Miracle-dz/UniFAR-FTUs huggingface dataset:
KABOOM! A new suffix array based algorithm for clustering expression data

MOTIVATION Second-generation sequencing technology has reinvigorated research using expression data, and clustering such data remains a significant challenge, with much larger datasets and with different error profiles. Algorithms that rely on all-versus-all comparison of sequences are not practical for large datasets. RESULTS We introduce a new filter for string similarity which has the potential to eliminate the need for all-versus-all comparison in clustering of expression data and other similar tasks. Our filter is based on multiple long exact matches between the two strings, with the additional constraint that these matches must be sufficiently far apart. We give details of its efficient implementation using modified suffix arrays. We demonstrate its efficiency by presenting our new expression clustering tool, wcd-express, which uses this heuristic. We compare it to other current tools and show that it is very competitive both with respect to quality and run time. AVAILABILITY Source code and binaries available under GPL at http://code.google. com/p/wcdest. Runs on Linux and MacOS X. CONTACT scott.hazelhurst@wits.ac. za; zsuzsa@cebitec.uni-bielefeld.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Information Sources for Travel Decisions: Toward a Source Process Model

This article contributes to the study of information sourcing behavior in the travel decision process. It focuses on the differences between information sourcing before and after a definite trip decision (characterized either by an irreversible choice with regard to destination or by a legal contract such as a reservation or purchase of one or multiple elements of a trip). The study identifies typical patterns of information search behavior for different travel types, grouped by means of clusters along two stages of the information sourcing process, thus forming paths of information sourcing. The data are representative for the case of Switzerland, serving as a model for a well-developed travel market. Descriptors such as type of trip, degree of packaging, choice of destination, and choice of accommodation showed significant explanatory power, while sociodemographic variables proved to be of less value. The results give the industry the possibility of improving information distribution systems throughout the travel decision process.
Strategically flexible production: the multi‐focused manufacturing paradigm

Defines a new manufacturing paradigm and investigates its adoption and performances, within the assembly industry on a global basis. The definition of the paradigm is based on a set of basic principles to design and manage production systems which discard the traditional way of organizing manufacturing activities, and pool companies which pursue different manufacturing strategies and implement different innovative techniques. The paradigm is characterized by the simultaneous implementation of three principles: strategic multi‐focusedness, integration of business processes across functions, and process ownership. Starting from an operationalization based on fuzzy logic, explores the hypotheses about the adoption and the performance improvements of the multi‐focused manufacturing paradigm using a sample from the International Manufacturing Strategy Survey (IMSS) database. The paradigm has been adopted widely across countries and industries involved in the IMSS survey. Shows that process ownership is poorly implemented by most of the companies at the moment, while multi‐focusedness and integration are more on hand. Companies which have adopted the paradigm are improving their performance significantly better and quicker than partial or non‐adopters. Highlights different possible patterns that the companies can follow to reach core adoption of the multi‐focused manufacturing paradigm.
Improving wholesale beef and pork product cross hedging

This study examines possible causes for the poor performance that has characterized the forward pricing and hedging practices used by participants in meat processing and merchandising operations. Alternative methods of managing price risk or meat merchandisers are presented and evaluated. The empirical analysis suggests pork and beef slaughter firms and merchandisers should seriously consider using more sophisticated cross hedge models to improve upon the poor performance of some forward contracting and hedging programs currently in use. © 1996 John Wiley & Sons, Inc.
Organizational complexity and innovation: developing and testing multiple contingency models

Current research in organizational innovation is extensive, yet, because of limitations in scope, most studies are not adequately encompassing. These studies typically relate organizational variables to innovation and control at most for the effect of one contingency factor. Because innovation depends upon a complex host of factors, such theories have limited predictive application. This study intends to develop and test theories that explain the variation in the organizational complexity-innovation relationship in greater detail. The study considers two major indicators of organizational complexity-structural complexity and organizational size. Hypotheses are proposed on the effects of 14 contingency factors on the relationships between structural complexity and innovation and organizational size and innovation. The contingency factors include environmental uncertainty, organizational size, industrial sectors, types of innovation, and stages of innovation adoption. Using a meta-analytic procedure for multivariate analysis, the hypotheses are then tested with data from published studies in organizational innovation during the last three decades. The effects of four methods variables-operational definitions of innovation, structural complexity and size, and similarity of data sources-are controlled for in testing the hypotheses. This process results in two powerful and encompassing models: 1 the association between structural complexity and innovation depends upon operational definition of complexity, environmental uncertainty, use of manufacturing organizations, use of service organizations, focus on technical innovations, focus on product innovations, and focus on implementation of innovation; and 2 the association between organizational size and innovation depends upon operational definition of size, environmental uncertainty, use of service organizations, use of for-profit organizations, focus on technical innovations, and focus on product innovations. These models suggest avenues for further theory development and research, which we discuss.
The link between a global 2 °C warming threshold and emissions in years 2020, 2050 and beyond

