Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression of Tumor Necrosis Factorα and Interferonγ in the Lungs of Mycoplasma pulmonis‐Infected Mice

ICR mice were infected intranasally with Mycoplasma pulmonis isolated freshly from the lungs of a rat with pneumonia. We demonstrated with high reproducibility the expressions of messenger RNAs of cytokines, tumor necrosis factor alpha (TNFα) and interferon gamma (IFNγ) in the lung tissue of M. pulmonis‐infected mice by the reverse transcriptase‐polymerase chain reaction and confirmed specific mRNA of the cytokines by restriction endonuclease digestion. Both the viable population of M. pulmonis in the lung tissue and the titers of the neutralizing antibody in the serum increased between 7 and 21 days, and reached their maximum 35 days after infection. The pneumonia in mice progresses with the development of lung lesions after 7 days of infection. The early lesions are characterized primarily by neutrophils and edema in the alveolar spaces. mRNAs prepared from the lung tissue of M. pulmonis‐infected and ‐uninfected mice were also tested for the presence of messages specific to TNFα and IFNγ by the reverse transcriptase‐polymerase chain reaction. The expression of the genes encoding TNFα and IFNγ was constitutively demonstrated from 24 hr through 35 days after the intranasal inoculation of M. pulmonis. Furthermore, cells of two types, adherent and nonadherent cells, in bronchoalveolar lavage fluids obtained from the mice 3 weeks after inoculation of M. pulmonis were also found to express the genes of TNFα and IFNγ respectively. These data suggest that these cytokines would play a role in both stimulation in the development of pathological changes in mycoplasmal infection, affecting the inflammatory responses.
Comment

Calhoun, G. (2011), “Out-of-Sample Comparisons of Overfit Models,” Working Paper 10002, Iowa State University. [12] Clark, T. E. , and McCracken, M. W. (2013), “Advances in Forecast Evaluation,” in Handbook of Economic Forecasting (Vol. 2), eds. G. Elliott and A. Timmermann, Amsterdam: Elsevier. [12] ——— (2014), “Nested Forecast Model Comparisons: A New Approach to Testing Equal Accuracy,” Journal of Econometrics, forthcoming. [12] Diebold, F. X. , and Mariano, R. S. (1995), “Comparing Predictive Accuracy,” Journal of Business and Economic Statistics, 13, 253–263. [12] Giacomini, R. , and White, H. (2006), “Tests of Conditional Predictive Ability,” Econometrica, 74, 1545–1578. [12] Harvey, D. I. , Leybourne, S. J., and Newbold, P. (1997), “Testing the Equality of Prediction Mean Squared Errors,” International Journal of Forecasting, 13, 281–291. [12]
Stumped by Trees? A Generalized Null Model for Patterns of Organismal Diversity

Evolutionary biologists increasingly have become interested in the factors determining the structure of phylogenetic trees. For example, highly asymmetric trees seem to suggest that the probability of extinction and/or speciation differs among lineages. Before looking for the cause of such differences, one must establish that the structure of the trees differs significantly from results of an appropriate null model. A commonly invoked null model assumes that speciation is equally probable along all branches of a diversifying tree and predicts that highly asymmetric trees are not unexpected. However, this model of diversification assumes more than equality of rates among lineages. We demonstrate theoretically and via simulations that relaxation of the hidden assumptions that speciation is essentially instantaneous and occurs independently in separate lineages leads to qualitatively different expectations concerning the expected phylogenetic topology. In particular, highly asymmetric trees are considerably less likely to arise by chance when the speciation process takes up a significant fraction of the expected time between initiation of speciation events or when lineages tend to speciate simultaneously. As with most null models in ecology and evolution, the assumptions encoded in the model play an important role in determining the null expectation.
Perfil físico-químico do soro de queijos mozarela e minas-padrão produzidos em várias regiões do estado de Minas Gerais

