Temporal Ordering and the Chouteau Aspect

Abstract

Temporal ordering of closely-related sites in the Oahe, Big Bend and Fort Randall Reservoirs of South Dakota may be accomplished by a simple seriation of selected traits common to, and diagnostic of, the related sites. The resultant ordering is best interpreted as three “blocks” of time within a temporal unit. The chronology inferred from the ordering reinforces the present known dates of the Chouteau Aspect as well as sites culturally and temporally marginal to the Chouteau Aspect.     

A Factor Analytic Approach to Seriation

Abstract

Seriation, a unidimensional ordering technique, is one of archaeology’s oldest and most useful tools. Its mathematical aspects have drawn the attention of mathematicians and statisticians in recent years, even as archaeologists themselves have begun to question its underlying assumptions. In this paper I describe some techniques appropriate at each step in the mathematical seriation problem: discovering trendsensitive variables and ordering items on the basis of these variables.     

A seriation approach for visualization-driven discovery of co-expression patterns in Serial Analysis of Gene Expression (SAGE) data

Background

Serial Analysis of Gene Expression (SAGE) is a DNA sequencing-based method for large-scale gene expression profiling that provides an alternative to microarray analysis. Most analyses of SAGE data aimed at identifying co-expressed genes have been accomplished using various versions of clustering approaches that often result in a number of false positives.

Principal Findings

Here we explore the use of seriation, a statistical approach for ordering sets of objects based on their similarity, for large-scale expression pattern discovery in SAGE data. For this specific task we implement a seriation heuristic we term ‘progressive construction of contigs’ that constructs local chains of related elements by sequentially rearranging margins of the correlation matrix. We apply the heuristic to the analysis of simulated and experimental SAGE data and compare our results to those obtained with a clustering algorithm developed specifically for SAGE data. We show using simulations that the performance of seriation compares favorably to that of the clustering algorithm on noisy SAGE data.

Conclusions

We explore the use of a seriation approach for visualization-based pattern discovery in SAGE data. Using both simulations and experimental data, we demonstrate that seriation is able to identify groups of co-expressed genes more accurately than a clustering algorithm developed specifically for SAGE data. Our results suggest that seriation is a useful method for the analysis of gene expression data whose applicability should be further pursued.     

The interplay between chromosome stability and cell cycle control explored through gene–gene interaction and computational simulation

Chromosome stability models are usually qualitative models derived from molecular-genetic mechanisms for DNA repair, DNA synthesis, and cell division. While qualitative models are informative, they are also challenging to reformulate as precise quantitative models. In this report we explore how (A) laboratory experiments, (B) quantitative simulation, and (C) seriation algorithms can inform models of chromosome stability. Laboratory experiments were used to identify 19 genes that when over-expressed cause chromosome instability in the yeast Saccharomyces cerevisiae. To better understand the molecular mechanisms by which these genes act, we explored their genetic interactions with 18 deletion mutations known to cause chromosome instability. Quantitative simulations based on a mathematical model of the cell cycle were used to predict the consequences of several genetic interactions. These simulations lead us to suspect that the chromosome instability genes cause cell-cycle perturbations. Cell-cycle involvement was confirmed using a seriation algorithm, which was used to analyze the genetic interaction matrix to reveal an underlying cyclical pattern. The seriation algorithm searched over 10¹⁴ possible arrangements of rows and columns to find one optimal arrangement, which correctly reflects events during cell cycle phases. To conclude, we illustrate how the molecular mechanisms behind these cell cycle events are consistent with established molecular interaction maps.     

Nest-site selection of the Long-eared Owl Asio otus in northwestern Switzerland

Capsules Sites are selected as part of an antipredator strategy.

Aims To assess if site choice depends on habitat variables at nest sites and if habitat quality influences reproduction.

Methods Breeding density was explored in northwestern Switzerland from 1992 to 1996. Habitat variables were examined at 38 breeding sites and were compared with data collected from random sites. Habitat quality was estimated using the discriminant function scores of the nesting sites.

Results Breeding density was found to vary between years; more pairs bred and raised more young in 1993, a year of high vole abundance. Long-eared Owls tended to avoid the vicinity of buildings; they occupied sites with denser forest edges, greater canopy cover, and with more conifers than random sites. I found no statistical evidence that they used less optimal sites when the population was high. The number of fledglings increased with habitat quality, but did not vary with any of the habitat variables taken separately.

Conclusion Long-eared Owl selects nesting habitat as part of an anti-predator strategy, but the measures of territory quality did not seem to be a limiting factor for the population.     

Selection of foraging habitat and nestling diet by Meadow Pipits Anthus pratensis breeding on intensively grazed moorland

Capsule Foraging sites with low vegetation height and density, but with high arthropod biomass, are selected.