In the Copenhagen Accord, nations agreed on the need to limit global warming to two degrees to avoid potentially dangerous climate change, while in policy circles negotiations have placed a particular emphasis on emissions in years 2020 and 2050. We investigate the link between the probability of global warming remaining below two degrees (above pre-industrial levels) right through to year 2500 and what this implies for emissions in years 2020 and 2050, and any long-term emissions floor. This is achieved by mapping out the consequences of alternative emissions trajectories, all in a probabilistic framework and with results placed in a simple-to-use set of graphics. The options available for carbon dioxide-equivalent (CO2e) emissions in years 2020 and 2050 are narrow if society wishes to stay, with a chance of more likely than not, below the 2 °C target. Since cumulative emissions of long-lived greenhouse gases, and particularly CO2, are a key determinant of peak warming, the consequence of being near the top of emissions in the allowable range for 2020 is reduced flexibility in emissions in 2050 and higher required rates of societal decarbonization. Alternatively, higher 2020 emissions can be considered as reducing the probability of limiting warming to 2 °C. We find that the level of the long-term emissions floor has a strong influence on allowed 2020 and 2050 emissions for two degrees of global warming at a given probability. We place our analysis in the context of emissions pledges for year 2020 made at the end of and since the 2009 COP15 negotiations in Copenhagen.
Poisoning by Talisia esculenta (A. St.-Hil.) Radlk in sheep and cattle

Talisia esculenta is a tree that produces pitomba, a fruit consumed by human beings in several regions of Brazil. The current study reports 3 outbreaks of poisoning by leaves and fruits of T. esculenta affecting sheep and cattle and the experimental reproduction of the disease in sheep. In the first investigated outbreak, sheep ingested the leaves of the plant; another outbreak affected cattle and sheep that ingested leaves and fruits; and in a third outbreak, sheep ingested only the fruits. The animals developed severe nervous signs, but most recovered. Poisoning was reproduced experimentally in 5 sheep by the administration of 30–60 g of leaves/kg body weight and in 2 sheep with doses of 5 and 10 g of seeds/kg body weight, respectively. No significant necropsy or histologic lesions were found.
The schooling experiences of Pasifika students

The growing diversity of students in mainstream schools in Aotearoa New Zealand is challenging for educators and policy makers alike. Educational researchers in the 21st century have shown that listening to what students have to say about what works best for them is more important than ever. This article discusses the narratives of schooling experiences of two generations of Pasifika students, comparing the experiences of Pasifika students from Auckland secondary schools involved in the Te Kotahitanga project in 2009 with the author's schooling experiences in the mid-1970s to the early 1980s.
Body mass and individual fitness in female ungulates: bigger is not always better

In female vertebrates, differences in fitness often correspond to differences in phenotypic quality, suggesting that larger females have greater fitness. Variation in individual fitness can result from variation in life span and/or variation in yearly reproductive success, but no study has yet assessed the relationships between the components of fitness and phenotypic quality while controlling for life span. We tried to fill this gap using data from long–term monitoring (23 years) of marked roe deer and bighorn sheep, two ungulates with very different life histories. In both species, we found a strong positive relationship between an adult female's mass and her probability of reaching old age: over the long term, bigger is indeed better for ungulate females. On the other hand, we found no evidence in either species that heavier females had higher fitness when differences in life span were accounted for: over the short term, bigger is not necessarily better. Our results indicate that, while broad differences in phenotypic quality affect individual fitness, when differences in life span are accounted for phenotypic quality has no residual effect on fitness. Therefore, within a given range of phenotypic quality, bigger is not always better, for reasons which may differ between species.
Quantifying Apoplastic Flux through Red Pine Root Systems Using Trisodium, 3-hydroxy-5,8,10-pyrenetrisulfonate.

