Sex determination by tooth size in a sample of Greek population

Sex assessment from tooth measurements can be of major importance for forensic and bioarchaeological investigations, especially when only teeth or jaws are available. The purpose of this study is to assess the reliability and applicability of establishing sex identity in a sample of Greek population using the discriminant function proposed by Rösing et al. (1995).     

Forensic Anthropology and Bioarchaeology in the American Anthropologist Rare but Exquisite Gems

This article explores forensic anthropological and bioarchaeological publishing patterns in the American Anthropologist (n.s.). Early contributions by Harris Hawthorne Wilder on both subjects are considered in detail, including previously unrecognized discussions of taphonomic variables. Articles on forensic anthropology in the American Anthropologist appear only during the first four decades of publication. While relatively well represented in early issues, bioarchaeological articles decrease in number over time. Comparative data from six other journals suggest that their presence has had a profound effect on the American Anthropologist . The impact of the "new" physical anthropology on publishing patterns in bioarchaeology is also assessed. [Keywords: forensic anthropology, funerary archaeology, paleodemography, paleopathology, taphonomy]     

Evaluation of missing data imputation methods for human osteometric measurements

It is not uncommon for biological anthropologists to analyze incomplete bioarcheological or forensic skeleton specimens. As many quantitative multivariate analyses cannot handle incomplete data, missing data imputation or estimation is a common preprocessing practice for such data. Using William W. Howells' Craniometric Data Set and the Goldman Osteometric Data Set, we evaluated the performance of multiple popular statistical methods for imputing missing metric measurements. Results indicated that multiple imputation methods outperformed single imputation methods, such as Bayesian principal component analysis (BPCA). Multiple imputation with Bayesian linear regression implemented in the R package norm2, the Expectation–Maximization (EM) with Bootstrapping algorithm implemented in Amelia, and the Predictive Mean Matching (PMM) method and several of the derivative linear regression models implemented in mice, perform well regarding accuracy, robustness, and speed. Based on the findings of this study, we suggest a practical procedure for choosing appropriate imputation methods.     

A hierarchical Bayesian approach for handling missing classification data

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Model life table for captive chimpanzees

Mortality statistics from three captive populations of chimpanzees (Pan troglodytes) were combined to generate standard model life tables for each sex in this species. The model is compared to an estimate of survivorship of a group of wild animals, and is applied to an incomplete data set to illustrate how the model may be used to extend estimates of mortality statistics to missing older ages. © 1995 Wiley-Liss, Inc.     

Missing data in craniometrics: a simulation study

Craniometric measurements represent a useful tool for studying the differentiation of mammal populations. However, the fragility of skulls often leads to incomplete data matrices. Damaged specimens or incomplete sets of measurements are usually discarded prior to statistical analysis. We assessed the performance of two strategies that avoid elimination of observations: (1) pairwise deletion of missing cells, and (2) estimation of missing data using available measurements. The effect of these distinct approaches on the computation of inter-individual distances and population differentiation analyses were evaluated using craniometric measurements obtained from insular populations of deer micePeromyscus maniculatus (Wagner, 1845). In our simulations, Euclidean distances were greatly altered by pairwise deletion, whereas Gower’s distance coefficient corrected for missing data provided accurate results. Among the different estimation methods compared in this paper, the regression-based approximations weighted by coefficients of determination (r ²) outperformed the competing approaches. We further show that incomplete sets of craniometric measurements can be used to compute distance matrices, provided that an appropriate coefficient is selected. However, the application of estimation procedures provides a flexible approach that allows researchers to analyse incomplete data sets.     

Resistance of melanized feathers to bacterial degradation: is it really so black and white?