The physical-chemical profile of the whey of mozzarella and minas-padrao cheeses was studied in four regions ("Alto Sao Francisco", "Zona Metalurgica", "Zona da Mata" and "Sul de Minas") which produce milk and cheese in Minas Gerais. Due to the lack of a specific identity and a quality pattern for cheese whey, the results can be taken as a base to develop such patterns. The mean values found for mozzarella cheese whey were: - 0.565± 0.031oH for freezing point; 6.19± 0.26 for pH; 13.16± 3.08oD for titratable acidity; 6.33± 0.43g/100g for total solids; 93.67± 0.43g/100g for moisture; 0.77± 0.26g/100g for fat; 0.84± 0.04g/100g for protein; 4.42± 0.68g/100g for lactose; 0.47± 0.04 g/100g for ashes; 0.18± 0.01g/100g for chlorine and 1.0253± 0.0006 for density. In relation to minas-padrao cheese whey, the following mean results were obtained: - 0.555± 0.030oH for freezing point; 6.30± 0.31 for pH; 12.48± 2.07oD for titratable acidity; 6.28± 0.51g/100g for total solids; 93.97± 0.54 g/100g for moisture; 0.70± 0.21g/100g for fat; 0.80± 0.04g/100g for protein; 4.12± 0.36g/100g for lactose; 0.49± 0.03g/100g for ashes; 0.20± 0.01g/100g for chlorine and 1.0249± 0.0009 for density. No statistical difference between those types of whey was observed, but difference among wheys from regions for freezing point, total solids, moisture and density as well as interaction whey x regions for protein, titratable acidity, fat, and chorine were found. Only lactose and ash contents did not present any statistical difference.
Comment

The article by Crainiceanu et al. addresses an important and relatively undeveloped area of statistical research: the analysis of populations in which the data objects are matrices. In particular, they focus on collections of matrices that have the same row and column dimensions. Such datasets are increasingly prevalent in a number of scientific fields. Examples range from the analysis of facial data in image analysis, EEG data in neuroscience, fMRI data in medical imaging, and browsing data in the study of Internet traffic (see Table 1). The method proposed by the authors, population value decomposition (PVD), is a useful way to simultaneously reduce the dimensionality of a collection of matrices. For matrices Y1,Y2, . ,Yn, each of dimension F × T , the PVD yields an approximation Yi ≈ PViD for i = 1, . ,n. The lowdimensional representation Vi for each matrix is on a common set of coordinates determined by P and D. This allows for the application of standard statistical approaches, such as regression and cluster analysis, to the lower-dimensional matrices Vi, rather than the Yi’s. Furthermore, inspection of the populationwide left and right loading matrices P and D can aid in identifying the primary modes of variation among a population of matrices. The authors present an interesting data analysis; however, we note that a model formally equivalent to PVD has been proposed in the computer science literature under the name twodimensional singular value decomposition (2DSVD) (Ding and Ye 2005; Ye 2005). This literature also provides natural additional approaches for choosing the population-wide matrices P and D. We discuss these approaches in Section 1. We may regard the problem addressed in these articles by viewing the data as a three-way (F × n × T) array. In Section 2 we discuss and compare alternative approaches that treat the data structure as a three-way array. We show that two SVDlike decompositions for higher-order arrays, those of Candecomp/Parafac (Carroll and Chang 1970) and Tucker (Tucker 1966), are related to the PVD decomposition. In fact, both can be represented in the form PViD, in which the Vi matrices have a particular structure. In Section 3 we discuss some important issues and caveats related to the application of PVD and related methods. In Section 4 we compare PVD and other methods in an application to facial image data.
SURVIVAL OF AVIAN CARCASSES AND PHOTOGRAPHIC EVIDENCE OF PREDATORS AND SCAVENGERS

Abstract Scavenging of carcasses may bias estimates of mortality following the use of pesticides. To assess carcass survival, we monitored bird carcasses in crop stubble, grassland, roadside, and wooded habitats in east-central South Dakota in early spring. Survival rates differed among habitat types in 1997 but not in 1998. Survival rates did not differ among species of carcass in 1997 or 1998. Within 5 d, 66% of carcasses had been scavenged in both 1997 and 1998. To assess potential hazards of secondary poisoning, we used infrared-triggered camera systems to identify predators and scavengers of live birds and bird carcasses. Mammals (n = 164), particularly striped skunks (Mephitis mephitis) (n = 105), were the most commonly photographed predators and scavengers. The number of avian predators and scavengers photographed (n = 39) was relatively low. Because scavenger activity can be high, we recommend that searches for carcasses should be conducted within 24 h of pesticide application to ensure accurate estimates of mortality.
Comment

