Species-area and species-individual relationships for tropical trees: A comparison of three 50-ha plots

1 Species-accumulation curves for woody plants were calculated in three tropical forests, based on fully mapped 50-ha plots in wet, old-growth forest in Peninsular Malaysia, in moist, old-growth forest in central Panama, and in dry, previously logged forest in southern India. A total of 610 000 stems were identified to species and mapped to < Im accuracy. Mean species number and stem number were calculated in quadrats as small as 5 m x 5 m to as large as 1000 m x 500 m, for a variety of stem sizes above 10 mm in diameter. Species-area curves were generated by plotting species number as a function of quadrat size; species-individual curves were generated from the same data, but using stem number as the independent variable rather than area. 2 Species-area curves had different forms for stems of different diameters, but species-individual curves were nearly independent of diameter class. With < 10(4) stems, species-individual curves were concave downward on log-log plots, with curves from different forests diverging, but beyond about 104 stems, the log-log curves became nearly linear, with all three sites having a similar slope. This indicates an asymptotic difference in richness between forests: the Malaysian site had 2.7 times as many species as Panama, which in turn was 3.3 times as rich as India. 3 Other details of the species-accumulation relationship were remarkably similar between the three sites. Rectangular quadrats had 5-27% more species than square quadrats of the same area, with longer and narrower quadrats increasingly diverse. Random samples of stems drawn from the entire 50 ha had 10-30% more species than square quadrats with the same number of stems. At both Pasoh and BCI, but not Mudumalai. species richness was slightly higher among intermediate-sized stems (50-100mm in diameter) than in either smaller or larger sizes, These patterns reflect aggregated distributions of individual species, plus weak density-dependent forces that tend to smooth the species abundance distribution and 'loosen' aggregations as stems grow. 4 The results provide support for the view that within each tree community, many species have their abundance and distribution guided more by random drift than deterministic interactions. The drift model predicts that the species-accumulation curve will have a declining slope on a log-log plot, reaching a slope of O.1 in about 50 ha. No other model of community structure can make such a precise prediction. 5 The results demonstrate that diversity studies based on different stem diameters can be compared by sampling identical numbers of stems. Moreover, they indicate that stem counts < 1000 in tropical forests will underestimate the percentage difference in species richness between two diverse sites. Fortunately, standard diversity indices (Fisher's sc, Shannon-Wiener) captured diversity differences in small stem samples more effectively than raw species richness, but both were sample size dependent. Two nonparametric richness estimators (Chao. jackknife) performed poorly, greatly underestimating true species richness.

A comparison of plotless density estimators using Monte Carlo simulation on totally enumerated field data sets

Background: Plotless density estimators are those that are based on distance measures rather than counts per unit area (quadrats or plots) to estimate the density of some usually stationary event, e.g. burrow openings, damage to plant stems, etc. These estimators typically use distance measures between events and from random points to events to derive an estimate of density. The error and bias of these estimators for the various spatial patterns found in nature have been examined using simulated populations only. In this study we investigated eight plotless density estimators to determine which were robust across a wide range of data sets from fully mapped field sites. They covered a wide range of situations including animal damage to rice and corn, nest locations, active rodent burrows and distribution of plants. Monte Carlo simulations were applied to sample the data sets, and in all cases the error of the estimate (measured as relative root mean square error) was reduced with increasing sample size. The method of calculation and ease of use in the field were also used to judge the usefulness of the estimator. Estimators were evaluated in their original published forms, although the variable area transect (VAT) and ordered distance methods have been the subjects of optimization studies. Results: An estimator that was a compound of three basic distance estimators was found to be robust across all spatial patterns for sample sizes of 25 or greater. The same field methodology can be used either with the basic distance formula or the formula used with the Kendall-Moran estimator in which case a reduction in error may be gained for sample sizes less than 25, however, there is no improvement for larger sample sizes. The variable area transect (VAT) method performed moderately well, is easy to use in the field, and its calculations easy to undertake. Conclusion: Plotless density estimators can provide an estimate of density in situations where it would not be practical to layout a plot or quadrat and can in many cases reduce the workload in the field.

