Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased Algal Dominance Despite Presence of Diadema Antillarum Populations on a Caribbean Coral Reef

Populations of Diadema antillarum (Philippi, 1845) have been slow to recover after their 1983 Caribbean-wide massive mortality. The continued absence of this important coral reef herbivore as well as further impacts on local and regional-scales have severely threatened the health of coral reefs. From 2008 to 2011, the population of D. antillarum and structure of the benthic community were monitored within Akumal Bay, Mexico, a heavily impacted ecosystem. Across the 4 yrs of the study, densities of adult D. antillarum did not significantly change and were highest on backreef sites (mean 1.30 and 1.44 m−2). Coral cover was low at all sites (maximum 14%) and decreased during the 4 yrs of the study. Changes in crustose coralline algae (CCA) cover varied by year but was significantly higher on forereef sites, while cover by turf-algal-sediment (TAS) increased at all four sites. Diadema antillarum densities correlated positively with coral and CCA cover in the backreef sites where sea urchin densities were higher but no correlation occurred with TAS and turf. Where Echinometra lucunter (Linnaeus, 1758) sea urchins were more prevalent, their densities correlated negatively with coral and positively with CCA. Although densities of adult D. antillarum were comparable to other regions of the Caribbean, increases in TAS over the 4 yrs of this study may be evidence that even an important herbivore cannot prevent continued decline of a reef in an impacted ecosystem. Coral reefs in the Caribbean have experienced major disturbances over the past few decades and continue to be under a combination of stressors including bleaching, overexploitation of herbivores, coral diseases, and declining water quality, which has resulted in an increase in macroalgae cover (Knowlton 1992, Aronson and Precht 2001, Hughes et al. 2003, Bellwood et al. 2004). The importance of long-spined sea urchin, Diadema antillarum (Philippi, 1845), in removing macroalgae cover became evident after their massive mortality in 1983, when algal biomass abruptly increased (de Ruyter van Steveninck and Bak 1986, Carpenter 1988, Hughes 1994). As the populations of D. antillarum recover after their 1983 Caribbean-wide massive mortality (Lessios et al. 1984b, Lessios 2005), it remains unclear if grazing by this herbivore provides a suitable driver from which to expect a decrease in macroalgal cover on impacted coral reefs. Modeled scenarios indicate that sea urchins impart significant resilience to Caribbean reefs such that continued decline is inevitable when sea urchins are scarce (Mumby et al. 2006). However, abundant literature indicates it is a combination of factors which impacts the benthic dynamics on coral reefs and the propensity for shifts between dominant states [e.g., competition for space (Sandin and McNamara 2012), herbivore diversity (Cheal et al. 2010), biotic histories (Aronson et al. 2004), global climate change and marine diseases (Aronson and Precht 2006)]. CORAL REEF PAPER FastTrack➲ publication
Provenance for SQL through Abstract Interpretation: Value-less, but Worthwhile

We demonstrate the derivation of fine-grained where- and why-provenance for a rich dialect of SQL that includes recursion, (correlated) subqueries, windows, grouping/aggregation, and the RDBMS's library of built-in functions. The approach relies on ideas that originate in the programming language community---program slicing and abstract interpretation, in particular. A two-stage process first records a query's control flow decisions and locations of data access before it derives provenance without consultation of the actual data values (rendering the method largely "value-less"). We will bring an interactive demonstrator that uses this provenance information to make input/output dependencies in real-world SQL queries tangible.
An IP Algorithm for RNA Folding Trajectories

