Leaving on migration: estimating departure dates of Barn Swallows Hirundo rustica from summer roosts using a capture–mark–recapture approach

Capsule Capture–mark–recapture data can be used to predict departure dates of Barn Swallows Hirundo rustica from summer roosts.

Aims To investigate how long Barn Swallows remain at their breeding grounds before migration by estimating departure dates.

Methods A capture–mark–recapture approach was applied to an extensive data set (65?303 ringed and 710 recaptured birds) from two summer roosts. Multiple-day constancy models were used to estimate apparent survival, which was subsequently translated to residence time.

Results The longest intervals between ringing and recapturing were between 66 and 67 days; estimated mean minimum durations were between 16.3 and 18.5 days. Apparent survival was high over most of the summer, indicating that there is little emigration during this period and was followed by a sharp departure-related decline in late August and September. Expected residence time, derived from apparent survival estimates, declined linearly from about 80 days in early July to less than 10 days in September. Estimated departure dates were highly consistent between years and occurred in late September.

Conclusions Barn Swallows stay much longer at post-breeding roost sites than is necessary to build up their fat reserves for migration. We suggest that the birds are likely to derive a number of benefits from such a prolonged stay that are not directly related to preparation for migration; for example, minimizing predation risk by foraging in familiar areas, and gathering information on the quality of future breeding sites.     

Improved frequency resolution in multidimensional constant-time experiments by multidimensional Bayesian analysis

Summary The resolution of spectral frequencies in NMR data obtained from discrete Fourier transformation (DFT) along D constant-time dimensions can be improved significantly through extrapolation of the D-dimensional free induction decay (FID) by multidimensional Bayesian analysis. Starting from Bayesian probability theory for parameter estimation and model detection of one-dimensional time-domain data [Bretthorst, (1990) J. Magn. Reson., 88, 533–551; 552–570; 571–595], a theory for the D-dimensional case has been developed and implemented in an algorithm called BAMBAM (BAyesian Model Building Algorithm in Multidimensions). BAMBAM finds the most probable sinusoidal model to account for the systematic portion of any D-dimensional stationary FID. According to the parameters estimated by the algorithm, the FID is extrapolated in D dimensions prior to apodization and Fourier transformation. Multidimensional Bayesian analysis allows for the detection of signals not resolved by the DFT alone or even by sequential one-dimensional extrapolation from mirror-image linear prediction prior to the DFT. The procedure has been tested with a theoretical two-dimensional dataset and with four-dimensional HN(CO)CAHA (Kay et al. (1992) J. Magn. Reson., 98, 443–450) data from a small protein (8 kDa) where BAMBAM was applied to the ¹³C and H constant-time dimensions.To whom correspondence should be addressed.     

Evolution of structure and information processing in the nervous system: Part IV of a general theory

Starting from fundamental principles, evolution of the nervous system is modelled as a random walk process in a multidimensional representation space (the F-space). This space is not flat, it is highly structured in terms of step probability. Fundamental considerations of evolutionary speed, efficiency of information processing, and priorities lead to specific theoretical predictions of the most probable pathways of evolution of the nervous system and its mechanisms of information processing. These processes are represented as vector paths (F-paths) in the F-space. Cognition becomes a process of correlations of the input signal to information stored in memories. Higher level brain processes involve extrapolation and interpolation along F-paths, input data reduction by clearly specifiable abstraction methods, and a unique process using abstracted analogs. These processes define and limit what the brain does and how it can do it. These considerations lead to certain inevitable conclusions (consequences of the fundamental principles) for the basis of our logical reasoning, decision-making, the process of dreaming (conscious and sleep), and explicit definitions of consciousness, unconsciousness, and personality. Detailed applications of this theory for analyzing empirical findings are suggested in the final paragraphs.     

Willow Warbler Phylloscopus trochilus habitat in woods with different structure and management in southern England

Capsule Use of Light Detection and Ranging (LiDAR) data identified suitable Willow Warbler habitat based on mean vegetation height. This habitat model provided maps of distribution and occupation of suitable habitat.

Aims To identify habitat associations in woods with different vegetation structure and management systems during a period of low Willow Warbler populations.

Methods Locations of all Willow Warblers were mapped during the breeding season in three woods of contrasting management; recent low intervention, actively coppiced woodland and high forest with clear‐fells. Height profile models of each wood were derived from airborne LiDAR. The mean vegetation height at locations with Willow Warblers and a sample from the rest of the wood were used to produce models of optimum habitat and breadth of habitat occupied in each wood. The habitat model was then used to produce maps of suitable habitat.