Melanins are common feather pigments that contribute to signaling and crypsis. Melanins may also help feathers resist feather‐degrading bacteria (FDB). Two recent studies (Goldstein et al. 2004, Grande et al. 2004) tested the resistance of melanized versus unmelanized feathers to FDB using in vitro experiments, but draw opposite conclusions. Goldstein et al. (2004) concluded that melanized feathers resist FDB more than unmelanized feathers, while Grande et al. (2004) concluded that unmelanized feathers resist FDB more than melanized feathers. To resolve this conflict in the literature, we replicated previous studies but included additional tests not previously used. We inoculated melanized and unmelanized feathers of domestic geese Anser anser domesticus, with the FDB Bacillus licheniformis and measured bacterial activity every two days over two weeks. Three metrics of bacterial activity on feathers were measured: soluble protein content around feathers in solution, bacterial growth on feathers, and loss of feather mass. The latter two metrics were not considered in the aforementioned studies, which indirectly measured bacterial activity. We conducted two trials, one in which feathers were sterilized by autoclaving before inoculation (Goldstein et al. 2004, Grande et al. 2004), and a second in which feathers were sterilized by ethylene oxide gas. This allowed us to test whether autoclaving, done in previous studies, influences bacterial activity on feathers and could confound results. In both trials, unmelanized feathers degraded earlier, supported greater bacterial growth, and lost more mass than melanized feathers. These results support the findings of Goldstein et al. (2004); melanized feathers are more resistant to FDB than unmelanized feathers. Thus, using direct metrics of bacterial activity, we resolve a current conflict in the literature. We also found that autoclaving feathers influences FDB activity on them, and thus autoclaving should be avoided in future studies.     

Evaluating the association between latent classes and competing risks outcomes with multiphenotype data

Latent class analysis is an intuitive tool to characterize disease phenotype heterogeneity. With data more frequently collected on multiple phenotypes in chronic disease studies, it is of rising interest to investigate how the latent classes embedded in one phenotype are related to another phenotype. Motivated by a cohort with mild cognitive impairment (MCI) from the Uniform Data Set (UDS), we propose and study a time-dependent structural model to evaluate the association between latent classes and competing risk outcomes that are subject to missing failure types. We develop a two-step estimation procedure which circumvents latent class membership assignment and is rigorously justified in terms of accounting for the uncertainty in classifying latent classes. The new method also properly addresses the realistic complications for competing risks outcomes, including random censoring and missing failure types. The asymptotic properties of the resulting estimator are established. Given that the standard bootstrapping inference is not feasible in the current problem setting, we develop analytical inference procedures, which are easy to implement. Our simulation studies demonstrate the advantages of the proposed method over benchmark approaches. We present an application to the MCI data from UDS, which uncovers a detailed picture of the neuropathological relevance of the baseline MCI subgroups.     

上海市二、三级医院肿瘤化疗病案质量现状与分析

目的 了解上海市二、三级医院肿瘤化学药物治疗（以下简称“化疗”）质量情况,完善肿瘤化疗质量控制体系。方法 依据上海市肿瘤化疗质控中心督查方案,对全市103家从事肿瘤化疗的二、三级医院开展了2015年肿瘤化疗质量现场核查,采用SPSS 13.0进行数据汇总和分析。结果 上海市二、三级医院之间,肿瘤专业科室和非专业科室之间,肿瘤化疗病案的质量存在显著的不平衡,主要问题包括知情同意书内容不完整（33.04%）,病理诊断不齐全或缺失（15.50%）,肿瘤分期不规范或未分期（56.27%）,化疗目的（42.44%）、化疗适应证（37.47%）和禁忌证（12.21%）不齐全或缺失,化疗疗效评价记录不全或未评价（24.10%）,中期评估记录不全或未评价（27.72%）,入院病史（16.28%）及化疗当日记录（32.04%）不完整或缺失等。结论 上海市医院肿瘤化疗病案的质量与医院的级别和是否为专科显著相关。各医院应该针对自身存在的问题,加强对化疗质量控制标准的学习。     

A pseudo-bayesian shrinkage approach to regression with missing covariates

Summary We consider the linear regression of outcome Y on regressors W and Z with some values of W missing, when our main interest is the effect of Z on Y, controlling for W. Three common approaches to regression with missing covariates are (i) complete‐case analysis (CC), which discards the incomplete cases, and (ii) ignorable likelihood methods, which base inference on the likelihood based on the observed data, assuming the missing data are missing at random ( Rubin, 1976b ), and (iii) nonignorable modeling, which posits a joint distribution of the variables and missing data indicators. Another simple practical approach that has not received much theoretical attention is to drop the regressor variables containing missing values from the regression modeling (DV, for drop variables). DV does not lead to bias when either (i) the regression coefficient of W is zero or (ii) W and Z are uncorrelated. We propose a pseudo‐Bayesian approach for regression with missing covariates that compromises between the CC and DV estimates, exploiting information in the incomplete cases when the data support DV assumptions. We illustrate favorable properties of the method by simulation, and apply the proposed method to a liver cancer study. Extension of the method to more than one missing covariate is also discussed.     

