Child mortality, social status, and fertility in India

The incidence of child mortality in relation to the social status and fertility of Indian women was investigated on the assumptions that: 1) the higher the social status, the lower the child mortality rate; and 2) the lower the child mortality rate, the lower the family size. 311 married women in Chandigarh were grouped into 4 status categories: (1) higher educated working women (95); (2) higher educated nonworking women (75); (3) less educated nonworking women (75); and (4) less educated working women (66). The 311 women gave birth to a total of 1075 children (960 living and 115 who had died, mostly between the ages 0-5 years). Percentage of children living (89%) was different for each status category: 93% for category 1; 92% for category 2; 91% for category 3; and 81% for category 4. When analyzed by proportion of women who had lost children in each status category, the relationship between child mortality and social status confirmed the assumption that the higher the social status, the lower the mortality. In category 1, 87% had not experienced any child mortality in their family; in category 2, the figure was 77%; category 3, 72%; and category 4, 48%. The findings also confirmed the other assumption that the lower the mortality rate, the lower the fertility (Table 2).     

Is the biological classification of benthic diatom communities concordant with ecotypes?

In this study a biological classification based on diatom communities (a posteriori classification) was used to search for the most appropriate a priori classification in reference conditions, on the basis of 31 reference sites encompassing eight watersheds in the NE Iberian Peninsula. We considered three different a priori systems for comparison: (i) a typological classification (ecotypes and subecotypes) based on geomorphology and water flow; (ii) the watershed as a unit, irrespective of its size; and (iii) a classification based on the geographical distance between sites under the assumption that biological characteristics are increasingly similar in geographically closer sites. Classification in ecotypes and subecotypes was the most robust with minor differences between them. The watershed (hydrological units) classification was significant though weaker than the typological classification and there was a larger environmental variation within watersheds than within ecotypes. Finally, results showed that geographically closer sites were not more biologically similar in terms of diatom community composition. We can conclude that the ecotypological environmental-based classifications developed by the local water agency did adequately describe the biological classification based on epilithic diatoms.     

A model for determining alveolar and small airway dimensions from aerosol recovery data

A mathematical model is presented that allows the determination of alveolar and small airway dimensions from a series of aerosol recovery measurements performed at different inspiration volumes. The model assumes 1) a symmetric dichotomous lung, 2) representation of airway and alveoli as ensembles of straight tubes, and 3) Gaussian dispersion of the aerosol bolus. Calculations with this model using dimensions given by Weibel show general agreement with experimental data on six human subjects obtained by Palmes et al. (J. Appl. Physiol. 34: 356-360, 1973). Close agreement is found by varying two parameters describing alveolar size and airway size to obtain the best fit. The resulting estimates of size are almost independent of the choice of the dispersion coefficient; however, the estimate of alveolar size is quite dependent on the form of settling assumed during breath holding. The values of alveolar diameter in the six subjects, determined under the assumption of stirred settling, ranged from 0.13 to 0.33 mm, whereas under the assumption of still settling the range was 0.24-0.65 mm. Small airway (generations 18-24) dimensions ranged from 0.41 to 0.66 mm under the still-settling assumption and 0.39 to 0.63 mm under the stirred-settling assumption. With the assumption of an intermediate (partially stirred) form of settling, the alveolar diameter in the six subjects is 0.28 +/- 0.02 mm, in close agreement with morphometric measurements by other investigators. A partially stirred form of settling is also consistent with model predictions of recovery vs. breath-holding time and with cardiogenic gas mixing in the lung.     

Evaluation of Gene Expression Classification Studies: Factors Associated with Classification Performance

Classification methods used in microarray studies for gene expression are diverse in the way they deal with the underlying complexity of the data, as well as in the technique used to build the classification model. The MAQC II study on cancer classification problems has found that performance was affected by factors such as the classification algorithm, cross validation method, number of genes, and gene selection method. In this paper, we study the hypothesis that the disease under study significantly determines which method is optimal, and that additionally sample size, class imbalance, type of medical question (diagnostic, prognostic or treatment response), and microarray platform are potentially influential. A systematic literature review was used to extract the information from 48 published articles on non-cancer microarray classification studies. The impact of the various factors on the reported classification accuracy was analyzed through random-intercept logistic regression. The type of medical question and method of cross validation dominated the explained variation in accuracy among studies, followed by disease category and microarray platform. In total, 42% of the between study variation was explained by all the study specific and problem specific factors that we studied together.     