Cox, D. R. , and Hinkley, D. V. (1974), Theoretical Statistics, New York: Chapman and Hall. [330] Hansen, B. E. (1999), “The Grid Bootstrap and the Autoregressive Model,” Review of Economics and Statistics, 81, 594–607. [332] McCloskey, A. (2012), “Bonferroni-Based Size-Correction for Nonstandard Testing Problems,” Working paper, Department of Economics, Brown University. Available at http://faculty.wcas. northwestern.edu/∼ate721/ McCloskey_BBCV. pdf. [332] Mikusheva, A. (2014), “Second Order Expansion of the t-Statistic in AR(1) Models,” Econometric Theory, forthcoming. [332] Müller, U. K. (2007), “A Theory of Robust Long-Run Variance Estimation,” Journal of Econometrics, 141, 1331–1352. [331] Phillips, P. C. B. (2005), “HAC Estimation by Automated Regression,” Econometric Theory, 21, 116–142. [331] ——— (2014), “On Confidence Intervals for Autoregressive Roots and Predictive Regression,” Econometrica, 82, 1177–1195. [332] Phillips, P. C. B. , Magdalinos, T. , and Giraitis, L. (2010), “Smoothing Localto-Moderate Unit Root Theory,” Journal of Econometrics, 158, 274–279. [331] Stock, J. (1991), “Confidence Intervals for the Largest Autoregressive Root in US Macroeconomic Time Series,” Journal of Monetary Economics, 28, 435–459. [332] Stoica, P., and Moses, R. (2005), Spectral Analysis of Signals, Upper Saddle River, NJ: Pearson Prentice Hall. [331] Sun, Y. (2006), “Best Quadratic Unbiased Estimators of Integrated Variance in the Presence of Market Microstructure Noise,” Working paper, Department of Economics, UC San Diego. Available at http://econweb.ucsd. edu/∼yisun/bqu.pdf. [331] ——— (2011), “Autocorrelation Robust Trend Inference With Series Variance Estimator and Testing-optimal Smoothing Parameter,” Journal of Econometrics, 164, 345–366. [331] ——— (2013), “A Heteroscedasticity and Autocorrelation Robust F Test Using Orthonormal Series Variance Estimator,” Econometrics Journal, 16, 1–26. [331] ——— (2014a), “Let’s Fix It: Fixed-b Asymptotics versus Small-b Asymptotics in Heteroscedasticity and Autocorrelation Robust Inference,” Journal of Econometrics, 178(3), 659–677. [332] ——— (2014b), “Fixed-Smoothing Asymptotics and Asymptotic F and t Tests in the Presence of Strong Autocorrelation,” Working paper, Department of Economics, UC San Diego. Available at http://econweb.ucsd. edu/∼yisun/ HAR_strong13_revised. pdf. [331] Thomson, D. J. (1982), “Spectrum Estimation and Harmonic Analysis,” IEEE Proceedings, 70, 1055–1096. [331]
Comment

(2004), Fields: Tools for Spatial Data, available at http://www.cgd. ucar.edu/stats/Software/Fields. Nychka, D. W. , and Saltzman, N. (1998), “Design of Air Quality Monitoring Networks,” in Case Studies in Environmental Statistics, eds. D. Nychka, W. W. Piegorsch, and L. H. Cox, New York: Springer-Verlag, pp. 51–76. R Development Core Team (2004), R: A Language and Environment for Statistical Computing, Vienna, Austria: R Foundation for Statistical Computing, available at http://www.R-project.org. Rue, H. , and Tjelmeland, H. (2002), “Fitting Gaussian Markov Random Fields to Gaussian Fields,” Scandinavian Journal of Statistics, 29, 31–50. Ruppert, D. (2002), “Selecting the Number of Knots for Penalized Splines,” Journal of Computational and Graphical Statistics, 11, 735–757. Ruppert, D. , Wand, M. P., and Carroll, R. J. (2003), Semiparametric Regression, Cambridge, U.K.: Cambridge University Press. Seketeli, A. et al. (2002), “The Achievements and Challenges of the African Programme for Onchocerciasis Control (APOC),” Annals of Tropical Medicine and Parasitology, 96, 15–28. Self, S. G. , and Liang, K. -Y. (1987), “Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests Under Nonstandard Conditions,” Journal of the American Statistical Association, 82, 605–610. Takoungang, I. et al. (2002), “Rapid Assessment Method for Prevalence and Intensity of L. loa Infection,” Bulletin of the World Health Organisation, 80, 852–858. van Rossum, G. , and Drake, F. L. Jr. (Eds.) (2003), The Python Language Reference Manual, http://docs.python. org/ref/ref.html, Network Theory Ltd. Wahba, G. (1990), Spline Models for Observational Data, Philadelphia: Society for Industrial and Applied Mathematics. Walter, G. , Warmerdam, F. , and Farris-Manning, P. (2002), “An Open Source Tool for Geospatial Image Exploitation,” in Proceedings of the IGARSS 2002 Conference, Vol. 6, pp. 3522–3524. World Health Organization (1995), Onchocerciasis and Its Control: Report of a WHO Expert Committee on Onchocerciasis Control, World Health Organisation Technical Report Series 852, Geneva: Author. Wood, S. N. (2003), “Thin Plate Regression Splines,” Journal of the Royal Statistical Society, Ser. B, 65, 95–114.
Population structure, distribution patterns and precopulatory mate-guarding in the feather mite Alloptes Canestrini, 1879 (Acari: Analgoidea: Alloptidae) on auks (Charadriiformes: Alcidae) at the Gannet Islands, Labrador, Canada