The fluorescent compound trisodium, 3-hydroxy-5,8,10-pyrenetrisulfonate (PTS) was used to quantify the apoplastic flux through red pine (Pinus resinosa Ait.) root systems-that portion of the total water flux reaching the xylem without ever crossing a semipermeable membrane. Flow was induced by pressure through detopped root systems, and by transpiration through intact seedlings. Apoplastic flux was determined by multiplying total flux by the ratio of PTS concentration in the xylem exudate to PTS concentration in the bathing medium.Under aeration, apoplastic flux was less than 1% of total flux. Under anaerobic conditions, up to 50% of total flux was apoplastic suggesting that anaerobic conditions change the pathway of water flow into root xylem. The change under anaerobic conditions was reversible. Detopped root systems under pressure and intact seedlings under transpiration gave similar results. In detopped root systems, the magnitude of the pressure gradient may alter the apoplastic contribution to total flux.
Accent Command Model Parameter Alignment in Argentine Spanish Absolute Interrogatives

The goal of this study is to explore the position of pitch accent commands relative to the accented syllable in final and non-final words for absolute interrogative sentences in Spanish. Fundamental frequency parameters are obtained from the Fujisaki model. Results indicate that accent commands for three-syllable words in final position are associated with late peaks no matter which the stressed syllable position is. In non-final words, accent commands are associated with early peaks also for all stressed syllable positions. These results are compared and presented with those obtained for declarative sentences. The influence of both phrase accents and boundary tones over pitch accents show that: 1) F0 contours ending with a high tone produce an attraction of H* accents; 2) F0 contours ending with a low tone have a tendency to keep distance from the realization of H* accents.
Resident Perceptions Toward the Impacts of the Macao Grand Prix

This article examines host residents’ perceptions toward a major sporting event, the Macao Fomula-3 car racing Grand Prix. It is an empirical study that involved 598 surveys with local Macao residents. An impact scale comprising 20 impact items with 5 factors, namely, social-psychological impacts, society benefits, society costs, social life costs, and physical impacts, was established to assess resident perceptions toward the impacts of the event. The study confirmed that most respondents perceived the impacts of the Macao Grand Prix positively. Based on their different perceptions of the Grand Prix impacts, residents were classified into two groups: embracers and tolerators. The three most significant factors that influenced resident perceptions toward the impacts of the Grand Prix are their age group, their attitude about government performance in the organization of the Grand Prix, and their preferences regarding having more tourists visit Macao.
Uncertainty, Learning, and Gradual Monetary Policy

The value of a vast array of financial assets are functions of rates or prices determined in OTC, interbank, or other off-exchange markets. In order to price such derivative assets, underlying rate and price indexes are routinely sampled and estimated. To guard against misreporting, whether unintentional or for market manipulation, many standard contracts utilize a technique known as trimmed-means. This paper points out that this polling problem falls within the statistical framework of robust estimation. Intuitive criteria for choosing among robust valuation procedures are discussed. In particular, the approach taken is to minimize the worst-case scenario arising from a false report. The finite sample performance of the procedures that qualify, the trimmed-mean and the Huber-estimator, are examined in a set of simulation experiments.
Effect of single and contiguous teeth extractions on alveolar bone remodeling: a study in dogs.

BACKGROUND Tooth extraction is associated with dimensional changes in the alveolar ridge. The aim was to examine the effect of single versus contiguous teeth extractions on the alveolar ridge remodeling. MATERIAL AND METHODS Five female beagle dogs were randomly divided into three groups on the basis of location (anterior or posterior) and number of teeth extracted - exctraction socket classification: group 1 (one dog): single-tooth extraction; group 2 (two dogs): extraction of two teeth; and group 3 (two dogs): extraction of three teeth in four anterior sites and four posterior sites in both jaws. The dogs were sacrificed after 4 months. Sagittal sectioning of each extraction site was performed and evaluated using microcomputed tomography. RESULTS Buccolingual or palatal bone loss was observed 4 months after extraction in all three groups. The mean of the alveolar ridge width loss in group 1 (single-tooth extraction) was significantly less than those in groups 2 and 3 (p < .001) (multiple teeth extraction). Three-teeth extraction (group 3) had significantly more alveolar bone loss than two-teeth extraction (group 2) (p < .001). The three-teeth extraction group in the upper and lower showed more obvious resorption on the palatal/lingual side especially in the lower group posterior locations. CONCLUSION Contiguous teeth extraction caused significantly more alveolar ridge bone loss as compared with when a single tooth is extracted.
MAPPING THE REPRESENTATIONAL DIMENSIONS OF NON‐PROFIT ORGANIZATIONS IN CHINA

To what extent do China's non-profit and voluntary organizations have the capacities to represent effectively the interests of their constituents? In this paper, we examine the prevalence of various representational dimensions in these organizations. Our survey findings provide evidence that, other things being equal, an organization's levels of descriptive and participatory representation have a positive and significant impact on its levels of substantive and symbolic representation. Our findings also show that organizational type matters: social organizations are more substantively and symbolically representative than private non-enterprise organizations, whereas advocacy-oriented organizations are more symbolically representative than those that are not advocacy-oriented. Our case studies further illustrate how the typical advocacy-oriented organization differs from the service-oriented organization in the development of its ‘representational mix’, how an organization's ‘representational mix’ evolves over time, and how the relationship between the organization and its supervisory agency affects its various representational dimensions.
Banking Reform in China: Catalyzing the Nation's Financial Future

