Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds

The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment.
Evaluating the green advertising practices of international firms: a trend analysis

Purpose – Consumer scepticism about the credibility of green advertising around the world is growing. The article aims to provide a comprehensive assessment and trend analysis of green advertising practices of international firms over a 20‐year period.Design/methodology/approach – The study identifies 473 international green advertisements during the 1988‐2007 period and content‐analyses them on five major axes: advertiser profile, targeting features, message aspects, copy characteristics, and situation points.Findings – The content analysis reveals significant trends in all major areas examined and identifies important interaction effects between certain dimensions of green advertisements.Research limitations/implications – The findings could be augmented by combining them with changes in the external environment, input from consumers about advertising effectiveness, the views of advertisers and advertising agencies, and secondary data referring to the performance of the specific company/product advertis.
Stock Market Returns and Weather Anomaly: Evidence from an Emerging Economy

Financial economists believe that the arbitrage forces in the market are the main reason of market efficiency and these forces are the fundamental concept of efficient market hypothesis (EMH). During last few years, various theoretical and empirical evidences have been presented to support the work of financial modeling for the markets with less than rational investors whose trading strategies are based on psychological factors like mood and emotions. Weather condition is among the substantial factors affecting investors’ mood and emotions. Present study investigates the impact of temperature on stock market returns in emerging economy of Pakistan. Using the daily temperature records and stock market indices of Karachi and Islamabad, the study has employed auto regressive (AR) – generalized autoregressive conditional heteroscedasticity (GARCH) model from 2006 to 2010. Based on AR (1)-GARCH (1, 1) estimation the study has found that weather temperatures of both Karachi and Islamabad are negatively related with Karachi Stock Exchange (KSE) and Islamabad Stock Exchange (ISE) index returns, respectively.
Does Accounting and Financial Expertise in the C-Suite Aid or Mitigate Earnings Management?

Despite the obvious impact of the CFO and the CEO on a firm’s financial statements, there is limited empirical evidence on whether and how the personal characteristics of senior management are associated with earnings management. We provide empirical evidence on the relation between earnings management and the accounting and financial expertise of these C-suite managers. For a sample of S&P 500 firms we find that CEOs and CFOs with accounting and financial expertise appear to manage earnings more aggressively than CEOs and CFOs without such expertise. We document greater earnings management by C-suite managers with accounting/financial expertise via accruals as well as real activities, such as overproducing goods, cutting back on discretionary spending, such as advertising and research and development expenses, manipulating sales and shifting of core expenses to special items. Our findings have important implications for boards of directors, members of the audit committee, investors and others.
CovertBand

This paper contributes a novel method for low-cost, covert physical sensing and, by doing so, surfaces new privacy threats. We demonstrate how a smartphone and portable speaker playing music with embedded, inaudible signals can track multiple individuals’ locations and activities both within a room and through barriers in 2D space. We achieve this by transforming a smartphone into an active sonar system that emits a combination of a sonar pulse and music and listens to the reflections off of humans in the environment. Our implementation, CovertBand, monitors minute changes to these reflections to track multiple people concurrently and to recognize different types of motion, leaking information about where people are in addition to what they may be doing. We evaluated CovertBand by running experiments in five homes in the Seattle area, showing that we can localize both single and multiple individuals through barriers. These tests show CovertBand can track walking subjects with a mean tracking error of 18 cm and subjects moving at a fixed position with an accuracy of 8 cm at up to 6 m in line-of-sight and 3 m through barriers. We test a variety of rhythmic motions such as pumping arms, jumping, and supine pelvic tilts in through-wall scenarios and show that they produce discernibly different spectrograms from walking in the acoustic reflections. In tests with 33 subjects, we also show that even in ideal scenarios, listeners were unlikely to detect a CovertBand attack.
A Graph Manipulation System Abstracted from e-Learning

In this position paper, we have an outlook on a graph manipulation system applicable to a visual interface of managing educational courses for an e-Learning system. We paraphrase a process of learning into a scheme of state-transitions related to graph manipulations. By the scheme, techniques and tools for educational courses can be abstracted to the treatments of graphs. Thus we construct a methodology of graph manipulations for a management of educational courses by extending the established graph viewer. We also propose a simple sketch-based interface to manipulate graphs. We here list up several tools of the sketch-based interface, based on the algorithm to detect mouse movements for indicating operations of the system.
A hybrid method for transportation with stochastic demand