Palaeomorphology: fossils and the inference of cladistic relationships

Edgecombe, G.D. 2010. Palaeomorphology: fossils and the inference of cladistic relationships. —Acta Zoologica (Stockholm) 91 : 72–80 Twenty years have passed since it was empirically demonstrated that inclusion of extinct taxa could overturn a phylogenetic hypothesis formulated upon extant taxa alone, challenging Colin Patterson’s bold conjecture that this phenomenon ‘may be non‐existent’. Suppositions and misconceptions about missing data, often couched in terms of ‘wildcard taxa’ and ‘the missing data problem’, continue to cloud the literature on the topic of fossils and phylogenetics. Comparisons of real data sets show that no a priori (or indeed a posteriori) decisions can be made about amounts of missing data and most properties of cladograms, and both simulated and real data sets demonstrate that even highly incomplete taxa can impact on relationships. The exclusion of fossils from phylogenetic analyses is neither theoretically nor empirically defensible.     

Sex identification of wolf (Canis lupus) using non-invasive samples

We have developed new specific primers for sex determination from forensic samples of wolves (Canis lupus), such as hair, saliva, faecal, tooth and urine samples. In order to improve molecular sexing, we performed a multiplex semi-nested polymerase chain reaction (PCR) and several replicated amplifications per sample to avoid errors in low quantity DNA samples, such as allelic dropout and false alleles. The sex of individuals is automatically determined by capillary electrophoresis with a fluorescently labelled internal sex-specific primer from each pair. Our method yielded sex identification on 100% of invasive samples and 93% of forensic samples, being one of the highest success rates obtained from wild animals.     

MORPHOLOGICAL EVOLUTION IN MUROID RODENTS I. CONSERVATIVE PATTERNS OF CRANIOMETRIC COVARIANCE AND THEIR ONTOGENETIC BASIS IN THE NEOTROPICAL GENUS ZYGODONTOMYS

Analyses of craniodental measurement data from 15 wild-collected population samples of the Neotropical muroid rodent genus Zygodontomys reveal consistent patterns of relative variability and correlation that suggest a common latent structure. Eigenanalysis of each sample covariance matrix of logarithms yields a first principal component that accounts for a large fraction of the total variance. Variances of subsequent sample principal components are much smaller, and the results of bootstrap resampling together with asymptotic statistics suggest that characteristic roots of the covariance matrix after the first are seldom distinct. The coefficients of normalized first principal components are strikingly similar from sample to sample: inner products of these vectors reveal an average between-sample correlation of 0.989, and the mean angle of divergence is only about eight degrees. Since first principal component coefficients identify the same contrasts among variables as comparisons of relative variability and correlation, we conclude that a single factor accounts for most of the common latent determination of these sample dispersions. Analyses of variance based on toothwear (a coarse index of age) and sex in the wild-collected samples, and on known age and sex in a captive-bred population, reveal that specimen scores on sample first principal components are age- and sex-dependent; residual sample dispersion, however, is essentially unaffected by age, sex, or age × sex interaction. The sample first principal component therefore reflects the covariance among measured dimensions induced by general growth, and its coefficients are interpretable as exponents of postnatal growth allometry. Path-analytic models that incorporate prior knowledge of the equivalent allometric effects of general growth within these samples can be used to decompose the between-sample variance by factors corresponding to other ontogenetic mechanisms of form change. The genetic or environmental determinants of differences in sample mean phenotypes induced by such mechanisms, however, can be demonstrated only by experiment.     

Estimating the Order of a Sequence of Physiological Changes from Incomplete Data

The problem considered in this paper is the estimation of the underlying order of m physiological changes from incomplete observations. The observations are incomplete in the sense that, for each individual in the sample, only the identity, but not the order, of the first k < m changes are observed, with k varying between individuals. An application to some data on physiological changes in fish undergoing sex change is presented.     

