Predicting nose projection and pronasale position in facial approximation: a test of published methods and proposal of new guidelines

Many prediction guidelines exist in facial approximation for determining the soft-tissue features of the face, and the reliability of each is generally unknown. This study examines four published and commonly used soft-tissue prediction guidelines for estimating nose projection, two of which also estimate the position of the pronasale. The methods tested are those described by: 1) Gerasimov ([1971] The Face Finder; London: Hutchinson & Co.), using the distal third of the nasal bones and the nasal spine; 2) Krogman ([1962] The Human Skeleton in Forensic Medicine; Springfield: Charles C. Thomas), using the average soft-tissue depth at midphiltrum, plus three times the length of the nasal spine (and a variation of this technique: plus three times the distance of the tip of the nasal spine from the nasal aperture); 3) Prokopec and Ubelaker ([2002] Forensic Sci Commun 4:1-4), using the reflected profile line of the nasal aperture; and 4) George ([1987] J Forensic Sci 32:1305-1330), using a variation of the Goode method. Four identical hard-tissue tracings were made of 59 adult lateral head cephlograms (29 males, mean age 24, SD 10 years; 30 females, mean age 23, SD 5 years) on separate sheets of tracing paper. One soft-tissue tracing was also made for each radiograph. All tracings were marked with three identical reference points. Soft-tissue tracings were isolated from one of us (C.N.S.), who attempted under blind conditions to predict pronasale position and nose projection on the hard-tissue tracings, using the soft-tissue prediction guides above. Actual soft-tissue tracings were then compared to each of the predicted tracings, and differences in projection/pronasale position were measured. Results indicate that for nose projection, methods 3 and 4 performed well, while methods 1 and 2 performed poorly. Features which are most related to nose projection/pronasale are described in this paper, as are regression equations generated from these variables that predict pronasale/nose projection better than the traditional methods mentioned above. The results of this study are significant because they: 1) indicate that the popular facial approximation methods used to build the nose are inaccurate and produce incorrect nose anatomy; and 2) indicate that the new pronasale prediction methods developed here appear to have less error than traditional methods.     

Proteome analysis of Escherichia coli using high-performance liquid chromatography and Fourier transform ion cyclotron resonance mass spectrometry

The basic problem of complexity poses a significant challenge for proteomic studies. To date two-dimensional gel electrophoresis (2-DE) followed by enzymatic in-gel digestion of the peptides, and subsequent identification by mass spectrometry (MS) is the most commonly used method to analyze complex protein mixtures. However, 2-DE is a slow and labor-intensive technique, which is not able to resolve all proteins of a proteome. To overcome these limitations gel-free approaches are developed based on high performance liquid chromatography (HPLC) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The high resolution and excellent mass accuracy of FT-ICR MS provides a basis for simultaneous analysis of numerous compounds. In the present study, a small protein subfraction of an Escherichia coli cell lysate was prepared by size-exclusion chromatography and proteins were analyzed using C4 reversed phase (RP)-HPLC for pre-separation followed by C18 RP nanoHPLC/nanoESI FT-ICR MS for analysis of the peptide mixtures after tryptic digestion of the protein fractions. We identified 231 proteins and thus demonstrated that a combination of two RP separation steps - one on the protein and one on the peptide level - in combination with high-resolution FT-ICR MS has the potential to become a powerful method for global proteomics studies.     

Variations of the mandibular shape in extant hominoids: Generic, specific, and subspecific quantification using elliptical fourier analysis in lateral view

While a number of studies have documented the mandibular variations in hominoids, few focused on evaluating the variation of the whole outline of this structure. Using an efficient morphometrical approach, i.e. elliptical Fourier analysis, mandibular outlines in lateral view from 578 adult hominoids representing the genera Hylobates, Pongo, Gorilla, Pan, and Homo were quantified and compared. This study confirms that elliptical Fourier analysis provides an accurate characterization of the shape of the mandibular profile. Differences in mandibular shape between hominoid genera, species, subspecies, and to a lesser extent between sexes were demonstrated. Mandibles in great apes and hylobatids subspecies were generally less distinct from each other than were species. However, the magnitudes of differences among subspecies of Gorilla and Pongo approached or exceeded those between Pan troglodytes and P. paniscus. The powerful discrimination between taxa from the genus down to subspecific level associated to the relatively low level of intrageneric mandibular polymorphism in great apes provides strong evidences in support of the taxonomic utility of the shape of the mandibular profile in hominoids. In addition, morphological affinities between Pongo and Pan and the clear distinction between Homo and Pan suggest that the mandibular outline is a poor estimate of phylogenetic relationships in great apes and humans. The sexual dimorphism in mandibular shape exhibits two patterns of expression: a high degree of dimorphism in Gorilla, Pongo, and H. s. syndactylus and a relatively low one in modern humans and Pan. Besides, degree of mandibular shape dimorphism can vary considerably among closely related subspecies as observed in gorillas, arguing against the use of mandibular shape dimorphism patterns as characters in phylogenetic analyses. However, the quantification of the mandibular shape and of the variations among hominoids provides an interesting comparative framework that is likely to supply further arguments for a better understanding of the patterns of differentiation between living hominoids.     