Documenting the inevitable: Voting behaviour at the 2013 Australian election

This chapter uses data from the 2013 Australian Election Study (AES), conducted by Clive Bean, Ian McAllister, Juliet Pietsch and Rachel Gibson (Bean et al. 2014) to investigate political attitudes and voting behaviour in the election. The study was funded by the Australian Research Council and involved a national survey of political attitudes and behaviour using a self-completion questionnaire mailed to respondents on the day before the 7 September election. The sample was a systematic random sample of enrolled voters throughout Australia, drawn by the Australian Electoral Commission. Respondents were given the option of returning the completed questionnaire by reply-paid mail or completing the survey online. Non-respondents were sent several follow-up mailings and the final sample size was 3955, representing a response rate of 34 per cent. The data were weighted to reflect population parameters for gender, age, state and vote.

Dispersal and related life history traits in the Glanville fritillary butterfly

Most studies of life history evolution are based on the assumption that species exist at equilibrium and spatially distinct separated populations. In reality, this is rarely the case, as populations are often spatially structured with ephemeral local populations. Therefore, the characteristics of metapopulations should be considered while studying factors affecting life history evolution. Theoretical studies have examined spatial processes shaping the evolution of life history traits to some extent, but there is little empirical data and evidence to investigate model predictions. In my thesis I have tried to bridge the gap between theoretical and empirical studies by using the well-known Glanville fritillary (Melitaea cinxia) metapopulation as a model system. The long-term persistence of classic metapopulations requires sufficient dispersal to establish new local populations to compensate for local extinctions. Previous studies on the Glanville fritillary have shown that females establishing new populations are not a random sample from the metapopulation, but they are in fact more dispersive than females in old populations. Many other life-history traits, such as body size, fecundity and lifespan, may be related to dispersal rate. Therefore, I examined a range of correlated traits for their evolutionary and ecological consequences. I was particularly interested in how the traits vary under natural environmental conditions, hence all studies were conducted in a large (32 x 26 m) outdoor population cage built upon a natural habitat patch. Individuals for the experiments were sampled from newly-established and old populations within a large metapopulation. Results show that females originating from newly-established populations had higher within-habitat patch mobility than females from old populations. I showed that dispersal rate is heritable and that flight activity is related to variation in a gene encoding the glycolytic enzyme phosphoglucose isomerase. Both among-individual and among-population variation in dispersal are correlated with the reproductive performance of females, though I found no evidence for a trade-off between dispersal and fecundity in terms of lifetime egg production or clutch size. Instead, the results suggest that highly dispersive females from newly-established populations have a shorter lifespan than females from old populations, and that dispersive females may pay a cost in terms of reduced lifetime reproductive success due to increased time spent outside habitat patches. In summary, the results of this thesis show that genotype-dependent dispersal rate correlates with other life history traits in the Glanville fritillary, and that the rapid turnover of local populations (extinctions and re-colonisations) is likely to be the mechanism that maintains phenotypic variation in many life history traits at the metapopulation level.

Paradigms in Statistical Inference for Finite Populations; Up to the 1950s

Modern sample surveys started to spread after statistician at the U.S. Bureau of the Census in the 1940s had developed a sampling design for the Current Population Survey (CPS). A significant factor was also that digital computers became available for statisticians. In the beginning of 1950s, the theory was documented in textbooks on survey sampling. This thesis is about the development of the statistical inference for sample surveys. For the first time the idea of statistical inference was enunciated by a French scientist, P. S. Laplace. In 1781, he published a plan for a partial investigation in which he determined the sample size needed to reach the desired accuracy in estimation. The plan was based on Laplace s Principle of Inverse Probability and on his derivation of the Central Limit Theorem. They were published in a memoir in 1774 which is one of the origins of statistical inference. Laplace s inference model was based on Bernoulli trials and binominal probabilities. He assumed that populations were changing constantly. It was depicted by assuming a priori distributions for parameters. Laplace s inference model dominated statistical thinking for a century. Sample selection in Laplace s investigations was purposive. In 1894 in the International Statistical Institute meeting, Norwegian Anders Kiaer presented the idea of the Representative Method to draw samples. Its idea was that the sample would be a miniature of the population. It is still prevailing. The virtues of random sampling were known but practical problems of sample selection and data collection hindered its use. Arhtur Bowley realized the potentials of Kiaer s method and in the beginning of the 20th century carried out several surveys in the UK. He also developed the theory of statistical inference for finite populations. It was based on Laplace s inference model. R. A. Fisher contributions in the 1920 s constitute a watershed in the statistical science He revolutionized the theory of statistics. In addition, he introduced a new statistical inference model which is still the prevailing paradigm. The essential idea is to draw repeatedly samples from the same population and the assumption that population parameters are constants. Fisher s theory did not include a priori probabilities. Jerzy Neyman adopted Fisher s inference model and applied it to finite populations with the difference that Neyman s inference model does not include any assumptions of the distributions of the study variables. Applying Fisher s fiducial argument he developed the theory for confidence intervals. Neyman s last contribution to survey sampling presented a theory for double sampling. This gave the central idea for statisticians at the U.S. Census Bureau to develop the complex survey design for the CPS. Important criterion was to have a method in which the costs of data collection were acceptable, and which provided approximately equal interviewer workloads, besides sufficient accuracy in estimation.