Biology ofTrichogrammatoidea simmondsi (Hym.: Trichogrammatidae) on sorghum shoot fly,Atherigona soccata (Dipt.: Muscidae) eggs

Experiments were conducted in a rearing room to study the biology ofTrichogrammatoidea simmondsi Nagaraja (Hym.: Trichogrammatidae) on sorghum shoot fly,Atherigona soccata Rondani (Dipt.: Muscidae) eggs. Shoot fly eggs were divided in two groups: 1) eggs < 24 h old and, 2) > 24 h old eggs. Thirty eggs of each group were used in a randomized complete block design with four replicates. Shoot fly eggs less than 24 h old were preferred (73% of parasitism) over 24 h old eggs (7.25%). Three larval instars ofT. simmondsi were observed. Few eggs with twoT. simmondsi exit holes (1.87%) were recorded in > 24 h old eggs compared with < 24 h ones (3.74%). The sex ratio male: female was 1 ∶ 1.47. The development from oviposition to adult emergence ranged from 7 to 12 days (average=9.8±1.31, n=40), and the average life span of male and femaleT. simmondsi was 25±1.46 h (range 22–26 h, n=12) and 35.17±10.9 (range 25–50 h, n=28) respectively at 26° C, 60–65% R.H. and 12 ∶ 12 (L/D) photoperiod. This paper constitutes the first published information on the biology ofT. simmondsi on the sorghum shoot fly eggs.

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Résumé Des essais ont été conduits en salle d'élevage en vue d'étudier la biologie deTrichogrammatoidea simmondsi Nagaraja (Hym.: Trichogrammatidae) sur les œufs de la mouche des pousses du sorgho,Atherigoa soccata Rondani (Dipt.: Muscidae). Les œufs de la mouche ont été divisés en deux groupes: 1) ℧ufs agés de < 24 h, 2) > 24 h. Trente œufs de chaque groupe ont été utilisés dans un dispositif en blocs complets randomisés à quatre répétitions. Les œufs de moins de 24 h d'age ont été plus parasités (73% de parasitisme) que ceux de plus de 24 h d'age (7,25% de parasitisme). Trois stades larvaires deT. simmondsi ont été observés. La présence de deux trous d'émergence deT. simmondsi était moins élevée (1,87%) dans les œufs de > 24 h que dans ceux de < 24 h (3,74%). Le sex ratio male: femelle était de 1 ∶ 1,47 Le cycle de développement de l'œuf à l'émergence de l'adulte variait de 7 à 12 jours avec une moyenne de 9,8±1,31 (n=40). La durée moyenne de vie du male et de la femelle deT. simmondsi était respectivement de 25±1,46 h (variation 22–26 h, n=12) et 35,17±10,9 (variation 25–50 h, n=28) à 26°C, 60–65% H.R. et une photopériode de 12 ∶ 12. Cet article constitue la première information publiée sur la biologie deT. simmondsi sur les œufs de la mouche des pousses du sorgho.

     

Digit flexor muscles in the cat: their action and motor units

The relation between muscle action and the mechanical properties of motor units has been explored in the main digit flexors of the cat hind limb: plantaris (PL); flexor digitorum brevis (FDB); flexor hallucis longus (FHL); and, flexor digitorum longus (FDL). General observations on muscle action revealed that PL is an ankle extensor as well as a digit flexor. PL and FHL were shown to be the major force contributors to digit flexion with FDL playing a lesser but still significant role. The mechanical properties of PL, FHL and FDB motor units were studied by noting twitch and tetanic tensions produced by electrical stimulation of single alpha axons, functionally isolated from the ventral root filaments. These data were compared to similar data reported by Olson and Swett (1966) for flexor digitorum longus (FDL). Our sample (114 PL, 60 FDB and 124 FHL units) disclosed that PL, FDB and FHL have units of uniformly fast contraction times (means 22, 27 and 27 msec respectively). PL units developed the most tetanic tension (3 to 160, mean 62 gm-wt) followed by FHL (2 to 87, mean 31 gm-wt) with FDB units producing very little tension (1 to 20, mean 6 gm-wt). Swett and Olson's FDL sample (108 units) showed tensions ranging from 0.3 to 100 gm-wt (mean 10 gm-wt). A division of labor among the four muscles is proposed. The large PL units are advantageous for forceful phasic inputs to the digits during the locomotion and in keeping with PL's additional role as an ankle exstensor. The low output forces of FDB units are optimal for discrete input to the digits during subtle adjustments of posture. We propose that the larger fast contracting units of FHL are used primarily for forceful digit flexions required in locomotion and for phasic protrusion of the claws while the predominately small and slow contracting units of FDL are used for sustained claw protrusion.     