Aims To test the hypothesis that on intensively grazed moorland, breeding Meadow Pipits forage for nestling food where arthropod prey are most readily available, and therefore that foraging site choice is a function of prey abundance and vegetation structure.

Methods Observations of adults provisioning nestlings were made from hides positioned close to 19 nests within grazed, 3.3-hectare experimental plots at Glen Finglas, Scotland. Vegetation height and density and arthropod abundance from mapped foraging sites were compared with control sites. Prey items fed to nestlings were quantified and compared with their relative abundance.

Results Meadow Pipits selected foraging sites with significantly lower vegetation height and density, but with significantly higher arthropod biomass. Our data suggest that within foraging sites, Meadow Pipits select particular prey types to provision nestlings, in particular, Lepidoptera larvae, adult Tipulidae and Arachnida.

Conclusions In intensively grazed upland systems, it appears that Meadow Pipits select foraging sites that optimize total food abundance and accessibility. In order to understand how anticipated changes to livestock farming in Europe will affect grassland birds, we recommend that future studies should investigate the foraging and vigilance behaviour, diet composition and breeding success of a variety of bird species provisioning nestlings under a range of livestock management scenarios.     

Behavioural responses of non-breeding waterbirds to drone approach are associated with flock size and habitat

ABSTRACT

Capsule: Non-breeding waterbirds are more likely to respond to drone approach when in larger flocks, and responses are more likely in arable and coastal habitats than at inland lochs.

Aims: To investigate the extent to which drones are a potential source of disturbance to non-breeding waterbirds.

Methods: Using a commercially available quadcopter drone, we approached waterbird flocks of varying sizes in coastal, freshwater, and arable habitats following a standardized protocol.

Results: Waterbirds at coastal sites and in arable fields were more likely to respond to drone approach than those at inland freshwater bodies. Larger flocks were more likely to respond to drone approach and responded at a greater distance than smaller flocks.

Conclusion: Repeated drone use at coastal and arable sites with large aggregations of feeding or roosting waterbirds could cause energetically costly flight responses, increased stress, and effective loss of available habitat. At such sites, it may be beneficial to regulate recreational and commercial drone use to minimize potential disturbance effects.     

Composition and community structure of the coralline algal reefs from Atol das Rocas, South Atlantic, Brazil

 Coralline-algal frameworks from Atol das Rocas reefs were sampled along windward and leeward transects, and multivariate statistical analysis was used to investigate the composition and community structure of the encrusting community. The following components of the reefs were identified in slabbed and polished reef blocks sampled along each transect: encrusting coralline algae dominated by Porolithon cf. pachydermum, vermetid gastropods, Homotrema rubrum, acervulinid foraminiferans, molluscs, corals, polychaete tubes, clionid sponge borings, polychaete/sipunculid borings, cemented sediments, and growth cavities. Q-mode cluster analysis correctly classified 78% of all windward samples and 69% of all leeward samples, and R-mode separated reef components adapted to high wave energy environments from those adapted to low wave energy. Separate classification and ordination of samples from each transect indicate that seriation breakdown occurs in the windward reef between 25 and 45 m from the reef front. In the leeward reef between 75 and 90 m from the leeward reef front, seriation breakdown was not found to be significant. These results confirm that seriation (zonation) is best developed in the windward reef, as has been documented in coral-dominated reefs. Accepted: 28 February 2000     

Nest and foraging‐site selection in Yellowhammers Emberiza citrinella: implications for chick provisioning

Capsule Vegetation structure and invertebrate abundance interact to influence both foraging sites and nestling provisioning rate; when invertebrate availability is low, adults may take greater risks to provide food for their young.

Aims To investigate nesting and foraging ecology in a declining farmland bird whose fledging success is influenced by the availability of invertebrate prey suitable for feeding to offspring, and where perceived predation risk during foraging can be mediated by vegetation structure.

Methods Provisioning rates of adult Yellowhammers feeding nestlings were measured at nests on arable farmland. Foraging sites were compared with control sites of both the same and different microhabitats; provisioning rate was related to habitat features of foraging‐sites.

Results Foraging sites had low vegetation density, probably enhancing detection of predators, or high invertebrate abundance at high vegetation density. Parental provisioning rate decreased with increasing vegetation cover at foraging sites with high invertebrate abundance; conversely, where invertebrate abundance was low, provisioning rate increased with increasing vegetation cover.

Conclusions Vegetation structure at foraging sites suggests that a trade‐off between predator detection and prey availability influences foraging site selection in Yellowhammers. Associations between parental provisioning rate and vegetation variables suggest that where invertebrate abundance is high birds increase time spent scanning for predators at higher vegetation densities; however, when prey are scarce, adults may take more risks to provide food for their young.     