Snoring and sleep apnea in children

Snoring is a primary and major clinical symptom of upper airway obstruction during sleep. Sleep-disordered breathing ranges from primary snoring to significant partial upper airway obstruction, and obstructive sleep apnea. Adult snoring and obstructive sleep apnea have been extensively studied, whereas less is known about these disorders in children. Snoring and more severe obstructive sleep apnea have been shown to have a harmful effect on the neurobehavioral development of children, but the mechanisms of this effect remains unknown. Furthermore, the correlation of this effect to objective sleep study parameters remains poor. This study evaluated the prevalence of snoring in preschool-aged children in Finland. Host and environmental risk factors, and neurobehavioral and neurocognitive symptoms of children suffering from snoring or obstructive sleep apnea were also investigated. The feasibility of acoustic rhinometry in young children was assessed. The prevalence and risk factors of snoring (I) were evaluated by a questionnaire. The random sample included 2100 children aged 1-6 years living in Helsinki. All 3- to 6-year-old children whose parents reported their child to snore always, often, or sometimes were categorized as snorers, and invited to participate to the clinical study (II-IV). Non-snoring children whose parents were willing to participate in the clinical study were invited to serve as controls. Children underwent a clinical ear-nose-throat examination. Emotional, behavioral, and cognitive performances were evaluated by Child Behavioral Checklist (CBCL), Wechsler Preschool and Primary Scale of Intelligence (WPPSI-R) and NEPSY-A Developmental Neuropsychological Assessment (NEPSY). Nasal volume was measured by acoustic rhinometry, and nasal resistance by rhinomanometry. Lateral and posteroanterior cephalometry were performed. A standard overnight ambulatory polysomnography was performed in the home environment. Twenty-six healthy children were tested in order to assess the feasibility of acoustic rhinometry in young children (V). Snoring was common in children; 6.3% of children snored always or often, whereas 81.3% snored never or occasionally. No differences were apparent between snorers and non-snorers regarding age, or gender. Pediatric snoring was associated with recurrent upper respiratory infections, otitis media, and allergic rhinitis. Exposure to parental tobacco smoke, especially maternal smoking, was more common among snorers. Rhinitis was more common among children who exposured to tobacco smoke. Overnight polysomnography (PSG) was performed on 87 children; 74% showed no signs of significant upper airway obstruction during sleep. Three children had obstructive apnea/hypopnea index (OAHI) greater than 5/h. Age, gender, or a previous adenoidectomy or tonsillectomy did not correlate with OAHI, whereas tonsillar size did correlate with OAHI. Relative body weight and obesity correlated with none of the PSG parameters. In cephalometry, no clear differences or correlations were found in PSG parameters or between snorers and non-snorers. No correlations were observed between acoustic rhinometry, rhinomanometry, and PSG parameters. Psychiatric symptoms were more frequent in the snoring group than in the nonsnoring group. In particular, anxious and depressed symptoms were more prevalent in the snoring group. Snoring children frequently scored lower in language functions. However, PSG parameters correlated poorly with neurocognitive test results in these children. This study and previous studies indicate that snoring without episodes of obstructive apnea or SpO2 desaturations may cause impairment in behavioral and neurocognitive functions. The mechanism of action remains unknown. Exposure to parental tobacco smoke is more common among snorers than non-snorers, emphasizing the importance of a smoke-free environment. Children tolerated acoustic rhinometry measurements well.