Abstract Feather mites are ubiquitous avian ectoparasites whose population structure is expected to vary with degree of coloniality and other aspects of host bird species' ecology. We investigated aggregation . and infrapopulation structure of feather mites of the genus Alloptes Canestrini on four auk species (with different levels of nesting aggregations) breeding at the Gannet Islands, Labrador, Canada. Feather mite populations were more prevalent and had higher relative abundance in Razorbills, Alca torda Linnaeus, and Atlantic Puffins, Fratercula arctica Linnaeus, compared to murres (Uria spp.). Prevalence increased moving from highly aggregated ledge-nesting hosts (53% in murres) to less aggregated, burrow-nesting hosts (87% in puffins), with similar trends in relative abundance. Prevalence and relative abundance of individual age-classes of feather mites varied among host species without any clear relationship to host coloniality. Infrapopulations were strongly female-biased (4–36% males), with a largeproportion of tritonymphs and adult females. Precopulatory mate guarding was observed in all sevencases of coupled individuals, each involving an adult male and a female tritonymph. This study constitutes the first record of precopulatory mate guarding in the genus Alloptes, a male strategy to ensure insemination of adult females as soon as they molt. Female-biased sex ratios may be produced in order to reduce local mate competition among male feather mites. Our study revealed several nonintuitive patterns of mite population structure, underlining the need for more detailed work on these ecologically important but poorly known species.
Leading Six Sigma

The  rst few chapters (or essays) deal with the methods for developing predictions for dependent responses: correlation and multiple regression for measured responses and logistic regression for categorical responses. A number of chapters discuss a methodology for including interactions in the logistic regression model. This method, called CHAID, is an automatic interaction detection procedure from the machine-learning world that utilizes regression trees. Applications for CHAID include market segment classi cation and modeling and the  nding of replacements for missing-data values and categories. With the modeling tools and methods in hand, the author next provides several chapters that deal with database marketing, customer identi cation developed from all of the information in these big databases. Separate chapters cover using bootstrapping and visualization to validate and evaluate the database models. Two chapters explore the use of genetic modeling, which is proposed as a method for variable selection. The book ends with a chapter on coef cient-free models, another product of the machine-learning world. Note that this book’s content is the antithesis for technical dif culty to the  ne statistical learning book by Hastie, Tibshirani, and Friedman (2001); see the long-winded Technometrics review by Ziegel (2003). Where that book was replete with technical detail, this book is almost devoid of technical content. More than half of these essays previously appeared in the Journal of Targeting, Measurement and Analysis for Marketing. However, the author’s background and experience make this book a useful addition to the library of any statistician involved with data mining. There is even SAS® code in a few of the chapters.
De la fiabilité des liaisons ostéologiques

Resume. — L'etude archeologique et anthropologique des grands ensembles funeraires, notamment des sepultures collectives, se heurte principalement au probleme de l'identification des os appartenant a un meme individu parmi des series qui comptent souvent plusieurs centaines de restes humains. Or, cette donnee est indispensable pour discuter la chronologie relative des depots et comprendre les gestes rituels dont la succession conditionne la dynamique interne du gisement funeraire. La solution theorique a ce probleme reside dans la recherche systematique des «liaisons osteologiques ». Les liaisons par symetrie et par contiguite articulaire presentent certainement de tres grandes potentialites d'exploitation. Mais ce sont aussi celles pour lesquelles l'argumentation theorique est la plus fragile car on peut legitimement s'interroger sur la validite des associations qui sont alors affirmees. La bibliographie relative a ces donnees est pratiquement inexistante. C'est pourquoi nous avons elabore une etude systematique des methodes qui ont ete mises en oeuvre de facon que la recherche des appartements et des contiguites puisse desormais se fonder sur des bases connues et non plus sur des convictions empiriques.
A Step-by-Step Approach to Using SAS® for Univariate & Multivariate Statistics, JMP® for Basic Univariate and Multivariate Statistics