A common, high-dimensional model of the representational space in human ventral temporal cortex

We present a high-dimensional model of the representational space in human ventral temporal (VT) cortex in which dimensions are response-tuning functions that are common across individuals and patterns of response are modeled as weighted sums of basis patterns associated with these response tunings. We map response-pattern vectors, measured with fMRI, from individual subjects' voxel spaces into this common model space using a new method, "hyperalignment." Hyperalignment parameters based on responses during one experiment--movie viewing--identified 35 common response-tuning functions that captured fine-grained distinctions among a wide range of stimuli in the movie and in two category perception experiments. Between-subject classification (BSC, multivariate pattern classification based on other subjects' data) of response-pattern vectors in common model space greatly exceeded BSC of anatomically aligned responses and matched within-subject classification. Results indicate that population codes for complex visual stimuli in VT cortex are based on response-tuning functions that are common across individuals.     

Methods for estimating the parameters of a linear model for ordered categorical data.

In many empirical analyses, the response of interest is categorical with an ordinal scale attached. Many investigators prefer to formulate a linear model, assigning scores to each category of the ordinal response and treating it as continuous. When the covariates are categorical, Haber (1985, Computational Statistics and Data Analysis 3, 1-10) has developed a method to obtain maximum likelihood (ML) estimates of the parameters of the linear model using Lagrange multipliers. However, when the covariates are continuous, the only method we found in the literature is ordinary least squares (OLS), performed under the assumption of homogeneous variance. The OLS estimates are unbiased and consistent but, since variance homogeneity is violated, the OLS estimates of variance can be biased and may not be consistent. We discuss a variance estimate (White, 1980, Econometrica 48, 817-838) that is consistent for the true variance of the OLS parameter estimates. The possible bias encountered by using the naive OLS variance estimate is discussed. An estimated generalized least squares (EGLS) estimator is proposed and its efficiency relative to OLS is discussed. Finally, an empirical comparison of OLS, EGLS, and ML estimators is made.     

Oscillatory neural network for pattern recognition: trajectory based classification and supervised learning

Computer algorithms that match human performance in recognizing written text or spoken conversation remain elusive. The reasons why the human brain far exceeds any existing recognition scheme to date in the ability to generalize and to extract invariant characteristics relevant to category matching are not clear. However, it has been postulated that the dynamic distribution of brain activity (spatiotemporal activation patterns) is the mechanism by which stimuli are encoded and matched to categories. This research focuses on supervised learning using a trajectory based distance metric for category discrimination in an oscillatory neural network model. Classification is accomplished using a trajectory based distance metric. Since the distance metric is differentiable, a supervised learning algorithm based on gradient descent is demonstrated. Classification of spatiotemporal frequency transitions and their relation to a priori assessed categories is shown along with the improved classification results after supervised training. The results indicate that this spatiotemporal representation of stimuli and the associated distance metric is useful for simple pattern recognition tasks and that supervised learning improves classification results.     

The use of most predictable surfaces for the classification and mapping of taxon assemblages

Most Predictable Surface (MPS) analysis provides a spatially explicit, multivariate technique for the classification and contour maping of taxon assemblages. In this paper, the technique of producing Most Predictable Surfaces is outlined and the application of MPS for the classification and mapping of taxon assemblages is demonstrated using modern pollen spectra from western Canada. The MPS maps are compared with maps of scores from principal components analysis. The strength of MPS is that it provides a classification of sites, a local mapped surface of assemblage distribution, and a global model of the relationship between taxon assemblages and geographic coordinates. The global model relating taxon assemblages to geographic coordinates may be used for indirect gradient analysis if the geographic coordinates can be related to specific environmental factors. Alternatively, independent environmental variables may be used directly in place of geographic coordinates. Potential limitations of MPS include (1) the assumption that the distribution of sites with similar assemblages can be approximated by a polynomial (2) the assumption that only two major taxon assemblages are present in the study area and further subdivision of the assemblages is hierarchical, (3) the assumption of a linear relationship between the taxa, and (4) the requirement of a relatively high ratio of sample sites to taxa. However, the results presented here indicate that MPS can have wide application in analysis of vegetation or any other types of taxon assemblages.Abbreviations MPS Most Predictable Surface     