NETGEM: Network Embedded Temporal GEnerative Model for gene expression data

Background: Temporal analysis of gene expression data has been limited to identifying genes whose expression varies with time and/or correlation between genes that have similar temporal profiles. Often, the methods do not consider the underlying network constraints that connect the genes. It is becoming increasingly evident that interactions change substantially with time. Thus far, there is no systematic method to relate the temporal changes in gene expression to the dynamics of interactions between them. Information on interaction dynamics would open up possibilities for discovering new mechanisms of regulation by providing valuable insight into identifying time-sensitive interactions as well as permit studies on the effect of a genetic perturbation. Results: We present NETGEM, a tractable model rooted in Markov dynamics, for analyzing the dynamics of the interactions between proteins based on the dynamics of the expression changes of the genes that encode them. The model treats the interaction strengths as random variables which are modulated by suitable priors. This approach is necessitated by the extremely small sample size of the datasets, relative to the number of interactions. The model is amenable to a linear time algorithm for efficient inference. Using temporal gene expression data, NETGEM was successful in identifying (i) temporal interactions and determining their strength, (ii) functional categories of the actively interacting partners and (iii) dynamics of interactions in perturbed networks. Conclusions: NETGEM represents an optimal trade-off between model complexity and data requirement. It was able to deduce actively interacting genes and functional categories from temporal gene expression data. It permits inference by incorporating the information available in perturbed networks. Given that the inputs to NETGEM are only the network and the temporal variation of the nodes, this algorithm promises to have widespread applications, beyond biological systems. The source code for NETGEM is available from https://github.com/vjethava/NETGEM

A Randomized Algorithm for Large Scale Support Vector Learning

We propose a randomized algorithm for large scale SVM learning which solves the problem by iterating over random subsets of the data. Crucial to the algorithm for scalability is the size of the subsets chosen. In the context of text classification we show that, by using ideas from random projections, a sample size of O(log n) can be used to obtain a solution which is close to the optimal with a high probability. Experiments done on synthetic and real life data sets demonstrate that the algorithm scales up SVM learners, without loss in accuracy. 1

Increased time-dependent room temperature plasticity in metallic glass nanopillars and its size-dependency

Room temperature, uniaxial compression creep experiments were performed on micro-/nano-sized pillars (having diameters in the range of 250-2000 nm) of a Zr-based bulk metallic glass (BMG) to investigate the influence of sample size on the time-dependent plastic deformation behavior in amorphous alloys. Experimental results reveal that plastic deformation indeed occurs at ambient temperature and at stresses that are well below the nominal quasi-static yield stress. At a given stress, higher total strains accrue in the smaller specimens. In all cases, plastic deformation was found to be devoid of shear bands, i.e., it occurs in homogeneous manner. The stress exponent obtained from the slope of the linear relation between strain rate and applied stress also shows a strong size effect, which is rationalized in terms of the amount of free volume created during deformation and the surface-to-volume ratio of the pillar. (C) 2012 Elsevier Ltd. All rights reserved.

Noise Detected NMR Spectroscopy

Spin noise phenomenon was predicted way back in 1946. However, experimental investigations regarding spin noise became possible only recently with major technological improvements in NMR hardware. These experiments have several potential novel applications and also demand refinements in the existing theoretical framework to explain the phenomenon. Elegance of noise spectroscopy in gathering information about the properties of a system lies in the fact that it does not require external perturbation, and the system remains in thermal equilibrium. Spin noise is intrinsic magnetic fluctuations, and both longitudinal and transverse components have been detected independently in many systems. Detection of fluctuating longitudinal magnetization leads to field of Magnetic Resonance Force Microscopy (MRFM) that can efficiently probe very few spins even down to the level of single spin utilizing ultrasensitive cantilevers. Transverse component of spin noise, which can simultaneously monitor different resonances over a given frequency range enabling one to distinguish between different chemical environments, has also received considerable attention, and found many novel applications. These experiments demand a detailed understanding of the underlying spin noise phenomenon in order to perform perturbation-free magnetic resonance and widen the highly promising application area. Detailed investigations of noise magnetization have been performed recently using force microscopy on equilibrium ensemble of paramagnetic alkali atoms. It was observed that random fluctuations generate spontaneous spin coherences which has similar characteristics as generated by macroscopic magnetization of polarized ensemble in terms of precession and relaxation properties. Several other intrinsic properties like g-factors, isotope-abundance ratios, hyperfine splitting, spin coherence lifetimes etc. also have been achieved without having to excite the sample. In contrast to MRFM-approaches, detection of transverse spin noise also offers novel applications, attracting considerable attention. This has unique advantage as different resonances over a given frequency range enable one to distinguish between different chemical environments. Since these noise signatures scale inversely with sample size, these approaches lead to the possibility of non-perturbative magnetic resonance of small systems down to nano-scale. In this review, these different approaches will be highlighted with main emphasis on transverse spin noise investigations.