Perhaps books like this would not be reported if I could ever bring myself to seriously use S–PLUS®, not just dabble with the GUI. Being on the airplane again with my laptop, it seemed like a nice time to try. This book has been reported a couple of times, mot recently Ziegel (2003) for the third edition, which was issued for Version 6 of S–PLUS. Now that there is Version 7, here is a fourth edition. In some of the author’s words, “This edition is an update. to cover new functions and features. adding more practical tips and examples” (Preface, p. v). As the authors note, “if you want to work permanently with S–PLUS, you will need to use the command line and appreciate it soon” (Preface, p. vi). This book continues to be a very good place to get started. If you have had a copy of one of the last two versions of the book, you still have the essentials of the content, which has been adequately described in my reports on the two previous editions (see especially Ziegel 2001). New to the third edition was the chapter on R, though perhaps R novices would be better served by the recent book by Crawley (2005), for which the review by Ng (2006) appears elsewhere in this issue. The book is comprehensive for learning S–PLUS—only a single chapter deals strictly with statistic analysis.
Morphological relationships of passerine birds from Australia and New Guinea in relation to their diets

Beak, wing, leg and intestinal lengths, and gizzard widths, were all significantly related to body mass in 51 honeyeater species from Australia, 48 honeyeater species from New Guinea and 31 purely insectivorous passerine bird species from Australia. The nectar-feeding honeyeaters had smaller gizzards and intestines than wholly insectivorous birds of comparable size, although their wing and leg lengths did not differ; New Guinean and Australian honeyeaters were similar in these respects. Overall, honeyeaters had longer beaks than pure insectivores. Among Australian honeyeaters, those genera consuming more nectar than insects had longer beaks than the less nectarivorous, more insectivorous genera. Indeed, the latter group had beaks comparable in length to wholly insectivorous birds. All morphological differences revealed were attributable to known differences in diet.
Characteristics and Peculiarities of Rural Tourism in the Balearic Islands

Abstract Rural tourism is a complement to quality food production efforts in its goal toward restoring vitality among rural areas in Europe, affronting the rest of the world's more productive and less costly food-producing industry. Countries such as France, Italy, Austria and Germany have pioneered rural tourism projects and have proved its revitalizing capacity. Generally, the growth of rural tourism in Spain has resulted in establishments with a wide variety of typologies, prices and levels of comfort. The Balearic Islands have also developed this new sector and the result is a style with characteristics differing from those of other regions. In the Balearic Islands, it is a sector that complements traditional tourism by offering small establishments located in rural areas. Often their services could be ranked as four or five stars and the establishments are commonly managed by people with previous work experience in the sector. The average costumer can be described as a foreigner who stays on the island for around a week and a half. The aim of this paper is to summarize rural tourism's legislation, quantitative development and the most common characteristics of its services and customers (including the differences between islands). Important differences when comparing with other forms of rural tourism in mainland Spain are also highlighted and the synergies existing with the predominant “sun and beach” mass tourism.
Book Reviews

Grubb, M. , Vrolijk, C. , Brack, D. , 1999. The Kyoto Protocol. Earthscan, London. Leggett, J., 1999. The Carbon War. Penguin, London. Missbach, A. , 1999. Das Klima zwischen Nord und Süd, Westfälisches Dampfboot, Münster. Mwandosya, M. , 1999. Survival Emissions. Dar es Salaam. Oberthür, S. , Ott, H. , 1999. The Kyoto Protocol. Springer, Berlin. Rahman, A. , Roncerel, A. , 1994. A view from the ground up. In: Mintzer, Irving Leonard, Amber (Eds.), Negotiating Climate Change. Cambridge, pp. 239–272. Taalab, A. , 1998. Voices Against Climate Change. Frankfurt.
Silica‐scaled Chrysophytes from Portugal

Phytoplankton samples from lakes, reservoirs and ponds in Central Portugal were obtained and the scale-bearing chrysophytes investigated by electron microscopy. This is the first study on the occurrence and distribution of these organisms in Portugal and in the Iberian Peninsula as a whole. It reports the presence of 23 species of the genera Chrysosphaerella, Paraphysomonas, Spiniferomonas, Mallomonas and Synura. Most of the species found are of worldwide distribution but a few rare organisms were present in some samples. To conclude, the perspectives of future research in Portugal are briefly outlined.