LPA protects intestinal epithelial cells from apoptosis by inhibiting the mitochondrial pathway

We previously showed (Gastroenterology 123: 206-216, 2002) that lysophosphatidic acid (LPA) protects and rescues rat intestinal epithelial cells (IEC-6) from apoptosis. Here, we provide evidence for the LPA-elicited inhibition of the mitochondrial apoptotic pathway leading to attenuation of caspase-3 activation. Pretreatment of IEC-6 cells with LPA inhibited campothecin-induced caspase-9 and caspase-3 activation and DNA fragmentation. A caspase-9 inhibitor peptide mimicked the LPA-elicited antiapoptotic activity. LPA elicited ERK1/ERK2 and PKB/Akt phosphorylation. The LPA-elicited antiapoptotic activity and inhibition of caspase-9 activity were abrogated by pertussis toxin, PD 98059, wortmannin, and LY 294002. LPA reduced cytochrome c release from mitochondria and prevented activation of caspase-9. LPA prevented translocation of Bax from cytosol to mitochondria and increased the expression of the antiapoptotic Bcl-2 mRNA and protein. LPA had no effect on Bcl-xl, Bad, and Bak mRNA or protein expression. These data indicate that LPA protects IEC-6 cells from camptothecin-induced apoptosis through G(i)-coupled inhibition of caspase-3 activation mediated by the attenuation of caspase-9 activation due to diminished cytochrome c release, involving upregulation of Bcl-2 protein expression and prevention of Bax translocation.     

Infinite hidden Markov models for multiple multivariate time series with missing data

Exposure to air pollution is associated with increased morbidity and mortality. Recent technological advancements permit the collection of time-resolved personal exposure data. Such data are often incomplete with missing observations and exposures below the limit of detection, which limit their use in health effects studies. In this paper, we develop an infinite hidden Markov model for multiple asynchronous multivariate time series with missing data. Our model is designed to include covariates that can inform transitions among hidden states. We implement beam sampling, a combination of slice sampling and dynamic programming, to sample the hidden states, and a Bayesian multiple imputation algorithm to impute missing data. In simulation studies, our model excels in estimating hidden states and state-specific means and imputing observations that are missing at random or below the limit of detection. We validate our imputation approach on data from the Fort Collins Commuter Study. We show that the estimated hidden states improve imputations for data that are missing at random compared to existing approaches. In a case study of the Fort Collins Commuter Study, we describe the inferential gains obtained from our model including improved imputation of missing data and the ability to identify shared patterns in activity and exposure among repeated sampling days for individuals and among distinct individuals.     

Endocranial volume of Australopithecus africanus: new CT-based estimates and the effects of missing data and small sample size

Estimation of endocranial volume in Australopithecus africanus is important in interpreting early hominin brain evolution. However, the number of individuals available for investigation is limited and most of these fossils are, to some degree, incomplete and/or distorted. Uncertainties of the required reconstruction (‘missing data uncertainty’) and the small sample size (‘small sample uncertainty’) both potentially bias estimates of the average and within-group variation of endocranial volume in A. africanus.We used CT scans, electronic preparation (segmentation), mirror-imaging and semilandmark-based geometric morphometrics to generate and reconstruct complete endocasts for Sts 5, Sts 60, Sts 71, StW 505, MLD 37/38, and Taung, and measured their endocranial volumes (EV). To get a sense of the reliability of these new EV estimates, we then used simulations based on samples of chimpanzees and humans to: (a) test the accuracy of our approach, (b) assess missing data uncertainty, and (c) appraise small sample uncertainty.Incorporating missing data uncertainty of the five adult individuals, A. africanus was found to have an average adult endocranial volume of 454-461 ml with a standard deviation of 66-75 ml. EV estimates for the juvenile Taung individual range from 402 to 407 ml. Our simulations show that missing data uncertainty is small given the missing portions of the investigated fossils, but that small sample sizes are problematic for estimating species average EV. It is important to take these uncertainties into account when different fossil groups are being compared.