A histopathologic evaluation of gross lesions excised from commercially important North Altantic marine fishes

Histopathologic studies of lesions found in commercially important North Atlantic marine fishes are uncommon. As part of a comprehensive Northeast Fisheries Center program ("Ocean Pulse") to evaluate environmental and resource health on the U.S. Continental Shelf from Cape Hatteras to Nova Scotia, grossly visible lesions of the gills, integument, muscle, and viscera of primarily bottom-dwelling fishes were excised and examined using light microscopy. Several gadid and pleuronectid fishes accounted for most of the lesions observed. Most pathological examinations were incidental to samples taken for age and growth determination and evaluation of predator/prey relationships. Several gadids, with either gill, heart, or spleen lesions, were sampled more intensively. Gill lesions principally affected gadids and were caused by either microsporidans or an unidentified oocyte-like cell. The majority of gastrointestinal lesions consisted of encapsulated or encysted larval worms or microsporidan-induced cysts. Few heart lesions were found. Integumental lesioos included ulcers, lymphocystis, and trematode metacercariae. Liver lesions almost always consisted of encapsulated or encysted larval helminths. Necrotic granulomata were seen in muscle and microsporidan-induced granulomata in spleen. Although not numerous, histologically interesting lesions were noted in integument, heart, liver, spleen, and muscle of several fish species. Histologic study of tissues excised from a variety of demersal and pelagic fishes from the eastern North Atlantic (France, Germany, Spain) revealed assorted integumental, renal, hepatic, and splenic lesions. Small sample size and non-random sampling precluded obtaining a meaningful quantitative estimate of the prevalence of the observed lesions in the population at risk; however, a useful census has been made of the types of lesions present in commercially important marine fishes. (PDF file contains 20 pages.)

