Associative symmetry and stimulus-class formation by pigeons: The role of non-reinforced baseline relations

Two experiments tested the assumption of Urcuioli's (2008) theory of pigeons’ equivalence-class formation that consistent non-reinforcement of certain stimulus combinations in successive matching juxtaposed with consistent reinforcement of other combinations generates stimulus classes containing the elements of the reinforced combinations. In Experiment 1, pigeons were concurrently trained on symbolic (AB) and two identity (AA and BB) successive tasks in which half of all identity trials ended in non-reinforcement but all AB trials were reinforced, contingent upon either responding or not responding to the comparisons. Subsequent symmetry (BA) probe trials showed evidence of symmetry in one of four pigeons. In Experiment 2, pigeons learned three pair-comparison tasks in which left versus right spatial choices were reinforced after the various sample-comparison combinations comprising AB, AA, and BB conditional discriminations. Non-differentially reinforced BA probe trials following acquisition showed some indication of symmetrical choice responding. The overall results contradict the theoretical predictions derived from Urcuioli (2008) and those from Experiment 2 challenge other stimulus-class analyses as well.     

Species composition and distribution of free-living marine nematodes in Vostok Bay, Sea of Japan

The qualitative and quantitative composition of free-living marine nematodes have been studied in Vostok Bay (Peter the Great Bay, Sea of Japan). It is found that the population density of nematodes in the bottom sediments of Vostok Bay shows an uneven distribution. The mean population density equaled 56800 ± 23400 specimens/m². A correlation has been revealed between the population density of nematodes and the substrate type. Altogether, 85 species of nematodes have been found; they were dominated by Sabatieria palmaris, Rhabdodemania orientalis, Araeolaimus parvibulbosus, Oncholaimium paraolium, Doryolaimopsis peculiaris, and Metachromadora itoi. Six taxocenoses of nematodes were distinguished, taking into account the species dominating in the population density and using cluster analysis of the obtained data. The dominating trophic assemblage of nematodes was “scrapers.” In general, the species composition of nematodes in Vostok Bay is characterized by the relatively great similarity with that in other areas of Peter the Great Bay (Sea of Japan).     

Modelling seasonal increments in size to determine the onset of annual growth in fishes

A new method based on modelling of seasonal growth increments ( G _SI) in total length was found useful for assessing the date of onset of annual growth for 16 fish species in a temperate fluvial lake. Model comparisons indicated that polynomial (linear or quadratic) functions provided better fits to seasonal growth and were more likely to avoid convergence problems than alternative non-linear models. There was little evidence for differences in the date of onset of growth between years, nor among age classes within individual species. The onset of growth also was to some extent synchronized among species and was concentrated within a narrow temporal window of c. 2 weeks, between 18 May and 2 June, which corresponded to mean water temperatures between 16·1 and 17·3° C. There was no apparent relationship between date of onset and species' thermal preferenda or thermal preferences. By producing a point estimate along with appropriate 95% CI, the G _SI method provides useful information on the onset of growth and the uncertainty about that estimate. The G _SI analyses can contribute to a better understanding of environmental influences on the onset of growth and the length of the growing season, and of thermal thresholds for growth, including their use in calculation of degree-day metrics.     

Predicting protein structural class based on multi-features fusion

Structural class characterizes the overall folding type of a protein or its domain and the prediction of protein structural class has become both an important and a challenging topic in protein science. Moreover, the prediction itself can stimulate the development of novel predictors that may be straightforwardly applied to many other relational areas. In this paper, 10 frequently used sequence-derived structural and physicochemical features, which can be easily computed by the PROFEAT (Protein Features) web server, were taken as inputs of support vector machines to develop statistical learning models for predicting the protein structural class. More importantly, a strategy of merging different features, called best-first search, was developed. It was shown through the rigorous jackknife cross-validation test that the success rates by our method were significantly improved. We anticipate that the present method may also have important impacts on boosting the predictive accuracies for a series of other protein attributes, such as subcellular localization, membrane types, enzyme family and subfamily classes, among many others.     