A classification of compounds in American Sign Language: an evaluation of the Bisetto and Scalise framework

Cross-linguistic comparisons of compounds are difficult because of the varied criteria and terms used by different linguists (Scalise and Bisetto 2009). To address this problem, Scalise and Bisetto proposed a universal three-level classification of compound types. Although several researchers have shown that American Sign Language (ASL) has compound signs, a classification of compound types in ASL has not been completed. All of the potential compounds in an ASL dictionary (Costello 1994) were identified, then verified as compounds with the help of a fluent deaf signer by applying standard tests for composition. These compounds were then classified using the Scalise and Bisetto classification. We found that Scalise and Bisetto??s three-level hierarchical classification successfully captured cross-category relationships among subtypes of compounds but fails to predict the existence of one type of compound attested in ASL. In our revised classification, a?consistent set of criteria is used at each level, resulting in a classification that is both conceptually simpler and empirically more adequate. The second tier category for hierarchical compounds are bifurcated into the categories expressed predicate and unexpressed predicate, according to whether each predicate in a compound??s semantic structure is expressed by one of the overt constituents. The revision has the further advantage of allowing us to avoid any reference to word class/grammatical category in applying our taxonomy, a goal that we show to be desirable on both theoretical and empirical grounds.     

Distribution model of organism development times

It is shown in this analysis that the distribution of organism development times for constant and variable temperatures can be described based upon one simple assumption. This assumption is that the concentration of enzymes which are rate controlling for development are symmetrically distributed about some genetically determined mean concentration. It then follows mathematically that the skew in the distribution in development times, observed by Stinner, Butler, Bacheler & Tuttle (1975) and others, results naturally from the transformation from development rates to emergence times. The distribution model is shown to agree with observed data for (i) boll weevil, Anthonomus grandis Boheman, and (ii) cotton fleahopper, Pseudatomoscelis seriatus Reuter, reared under both constant and variable temperature regimes. The resulting model enables predictions of the distribution of emergence times for organisms reared under any set of variable temperature field conditions.     

Sexual isolation in Drosophila. II. Intraspecific variation in mate recognition systems

A simple behavioral model is used to investigate whether differences in the specific-mate-recognition system (SMRS), occur within species of the Drosophila genus. This model takes into account, and overcomes, the distorting effect of vigor differences on experimental results. Analysis shows significant deviations from the expected values under the assumption of identical SMRSs in around one fifth of the multiple-choice experiments performed with natural strains of twelve different Drosophila species. Different selection procedures raise the number of significant assortative mating results between strains of D. melanogaster and D. pseudoobscura from 3.0% to 32.8%. Finally, sub- or semispecific taxa show variations in their SMRS even more frequently (74.5%). Differences in male vigor and female receptivity are also found. These results show that a classification of Drosophila species based on SMRS stability, as proposed by the “Recognition concept of species”, is virtually impossible.     

Can the Tumor Deposits Be Counted as Metastatic Lymph Nodes in the UICC TNM Staging System for Colorectal Cancer?

Objective

The 7th edition of AJCC staging manual implicitly states that only T1 and T2 lesions that lack regional lymph node metastasis but have tumor deposit(s) will be classified in addition as N1c, though it is not consistent in that pN1c is also an option for pT3/T4a tumors in the staging table. Nevertheless, in this TNM classification, how to classify tumor deposits (TDs) in colorectal cancer patients with lymph node metastasis (LNM) and TDs simultaneously is still not clear. The aim of this study is to investigate the possibility of counting TDs as metastatic lymph nodes in TNM classification and to indentify its prognostic value for colorectal cancer patients.