O fundamento das improbidades na administração pública municipal brasileira

Ao longo da história, poucos fenômenos despertaram tanto interesse dos cidadãos, dispenderam tantos recursos do Estado e contribuíram tanto para o atraso de seu desenvolvimento quanto o problema da corrupção dos agentes públicos. Nesta tese, uso o conceito de improbidade para definir um tipo particular de fenômeno e distingui-lo de outros geralmente abrangidos pelo conceito de corrupção. A partir daí procuro responder as seguintes questões: quais elementos influenciam o processo de tomada de decisão do agente público para que considere o engajamento em uma improbidade? Que fatores estão associados à ocorrência de improbidades na Administração Pública municipal brasileira? Sob a perspectiva da nova economia institucional, a primeira parte da tese procede com a análise conceitual e metodológica do fenômeno, consubstanciado no referencial analíticos das improbidades, sustentando que: a) as improbidades correspondem a um gênero de atitudes oportunistas, dentre as quais se destaca uma espécie denominada transação corrupta; b) o processo de tomada de decisão do agente público, inserido no contexto de racionalidade limitada, orienta-se igualmente por elementos da análise custo-benefício (maximização da utilidade esperada), da dinâmica dos processos de aprendizagem e da barreira ético-moral dos próprios indivíduos. As demais partes da tese apresentam os resultados de uma investigação empírica sistemática, baseada nas informações de uma amostra aleatória de 960 municípios brasileiros auditados pela Controladoria-Geral da União. A análise evidencia os fatores associados à ocorrência das improbidades, tanto sob o ponto vista da literatura tradicional (modernização, capital social e rent-seeking), quanto da nova perspectiva analítica proposta, baseada nos mecanismos de governança. O teste a partir dos modelos tradicionais da literatura demonstra: a) a associação negativa entre a ocorrência das improbidades e os indicadores de desempenho institucional e de desenvolvimento socioeconômico dos municípios (em consonância com os efeitos comumente atribuídos as improbidades); b) a associação negativa entre a ocorrência das improbidades e os indicadores de modernização e de capital social dos municípios (em consonância com as causas comumente atribuídas as improbidades); c) a não associação entre a ocorrência das improbidades nos municípios brasileiros e os indicadores de incentivo ao comportamento rent-seeking (em oposição à clássica proposição de que quanto maior o tamanho do Estado, maior será a ocorrência de improbidades em razão dos incentivos oriundos de seu monopólio). Com base nos resultados obtidos, incorporo os supostos neoinstitucionalistas a análise das improbidades, interpretando-os como decorrência da inadequação das estruturas de governança dos contratos. Assim, para além do impacto do arranjo institucional, que abarca o controle parlamentar, administrativo e jurisdicional interno e externo dos recursos públicos federais transferidos aos municípios, apresento evidências de que as variações observadas na contagem de improbidades nos municípios brasileiros estão diretamente relacionadas à qualidade de seus mecanismos de governança. Dentre esses, destacam-se aqueles de natureza democrática: os mecanismos de controle social (os conselhos municipais de políticas públicas); os mecanismos de promoção da transparência (a qualidade do governo eletrônico); e os mecanismos de accountability (a disputa político-eleitoral). De acordo com o referencial analítico das improbidades, a existência e operação desses mecanismos elevam os custos de transação do agente público que, mesmo superando as limitações da barreira ético-moral e de aprendizado, ainda considera um eventual engajamento nesse gênero de atitudes oportunistas.

Precision estimates and suggested sample sizes for length-frequency data

For most fisheries applications, the shape of a length-frequency distribution is much more important than its mean length or variance. This makes it difficult to evaluate at which point a sample size is adequate. By estimating the coefficient of variation of the counts in each length class and taking a weighted mean of these, a measure of precision was obtained that takes the precision in all length classes into account. The precision estimates were closely associated with the ratio of the sample size to the number of size classes in each sample. As a rule-of-thumb, a minimum sample size of 10 times the number of length classes in the sample is suggested because the precision deteriorates rapidly for smaller sample sizes. In absence of such a rule-of-thumb, samplers have previously under-estimated the required sample size for samples with large fish, while over-sampling small fish of the same species.

Longitudinal logbook survey designs for estimating recreational fishery catch, with application to ayu (Plecoglossus altivelis)

Longitudinal surveys of anglers or boat owners are widely used in recreational fishery management to estimate total catch over a fishing season. Survey designs with repeated measures of the same random sample over time are effective if the goal is to show statistically significant differences among point estimates for successive time intervals. However, estimators for total catch over the season that are based on longitudinal sampling will be less precise than stratified estimators based on successive independent samples. Conventional stratified variance estimators would be negatively biased if applied to such data because the samples for different time strata are not independent. We formulated new general estimators for catch rate, total catch, and respective variances that sum across time strata but also account for correlation stratum samples. A case study of the Japanese recreational fishery for ayu (Plecoglossus altivelis) showed that the conventional stratified variance estimate of total catch was about 10% of the variance estimated by our new method. Combining the catch data for each angler or boat owners throughout the season reduced the variance of the total catch estimate by about 75%. For successive independent surveys based on random independent samples, catch, and variance estimators derived from combined data would be the same as conventional stratified estimators when sample allocation is proportional to strata size. We are the first to report annual catch estimates for ayu in a Japanese river by formulating modified estimators for day-permit anglers.

Developing a toolkit for assessing the impact of health library services on patient care

Urquhart,C., Spink, S., Thomas, R. & Weightman, A. (2007). Developing a toolkit for assessing the impact of health library services on patient care. Report to LKDN (Libraries and Knowledge Development Network). Aberystwyth: Department of Information Studies, Aberystwyth University. Sponsorship: Libraries and Knowledge Development Network/ NHS