Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of the Escape Swim Motor Network in the Organization of Behavioral Hierarchy and Arousal in Pleurobranchaea1

Abstract The escape swimming pattern generator of the notaspid opisthobranch Pleurobranchaea drives a high threshold, override behavior. The pattern generator is integrated with neural networks of other behaviors so as to coordinate unitary behavioral expression and to promote general behavioral arousal. These functions are separately produced by different swim network elements. One set of swim premotor neurons, the A1/A10 ensemble, A3 and IVS, generate the swim pattern and, through corollary activity, suppress potentially conflicting feeding behavior by exerting broad inhibition at major feeding network interneurons. A second set of swim neurons, the serotonergic As1–4 neurons, provides intrinsic neuromodulatory excitation to the swim pattern generator that sustains the escape swim episode through multiple cycles. The As1–4 also provide neuromodulatory excitation to important modulatory, serotonergic cells in the feeding motor network and locomotor network, and may have a general regulatory role in the distributed serotonergic arousal network of the mollusk. The As1–4 appear to be also necessary to both avoidance and orienting turning, and are therefore likely to be critical, multi-functional components upon which much of the organization of the animal's behavior rests.
Seismic Signal Use by Fossorial Mammals1

Abstract The subterranean environment is not favorable for the use of vision or the audition of airborne sounds as means of long-distance sensory perception. However, seismic vibrations have been shown to propagate at least an order of magnitude better than airborne sound between the burrow systems of the mole-rat Georychus capensis. The use of the seismic channel for communication underground is well documented for other species of bathyergids, as well as the spalacine mole-rat Nannospalax. It has recently been suggested that the golden mole Eremitalpa granti namibensis may also be sensitive to ground vibrations, in this case used in foraging in its desert habitat. In this paper, the use of seismic signals among these and other fossorial mammals is reviewed from theoretical, behavioral and anatomical standpoints. The question of whether auditory or somatosensory means are used to detect vibratory signals is examined. Attempts to explain the distribution of seismic sensitivity and communication mechanisms among fossorial mammals are considered. The potential influences of different soil type and digging methods are discussed, and it is proposed that digging mechanisms involving the head might preadapt a fossorial mammal towards the development of seismic sensitivity.
Regulation of Drosophila Visual System Development by Nitric Oxide and Cyclic GMP1

Abstract Photoreceptors undergoing target selection in the optic lobe of Drosophila express a nitric oxide sensitive soluble guanylate cyclase (sGC). At the same time, cells in the target region of the optic lobe express nitric oxide synthase (NOS). Pharmacological inhibition of NOS, NO or sGC leads to disruption of the retinal projection pattern in vitro, and the extension of individual retinal axons beyond their appropriate targets. The disruptive effects of NOS inhibition in vitro are prevented by adding a cGMP analog. Mutations in the sGC alpha subunit gene, Gcα1, reduce sGC expression and attenuate NO-sensitive retinal cGMP production in the visual system. Although the retinal projection pattern is undisturbed in Gcα1 mutants, they lack positive phototaxis as adults, suggesting inappropriate connections exist between the photoreceptors and optic lobe interneurons in these flies. Preliminary results show that heat-shock expression of wild-type Gcα1 during metamorphosis can restore positive phototaxis in severe Gcα1 mutants. These in vivo results support the in vitro findings that NOS and sGC activity are required to promote the appropriate retinal innervation of the optic lobe.
A PALEONTOLOGIST'S CONTRIBUTION TO UNDERSTANDING THE ORIGINS OF MAMMALIAN BIOLOGY1

The fossil record of mammals and their amniote precursors, especially when combined with evidence from the rapidly emerging field of molecular taxonomy, provides the most complete documentation available for any animal group about the rate and nature of its evolutionary change. That is an allpervasive theme within this generally excellent new book. Thomas Kemp is a recognized authority on the diversification of nonmammalian synapsids, and the book reflects the truly ancient origins of anatomical and physiological trends that characterize mammalian biology. This is a thoroughly rewritten version of his 1982 book with the addition of a summary of Cenozoic mammalian history. I’m happy to have Kemp’s book available, and I will use it for many reference purposes. Except for the kingly price, I would be happy to assign it as a textbook. There is much to praise. Every such work will have its weaknesses, however, and I’ll speak to some of those before returning to the book’s more positive qualities. Some of these critical comments represent no more than my own biases and opinions. The technical editing is spotty. Scientific names are commonly misspelled, and figure captions seem especially prone to that problem. The text is perfused with confusion of timeversus rock-based terminology (e.g., Ophiacodon ‘‘appears in the latest Upper Carboniferous’’). The abbreviation Ma, which is intended to refer to a specific geologic interval identified as millions of years ago, is consistently confused (e.g., ‘‘during the 140 Ma duration of the Jurassic and Cretaceous Periods’’) with my, which is intended to indicate any general duration that extended some millions of years. The strengths of this book do not reside in its geological aspects. Such topics as the practical uncertainties in correlation and discussions of paleogeography and paleoclimatology are given relatively unsophisticated treatments. Numerous outright errors exist, including the following examples: ‘‘The docodontan Henkelotherium’’; ‘‘condylarths such as Purgatorius’’; [in reference to marsupials] ‘‘Unique characters of the postcranial skeleton are few but include the presence of a prepubic bone’’; and suggesting Asiatic ‘‘introduction’’ of antilocaprids to North America via the Bering Strait. To his credit, Kemp was not hesitant to express his own opinions about the mammalian fossil record. However, he made occasional overarching statements that I think are unjustified. For example, in reference to the mammalian clade holding the common ancestor of aegialodonts and living groups that primitively had a well-developed talonid on lower
Dynamic Topology Extraction in Cloud Infrastructures