Results The habitat models did not differ between woods, with highest probability of Willow Warbler occurrence in mean vegetation heights of 3.7–5.3 m. Habitat of heights 6–11 m appeared less suitable, being only partly occupied. Habitat maps showed that habitat of suitable height was only occupied when it occurred as large patches; smaller patches (mostly <0.5 ha) and edges along rides and fields were not used.

Conclusion The use of LiDAR derived measures of vegetation height identified areas of suitable habitat for Willow Warblers. Willow Warblers occupied areas of low mean vegetation height either as early successional or open canopy woodland in all woods. Height‐based habitat maps can identify areas of suitable habitat within larger expanses of heterogeneous woodland and are a potentially useful tool in assessing changes in extent of what are often temporary patches of habitat.     

Comparing fruiting phenology across two historical datasets: Thoreau’s observations and herbarium specimens

Background and AimsFruiting remains under-represented in long-term phenology records, relative to leaf and flower phenology. Herbarium specimens and historical field notes can fill this gap, but selecting and synthesizing these records for modern-day comparison requires an understanding of whether different historical data sources contain similar information, and whether similar, but not equivalent, fruiting metrics are comparable with one another.MethodsFor 67 fleshy-fruited plant species, we compared observations of fruiting phenology made by Henry David Thoreau in Concord, Massachusetts (1850s), with phenology data gathered from herbarium specimens collected across New England (mid-1800s to 2000s). To identify whether fruiting times and the order of fruiting among species are similar between datasets, we compared dates of first, peak and last observed fruiting (recorded by Thoreau), and earliest, mean and latest specimen (collected from herbarium records), as well as fruiting durations.Key ResultsOn average, earliest herbarium specimen dates were earlier than first fruiting dates observed by Thoreau; mean specimen dates were similar to Thoreau’s peak fruiting dates; latest specimen dates were later than Thoreau’s last fruiting dates; and durations of fruiting captured by herbarium specimens were longer than durations of fruiting observed by Thoreau. All metrics of fruiting phenology except duration were significantly, positively correlated within (r: 0.69–0.88) and between (r: 0.59–0.85) datasets.ConclusionsStrong correlations in fruiting phenology between Thoreau’s observations and data from herbaria suggest that field and herbarium methods capture similar broad-scale phenological information, including relative fruiting times among plant species in New England. Differences in the timing of first, last and duration of fruiting suggest that historical datasets collected with different methods, scales and metrics may not be comparable when exact timing is important. Researchers should strongly consider matching methodology when selecting historical records of fruiting phenology for present-day comparisons.     

On The Significance of Additional Radiocarbon Dates from Bonfire Shelter,Texas

Abstract

Two hitherto unreported dates from charcoal samples associated with remains attributed to a Paleo-Indian bison kill at this site are provided. These dates further substantiate a minimal antiquity of ca. 10,000 years for the deposit and, by inference, give evidence of the use of a “bison jump” technique of hunting at this early time period. Definitional problems, differing views on the antiquity, basic comparability of cited examples, and temporal continuity of this mode of mass killing are briefly discussed. Some suggestions are made as to the cultural implications made probable by acceptance of an early date for this practice.     

Computer-aided construction of nucleic acid restriction maps using defined vectors

A new algorithm is described that will rapidly produce restrictionmaps of cloned DNA fragments. Information concerning the vectoris stored as a data file and used in constructing probable maps.As the program is based upon a permutation analysis it has twoprimary uses. First, preliminary restriction maps can be createdfrom fragment length data as a starting point for further analysis.Second, existing maps can be confirmed as being highly probable,and other probable maps examined to ensure certain combinationshave not been overlooked. Although primarily designed for linearvectors, the program can be used to calculate circular maps. Received on June 5, 1985; accepted on September 27, 1985     

Prediction of probable pathways of folding in globular proteins

A method is described for the prediction of probable folding pathways of globular proteins, based on the analysis of distance maps. It is applicable to proteins of unknown spatial structure but known amino acid sequence as well as to proteins of known structure. It is based on an objective procedure for the determination of the boundary of compact regions that contain high densities of interresidue contacts on the distance map of a globular protein. The procedure can be used both with contact maps derived from a known three-dimensional protein structure and with predicted contact maps computed by means of a statistical procedure from the amino acid sequence alone. The computed contact map can also be used to predict the location of compact short-range structures, viz. -helices and -turns, thereby complementing other statistical predictive procedures. The method provides an objective basis for the derivation of a theoretically predicted pathway of protein folding, proposed by us earlier [Tanaka and Scheraga (1977) Macromolecules10, 291–304; Némethy and Scheraga (1979) Proc. Natl. Acad. Sci., U.S.A.76, 6050–6054].     

