Miracle-dz/UniFAR-FTUs huggingface dataset:
Taxonomic revision of the stone geckos (Squamata: Diplodactylidae: Diplodactylus ) of southern Australia

The stone geckos of the Diplodactylus vittatus species-group are robust terrestrial geckos, mainly distributed through the southern half of Australia. Recent molecular analyses indicate that the current taxonomy significantly under-represents the true diversity in this group. Here we assess the morphological variation in the currently recognized species D. vittatus and D. granariensis, including the subspecies D. g. rex. We redescribe D. vittatus and D. granariensis, resurrect D. furcosus from the synonymy of D. vittatus and describe D. calcicolus sp. nov. and D. wiru sp. nov. from semiarid habitats in western and southern Australia. Other than D. g. rex, most taxa are very similar for such characters as scalation, body and tail shape and size, but colour patterns show species-specific modal conditions, and the largely allopatric distributions mean that most areas support only one or two species which can be distinguished through a combination of characters. Further genetic data is required to resolve the systematic status and geographic distribution of additional deeply divergent genetic lineages in eastern Australia.
Marking theory and kinship analysis

The concept of marking was discovered in phonology by Trubetzkoy and generalized to morphology and grammar by Jakobson. In a fundamental application to anthropology, Greenberg integrated a generalized concept of marking into a cognitivelinguistic theory of kinship universals. Greenberg's theory is important for three reasons: (1) it leads to the discovery and explanation of cross-cultural universals in kinship classification; (2) it predicts the order in which kin terms evolve and establishes, thereby, criteria for evaluating alternative, competing reconstructions of kinship systems; (3) it provides a means for inferring features of prehistoric social organization. This paper illustrates these applications and points out the typological and cognitive implications of marking effects in kinship systems. The analysis demonstrates that a formal deductive approach to kinship can yield results not obtainable by more usual informal and inductive methods.
Variable amounts of DNA related to the size of chloroplasts. IV. Three-dimensional arrangement of DNA in fully differentiated chloroplasts of Beta vulgaris L.

Glutaraldehyde-fixed strips of fully differentiated leaves of Beta vulgaris L. were treated with proteases. With this method it is possible to display DNA-regions in chloroplasts selectively and to reconstruct them from serial sections. As in young plastids, the DNA in mature plastids is also distributed within several regions which are separated rather clearly by thylakoids. The number of such regions depends upon the size of the organelle and thus upon its developmental state. The shape of the regions is, in contrast to less-differentiated plastids, mostly elongated. The individual regions seem to contain unequal quantities of DNA-fibrils. A comparison of our ultrastructural results and biochemical data (DNA-amounts per plastid depending on the size of the organelle; kinetic complexity of chloroplast-DNA of Beta ) as well as a comparison of the chloroplast with similar prokaryotic systems (as in bacteria, blue-green algae, and mitochondria) leads to the suggestion that each DNA-containing region can be regarded as a single nucleoid. In addition, each nucleoid already contains several (on average, 4-8) genetic units. Thus the chloroplast of Beta seems genetically polyvalent in at least 2 respects: (i) it is of polyenergidic organization, and (ii) the individual nucleoids can be polyploid to varying degrees.
Web page classification based on k-nearest neighbor approach

Automatic categorization is the only viable method to deal with the scaling problem of the World Wide Web. In this paper, we propose a Web page classifier based on an adaptation of k-Nearest Neighbor (k-NN) approach. To improve the performance of k-NN approach, we supplement k-NN approach with a feature selection method and a term-weighting scheme using markup tags, and reform document-document similarity measure used in vector space model. In our experiments on a Korean commercial Web directory, our proposed methods in k-NN approach for Web page classification improved the performance of classification.
Mass media and political accountability

Mass media can play a key role in enabling citizens to monitor the actions of incumbents and to use this information in their voting decisions. This can lead to government which is more accountable and responsive to its citizens' needs. In spite of the intuitive plausibility of the proposition, there is comparatively little work in political economy literature that scrutinises the role and effectiveness of the media in fulfilling this function. A literature, however, is emerging which focuses attention on the importance of the so-called 'fourth estate of government' in the policy process. A key feature of the approach taken here is to focus on incentives the media have to produce and disseminate information.
Food choice, appetite and physical activity