In industrial transportation, the forecast demand at each destination may be affected by a number of factors. Consequently, a conventional transport plan often fails to match the reality, and the planned transport capacity is either insufficient to meet the demand or wastefully excessive. In this paper, we introduce a new algorithm to generate a minimal cost transport plan that meets a given level of reliability. The reliability of a candidate solution is measured through simulating each candidate solution against a large number of scenarios. To search for reliable solutions, a genetic algorithm method is applied as an external loop. The minimal transport cost is achieved through a deterministic optimisation algorithm. We show that this problem decomposition in principle enables the optimal solution of the original non-deterministic problem to be found. Experimental results establish the practical usefulness of the proposed algorithm.
Process Innovation and Integration in Process-Oriented Settings: The Case of the Oil Industry

Scholars have long argued that in new product development integrated innovation processes replace sequentially organized ones because of changing capabilities, integration of knowledge, and the increasing importance of market orientation. The intention of this paper is to study whether this also applies in process-oriented industries. Process-oriented settings are fundamentally different from product-oriented ones as the emphasis is on efficiency, clear guidelines, and tacit knowledge, while radical innovation is less important. It is also less obvious why market orientation—a key driver of integration in new product development—should change the way the innovation process is organized, as there is no product to be developed in the first place. A Stage Gate Model could therefore be well-suited to achieve more efficiency and effectiveness. In order to investigate process innovation in a process-oriented setting, we decided to study the upstream oil and gas industry, a scale-intensive, process-oriented setting that substantially contrasts with traditional science-driven industries such as biotechnology and pharmaceuticals, where patents are relevant. The particular advantage of this setting is that virtually no product innovation occurs, allowing the isolation of process innovation. Relying on five inductive case studies of major projects (BP's Prudhoe Bay, Chevron's Kern River, Conoco Philips's Ekofisk, ENI's el-Bouri, and Shell's Troll field), we find that integration occurs in process-oriented settings but does so for different reasons than in product-oriented ones. Integration emerges from an innovation mode characterized by: (1) trial and error (not RD (2) the cooperation of experts from different knowledge backgrounds; (3) the development of Information and Communication Technology (ICT), which facilitates this cooperation across disciplines and projects; and (4) the need to increase efficiency as demand outstrips supply. More precisely, demand shapes reward systems and determines whether new raw materials will be used (creating new supply that requires innovation of processes in periods when demand outstrips supply). Supply and reward systems therefore create the conditions where trial and error, integration of knowledge, and ICT development mutually enforce each other, leading to the integration of the innovation process. Besides contributing to the literature on innovation the paper also offers interesting insights for managers. In order to foster innovation in process-oriented settings they need to provide specialists with room to experiment over extended periods of time, encourage cooperation across disciplines, and create both incentives and systems to facilitate this process. Finally, managers need to consider the ability of staff to cooperate at the outset, when they set up their recruitment process.
Isolation and characterization of biosurfactants-producing bacteria isolated from palm oil industry and evaluation for biosurfactants production using low-cost substrates

Biosurfactants-producing bacteria were isolated from various palm oil refinery industrial sites in the south of Thailand. Isolates were screened for biosurfactant production by using low-cost, agro-industrial by-products or wastes as a substrate. Based on drop collapsing test and emulsification activity, 25 isolates were selected. All the selected isolates reduced the growth medium surface tension to 40 mN/m and produced emulsions with xylene. Twenty isolates exhibited high emulsion-stabilizing capacity, maintaining more than 50% of the original emulsion volume for 24 h. The phylogenetic position of these 25 isolates was evaluated by 16S rRNA gene sequence analysis.The production of biosurfactants was determined for strains representative of 15 different bacterial genera, six of them (Azorhizobium, Buttiauxella, Comamonas, Halopenitus, Haloplanus and Sinorhizobium ) have been for the first time reported in this study as biosurfactant-producing strains. Additionally, Sinorhizobium meliloti AS91 and Marinobacter hydrocarbonoclasticus AS51 produced extracellular biosurfactant which exhibited the lowest surface tension (32 mN/m) and emulsification activity (69%) when cashew apple juice and used vegetable oil were used as the carbon source, respectively. Overall, this is the first study of a phylogenetic analysis of biosurfactant-producing bacteria from palm oil refinery industry site and their ability to produce biosurfactant on renewable substrates.
Liver disease and HPLC quantification of disialotransferrin for heavy alcohol use: a case series.