Vienna RNA Package software Kinfold implements the Gillespie algorithm for RNA secondary structure folding kinetics, for the move sets MS1 [resp. MS2], consisting of base pair additions and removals [resp. base pair addition, removals and shifts]. In this paper, for arbitrary secondary structures s, t of a given RNA sequence, we present the first optimal algorithm to compute the shortest MS2 folding trajectory s = s0, s1, . , sm = t, where each intermediate structure si+1 is obtained from its predecessor by the addition, removal or shift of a single base pair. The shortest MS1 trajectory between s and t is trivially equal to the number of base pairs belonging to s but not t, plus the number of base pairs belonging to t but not s. Our optimal algorithm applies integer programming (IP) to solve (essentially) the minimum feedback vertex set (FVS) problem for the “conflict digraph” associated with input secondary structures s, t, and then applies topological sort, in order to generate an optimal MS2 folding pathway from s to t that maximizes the use of shift moves. Since the optimal algorithm may require excessive run time, we also sketch a fast, near-optimal algorithm (details to appear elsewhere). Software for our algorithm will be publicly available at http://bioinformatics.bc. edu/clotelab/MS2distance/. 1998 ACM Subject Classification G.1. 6 Optimization
Protein and antigen heterogeneity among strains of Mycoplasma fermentans

The proteins and antigens of three strains of Mycoplasma fermentans were compared with those of a mycoplasma, designated "Mycoplasma incognitus," recently identified in tissues of AIDS patients. Previous studies have shown that "M. incognitus" is most likely not a new species but rather a strain of M. fermentans. In the present study, one- and two-dimensional electrophoretic analysis demonstrated the expected similarity between these mycoplasmas, but it also demonstrated several distinct protein differences. Nine proteins were identified as strain variable by two-dimensional gel electrophoresis. Also, immunoblot analysis using rabbit antiserum against the type strain of M. fermentans (strain PG 18) documented the occurrence of size heterogeneity in at least one and possibly two other antigens.
On the Economics of the Software Replacement Problem

Software maintenance constitutes a significant fraction of the software budget. The cost of maintaining old applications has been escalating and this trend is likely to continue in the foreseeable future. The study of software maintenance strategies has become important to both researchers and practitioners in Information Systems. While there is a rich literature on the technical aspects of software maintenance, research on the economics of maintenance is in its infancy. In particular, the tradeoffs between maintaining and rewriting old software have not been investigated from a theoretical standpoint. In this paper, we present an economic model of the software replacement problem. Based on available empirical evidence, we hypothesize that, with frequent modifications and enhancements, the complexity of software increases rapidly. This deterioration of the code leads to a sharp increase in the maintenance cost. Thus, there may exist a time when it is optimal (in an economic sense) to rewrite the system, which reduces the system complexity and the subsequent maintenance cost. The proposed model allows us to compare the economics of various rewriting strategies and to determine the optimal rewriting point(s). Some interesting results with implications for the systems manager are obtained from the analysis. These include the impacts of system size, structuredness of the underlying technology, and the availability of superior technologies upon the rewriting point(s) and life cycle costs. A numerical example is provided to demonstrate the applicability of the model.
Men, women, and the birthing of modern science

In the early 1600s, Francis Bacon could encompass all knowledge of both the physical and the metaphysical in a single term: natural philosophy. Over the next two hundred years, however, natural philosophy gradually split into philosophy - the study of first causes and ways of knowing - and science - the study of the material world, based on direct observation and verifiable experiment. Initially, science was not an exclusively masculine domain. During the seventeenth and eighteenth centuries, women received doctorates in physics and taught at universities. They corresponded with Descartes and dared to question his premises and conclusions. In astronomy, they worked side by side with men to make observations and calculate cometary orbits. They not only translated and illustrated scientific works but also published original syntheses and reports based on their own research. Gradually, however, as access to the new knowledge became institutionalized, women were excluded. By the dawn of the nineteenth century, the roles open to women were deemed secondary to those of men. Women's ideas and discoveries were subsumed under the names of male colleagues, dismissed as the work of amateurs, or viewed as marginal and easily forgotten. This subtle combination of changed circumstances gave the new science a gendered dimension. "Men, Women, and the Birthing of Modern Science" traces the division of natural philosophy into the modern categories of philosophy and science and the gradual marginalization of women as intellectuals. Here, ten scholars of gender, women's history, and the history of philosophy and science write on these twin themes, allowing the opportunity for cross-cultural analysis and yielding insights into the history of both science and women.
Ecological Impacts of Pesticides in Agricultural Ecosystem