不同分化程度的原发性肝癌MRI初步临床研究

目的:探讨原发性肝癌不同分化程度、细胞类型的MRI图像特征、参数。方法:回顾性分析肝硬化再生结节27例、肝细胞癌75例81处病灶(高度分化15例,中度分化40例,低度分化26例)、肝内胆管癌20例的病理结果及MRI影像学数据,比较再生结节、肝细胞癌和肝内胆管癌之间,以及肝细胞癌各种组织分化程度之间的ADC值、强化程度差异。结果:常规MRI平扫结合LAVA可准确诊断大部分原发性肝癌病例。再生结节、肝细胞癌及肝内胆管癌ADC值均值的具有显著统计学差异(P0.01);肝细胞癌高分化组、中分化组及低分化组ADC值均值均具有显著统计学差异(P0.01),但中、低分化肝细胞癌ADC值均值的差异无实际临床意义;高分化肝细胞癌与肝内胆管癌ADC值均值的差异无统计学意义(P=0.27)。结论:常规MRI结合DWI、多期动态增强扫描有助于区分原发性肝癌各种组织分化程度及细胞类型。     

Methanogenic degradation kinetics of phenolic compounds in aquifer-derived microcosms

In this segment of a larger multidisciplinary study of the movement and fate of creosote derived compounds in a sand-and-gravel aquifer, we present evidence that the methanogenic degradation of the major biodegradable phenolic compounds and concomitant microbial growth in batch microcosms derived from contaminated aquifer material can be described using Monod kinetics. Substrate depletion and bacterial growth curves were fitted to the Monod equations using nonlinear regression analysis. The method of Marquardt was used for the determination of parameter values that best fit the experimental data by minimizing the residual sum of squares. The Monod kinetic constants ( _max , K _s, Y, and k _d) that describe phenol, 2-, 3-, and 4-methylphenol degradation and concomitant microbial growth were determined under conditions that were substantially different from those previously reported for microcosms cultured from sewage sludge. The K _s values obtained in this study are approximately two orders of magnitude lower than values obtained for the anaerobic degradation of phenol in digesting sewage sludge, indicating that the aquifer microorganisms have developed enzyme systems that are adapted to low nutrient conditions. The values for k _d are much less than _max, and can be neglected in the microcosms. The extremely low Y values, approximately 3 orders of magnitude lower than for the sewage sludge derived cultures, and the very low numbers of microorganisms in the aquifer derived microcosms suggest that these organisms use some unique strategies to survive in the subsurface environment.Abbreviations GC gas chromatography - HPLC high performance liquid chromatography - LBSSB likelihood based sum of squares boundaries - MPN most probable number - NLR nonlinear regression analysis - OFAG oxygen free Argon gas - PCP pentachlorophenol - RSS residual sum of squares - SRB sulfate reducing bacteria     

An updated global data set for diet preferences in terrestrial mammals: testing the validity of extrapolation

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A Reexamination of Roper’S Trend-Surface Analysis of Central Plains Radiocarbon Dates

Abstract

A reexamination of Roper’s (1976) trend-surface analysis of Central Plains radiocarbon dates indicates that 1) a nonlinear trend in the data was not recognized, and 2) the dates of the trend-surface contours given in her map of the Central Plains are in error. A revised trend-surface model is presented which better describes the site data and more closely agrees with the Central Plains cultural sequence.     

Combining archive territory mapping data and aerial photography to investigate bird–habitat relationships: a case study from the Lincolnshire coast

Capsule Habitat associations of breeding birds in a complex coastal environment are clear, interpretable and mostly consistent between years.

Aims To match archive territory mapping data with historical aerial photographs and develop data handling and analytical techniques for the study of bird–habitat relationships.

Methods Bird registrations were digitized from archive British Trust for Ornithology Common Birds Census maps and habitat characteristics from contemporaneous aerial photographs. The resulting maps were overlaid and ranks of habitat preference for 15 species calculated using compositional analysis. Similarity analysis identified species with consistent habitat profiles across years. Cluster analysis identified groups of species with similar patterns of habitat use.