MOLTING PHENOLOGY OF HARBOR SEALS ON TUGIDAK ISLAND, ALASKA

We documented the progression and timing of the annual molt of harbor seals on Tugidak Island, Alaska, from 1997 to 1999. In all years the timing of molting differed among age-sex classes. Yearlings molted first, subadults second, adult females third, and lastly adult males. Timing of molting was nearly identical in 1997–1998, whereas in 1999 molting occurred three to six days later for all age-sex classes except yearlings. Estimated dates when peak proportions of each age-sex class were molting ranged from 2 August (yearlings) to 2 September (adult males). The number of seals hauled out was positively related to the proportion of seals in the molt and negatively related to the proportion of seals in the postmolt. Population trend estimates, based on aerial counts conducted during a narrow window within the molting period, are likely biased toward certain age-sex classes. Statistical models used to estimate trend include covariates to help account for within-year variation in seal numbers, but do not account for compositional changes that occur during molting. Population modeling may elucidate the effects of within-year population structure on trend estimates. Monitoring molting phenology at additional sites is necessary to determine the extent of geographic variation in molting.     

Macaca thibetana at Mt. Emei,China: III. Group composition

Data on group composition at the end of the 1986 birth season were collected from six groups of Macaca thibetana. All adult males, the members of group A, and some conspicuous animals were recognized individually. Fourhundred survey sessions were completed. The mean group size was 38.3 (SD = 13.8, range: 28–65); the number of adult females was the best correlate of total group size. The mean adult sex ratio (F:M) across groups was 3:1 (SD = 1.9, range: 1.5–6.5:1), which significantly deviated from 1:1. Sex ratios (F:M) in newborns, juveniles, and all members did not significantly deviate from 1. The ratio of immature animals to adults was 1.5 to 1 (average of groups); that is, 60% of the population was composed of immature animals, and the population was growing.     

Controlling infestations of Parkinsonia aculeata in a riparian zone at the landscape scale

Abstract To prioritize weed management activities it is necessary to predict the extent of future infestations of individual weed species. Management effort should focus on populations which are likely to spread and produce new satellite populations. Deciding which aspects of an invading population to manage, new emerging distant satellites or the existing core from which most seed originates has been the subject of much debate. We use extensive survey data to define the core and satellite populations and dispersal function of Parkinsonia aculeata in the semi‐arid rangelands of the Northern Territory of Australia. We described populations in terms of three size classes, classified on the basis of plant height (small (<0.4 m), medium (>0.4 and <2.5 m) and large (>2.5 m)). Data were recorded as a spatial point pattern and a dispersal function was derived from the distribution of the distance of each medium plant to the nearest P. aculeata neighbour that was greater than 2.5 m. All large and medium P. aculeata were classified as members of core or satellite populations. From these classifications, we tested critical assumptions of Moody and Mack's model, namely (i) the satellites form multiple disjunct foci that do not overlap; (ii) the system is homogenous and there are no abiotic or biotic restrictions to the weeds expansion enabling it to expand radially in any direction; (iii) the densities of all foci are uniform; (iv) there is no extinction through stochastic processes; and (v) there are no threshold effects. When the medium size class was considered, the population density and area occupied by the weed increased. Two satellite populations were comprised solely of medium plants, suggesting the number of satellites increased marginally from eight to 10 when data from both size classes were considered. Most individuals were part of the core population. The core population increased in density and we argue this core population is most likely to give rise to new satellites and should be managed in preference to emerging satellite populations. We suggest the invasion is behaving like a source‐sink system, where the core population is the source of most new medium plants.     