To determine the threat exposure of a virtualized environment, attack graphs generation, coupled to a risk-based assessment can be used. The first roadblock to lift to that end is the extraction of the topology. We will present in this paper the stategy we intend to use to obtain a near real-time view of the connectivity existing in a virtual infrastructure .
Dynamics of Specific Antibody Responses Induced in Mallards After Infection by or Immunization With Low Pathogenicity Avian Influenza Viruses

Important Findings This study showed the long-lasting antibody response of mallards against low pathogenicity avian influenza virus (LPAIV) infections. Natural infections with different subtypes of LPAIVs are very common in wild duck populations. Recent outbreaks of high pathogenicity avian influenza virus (HPAIV) H5N1 in Eurasian and African countries stimulated monitoring activities in aquatic wild bird populations. Surveillance mainly focused on virus detection; only a few serologic investigations have been conducted so far.
FEMALES RECEIVE A LIFE-SPAN BENEFIT FROM MALE EJACULATES IN A FIELD CRICKET

Abstract Mating has been found to be costly for females of some species because of toxic products that males transfer to females in their seminal fluid. Such mating costs seem paradoxical, particularly for species in which females mate more frequently than is necessary to fertilize their eggs. Indeed, some studies suggest that females may benefit from mating more frequently. The effect of male ejaculates on female life span and lifetime fecundity was experimentally tested in the variable field cricket, Gryllus lineaticeps. In field crickets, females will mate repeatedly with a given male and mate with multiple males. Females that were experimentally mated either repeatedly or multiply lived more than 32% longer than singly mated females. In addition, multiply mated females produced 98% more eggs than singly mated females. Because females received only sperm and seminal fluid from males in the experimental matings, these life-span and fecundity benefits may result from beneficial seminal fluid products that males transfer to females during mating. Mating benefits rather than mating costs may be common in many animals, particularly in species where female mate choice has a larger effect on male reproductive success than does the outcome of sperm competition. Corresponding Editor: C. Boggs
Endocrine Disruptors of the Stress Axis in Natural Populations: How Can We Tell?1

Synopsis Often, as environmental endocrinologists, we observe animals in nature with the goal of describing their normal endocrinology. However, the contamination of virtually all natural habitats by chemicals of anthropogenic origins (e.g., PCBs, organochlorines, phytoestrogens, alkyphenols, heavy metals) that might alter endocrine conditions suggests we need to reevaluate many of our field studies with respect to points of reference or controls. The impaired response of the stress axis of feral brown trout, Salmo trutta, correlated with chronic exposure to heavy metals is examined as a case in point although the problems extend to other hypothalamic axes as well. Our studies emphasize that measurement of one static endocrine parameter to assess the health of any hypothalamus-pituitary axis (e.g., plasma cortisol levels to indicate stress) should not be used as a biomarker for field studies.
A LIKELIHOOD-BASED APPROACH TO ESTIMATING AND TESTING FOR ISOLATION BY DISTANCE

Abstract Simple regression of genetic similarities between pairs of populations on their corresponding geographic distances is frequently used to detect the presence of isolation by distance (IBD). However, these pairwise values are obviously not independent and there is no parametric procedure for estimating and testing for the IBD intercepts and slopes based on standard regression theory. Nonparametric tests, such as the Mantel test, and resampling techniques, such as bootstrapping, have been exploited with limited success. Here, I describe a likelihood-based analysis to allow for simultaneously detecting patterns of correlated residuals and estimating and testing for the presence of IBD. It is shown, through the analysis of two molecular datasets in pine species, that different covariance structures of the residuals exist. More over, the likelihood ratio tests under these covariance structures are less sensitive to the presence of IBD than the Mantel test and the simple regression analysis but more sensitive than the bootstrap and jackknife samples over independent populations or population pairs. Because the likelihood analysis directly models and accounts for nonindependence of residuals, it should legitimately detect the presence of IBD, thereby allowing for accurate inferences about evolutionary and demographic processes influencing the extent and patterns of IBD.
VIRULENCE FACTORS OF AVIAN PATHOGENIC ESCHERICHIA COLI STRAINS ISOLATED FROM CHICKENS WITH COLISEPTICEMIA IN JAPAN