Methods and Results

In this retrospective study, 513 cases of colorectal cancer with LNM were reviewed. We proposed a novel pN (npN) category in which TDs were counted as metastatic lymph nodes in the TNM classification. Cancer-specific survival according to the npN or pN category was analyzed using Kaplan-Meier survival curves. Univariate and multivariate analyses were performed to indentify significant prognostic factors. Harrell''s C statistic was used to test the predictive capacity of the prognostic models. The results revealed that the TD was a significant prognostic factor in colorectal cancer. Univariate and multivariate analyses uniformly indicated that the npN category was significantly correlated with prognosis. The results of Harrell''s C statistical analysis demonstrated that the npN category exhibited a superior predictive capacity compared to the pN category of the 7th edition TNM classification. Moreover, we also found no significant prognostic differences in patients with or without TD in the same npN categories.

Conclusions

The counting of TDs as metastatic lymph nodes in the TNM classification system is potentially superior to the classification in the 7th edition of the TNM staging system to assess prognosis and survival for colorectal cancer patients.     

Dependent competing risks: a stochastic process model

Analyses of human mortality data classified according to cause of death frequently are based on competing risk theory. In particular, the times to death for different causes often are assumed to be independent. In this paper, a competing risk model with a weaker assumption of conditional independence of the times to death, given an assumed stochastic covariate process, is developed and applied to cause specific mortality data from the Framingham Heart Study. The results generated under this conditional independence model are compared with analogous results under the standard marginal independence model. Under the assumption that this conditional independence model is valid, the comparison suggests that the standard model overestimates by 4% the effect on life expectancy at age 30 due to the hypothetical elimination of cancer and by 7% the effect for cardiovascular/cerebrovascular disease. By age 80 the overestimates were 11% for cancer and 16% for heart disease. These results suggest the importance of avoiding the marginal independence assumption when appropriate data are available — especially when focusing on mortality at advanced ages.     

A Posteriori and a Priori Methodologies for Testing Hypotheses of Causal Processes in Vicariance Biogeography

Methods used in vicariance biogeography fall into the categories of a posteriori methods (e.g., Component Compatibility Analysis and Brooks Parsimony Analysis) and a priori methods (e.g., Component Analysis, Reconciled Tree Analysis, and Three Area Statement Analysis). Each category corresponds to a particular methodology that arrives at general area cladograms by testing null hypotheses in a particular way. A posteriori methods assume the process of vicariance only (A0) as a common cause of the distribution of different monophyletic groups of taxa under the null hypothesis. Whenever a parsimony analysis of combined data from these monophyletic groups results in a general area cladogram with homoplasy, the null hypothesis is rejected and extinction and dispersal are invoked a posteriori as ad hoc process explanations. A priori methods assume not only vicariance (A0) but also combinations of vicariance with the processes of extinction (A1) and dispersal (A2) as possible causes of the distribution of the taxa of different monophyletic groups. Each assumed set of processes corresponds to a different null hypothesis. Under the assumption of independence and thus additivity of the processes involved, the sets of area cladograms obtained under A0, A1, and A2 from data of each monophyletic group must be inclusive (requirement I). Whenever no congruent area cladograms are found in the intersection of sets of area cladograms derived under the same assumption for different monophyletic groups (II), the corresponding null hypothesis is rejected.     

General Regression and Representation Model for Classification

Recently, the regularized coding-based classification methods (e.g. SRC and CRC) show a great potential for pattern classification. However, most existing coding methods assume that the representation residuals are uncorrelated. In real-world applications, this assumption does not hold. In this paper, we take account of the correlations of the representation residuals and develop a general regression and representation model (GRR) for classification. GRR not only has advantages of CRC, but also takes full use of the prior information (e.g. the correlations between representation residuals and representation coefficients) and the specific information (weight matrix of image pixels) to enhance the classification performance. GRR uses the generalized Tikhonov regularization and K Nearest Neighbors to learn the prior information from the training data. Meanwhile, the specific information is obtained by using an iterative algorithm to update the feature (or image pixel) weights of the test sample. With the proposed model as a platform, we design two classifiers: basic general regression and representation classifier (B-GRR) and robust general regression and representation classifier (R-GRR). The experimental results demonstrate the performance advantages of proposed methods over state-of-the-art algorithms.     