Pesticides are essential tools in integrated pest management (IPM) programs which can have the great influence if they are used properly. However, the adverse impacts of these compounds on the environment and ecosystem should not be ignored. The ecological effects of pesticides can be discussed from different points of view. Some of the significant consequences of use of pesticides are side effects of the pesticides on non-target organisms, sub-lethal effects of the pesticides on target and non-target organisms, emergence of resistant populations and pesticide residue and their entry into the trophic network. Side effect of the pesticides is a controversial issue in pesticides applications. They kill natural enemies present in the field and ecosystem and destroy the natural equilibrium between the hosts and their natural enemies. In the absence of natural enemies, pest populations increase rapidly and makes more controlling efforts, usually pesticides, necessary. In spite of pests, pesticide resistance in natural enemies is not common due to lower exposure to pesticides. Sub-lethal deposits of pesticides can change some biological traits of the organisms exposed to low and highly low concentrations of the toxicants. Sublethal impacts of pesticides are mostly ignored in ecological pesticide assessment because most pesticide assessments are performed as individual-level bioassays and population-level of toxicants has not been considered. Insects (pests and natural enemies) exposed to sub-lethal concentrations of pesticides show some changes in their life history’s traits. Resistant populations emerge due to the misuse of pesticides. The populations with high ecological potential are gradually selected generation by generation and subsequent populations are remarkably or completely insensitive to pesticides. Resistant populations are usually different from natural population in their fertility life table characteristics. Nowadays, the existence of pesticides residue in agricultural crops and their entrance into the trophic network has endangered human health and environment, and it has also necessitated the correct use of the pesticides. In the current chapter, the most significant ecological impacts of pesticides in agricultural ecosystems have been discussed.
Incivility: General attitudes towards the stranger: exploring fear and trust

In traditional societies most people lived in bands or in villages, their geographic horizons usually defined by how far one could walk in a day. Such familiar environments were largely without strangers. Passing migrants, gypsies, tinkers, charlatans and traders were noteworthy interruptions in biographies filled with known others, mostly family and neighbours. Even in courtly society unknown outsiders were something of a novelty. One thinks of the stir caused by the arrival of a company of travelling players in Shakespeare's Hamlet . By contrast, much of lived experience in modern societies takes place in the close physical presence of strangers. Urbanization and the evolution of affordable technologies for daily travel have led to the increased social densities and circulations that see strangers thrown against each other. Of course, at home and at work the stranger is relatively absent. Yet out in public the situation is very different. Remarkably little objective information is known about our social connectedness with, beliefs about, or quality of interactions among those anonymous people with whom we must share public space. Still, respondents to surveys seem to be confident in claiming that things have gone to the dogs and are getting worse. The Public Agenda (2002) survey of 2001 found 79 per cent of American respondents saying that ‘lack of respect and courtesy is a serious problem for our society’, and 73 per cent believing that there was more respect around in the past. These impressions are generally supported rather than critiqued in the academic literature.
The PiTSTOP study: a feasibility cluster randomized trial of delirium prevention in care homes for older people

Background and objectives: delirium is a distressing but potentially preventable condition common in older people in long-term care. It is associated with increased morbidity, mortality, functional decline, hospitalization and significant healthcare costs. Multicomponent interventions, addressing delirium risk factors, have been shown to reduce delirium by one-third in hospitals. It is not known whether this approach is also effective in long-term care. In previous work, we designed a bespoke delirium prevention intervention, called ‘Stop Delirium! ’ In preparation for a definitive trial of Stop Delirium, we sought to address key aspects of trial design for the particular circumstances of care homes. Design: a cluster randomized feasibility study with an embedded process evaluation. Setting and participants: residents of 14 care homes for older people in one metropolitan district in the UK. Intervention: Stop Delirium! : a 16-month-enhanced educational package to support care home staff to address key delirium risk factors. Control homes received usual care. Measurements: we collected data to determine the following: recruitment and attrition; delirium rates and variability between homes; feasibility of measuring delirium, resource use, quality of life, hospital admissions and falls; and intervention implementation and adherence. Results: two-thirds (215) of eligible care home residents were recruited. One-month delirium prevalence was 4.0% in intervention and 7.1% in control homes. Proposed outcome measurements were feasible, although our approach appeared to underestimate delirium. Health economic evaluation was feasible using routinely collected data. Conclusion: a definitive trial of delirium prevention in long-term care is needed but will require some further design modifications and pilot work.
Hyperbolic polynomials approach to Van der Waerden/Schrijver-Valiant like conjectures: sharper bounds, simpler proofs and algorithmic applications