BACKGROUND It had previously been suggested that individuals with cirrhosis may have a pattern of transferrin glycosylation that interferes with the interpretation of carbohydrate-deficient transferrin (CDT) testing for heavy alcohol use. The goal of this case series was to evaluate the prevalence of liver disease among individuals with poor resolution of transferrin glycoforms by high performance liquid chromatography. METHODS We reviewed the electronic medical records of 35 consecutive patients with poor chromatographic resolution of disialotransferrin from trisialotransferrin and recorded information on diagnosed liver disease, liver function testing, and other factors. RESULTS Thirty of the 35 subjects with poor chromatographic resolution of the transferrin glycoforms had sufficient data in the medical record for some estimation of liver function. Of these 30 subjects, 25 had previously diagnosed liver pathology. Of the remaining 5 subjects, 2 had liver imaging results suggestive of benign tumor; the remaining 3 had mildly elevated bilirubin and aminotransferase activity, and low albumin. CONCLUSIONS Liver abnormalities, but not necessarily cirrhosis, are common in individuals with poor chromatographic separation of transferrin glycoforms, which might lead to false-positive results on CDT testing. However, the chromatographic-based assay can detect this issue, minimizing the reporting of false positives, but not necessarily assisting in valid detection of heavy drinking.
Mitigating the Insider Threat with High-Dimensional Anomaly Detection

Abstract : In this project, we explored new techniques for detecting the threat of insider attacks in enterprise networks. In particular, we explored the use of high-dimensional search techniques such as Latent Semantic Indexing to mitigate the problem of high dimensionality that is inherent in intrusion detection. This new technique can be used for both labeled and unlabeled detection, and shows promise for detecting attacks and anomalies earlier than previously possible and detecting attacks that are similar to past ones.
Developing and testing a model of successful adoption ofactivity-based costing

This study aims to develop and test a model for successful adoption of activitybased costing (ABC). The model has been constructed to explore the relationship between organisational and technological factors and management evaluation of overall ABC success and suggest a pathway. Another objective of this study is the examination of the relationship between ABC and business unit performance. The study also aims to investigate why some business units have not adopted ABC and why some business units have discontinued their use of ABC.
Economic Impact of Bovine Tuberculosis on Minnesota’s Cattle and Beef Sector

Introduction In September 2005, the first case of bovine tuberculosis (BTB) in 34 years was discovered in Minnesota and led to a loss of Minnesota's bovine TB free status. In October 2007 and January and February 2008, four additional cattle herds and deer infected with BTB were discovered in Roseau and Beltrami counties and Minnesota's BTB status was changed from " modified accredited advanced " to " modified accredited " in April 2008. Each of these designations has increased regulatory requirements (and costs) for animal testing, record keeping, eradication practices, slaughtering and shipments of cattle within state and across state lines. As a result of the large anticipated costs of a Minnesota statewide designation of modified accredited status for bovine tuberculosis, Minnesota applied to the USDA Animal and Plant Health Inspection Service (APHIS) for split state status. The split state status would allow the northwest part of Minnesota where the BTB cases were found to remain classified as modified accredited for BTB and the rest of the state to be classified as modified accredited advanced, a less restrictive and less costly designation. The State of Minnesota completed a management plan and APHIS completed their risk assessment study (USDA, APHIS, June 24, 2008) informed by Minnesota's management plan. In October 2008, Minnesota was granted " split state status " Marshall and Lake of the Woods) approximate the region in Minnesota now designated as modified accredited (MA). The rest of the state is now designated as modified accredited advanced (MAA). This designation will greatly reduce the cost impacts of BTB on the Minnesota cattle industry. The APHIS report included the expected costs to the state of 3 managing and eradicating bovine TB, but did not evaluate what the expected cost of bovine TB would be to the beef industry itself. This report quantifies the economic impacts of BTB on Minnesota beef cattle producers and related industries. Representative cattle production systems are simulated and the costs of BTB response are incorporated into these systems using a partial budgeting approach. A partial equilibrium market model is then used to simulate the impact of these cost increases on the production of cattle and the prices received by the beef industry in Minnesota. This model also allows for changing assumptions regarding price discounts cattle producers might face given the BTB positive status. Finally, an input-output analysis using IMPLAN is used to evaluate the total economic impacts …
Activation of the dsRNA‐dependent protein kinase, PKR, induces apoptosis through FADD‐mediated death signaling