Results A total of 5400 registrations of 15 species in 14 habitats were analysed. Of these, 13 species showed stable patterns of habitat association across survey years. Clear differences and similarities in habitat preferences among the species were identified. The results may be used to inform conservation and management programmes in this and similar environments.

Conclusions Extensive archives of bird survey data can be used to study bird–habitat relationships and to measure the effects of natural and anthropogenic environmental change if contemporaneous aerial photographs can be sourced.     

An analysis of relationships among plant community phenology and seasonal metrics of Normalized Difference Vegetation Index in the northern part of the monsoon region of China

This study focuses on relationships between the phenological growing season of plant communities and the seasonal metrics of Normalized Difference Vegetation Index (NDVI) at sample stations and pixels overlying them, and explores the procedure for determining the growing season of terrestrial vegetation at the regional scale, using threshold NDVI values obtained by surface–satellite analysis at individual stations/pixels. The cumulative frequency of phenophases has been calculated for each plant community and each year in order to determine the growing season at the three sample stations from 1982 to 1993. The precise thresholds were arbitrarily set as the dates on which the phenological cumulative frequency reached 5% and 10% (for the beginning) and 90% and 95% (for the end). The beginning and end dates of the growing season were then applied each year as time thresholds, to determine the corresponding 10-day peak greenness values from NDVI curves for 8-km² pixels overlying the phenological stations. According to a trend analysis, a lengthening of the growing seasons and an increase of the integrated growing season NDVI have been detected in the central part of the research region. The correlation between the beginning dates of the growing season and the corresponding threshold NDVI values is very low, which indicates that the satellite-sensor-derived greenness is independent of the beginning time of the growing season of local plant communities. Other than in spring, the correlation between the end dates of the growing season and the corresponding threshold NDVI values is highly significant. The negative correlation shows that the earlier the growing season terminates, the larger the corresponding threshold NDVI value, and vice versa. In order to estimate the beginning and end dates of the growing season using the threshold NDVI values at sites without phenological data from 1982 to 1993, we calculated the spatial correlation coefficients between NDVI time-series at each sample station and other contiguous sites year by year. The results provide the spatial extrapolation area of the growing season for each sample station. Thus, we can use the threshold NDVI value obtained at one sample station/pixel for a year to determine the growing season at the extrapolation sites with a similar vegetation type for the same year. Received: 25 October 2000 / Revised: 19 June 2001 / Accepted: 19 June 2001     

Bloch Equations-Based Reconstruction of Myocardium T1 Maps from Modified Look-Locker Inversion Recovery Sequence

Modified Look-Locker Inversion recovery (MOLLI) sequence is increasingly performed for myocardial T1 mapping but is known to underestimate T1 values. The aim of the study was to quantitatively analyze several sources of errors when T1 maps are derived using standard post-processing of the sequence and to propose a reconstruction approach that takes into account inversion efficacy (η), T2 relaxation during balanced steady-state free-precession readouts and B1+ inhomogeneities. Contributions of the different sources of error were analyzed using Bloch equations simulations of MOLLI sequence. Bloch simulations were then combined with the acquisition of fast B1+ and T2 maps to derive more accurate T1 maps. This novel approach was evaluated on phantoms and on five healthy volunteers. Simulations show that T2 variations, B1+ heterogeneities and inversion efficiency represent major confounders for T1 mapping when MOLLI is processed with standard 3-parameters fitting. In vitro data indicate that T1 values are accurately derived with the simulation approach and in vivo data suggest that myocardium T1 are 15% underestimated when processed with the standard 3-parameters fitting. At the cost of additional acquisitions, this method might be suitable in clinical research protocols for precise tissue characterization as it decorrelates T1 and T2 effects on parametric maps provided by MOLLI sequence and avoids inaccuracies when B1+ is not homogenous throughout the myocardium.     