In 2003 China posted its highest economic growth rate in seven years, a robust 9.1 percent. Today the nation's gross domestic product (GDP) dwarfs by more than eight fold its level of 1978, the year China began taking its first tentative steps away from a centrally-planned communist economy towards a mixed socialist-market system. According to the World Bank, market reforms in China and the growth they have stimulated helped lift more than 250 million people from poverty (roughly equivalent to positively transforming the lives of the combined populations of England, France, Germany, and Italy). In 2003 China's per capita GDP surpassed the $1,000 mark for the first time in history. The greatest and most fundamental undertaking for China's financial reform over the coming years undeniably will occur in the banking sector. As with the situation throughout East Asia, businesses in China typically obtain external financing from banks rather than through the issuance of securities. Yet banking in China represents a glaringly fragile component in its economy. Poor lending policies of the past have produced a massive deadweight of nonperforming loans (NPLs). This article argues that investors and policy makers, while right to be concerned, would be patently wrong to ignore the tremendous upsides that should accompany China's banking reforms. Although now a soft spot in the Chinese economy, we contend that China's banking sector has the momentum and potential not only to be restored to health, but to play a catalytic role as a stimulant to further and sustained growth.
Individual Substitutions of Clustered Arginine Residues of the Sensor Kinase KdpD of Escherichia coli Modulate the Ratio of Kinase to Phosphatase Activity*

Escherichia coli responds to K+ limitation or high osmolarity by induction of thekdpFABC operon coding for the high affinity K+-translocating Kdp-ATPase. KdpD, the sensor kinase of this system, is a bifunctional enzyme catalyzing the autophosphorylation by ATP and the dephosphorylation of the corresponding response regulator KdpE. Here we demonstrate that individual replacements of clustered arginine residues located close to transmembrane domain TM4 modulate the ratio of kinase to phosphatase activity. Thus KdpD-Arg511 → Gln is characterized by an increase in the kinase activity and a loss of the phosphatase activity. However, when Arg at position 511 is replaced with Lys, activities of the corresponding protein are comparable with wild-type KdpD. In contrast, replacement of arginine residues at positions 503, 506, or 508 with glutamine or lysine causes a decrease of the kinase and an increase of the phosphatase activities. Changes of the activities of these KdpD proteins correspond with alterations in kdpFABCexpression. Thus KdpD-Arg511 → Gln causes constitutive expression of kdpFABC. KdpD proteins with Arg replacements at positions 503, 506, or 508 are unable to respond to osmolarity, whereas the sensing of K+ limitation is not influenced. Simultaneous replacement of arginine residues 508 and 511 or 506, 508, and 511 with glutamine leads to a decrease of the phosphatase activity. However, kdpFABC expression is dependent on K+and osmolarity. Finally, when Arg513 is replaced with glutamine the amount of KdpD detected in the membrane is drastically reduced. These results imply that there is an equilibrium between the kinase and phosphatase activities of KdpD, which can be shifted by the replacement of one arginine residue. An electrostatic switch mechanism within the protein is proposed through which the ratio of kinase to phosphatase is regulated. Finally, these results lend support to the notion that KdpD can be activated by two distinct stimuli, K+ limitation and osmolarity.
Educators' Perceptions of High-Stakes Testing in the Low and High Poverty Schools

Educators’ Perceptions of High-Stakes Testing in Low and High Poverty Schools by Natasha M. Domond EdS, Florida AM they also assist policymakers and stakeholders in identifying supports needed to ensure that all children succeed. Educators’ Perceptions of High-Stakes Testing in the Low and High Poverty Schools by Natasha M. Domond EdS, Florida A&M University, 2007 MS, Florida A&M University, 2006 Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Psychology Walden University November 2015
Neoliberalism and violence: The Big Society and the changing politics of domestic violence in England

Focusing on the domestic violence sector as a case study, this article examines how the Big Society agenda, coming alongside public spending cuts, is affecting the independence and ability of women’s organizations to engage in progressive policy shaping. By situating the analysis of the Big Society agenda within the broader context of international civil society strengthening programmes, the article considers how the processes currently unfolding in England, share certain similarities to what has happened globally wherever neoliberal policies aimed at instrumentalizing civil society for service delivery have been implemented. It contends that the policies of the Big Society agenda, which are aimed at strengthening the ‘capacity’ of civil society, are instead creating a situation where the independence and ability of civil society organizations to engage in progressive policy making is weakened.