Quantifying temporal variation in heterobranch (Mollusca: Gastropoda) sea slug assemblages: tests of alternate models

Assemblages of heterobranch sea slugs are notoriously variable in space and time which has sometimes led to their exclusion from broader studies of patterns of biodiversity. This variability may also result in a failure to detect underlying spatial and temporal patterns. Assemblage data (species abundances) from three intertidal sites over a period of 13 months, were used to compare the conclusions drawn from three different analytical approaches—a non-specific test for differences among months, and tests of cyclicity, and seriation, using specific model matrices. While no significant difference was detected for the non-specific test (i.e. concluding no significant temporal variation), the data were significantly correlated to both model matrices with the cyclicity model outperforming the seriation model at two of the three sites. The study also highlighted the spatial variability of assemblages over a scale of just a few kilometres. Wider testing using previously published datasets confirmed the utility of these models for exploring specific hypotheses about patterns of temporal change.     

Actin exposure upon tissue injury is a targetable wound site-specific protein marker

BackgroundIdentification of wound-specific markers would represent an important step toward damaged tissue detection and targeted delivery of biologically important materials to injured sites. Such delivery could minimize the amount of therapeutic materials that must be administered and limit potential collateral damage on nearby normal tissues. Yet, biological markers that are specific for injured tissue sites remain elusive.MethodsIn this study, we have developed an immunohistological approach for identification of protein epitopes specifically exposed in wounded tissue sites.ResultsUsing ex-vivo tissue samples in combination with fluorescently-labeled antibodies we show that actin, an intracellular cytoskeletal protein, is specifically exposed upon injury. The targetability of actin in injured sites has been demonstrated in vivo through the specific delivery of anti-actin conjugated particles to the wounded tissue in a lethal rat model of grade IV liver injury.ConclusionsThese results illustrate that identification of injury-specific protein markers and their targetability for specific delivery is feasible.General significanceIdentification of wound-specific targets has important medical applications as it could enable specific delivery of various products, such as expression vectors, therapeutic drugs, hemostatic materials, tissue healing, or scar prevention agents, to internal sites of penetrating or surgical wounds regardless of origin, geometry or location.     

Bioacoustic variation in Wren Troglodytes troglodytes populations on Welsh islands

ABSTRACT

Capsule: Duration and peak frequency of Wren Troglodytes troglodytes songs differ between Welsh islands (Skokholm, Flat Holm, and Sully Island) and a mainland site, suggesting random or cultural divergence.

Aims: The study tests for differences in bioacoustic traits in Wren song between four breeding sites.

Methods: Songs from breeding male Wrens were recorded from three Welsh islands and a representative location on the local mainland. Each sonogram was measured for six variables from the whole song and two distinct phrases from the beginning and middle. The variables were measured manually using an open source acoustic tool and compared between sites using generalized linear mixed-effects models.

Results: There was significant variation in song variables between island sites and the mainland. Skokholm Wren songs were significantly longer in duration than all other sites by up to 66%. Peak frequency was significantly different across all sites with Sully Island having the highest peak frequency and Skokholm the lowest.

Conclusion: The differences in song duration and frequency do not directly suggest a trend associated with selective pressures such as habitat or noise, but instead may be explained by non-selective drivers such as cultural drift or local dialect formation.     

Offshore refuges support higher densities and show slower population declines of wintering Ruddy Turnstones Arenaria interpres

ABSTRACT

Capsule: Wintering Ruddy Turnstones Arenaria interpres occur in higher densities and their populations decline less on, or close to, offshore refuges than on mainland sites subject to greater levels of human disturbance.

Aim: To compare wintering densities of Ruddy Turnstones and changes in counts across time from sites with differing levels of human disturbance.

Methods: Long-term counts of Ruddy Turnstones (1998/1999 to 2015/2016) were used from 19 sites (two offshore refuges and 17 mainland sites subject to higher levels of human disturbance) in northeast England. No direct measure of human disturbance was available for our mainland sites; instead we used questionnaires (n?=?690) to understand how far people travelled to visit the coast and then used this distance with human population densities in a buffer around each site as a proxy for human disturbance levels.

Results: After controlling for the extent of their preferred habitat at each site (rocky shore) we found: (i) the closer each of the 19 sites was to the nearest offshore refuge the higher the density of Ruddy Turnstones and (ii) bird counts were stable at the two refuge sites, whereas, on average, counts declined at the 17 mainland sites. However, no relationship was found between Ruddy Turnstone counts from 17 mainland sites and human population densities within differing distances from each site (up to 10?km).

Conclusions: Our work suggests that Ruddy Turnstones made greater use of relatively undisturbed areas (offshore refuges) than those subject to greater disturbance by humans (mainland sites). Although the use of refuges and mainland in our study area was not well known, observations from 11 radio-tagged Ruddy Turnstones suggest that individual birds did use both locations. In a broader context, our work concurs with other studies that highlight the need for refuges with limited or no human access.     