Avian pathogenic Escherichia coli (APEC) infections are responsible for significant economic losses in the poultry industry. The purpose of this study was to show the characteristics of virulence factors of APEC isolated in Japan. Comparative studies were made on the nature of O serogroups, presence/absence of K1 and K5 capsule polysaccharides and genotypes, between strains isolated from lesions or blood of diseased chickens (APEC) and strains isolated from cloacal contents of healthy chickens (commensal E. coli).
Efficient Structure Learning of Markov Networks using L1-Regularization

Markov networks are commonly used in a wide variety of applications, ranging from computer vision, to natural language, to computational biology. In most current applications, even those that rely heavily on learned models, the structure of the Markov network is constructed by hand, due to the lack of effective algorithms for learning Markov network structure from data. In this paper, we provide a computationally efficient method for learning Markov network structure from data. Our method is based on the use of L1 regularization on the weights of the log-linear model, which has the effect of biasing the model towards solutions wheremany of the parameters are zero. This formulation converts theMarkov network learning problem into a convex optimization problem in a continuous space, which can be solved using efficient gradient methods. A key issue in this setting is the (unavoidable) use of approximate inference, which can lead to errors in the gradient computation when the network structure is dense. Thus, we explore the use of different feature introduction schemes and compare their performance. We provide results for our method on synthetic data, and on two real world data sets: pixel values in the MNIST data, and genetic sequence variations in the human HapMap data. We show that our L1-based method achieves considerably higher generalization performance than the more standard L2-based method (a Gaussian parameter prior) or pure maximum-likelihood learning. We also show that we can learn MRF network structure at a computational cost that is not much greater than learning parameters alone, demonstrating the existence of a feasible method for this important problem.
American Statistical Association Conference on Radiation and HealthHoward Johnson Plaza Resort, Deerfield Beach, Florida, June 23–26, 2002

The 15th ASA Conference on Radiation and Health, held June 23–26, 2002 in Deerfield Beach, FL, offered a unique forum for radiation researchers from a variety of disciplines to present and discuss recent findings and current issues related to the effects of radiation exposures on human health. The Conference also furnished investigators the opportunity to learn about new approaches to problems within their disciplines. The focus of the 2002 conference was current issues in radiation and health with sessions on:
EVOLUTION OF INTRINSIC GROWTH AND ENERGY ACQUISITION RATES. II. TRADE-OFFS WITH VULNERABILITY TO PREDATION IN MENIDIA MENIDIA

The Atlantic silverside (Menidia menidia) exhibits countergradient latitudinal variation in somatic growth rate along the East Coast of North America. Larvae and juveniles from high-latitude populations display higher intrinsic rates of energy consumption and growth than genotypes from low-latitude populations. The existence of submaximal growth in some environments suggests that trade-offs must counter the oft-cited theoretical benefits of energy and growth maximization (e.g., ‘‘bigger is better,’’ ‘‘faster is better’’) in the immature life stages. We hypothesized that energy and growth maximization trades off against investment in defense from predators. We conducted laboratory selection experiments to compare vulnerability to predation of silversides from: (1) fast-growing northern (Nova Scotia, NS) versus slow-growing southern (South Carolina, SC) source populations; (2) phenotypically manipulated fast-growing versus moderately-growing NS fish; and (3) recently fed versus unfed NS and SC fish. Tests involved fish drawn from common-garden environments and were conducted by subjecting mixed-treatment schools of sizematched silversides to natural, common piscine predators. NS silversides suffered significantly higher predation mortality than SC silversides. Parallel results were found in phenotypic manipulation of growth: NS silversides reared on a fast-growth trajectory (;1.0 mm/day) were significantly more vulnerable to predation than those growing at a moderate rate (;0.5 mm/day). Food consumption also affected vulnerability to predators: Silversides with large meals in their stomachs suffered significantly higher predation mortality than unfed silversides. Differences in predation vulnerability were likely due to swimming performance, not attractiveness to predators. Our findings demonstrate that maximization of energy intake and growth rate engenders fitness costs in the form of increased vulnerability to predation.
Composition of grazed and cleared temperate grassy woodlands in eastern Australia: patterns in space and inferences in time