A comparative analysis of leaf shape of wheat, barley and maize using an empirical shape model

Background and Aims

The phenotypes of grasses show differences depending on growth conditions and ontogenetic stage. Understanding these responses and finding suitable mathematical formalizations are an essential part of the development of plant and crop models. Usually, a marked change in architecture between juvenile and adult plants is observed, where dimension and shape of leaves are likely to change. In this paper, the plasticity of leaf shape is analysed according to growth conditions and ontogeny.

Methods

Leaf shape of Triticum aestivum, Hordeum vulgare and Zea mays cultivars grown under varying conditions was measured using digital image processing. An empirical leaf shape model was fitted to measured shape data of single leaves. Obtained values of model parameters were used to analyse the patterns in leaf shape.

Key Results

The model was able to delineate leaf shape of all studied species. The model error was small. Differences in leaf shape between juvenile and adult leaves in T. aestivum and H. vulgare were observed. Varying growth conditions impacted leaf dimensions but did not impact leaf shape of the respective species.

Conclusions

Leaf shape of the studied T. aestivum and H. vulgare cultivars was remarkably stable for a comparable ontogenetic stage (leaf rank), but differed between stages. Along with other aspects of grass architecture, leaf shape changed during the transition from juvenile to adult growth phase. Model-based analysis of leaf shape is a method to investigate these differences. Presented results can be integrated into architectural models of plant development to delineate leaf shape for different species, cultivars and environmental conditions.     

The statistical analysis of tidal rhythms: Tests of the relative effectiveness of five methods using model simulations and actual data

Endogenous rhythms in intertidal organisms are often very complex and imprecise. Thus, confusing results are sometimes obtained when applying various interpretive analytical techniques. In an attempt to resolve this problem, ten different models representing typical organismic tidal‐rhythm displays were created and examined with five different inferential statistical techniques. The exercise was designed to test the relative effectiveness of these techniques in detecting the presence of known cycles in the models, and estimating their period lengths. The same comparison was then repeated on sets of animal‐derived data.

All of the five methods had their merits, but, depending on the model being examined, the results from the various methods were not identical. Three of the techniques produce harmonics, making data that contain multiple periods especially difficult to decipher. Often both tidal and circadian periods are displayed by shore dwellers; all five methods were able to find these two periods. But when the difference in circa period length was close, only one technique (array analysis) could make a distinction. This technique was also the only one able to handle data in which the period was not constant. Interestingly, this simplest of methods is probably the best all‐round method of discovery. Many more subtle, but important, differences were also noted, and it is recommended that more than one method always be used to ensure accuracy.     

Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis

A genome-scale metabolic network reconstruction for Clostridium acetobutylicum (ATCC 824) was carried out using a new semi-automated reverse engineering algorithm. The network consists of 422 intracellular metabolites involved in 552 reactions and includes 80 membrane transport reactions. The metabolic network illustrates the reliance of clostridia on the urea cycle, intracellular L-glutamate solute pools, and the acetylornithine transaminase for amino acid biosynthesis from the 2-oxoglutarate precursor. The semi-automated reverse engineering algorithm identified discrepancies in reaction network databases that are major obstacles for fully automated network-building algorithms. The proposed semi-automated approach allowed for the conservation of unique clostridial metabolic pathways, such as an incomplete TCA cycle. A thermodynamic analysis was used to determine the physiological conditions under which proposed pathways (e.g., reverse partial TCA cycle and reverse arginine biosynthesis pathway) are feasible. The reconstructed metabolic network was used to create a genome-scale model that correctly characterized the butyrate kinase knock-out and the asolventogenic M5 pSOL1 megaplasmid degenerate strains. Systematic gene knock-out simulations were performed to identify a set of genes encoding clostridial enzymes essential for growth in silico.     

PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis

Prediction of protein subcellular localization (PSL) is important for genome annotation, protein function prediction, and drug discovery. Many computational approaches for PSL prediction based on protein sequences have been proposed in recent years for Gram-negative bacteria. We present PSLDoc, a method based on gapped-dipeptides and probabilistic latent semantic analysis (PLSA) to solve this problem. A protein is considered as a term string composed by gapped-dipeptides, which are defined as any two residues separated by one or more positions. The weighting scheme of gapped-dipeptides is calculated according to a position specific score matrix, which includes sequence evolutionary information. Then, PLSA is applied for feature reduction, and reduced vectors are input to five one-versus-rest support vector machine classifiers. The localization site with the highest probability is assigned as the final prediction. It has been reported that there is a strong correlation between sequence homology and subcellular localization (Nair and Rost, Protein Sci 2002;11:2836-2847; Yu et al., Proteins 2006;64:643-651). To properly evaluate the performance of PSLDoc, a target protein can be classified into low- or high-homology data sets. PSLDoc's overall accuracy of low- and high-homology data sets reaches 86.84% and 98.21%, respectively, and it compares favorably with that of CELLO II (Yu et al., Proteins 2006;64:643-651). In addition, we set a confidence threshold to achieve a high precision at specified levels of recall rates. When the confidence threshold is set at 0.7, PSLDoc achieves 97.89% in precision which is considerably better than that of PSORTb v.2.0 (Gardy et al., Bioinformatics 2005;21:617-623). Our approach demonstrates that the specific feature representation for proteins can be successfully applied to the prediction of protein subcellular localization and improves prediction accuracy. Besides, because of the generality of the representation, our method can be extended to eukaryotic proteomes in the future. The web server of PSLDoc is publicly available at http://bio-cluster.iis.sinica.edu.tw/~ bioapp/PSLDoc/.     

Modeling the occurrence of 15 coniferous tree species throughout the Pacific Northwest of North America using a hybrid approach of a generic process‐based growth model and decision tree analysis

Question: Can we interpret how climatic variation limits photosynthesis and growth for one widely distributed species, and then relate these responses to model the geographic distributions of other species? Location: The forested region of the Pacific Northwest, United States and Canada. Methods: We first mapped monthly climatic data, averaged for the period 1950 to 1975 at 1 km resolution across the region. The recorded presence and absence of 15 native tree species were next mapped at 1 km resolution from data acquired on 22 771 field survey plots. To establish seasonal limits on photosynthesis and water use, a process‐based growth model (3‐PG, Physiological Processes to Predict Growth) was parameterized for Douglas‐fir (Pseudotsuga menziesii), one of the most widely distributed species in the region. Automated decision tree analyses were used to predict the distribution of different species by creating a suite of rules associated with the relative constraints that soil drought, atmospheric humidity deficits, suboptimal and subfreezing temperatures would impose on the growth of Douglas‐fir. Results: The 3‐PG process‐based modeling approach, combined with automated decision tree analyses, predicted presence and absence of 15 conifers on field survey plots with an average accuracy of 82±12%. Predictive models of current distribution for each species differed in the number of, order in, and physiological thresholds selected. A deficit in the soil water balance, followed by departures from optimum temperatures in the summer were the two most important variables selected in predicting species distributions. Conclusions: Although empirical models using different sampling techniques and statistical analyses may be more accurate in predicting current distribution of species, the hybrid approach presented in this paper provides a greater mechanistic understanding of the limits to growth and tree distributions. These attributes of process‐based models make them particularly useful in designing mitigating strategies to projected changes in climate.     

A new trajectory analysis method for migratory planthoppers, Sogatella furcifera (Horváth) (Homoptera: Delphacidae) and Nilaparvata lugens (Stål), using an advanced weather forecast model

Abstract 1 A new method of backward trajectory analysis for planthopper migration is presented. The method consists of two components: an advanced weather forecast model, MM5, for weather simulation, and a migration model for trajectory calculation. The weather forecast model simulates wind fields in which trajectories are calculated by the migration model. 2 It is assumed that planthoppers, Sogatella furcifera and Nilaparvata lugens, are transported at wind speeds and in wind directions. The method is evaluated using a migration event observed at Chikugo in Japan on 25 June 1969, which was recorded in hourly catch data. 3 The results indicate that the takeoff responsible for the migration occurred at 21 UTC (Coordinated Universal Time) on 23 June along the coastal region of Fujian province in China. This is the first time that the source region of this event has been accurately identified. Determinations of the migrating duration and height are also consistent with observations. 4 Although the landing process is not considered in the model, it is shown that the method is able to simulate the migration and accurately estimate various parameters. This study also shows the importance of high‐quality weather simulation.