The dsRNA‐dependent protein kinase (PKR) is considered to play a key role in interferon‐mediated host defense against viral infection and conceivably malignant transformation. To investigate further the mechanisms of PKR‐induced growth inhibition, we have developed tetracycline‐inducible murine cell lines that express wild‐type PKR or a catalytically inactive PKR variant, PKRΔ6. Following induction, the growth of the wild‐type PKR‐expressing cells was similar to that of cells transfected with vector alone, while cells expressing PKRΔ6 became malignantly transformed. Significantly, treatment with dsRNA caused the wild‐type PKR‐overexpressing cells to undergo programed cell death while, conversely, cells expressing PKRΔ6 were completely resistant. Our studies demonstrated that activation of PKR induces the expression of members of the tumor necrosis factor receptor (TNFR) family, including Fas (CD95/Apo‐1) and pro‐apopotic Bax. In contrast, transcripts representing Fas, TNFR‐1, FADD (Fas‐associated death domain), FLICE, Bad and Bax were ablated in cells expressing PKRΔ6. The involvement of the death receptors in PKR‐induced apoptosis was underscored by demonstrating that murine fibroblasts lacking FADD were almost completely resistant to dsRNA‐mediated cell death. Thus, PKR, a key cellular target for viral repression, is a receptor/inducer for the induction of pro‐apoptotic genes by dsRNA and probably functions in interferon‐mediated host defense to trigger cell death in response to virus infection and perhaps tumorigenesis.
Purification of Chymotrypsin-Trypsin Inhibitor from Winged Bean Seeds using Single Step Immunoaffinity Column

Problem statement: Winged bean is a rich source of protease inhibitors. The seeds of winged bean contain several serine protease inhibitors of which winged bean chymotrypsin-trypsin inhibitor (WbCTI) is of significant importance due to its dual inhibition of both chymotrypsin and trypsin. The purification of WbCTI has always been difficult and a time taking process that involved large number of steps and various purification columns. Approach: This study was focused on the single step method of purification of WbCTI to homogeneity from winged bean seeds using immunoaffinity column chromatography. Results: WbCTI was purified to homogeneity using anti-WbCTI antibody column in a single step which gave a single band on SDS-PAGE analysis and with almost one and half times more yield of purified protein than obtained from previously mentioned purification methods. Conclusion: This method using immunoaffinity column is high yielding and time saving process of purification.
Thesaurus expansion using similar word pairs from patent documents

In both written and spoken languages, we sometimes use different words in order to describe the same meaning. For instance, we use “constraint” ( seigen ) and “restriction” ( seiyaku ) as the same meaning. This makes text classiﬁcation and text summarization difﬁcult. In order to deal with this problem, dictionaries especially thesauri are used. However, in technical paper and patent documents, a lot of new words which are not given in the dictionary. In this paper, we propose a method to accurately extract words which are semantically similar to each other. Using this method, we extracted similar word pairs from patent documents. We also expand a thesaurus using the extracted similar words.
Geometrical Algorithms to Detect Patterns from a Set of Points

This article presents a new approach for detecting patterns, such as lines, parabolas and circles, from a two- dimensional cloud of points S. This scheme transforms the problem of detecting the patterns from S, to the problem of detecting simpler patterns from a set of points S1 computed from the Voronoi and Delaunay diagrams of S. It is based on the differential properties of the Voronoi diagram that reflect the patterns to be retrieved. For example, in the case of parabolas, the patterns to be detected in S' are straight lines. The general idea of using the Voronoi diagram to detect patterns is an alternative and a complementary approach to the Hough Transform. It does not need to code a space of parameters and can be generalized to higher dimensions, with some adaptations.