte in den Fokus von REDD+ Projekten, die auf eine Verringerung der Emissionen durch Entwaldung und Walddegradierung abzielen. Diese Projekte benotigen eine genaue Kontrolle und Abschatzung der Kohlenstoffbestande in den Waldern, welche von der oberirdischen Biomasse abgeleitet wird. Die Analyse von Fernerkundungsdaten erweist sich hierbei als die wirtschaftlichste Methode, abgelegene und kaum zugangliche Walder zu uberwachen. Auch wenn die Erhebung von Felddaten arbeitsintensiv, zeitaufwendig und teuer ist, sind diese dennoch zwingend erforderlich fur die Kalibrierung von luftoder satellitengestutzten Fernerkundungsdaten im Hinblick auf die Bestimmung der Biomasse.
CASTLE: Enhancing the Utility of Inequality Query Auditing Without Denial Threats

We consider a private data set composed of a set of individuals, and the data are outsourced to a remote cloud server. We revisit the classic <italic>query auditing</italic> problem in this outsourcing scenario; the cloud audits each newly arrived query on a single attribute, and the query is rejected if answering it compromises any individual’s privacy. Various query auditing issues have been studied and addressed before. However, previous auditing schemes either have the difficulty of removing denial threats, or lack the analysis of utility (which is defined as the number of answered queries). In this paper, we study the auditing of a sequence of polynomial-time computable queries. Each query is of format <inline-formula> <tex-math notation="LaTeX">$\mathit {f}(\tilde {X}) \leq \! \! \! \! \;\; a$ </tex-math></inline-formula>, where <inline-formula> <tex-math notation="LaTeX">$\mathit {f}$ </tex-math></inline-formula> is any polynomial function, <inline-formula> <tex-math notation="LaTeX">$\tilde {X}$ </tex-math></inline-formula> is a subset of the private data set, and the answer is either “yes” or “no”. Existing methods cannot be applied directly to audit such a query, because it intermingles several types of functions (e.g., sum and max/min). Hence, we propose CASTLE, which is an inequality query auditing scheme that evaluates the risk of answering a query based on the query history and determines whether a newly arrived query should be answered correctly against a <italic>denial threat</italic>. Furthermore, to overcome the limitations of the existing query auditing mechanisms, which are of low utility, we relax CASTLE to increase the utility by returning answers with slight perturbations. We show that our method can be applied to audit intermingled equality queries with an extension. Experiments are conducted to evaluate the efficiency and effectiveness of our methods.