A morphological classification of plants,with special reference to the New Zealand alpine flora

Abstract. A plant is a complex of integrated systems (leaves, leaf groups, stems, roots, inflorescences), coexisting side by side or superimposed on each other to produce the life form (orphysiognomy) of the individual. The classic Raunkiaer classification based fundamentally on one character (apex position) is insufficient for the purpose of a functional classification. Five keys are given to determine the categories of:

• 1) the plant silhouette or general shape resulting from a combination of other systems, with 11 categories proposed;
• 2) the leaf group, with 14 categories;
• 3) the stem, with 27 categories;
• 4) the root, with 5 categories; and
• 5) the inflorescence, with 3 categories.

Each plant can be named according to the category or model of each of the five different systems that they most resemble, or by using only the name(s) of systems which are more conspicuous than others. Characters are selected primarily for their influence on form and secondarily on size. This scheme allows for detailed studies of a flora in terms of morphological characteristics (alone or in systems), expressed as frequency of occurrence of each character in the flora. Characters can be analysed separately (e.g. entire margined leaves), as a combination of characters (e.g. leaf groups) or as a combination of systems (e.g. rosettes without stems). Thus correlations between environmental variables and plants canbe made with more precision than in previous classification schemes. The classification also serves as the framework for including additional morphological data and incorporating new models. The New Zealand alpine flora is used as a test case and to exemplify the classification.     

Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

Rates of Agonism by Diurnal Lemuroids: Implications for Female Social Relationships

Sterck and colleagues (Behaviour 134:749–774, 1997) focused attention on the evolutionary ecology of female social relationships within and between groups and proposed a model that distinguishes 4 categories of female relationships, which correspond to particular types of intra- and intergroup competition. They emphasized literature on haplorhines in their model because of numerous, detailed studies conducted on a range of species in the wild; in contrast, strepsirrhines such as the lemuroids are poorly represented. We evaluate more closely their classification of lemuroids as Dispersal-Egalitarian using a greater number of species of Lemur, Eulemur, Varecia, Hapalemur, Indri, and Propithecus. For the focal species we found that female philopatry occurs rarely, agonistic rates are relatively low, female dominance hierarchies are not stable and do not exist year-round, and intra- and intergroup female-female competition is infrequent. Therefore, our results support the suggestion that a majority of lemuroid taxa we surveyed correspond to the Dispersal-Egalitarian category with 2 probable exceptions: Lemur catta and Propithecus edwardsi. Because female Lemur catta are philopatric, have year-round dominance hierarchies with female matrilines, exhibit the highest rates of agonism in studied lemuroids, and have frequent intra- and intergroup female-female competition, it would seem that they more closely correspond to the category Resident-Nepotistic. However, maternal Lemur catta rarely support their offspring in agonistic contests and matrilineal rank is not inherited, which leads us to state that the species does not fit into any existing category that explains the nature of female social relationships. The relationships of female Propithecus edwardsi are also a challenge to categorize under the current model because some of their characteristics —typical female dispersal and low agonistic rates— fall into the Dispersal-Egalitarian category, yet other behaviors —intense targeted aggression and stable and year-round female dominance hierarchies— do not.     

Modelling eye movements in a categorical search task

We introduce a model of eye movements during categorical search, the task of finding and recognizing categorically defined targets. It extends a previous model of eye movements during search (target acquisition model, TAM) by using distances from an support vector machine classification boundary to create probability maps indicating pixel-by-pixel evidence for the target category in search images. Other additions include functionality enabling target-absent searches, and a fixation-based blurring of the search images now based on a mapping between visual and collicular space. We tested this model on images from a previously conducted variable set-size (6/13/20) present/absent search experiment where participants searched for categorically defined teddy bear targets among random category distractors. The model not only captured target-present/absent set-size effects, but also accurately predicted for all conditions the numbers of fixations made prior to search judgements. It also predicted the percentages of first eye movements during search landing on targets, a conservative measure of search guidance. Effects of set size on false negative and false positive errors were also captured, but error rates in general were overestimated. We conclude that visual features discriminating a target category from non-targets can be learned and used to guide eye movements during categorical search.