Optimizing biocontrol using phenological day degree models: the European earwig in pipfruit orchards

• 1 Phenological day degree models are often used as warning systems for the emergence of arthropod pests in agricultural crops or the occurrence of natural enemies of the pest species. In the present study, we report on a case study of the European earwig Forficula auricularia L., which is an important natural enemy in pipfruit orchards, and describe how such a day degree model can be used to avoid negative effects of crucial orchard management, such as spray applications and soil tillage. A precise timing of these interventions in relation to the phenology of natural enemies will enhance biocontrol.
• 2 Earwig population dynamics are characterized by single‐ and double‐brood populations, each with specific biological characteristics.
• 3 A day degree model capable of predicting the phenology of local earwig populations of both population types was developed. The model was checked for accuracy by comparing the first field observation dates of various life stages with predicted values using temperature data from the nearest weather station. In addition, variation in development time was assessed using field data.
• 4 The model was able to make predictions on a global scale. Although single‐ and double‐brood populations differ in phenology, the predictions of first appearance dates were similar. Variation in development time showed that single‐brood populations were more synchronized.
• 5 Our phenological model provides an accurate tool for predicting and simulating earwig population dynamics, as well as for enhancing the biocontrol of pests in pipfruit orchards.

     

Characterisation of H+ and Cu2+ binding to humic and fulvic acids

Abstract

The nature of H⁺ and Cu²⁺ binding by soil-derived humic (HA) and fulvic (FA) acid was characterised using potentiometric titrations. The experimental data obtained showed that the derived proton balance equation was valid and capable of describing proton consumption by both polyelectrolytes. HA was found to be more acidic and more reactive as shown by its lower equivalent weight compared to FA. Acid consumption by HA during titrations was little affected at ionic strength (μ) up to 0.1 M although it was enhanced at higher μ. Displacement of protons by Cu²⁺ resulted in a nonlinear sigmoidal pattern suggesting the formation of different Cu-HA chelates, or existence of sites that differed in their affinities for Cu on the ligand. Different concentrations of added Cu appeared to favour one or both mechanisms, although the titration method could not differentiate which of the probable mechanisms was more dominant at a specific level of Cu added. Similar values were obtained for conditional stability constants using either the equation of Scatchard or Ruzic.     

Mapping historical forest types in Baraga County Michigan,USA as fuzzy sets

Data on tree location and species in a portion of Northern Michigan were gathered from General Land Office (GLO) survey notes (ca. 1850), digitized, and generalized to represent forest types. Fuzzy membership values describing the degree of membership of each species in each forest type were derived from (a) semantic information in the forestry literature and (b) a fuzzy clustering routine applied to data from randomly placed circular plots. The fuzzy membership values assigned to each tree point for each forest type were interpolated to form continuous surfaces using kriging and co-kriging. Advantages of this method over traditional discrete mapping methods include: (a) multiple options are available for the display and analysis; (b) classification uncertainty and the continuity of natural vegetation can be represented; and (c) the classification scheme is applied systematically across the entire map area and can be altered to produce alternative maps. The subset of available display and analytical products presented include: discrete forest type maps; a surface representing the confusion between forest types; fuzzy logical overlays of forest types; and discrete class maps with color value altered within each class to indicate degree of confusion at each location.     

Radiomics classifier to quantify automatic segmentation quality of cardiac sub-structures for radiotherapy treatment planning

PurposeA radiomics features classifier was implemented to evaluate segmentation quality of heart structures. A robust feature set sensitive to incorrect contouring would provide an ideal quantitative index to drive autocontouring optimization.MethodsTwenty-five cardiac sub-structures were contoured as regions of interest in 36 CTs. Radiomic features were extracted from manually-contoured (MC) and Hierarchical-Clustering automatic-contouring (AC) structures. A robust feature-set was identified from correctly contoured CT datasets. Features variation was analyzed over a MC/AC dataset. A supervised-learning approach was used to train an Artificial-Intelligence (AI) classifier; incorrect contouring cases were generated from the gold-standard MC datasets with translations, expansions and contractions. ROC curves and confusion matrices were used to evaluate the AI-classifier performance.ResultsTwenty radiomics features, were found to be robust across structures, showing a good/excellent intra-class correlation coefficient (ICC) index comparing MC/AC. A significant correlation was obtained with quantitative indexes (Dice-Index, Hausdorff-distance). The trained AI-classifier detected correct contours (CC) and not correct contours (NCC) with an accuracy of 82.6% and AUC of 0.91. True positive rate (TPR) was 85.1% and 81.3% for CC and NCC. Detection of NCC at this point of the development still depended strongly on degree of contouring imperfection.ConclusionsA set of radiomics features, robust on “gold-standard” contour and sensitive to incorrect contouring was identified and implemented in an AI-workflow to quantify segmentation accuracy. This workflow permits an automatic assessment of segmentation quality and may accelerate expansion of an existing autocontouring atlas database as well as improve dosimetric analyses of large treatment plan databases.