Let p(x<sub>1</sub>,.,x<sub>n</sub>) = p(X) , X ∈ R<sup>n</sup> be a homogeneous polynomial of degree n in n real variables, e = (1,1,.,1) ∈ R<sup>n</sup> be a vector of all ones . Such a polynomial p is called e-hyperbolic if for all real vectors X ∈ R<sup>n</sup> the univariate polynomial equation p(te - X) = 0 has all real roots λ<sub>1</sub>(X) ≥ . ≥ λ<sub>n</sub>(X). The number of nonzero roots |i :λ<sub>i</sub>(X) ≠ 0 | is called Rank<sub>p</sub>(X). An e-hyperbolic polynomial p is called POS-hyperbolic if roots of vectors X ∈ R<sup>n</sup><sub>+</sub> with nonnegative coordinates are also nonnegative (the orthant R<sup>n</sup><sub>+</sub> belongs to the hyperbolic cone) and p(e) > 0. Below e<sub>1</sub>,. ,e<sub>n</sub> stands for the canonical orthogonal basis in R<sup>n</sup>. The main results of this paper states that if p(x<sub>1</sub>,x<sub>2</sub>,.,x<sub>n</sub>) is a POS-hyperbolic (homogeneous) polynomial of degree n, Rank<sub>p</sub> (e<sub>i</sub>) = R<sub>i</sub> and p(x<sub>1</sub>,x<sub>2</sub>,.,x<sub>n</sub>) ≥ ∏<sub>1 ≤ i ≤ n</sub> x<sub>i</sub> ; x<sub>i</sub> > 0, 1 ≤ i ≤ n, then the following inequality holds ∂<sup>n</sup>/∂ x<sub>1</sub>. ∂ x<sub>n</sub> p(0,.,0) ≥ ∏<sub>1 ≤ i ≤ n</sub> (G<sub>i</sub>-1/G<sub>i</sub>)<sup>G</sup>i<sub>-1</sub>, where G<sub>i</sub> = min(R<sub>i</sub> , n+1-i) . This inequality is a vast (and unifying) generalization of the van der Waerden conjecture on the permanents of doubly stochastic matrices as well as the Schrijver-Valiant conjecture on the number of perfect matchings in k-regular bipartite graphs. These two famous results correspond to the POS-hyperbolic polynomials which are products of linear forms with nonnegative coefficients.Our proof is relatively simple and "noncomputational"; it actually slightly improves Schrijver's lower bound, and uses very basic (more or less centered around Rolle's theorem) properties of hyperbolic polynomials. We present some important algorithmic applications of the result, including a polynomial time deterministic algorithm approximating the permanent of n x n entry-wise non-negative matrices within a multiplicative factor e<sup>n</sup>/n<sup>m</sup> for any fixed positive m; and a deterministic poly-time algorithm approximating the permanent of n x n matrix A having at most k nonzero entries in each column to within a multiplicative factor (k-1/k)<sup>(k-1)n</sup>. This paper introduces a new powerful "polynomial" technique , which allows us to simplify and unify hard and key known results as well as to prove new important theorems and get new algorithms.
An Intermediate Query Model for Structured Retrieval's Queries Construction