An Analysis Of Four Survey Collections From Armstrong County,South Dakota 39Ar2 (No Heart Creek Site), 39Ar4, 39Ar5 And 39Ar 7

Abstract

The materials collected from four sites on the Little Bend of the Missouri River are described and analyzed. In the conclusion, these manifestations, referred to as the No Heart Creek complex, are compared to seven other sites along the river in north.-central South Dakota. The sites are related to the Le Compte Focus and are characterized by a distinetive settlement pattern.     

Nesting habitat overlap between the Common Buzzard Buteo buteo and the Lesser Spotted Eagle Clanga pomarina for conservation planning in Natura 2000 sites

Capsule: The nesting habitat of the Common Buzzard Buteo buteo and Lesser Spotted Eagle Clanga pomarina extensively overlap, indicating that they exploit similar resources.

Aim: We aimed to determine the overlap in the nest platforms, nest trees and nest stands used by these raptors, find any evidence for the avoidance of the larger Lesser Spotted Eagle by the smaller Common Buzzard, and provide conservation implications for habitat protection of the former species in habitats that overlap extensively.

Methods: Nest sites were mapped during 2012–2014 in the Bir?ai Forest Spatial Protection Area, northern Lithuania. Fifty-three nest sites occupied by Common Buzzards and 26 by Lesser Spotted Eagles were compared.

Results: The nest platforms of both raptors were similarly placed in the tree canopies. Most Lesser Spotted Eagle nests were built in spruce, while the Common Buzzard usually nested in birch. The nest stands of the eagles were on wetter soil and located closer to the forest edge than those of the buzzards, otherwise, the nest stands did not differ significantly. There was no evidence for spatial avoidance of the larger raptor by the Common Buzzard.

Conclusions: The different components of the nesting habitats extensively overlapped, and the distribution of the interspecific pairs lacked spatial avoidance. We suggest that the nest sites of both raptors were a largely shared resource, especially if located close to the forest edges. We propose, as a rule of thumb, applying protection by way of buffer zones around buzzard nest sites if they are located close to eagle nest sites and the forest edge.     

基于荧光染料Cy5.5标记的引物延伸法鉴定细菌RNA剪切加工位点

【背景】传统引物延伸法常与放射性标记结合使用,但由于放射性元素半衰期短、危害人体健康及严格的操作要求等限制了其在一般实验室的广泛使用。因此,开发新型非放射性引物延伸法成为当前研究的热点。【目的】建立非放射性的引物延伸法,并利用该方法实现对细菌RNA剪切加工位点的鉴定。【方法】将包含RNA剪切位点的序列克隆至双荧光报告系统,然后利用荧光染料Cy5.5标记的特异性靶向mcherry寡核苷酸引物进行延伸,并辅以Northern blotting、RT-qPCR等技术,确定RNA剪切加工的精确位点。【结果】鉴定了来自解纤维梭菌cip-cel mRNA中的2个剪切加工位点均位于颈环结构下游的单链区域,且在剪切位点附近未发现保守序列。【结论】基于Cy5.5标记的引物延伸法能够精确鉴定RNA剪切加工位点,且与传统的放射性引物延伸法相比,该方法具有更高的安全性和更快的检测速度,能够满足一般实验室的实验要求。     

Characteristics of 3H-Tifluadom Binding in Guinea-Pig Brain Membranes

Abstract

³H-Tifluadom labels specifically recognition sites of opioid kappa receptors. Membranes of guinea-pig whole brain bind ³H-tifluadom with two affinities, in contrast to the cerebellum where almost all opioid sites are kappa.     

Nest-site selection and predation in Savi's Warblers Locustella luscinioides

Capsule Savi's Warblers preferred sites dominated by high and dense Juncus and Rubus with thick litter, and avoided pure reeds; predation was higher in sites with less litter.

Aim To describe nest-site selection and identify which habitat and nest features influence predation risk.

Methods Comparisons were made between habitat characteristics measured at nest-sites and random points, and between predated and successful nests.

Results Total vegetation cover, litter thickness, habitat type, undergrowth height and undergrowth cover, which were higher or denser at nest-sites, were the most important variables influencing the distribution of Savi's Warbler nests. Nests were most often predated in sites with low litter thickness.

Conclusion Savi's Warblers are dependent on the presence of dense low vegetation and litter for nesting, which should be maintained close to or within reed-beds for their benefit.     

Burned Rock Midden Sites on the Southwestern Edge of the Edwards Plateau,Texas

Abstract

Data from two groups of burned rock midden sites are presented. Occupation of the sites seems to have been heaviest during Archaic times, with some Late Prehistoric and possible Paleo-Indian components also recognized. A burial is described from one site. Problems pertaining to burned rock midden sites are briefly discussed.