Abstract Food choices and diet composition have been studied less often than energy intake in subjects with varying levels of physical activity. The reported effects of exercise on food choices are not fully consistent, especially on the short term. Type of exercise, intensity, duration can affect the results as well as subjects' characteristics (gender, age, previous training and fitness). A crucial role could also be played by psychological (chronic dieting, attitudes toward health and food, long-established food habits and preferences) and social (traditions, food availability, appropriate times and places) factors. In short-term intervention studies, where a meal is ingested a few minutes following a bout of exercise of varying duration and intensity, an increase in CHO intake is most often reported, while increased protein intake is an occasional observation. In long-term (several weeks) training interventions, intake is assessed from dietary records. Again CHO intake is augmented in exercised subjects as compared to controls, while that of saturated fats and cholesterol may also be affected. Epidemiological studies (without dietary or exercise intervention) often report that habitually active persons eat more and ingest more fruits and vegetables than less active peers. It is not known to what extent such food choices are driven by biological needs (e.g. replacement of glycogen) or elicited by social and psychological factors.
Katyusha: The First Truly Accelerated Stochastic Gradient Method

We introduce $\mathtt{Katyusha}$, the first direct stochastic gradient method that has an accelerated convergence rate. Given an objective that is an average of $n$ convex and smooth functions, $\mathtt{Katyusha}$ converges to an $\varepsilon$-approximate minimizer using $O((n + \sqrt{n \kappa})\cdot \log\frac{f(x_0)-f(x^*)}{\varepsilon})$ stochastic iterations, where $\kappa$ is the condition number. $\mathtt{Katyusha}$ also resolves the following open questions in optimization and machine learning $\bullet$ For weakly convex and smooth objectives (e.g., Lasso, Logistic Regression), $\mathtt{Katyusha}$ is the first stochastic method that achieves the optimal $1/\sqrt{\varepsilon}$ rate. $\bullet$ For strongly-convex but non-smooth ERM objectives (e.g., SVM), $\mathtt{Katyusha}$ gives the first stochastic method that achieves the optimal $1/\sqrt{\varepsilon}$ rate. $\bullet$ For weakly convex and non-smooth ERM objectives (e.g., L1SVM), $\mathtt{Katyusha}$ gives the first stochastic method that achieves the optimal $1/\varepsilon$ rate.
Querying XML documents made easy: nearest concept queries

Due to the ubiquity and popularity of XML, users often are in the following situation: they want to query XML documents which contain potentially interesting information but they are unaware of the mark-up structure that is used. For example, it is easy to guess the contents of an XML bibliography file whereas the mark-up depends on the methodological, cultural and personal background of the author(s). None the less, it is this hierarchical structure that forms the basis of XML query languages. We exploit the tree structure of XML documents to equip users with a powerful tool, the meet operator that lets them query databases with whose content they are familiar, but without requiring knowledge of tags and hierarchies. Our approach is based on computing the lowest common ancestor of nodes in the XML syntax tree: e.g., given two strings, we are looking for nodes whose offspring contains these two strings. The novelty of this approach is that the result type is unknown at query formulation time and dependent on the database instance. If the two strings are an author's name and a year mainly publications of the author in this year are returned. If the two strings are numbers the result mostly consists of publications that have the numbers as year or page numbers. Because the result type of a query is not specified by the user we refer to the lowest common ancestor as nearest concept. We also present a running example taken from the bibliography domain, and demonstrate that the operator can be implemented efficiently.
Sustainability at the Edge: The Opportunity and Responsibility of Local Governments to Most Effectively Plan for Natural Disaster Mitigation

The traditional link between disaster mitigation and local land use planning was highlighted by the Disaster Mitigation Act (DMA) of 2000, which emphasizes the need for mitigation coordination among state and local entities. This article looks at the role of local governments in natural disaster mitigation, specifically, how local governments may use traditional land use powers, such as the police power, to protect against disasters. The paper cites DMA provisions that offer financial incentives to states that work with local governments to plan for growth and disasters; and sets forth case studies to illustrate how states can create vertical links among federal,state, and local entities to coordinate disaster mitigation strategies.
Effects of Cigarette Smoke, Cessation, and Switching to Two Heat-Not-Burn Tobacco Products on Lung Lipid Metabolism in C57BL/6 and Apoe−/− Mice—An Integrative Systems Toxicology Analysis

The impact of cigarette smoke (CS), a major cause of lung diseases, on the composition and metabolism of lung lipids is incompletely understood. Here, we integrated quantitative lipidomics and proteomics to investigate exposure effects on lung lipid metabolism in a C57BL/6 and an Apolipoprotein E-deficient (Apoe−/−) mouse study. In these studies, mice were exposed to high concentrations of 3R4F reference CS, aerosol from potential modified risk tobacco products (MRTPs) or filtered air (Sham) for up to 8 months. The 2 assessed MRTPs, the prototypical MRTP for C57BL/6 mice and the Tobacco Heating System 2.2 for Apoe−/− mice, utilize “heat-not-burn” technologies and were each matched in nicotine concentrations to the 3R4F CS. After 2 months of CS exposure, some groups were either switched to the MRTP or underwent cessation. In both mouse strains, CS strongly affected several categories of lung lipids and lipid-related proteins. Candidate surfactant lipids, surfactant proteins, and surfactant metabolizing proteins were increased. Inflammatory eicosanoids, their metabolic enzymes, and several ceramide classes were elevated. Overall, CS induced a coordinated lipid response controlled by transcription regulators such as SREBP proteins and supported by other metabolic adaptations. In contrast, most of these changes were absent in the mice exposed to the potential MRTPs, in the cessation group, and the switching group. Our findings demonstrate the complex biological response of the lungs to CS exposure and support the benefits of cessation or switching to a heat-not-burn product using a design such as those employed in this study.
Computational Analysis of HIV-1 Protease Protein Binding Pockets