Abstract A regional vegetation survey of the temperate grassy woodlands (temperate savanna) in Australia was designed to assess the effects of clearing and grazing on the composition of vegetation remnants and the adjacent pasture matrix. Vegetation was sampled across a range of habitats using 77 0.1024-ha quadrats; the relative abundance of species was recorded. Classification analysis clustered the sites into three main groups that corresponded to intensity of grazing/clearing followed by groups based on underlying lithology (basalt, metasediment, granites). Using Canonical Correspondence Analysis, exogenous disturbance and environmental variables were related to the relative abundance of species; grazing intensity had the highest eigenvalue (0.27) followed by tree canopy cover (0.25), lithology (0.18), altitude (0.17) and slope (0.10). Based on two-dimensional ordination scores, six species response groups were defined relating to intensity of pastoralism and nutrient status of the landscape. Abundance and dominance of native shrubs, sub-shrubs, twiners and geophytes were strongly associated with areas of less-intense pastoralism on low-nutrient soils. The strongest effects on species richness were grazing followed by canopy cover. Continuously grazed sites had lower native species richness across all growth forms except native grasses. There was no indication that intermediate grazing intensities enhanced forb richness as a result of competitive release. Species richness for all native plants was lowest where trees were absent especially under grazed conditions. Canopy cover in ungrazed sites appeared to promote the co-existence of shrubs with the herbaceous layer. Predicted declines in forb richness in treeless, ungrazed, sites were not detected. The lack of a disturbance-mediated enhancement of the herbaceous layer was attributed to habitat heterogeneity at 0.1 ha sampling scale. Nomenclature: Harden 1990–1993.
Screening Effect Diverts the Swimming Directions from Diaphototactic to Positive Phototactic in a Disk-shaped Green Flagellate Mesostigma viride¶

Abstract We found diaphototactic behavior (i.e. the cells swim perpendicularly with respect to the incident light) in a strain with colorless eyespot of a unicellular disk-shaped green flagellate Mesostigma viride. Lacking pigments completely in the eyespot, the screening effect in this strain was due only to the central part of the chloroplast whose cross section was thin. The diaphototaxis was most obvious when unilateral green stimulus light (520–580 nm) was given, whereas positive phototaxis appeared when given blue light (430–490 nm). The choice between diaphototaxis and (ordinary) phototaxis depended entirely on the transmission (%T) of the cell body against each wavelength of the stimulus: the green light penetrated well (%T > 90%), whereas the blue light was considerably shaded by the chloroplast (50% < %T < 70%). The fraction of positive phototactically behaving cells against each wavelength was in proportion to the front-to-back contrast value obtained at each individual wavelength. The fraction of diaphototaxis was inversely proportional to it. In addition, bilateral stimulus irradiations to wild-type cell with colored eyespot provided useful information about the principle of the diaphototactic steering.
The PEASS Toolkit - Perceptual Evaluation methods for Audio Source Separation

We present the PEASS Toolkit designed for the perceptual evaluation of audio source separation. It includes a MUSHRA-based listening-test protocol adapted for the subjective evaluation of audio source separation; a set of subjective measures - sounds and subjective scores - obtained by applying the proposed test protocol; and a set of auditory-motivated objective measures based on a new algorithm to decompose the estimation error into some distortion components (target distortion, interference, artefacts) and on integrating the outputs of the auditory-based objective measure PEMO-Q. This presentation will be the opportunity to detail the recent release of the PEASS toolkit, as well as its use in the Signal Separation Evaluation Campaign (SiSEC) in 2010.
Declining Mortality in American Crow (Corvus brachyrhynchos) Following Natural West Nile Virus Infection

Important Findings Researchers developed a model to estimate the annual West Nile virus (WNV)-associated mortality rates among American (Corvus brachyrhynchos) and fish crows (Corvus ossifragus). The model supports the hypothesis that the WNV-associated mortality rate declined by 1.5% annually for the American crow and 1.1% for the fish crow. The probability that the trend in mortality was negative was 90% for the American crow and 60% for the fish crow. The American crow is known to suffer 100% mortality from infection with the New York 1999 strain of WNV. Following the initial detection of WNV in North America in 1999, researchers measured prevalence of WNV-reactive antibodies (‘‘seroprevalence’’) in free-ranging American and fish crows of central New Jersey after each transmission season through 2005. In 2002, seroprevalence increased to 14% from 5% of the previous year in American crow juveniles potentially indicating increased survival in this species.
ALLOMETRY OF MALE GENITALIA IN A SPECIES OF SOLDIER BEETLE: SUPPORT FOR THE ONE-SIZE-FITS-ALL HYPOTHESIS

Hypotheses about the functions of the male genitalia and the male scape in insects were tested by measuring the slopes of allometric relations in six populations of Chauliognathus scutellaris. All allometric relations used elytron length as the indicator of overall body size. Male genitalia have lower slopes than male pronota (a structure not involved in reproduction), male scapes (secondary sexual characters) have higher slopes than male pronota, and female scapes have slopes that are not different from the slopes of female pronota. These results support Eberhard’s onesize-fits-all hypothesis regarding the size of male genitalia in insects, and they raise questions about the role of the male scape in reproductive activities.