Looking at the amount of structured contents available on the web in recent years, we can be certain that the needs of structured retrieval systems are getting more prominent. In order to access the structured contents, information requests are formulated in the form of query languages supported by the structured retrieval systems. Nevertheless, information requests at this layer cannot be specified directly by end users. Hence, a common solution is to map information needs obtained from the application layer to the query language of a retrieval system automatically. Although rule-based approach can be used to generate query automatically, it is designed for a single target query language, whereas, there are not one but different types of structured queries with different forms of syntax used in a structured retrieval environment. In this paper, we address the problem of constructing structured queries for structured retrieval by proposing an intermediate query model that can be used to construct different types of structured queries. This model allows flexibility of accommodating new query language by separating the semantic of query from its syntax. Firstly, rule-based approach is used to construct a generic form of query known as semantic query structure. Then, generation of query into target language is carried out by matching templates obtained from example-based method. Evaluations were carried out based on how well information needs are captured and transformed into a target query language. In summary, the proposed model is able to express information needs specified using query like NEXI. Xquery records a lower percentage due to its language complexity. We also achieve satisfactory query conversion rate with our example-based method, i.e. 86% (for NEXI IMDB topics) and 87% (NEXI Wiki topics) respectively compare to benchmark of 78% by Sumita & Iida in language translation.
HELPING BEHAVIOR IN LARGE SCALE DISASTERS: A SOCIAL ORGANIZATIONAL APPROACH

Disasters are a significant and persistent theme in the mass media in every society. Newspapers give them banner headlines. Radio presents on-the-spot reports. Television uses them to set the tone for the evening news. Movies use them as a basis for plots to feature well-known stars. The reasons for the media preoccupation are perhaps not as clear as the image they present. The image usually focuses on the suddenness of human need, followed by the struggle to mobilize assistance. There is a duality to the image –one part focuses on damage, loss, tragedy and destruction while the other part focuses on heroism, optimism, healing, recovery, altruism and rebuilding. Because of this duality, disasters can become a collective projective test, providing an ambiguous form into which members of the society project their own meanings. Some only see tragedy; others see altruism. Some only see loss; others see opportunity. Some only see the end of aspirations; others see the beginnings of hope and change. Some see the need to help; others see the helping which is needed.
Building large-scale Bayesian networks

Bayesian networks (BNs) model problems that involve uncertainty. A BN is a directed graph, whose nodes are the uncertain variables and whose edges are the causal or influential links between the variables. Associated with each node is a set of conditional probability functions that model the uncertain relationship between the node and its parents. The benefits of using BNs to model uncertain domains are well known, especially since the recent breakthroughs in algorithms and tools to implement them. However, there have been serious problems for practitioners trying to use BNs to solve realistic problems. This is because, although the tools make it possible to execute large-scale BNs efficiently, there have been no guidelines on building BNs. Specifically, practitioners face two significant barriers. The first barrier is that of specifying the graph structure such that it is a sensible model of the types of reasoning being applied. The second barrier is that of eliciting the conditional probability values. In this paper we concentrate on this first problem. Our solution is based on the notion of generally applicable “building blocks”, called idioms, which serve solution patterns. These can then in turn be combined into larger BNs, using simple combination rules and by exploiting recent ideas on modular and object oriented BNs (OOBNs). This approach, which has been implemented in a BN tool, can be applied in many problem domains. We use examples to illustrate how it has been applied to build large-scale BNs for predicting software safety. In the paper we review related research from the knowledge and software engineering literature. This provides some context to the work and supports our argument that BN knowledge engineers require the same types of processes, methods and strategies enjoyed by systems and software engineers if they are to succeed in producing timely, quality and cost-effective BN decision support solutions.
Integrating African- American Literature in the Elementary Social Studies Classroom

African-Americans are one of the largest minority groups in the United States; therefore it is imperative that lit erature that features African-Americans as the main characters be in today’s classrooms. This literature is not only important for African-American children to see themselves, but for children of other races to see as well. Carlsen (1971) stated “. young people want to read about people like themselves, with whom they can identify” (p. 208). ”If African-American students cannot find themselves and people like them in the books they read and have read to them, they receive a powerful message about how they are undervalued in both schooland society” (Bishop, 1990, p. 561).