Mutations that arise in HIV-1 protease after exposure to various HIV-1 protease inhibitors have proved to be a difficult aspect in the treatment of HIV. Mutations in the binding pocket of the protease can prevent the protease inhibitor from binding to the protein effectively. In the present study, the crystal structures of 68 HIV-1 proteases complexed with one of the nine FDA approved protease inhibitors from the Protein Data Bank (PDB) were analyzed by (a) identifying the mutational changes with the aid of a developed mutation map and (b) correlating the structure of the binding pockets with the complexed inhibitors. The mutations of each crystal structure were identified by comparing the amino acid sequence of each structure against the HIV-1 wild-type strain HXB2. These mutations were visually presented in the form of a mutation map to analyze mutation patterns corresponding to each protease inhibitor. The crystal structure mutation patterns of each inhibitor (in vitro) were compared against the mutation patterns observed in in vivo data. The in vitro mutation patterns were found to be representative of most of the major in vivo mutations. We then performed a data mining analysis of the binding pockets from each crystal structure in terms of their chemical descriptors to identify important structural features of the HIV-1 protease protein with respect to the binding conformation of the HIV-1 protease inhibitors. Data mining analysis is performed using several classification techniques: Random Forest (RF), linear discriminant analysis (LDA), and logistic regression (LR). We developed two hybrid models, RF-LDA and RF-LR. Random Forest is used as a feature selection proxy, reducing the descriptor space to a few of the most relevant descriptors determined by the classifier. These descriptors are then used to develop the subsequent LDA, LR, and hierarchical classification models. Clustering analysis of the binding pockets using the selected descriptors used to produce the optimal classification models reveals conformational similarities of the ligands in each cluster. This study provides important information in understanding the structural features of HIV-1 protease which cannot be studied by other existing in vivo genomic data sets.
A Triptych Inquiry: Rethinking Sustainability, Innovation, and Financial Performance

Management scholars have sought to answer the question: is there a financial payoff for ad-dressing ecological and social issues? We move beyond this question and include a time com-ponent for corporate financial performance (CFP) and a firm’s innovativeness in order to ask: when does it pay? Combining a contingency perspective with the resource-based view of the firm clarifies the positive relationship between corporate environmental and social perform-ance (ESP) and CFP, which only holds in the long-term but not in the short-term. Further, we find support for a moderating effect of innovation on the relationship between the ESP and short-term CFP as suggested by the literature. However, we empirically show that in the long-term, innovation mediates the ESP-CFP relationship suggesting that innovation should be considered as a long-term investment required to unlock the full potential of ESP initiatives.
Quality‐control of an hourly rainfall dataset and climatology of extremes for the UK

Sub‐daily rainfall extremes may be associated with flash flooding, particularly in urban areas but, compared with extremes on daily timescales, have been relatively little studied in many regions. This paper describes a new, hourly rainfall dataset for the UK based on ∼1600 rain gauges from three different data sources. This includes tipping bucket rain gauge data from the UK Environment Agency (EA), which has been collected for operational purposes, principally flood forecasting. Significant problems in the use of such data for the analysis of extreme events include the recording of accumulated totals, high frequency bucket tips, rain gauge recording errors and the non‐operation of gauges. Given the prospect of an intensification of short‐duration rainfall in a warming climate, the identification of such errors is essential if sub‐daily datasets are to be used to better understand extreme events. We therefore first describe a series of procedures developed to quality control this new dataset. We then analyse ∼380 gauges with near‐complete hourly records for 1992–2011 and map the seasonal climatology of intense rainfall based on UK hourly extremes using annual maxima, n‐largest events and fixed threshold approaches. We find that the highest frequencies and intensities of hourly extreme rainfall occur during summer when the usual orographically defined pattern of extreme rainfall is replaced by a weaker, north–south pattern. A strong diurnal cycle in hourly extremes, peaking in late afternoon to early evening, is also identified in summer and, for some areas, in spring. This likely reflects the different mechanisms that generate sub‐daily rainfall, with convection dominating during summer. The resulting quality‐controlled hourly rainfall dataset will provide considerable value in several contexts, including the development of standard, globally applicable quality‐control procedures for sub‐daily data, the validation of the new generation of very high‐resolution climate models and improved understanding of the drivers of extreme rainfall.
Immigration and the Food Stamp Program