Ecological and genetic data indicate recovery of the endangered coral Acropora palmata in Los Roques, Southern Caribbean

The rapid decline of Acropora cervicornis and Acropora palmata has often been linked with coral reef deterioration in the Caribbean; yet, it remains controversial whether these species are currently recovering or still declining. In this study, the status of ten populations of A. palmata in Los Roques National Park (LRNP), Venezuela is presented. Six of these populations showed signs of recovery. Ten 80 m² belt-transects were surveyed at each of the ten reef sites. Within belt-transects, each colony was measured (maximum diameter and height) and its status (healthy, diseased or injured) was recorded. Populations in recovery were defined by a dominance of small to medium-sized colonies in densities >1 colony per 10 m², together with 75% undamaged colonies, a low prevalence of diseases (<10%), and a low density of predators (0.25 snails per colony). Based on allozyme analysis of seven polymorphic loci in four populations (N = 30), a moderate to high-genetic connectivity among these populations (F _ST = 0.048) was found with a predominance of sexual over asexual reproduction (N* : N = 1; N _go : N = 0.93–1). Both ecological and molecular data support a good prognosis for the recovery of this species in Los Roques.     

Skeletal and dental growth and development in chimpanzees of the Taï National Park, Côte D'Ivoire

An extraordinary collection of 22 immature skeletons from Taï National Park, Côte d'Ivoire, has provided a rare opportunity to establish the timing of dental eruption and its correlation with skeletal fusion and morphometrics in wild chimpanzees of known chronological ages. Comparison of the immature Taï chimpanzees Pan troglodytes verus with adults from the same population show that sex differences in skeletal maturation apparently appear during the Juvenile II stage, about age 8. A few skeletons from other chimpanzee field sites conform to the dental and skeletal growth in Taï chimpanzees. The tempo of wild chimpanzee growth contrasts sharply with the rate demonstrated for captive individuals. Captive chimpanzees may mature as much as 3 years earlier. The ability to link physical development with field observations of immature chimpanzees increases our understanding of their life-history stages. These data provide an improved dataset for comparing the rates of growth among chimpanzees, Homo sapiens and fossil hominids.     

Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction.

Loops are regions of nonrepetitive conformation connecting regular secondary structures. We identified 2,024 loops of one to eight residues in length, with acceptable main-chain bond lengths and peptide bond angles, from a database of 223 protein and protein-domain structures. Each loop is characterized by its sequence, main-chain conformation, and relative disposition of its bounding secondary structures as described by the separation between the tips of their axes and the angle between them. Loops, grouped according to their length and type of their bounding secondary structures, were superposed and clustered into 161 conformational classes, corresponding to 63% of all loops. Of these, 109 (51% of the loops) were populated by at least four nonhomologous loops or four loops sharing a low sequence identity. Another 52 classes, including 12% of the loops, were populated by at least three loops of low sequence similarity from three or fewer nonhomologous groups. Loop class suprafamilies resulting from variations in the termini of secondary structures are discussed in this article. Most previously described loop conformations were found among the classes. New classes included a 2:4 type IV hairpin, a helix-capping loop, and a loop that mediates dinucleotide-binding. The relative disposition of bounding secondary structures varies among loop classes, with some classes such as beta-hairpins being very restrictive. For each class, sequence preferences as key residues were identified; those most frequently at these conserved positions than in proteins were Gly, Asp, Pro, Phe, and Cys. Most of these residues are involved in stabilizing loop conformation, often through a positive phi conformation or secondary structure capping. Identification of helix-capping residues and beta-breakers among the highly conserved positions supported our decision to group loops according to their bounding secondary structures. Several of the identified loop classes were associated with specific functions, and all of the member loops had the same function; key residues were conserved for this purpose, as is the case for the parvalbumin-like calcium-binding loops. A significant number, but not all, of the member loops of other loop classes had the same function, as is the case for the helix-turn-helix DNA-binding loops. This article provides a systematic and coherent conformational classification of loops, covering a broad range of lengths and all four combinations of bounding secondary structure types, and supplies a useful basis for modelling of loop conformations where the bounding secondary structures are known or reliably predicted.