The growth of the welfare state in the past few decades coincided with the resurgence of large-scale immigration to the United States, adding a new and explosive question to the already contentious debate over immigration policy: Do immigrants "pay their way" in the welfare state? The available empirical evidence suggests that immigrant participation in cash benefit programs has risen dramatically since 1970. Congress reacted to this trend by enacting welfare reform legislation in 1996 that denied many types of means-tested assistance to non-citizens, including food stamps. Because of data constraints, much of the research analyzing immigrant participation in welfare programs investigates the extent to which immigrants enroll in cash benefit programs, with little attention being paid to the trends and determinants of immigrant participation in other programs. This paper uses data drawn from the decennial Censuses, the Survey of Income and Program Participation, and the Current Population Surveys to analyze trends in immigrant participation in the Food Stamp Program. The study describes the differential trends in immigrant and native participation in the Food Stamp Program; explores the factors that cause these differential trends; and examines the extent to which immigrant participation in public assistance programs affects the propensity of the second generation to receive food stamps. The evidence suggests that the immigrant-native gap in participation rates in the Food Stamp Program widened until about 1995. Since 1995, there has been a decline in the number of both native and immigrant households that receive food stamps, but the decline has been steeper in the immigrant population. A large part of the gap in participation rates between immigrant and native households can be attributed to differences in socioeconomic characteristics between the two groups, particularly educational attainment. The evidence also indicates that immigrant households have much higher entry rates into the Food Stamp Program, but roughly the same exit rates. Finally, there is a strong link between the use of cash benefits in the immigrant generation and the use of food stamps in the second generation.
Labor Markets, Economic Policy,& Business Cycles

My thesis is composed of three essays. In the first essay, I am the first to relate luck and employment protection: I study the effects of employment protection on the roles of luck, merit, and effort, in determining income inequality. To this end, I develop a model of heterogeneous workers and firms that meet subject to matching frictions. In the model, an increase in employment protection strengthens the role of luck and weakens the role of merit in generating income inequality. In the second essay, Alper Cenesiz and I study the effects of monetary policy on aggregate and sectoral outputs. The standard two sector (with durable and nondurable goods sectors) New Keynesian model generates either negative sectoral comovement and aggregate neutrality or no sectoral comovement. These results are at odds with conventional wisdom and VAR evidence: (i) aggregate and sectoral outputs move together, and (ii) price and output of the durable sector react more strongly than those of the nondurable sector. In this essay, we reconcile the standard two sector New Keynesian model with VAR evidence by introducing real wage rigidities. In the third essay, Alper Cenesiz and I focus on the unemployment volatility puzzle. The search and matching model, the workhorse model of the labor market, has a volatility problem: The standard deviation of unemployment is about 20 times smaller than that in data. Motivated by this puzzle, we extend a real business cycle model to allow for both intensive and extensive margins of labor in a novel way. In the model, workers differ in their skills, firms love variety of skills, and households incur in costs for adjusting the number of skills in the market. Our model generates highly volatile unemployment, highly volatile output,
Current Controversies in the Prediction, Diagnosis, and Management of Cerebral Vasospasm: Where Do We Stand?

Aneurysmal subarachnoid hemorrhage occurs in approximately 30,000 persons in the United States each year. Around 30 percent of patients with aneurysmal subarachnoid hemorrhage suffer from cerebral ischemia and infarction due to cerebral vasospasm, a leading cause of treatable death and disability following aneurysmal subarachnoid hemorrhage. Methods used to predict, diagnose, and manage vasospasm are the topic of recent active research. This paper utilizes a comprehensive review of the recent literature to address controversies surrounding these topics. Evidence regarding the effect of age, smoking, and cocaine use on the incidence and outcome of vasospasm is reviewed. The abilities of different computed tomography grading schemes to predict vasospasm in the aftermath of subarachnoid hemorrhage are presented. Additionally, the utility of different diagnostic methods for the detection and visualization of vasospasm, including transcranial Doppler ultrasonography, CT angiography, digital subtraction angiography, and CT perfusion imaging is discussed. Finally, the recent literature regarding interventions for the prophylaxis and treatment of vasospasm, including hyperdynamic therapy, albumin, calcium channel agonists, statins, magnesium sulfate, and endothelin antagonists is summarized. Recent studies regarding each topic were reviewed for consensus recommendations from the literature, which were then presented.