Perspectives of data analysis of enzyme inhibition and activation,Part 2: Parametrical classification of types of enzymatic reactions

A parametrical classification of types of enzymatic reactions that counts 15 types—7 inhibited reactions, 7 activated ones, and 1 type of initial (uninhibited and nonactivated) reaction—is considered. The system permits taking into account the number of parameters of enzymatic reactions and symmetricity of a course of their change. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:101–107, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20272     

Perspectives of data analysis of enzyme inhibition and activation,Part 3: Equations for calculation of the initial rates of enzymatic reactions

Equations for calculation of the initial rates of activated enzymatic reactions and the inhibited enzymatic reactions, unavailable in experimental enzymology, were obtained. Examples of practically using of these equations are given. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:108–118, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20271     

Perspectives of data analysis of enzyme inhibition and activation,part 4: Equations for calculation of constants of enzyme activation and inhibition

Equations for calculation of constants of enzyme activation and nontrivial types of enzyme inhibition, which are not reported in the literature, have been deduced. Examples of using these equations are also presented. © 2010 Wiley Periodicals, Inc. J Biochem Mol Toxicol 24:145–154, 2010; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20316     

The combination of two‐dimensional and three‐dimensional analysis methods contributes to the understanding of glioblastoma spatial heterogeneity

Heterogeneity is regarded as the major factor leading to the poor outcomes of glioblastoma (GBM) patients. However, conventional two‐dimensional (2D) analysis methods, such as immunohistochemistry and immunofluorescence, have limited capacity to reveal GBM spatial heterogeneity. Thus, we sought to develop an effective analysis strategy to increase the understanding of GBM spatial heterogeneity. Here, 2D and three‐dimensional (3D) analysis methods were compared for the examination of cell morphology, cell distribution and large intact structures, and both types of methods were employed to dissect GBM spatial heterogeneity. The results showed that 2D assays showed only cross‐sections of specimens but provided a full view. To visualize intact GBM specimens in 3D without sectioning, the optical tissue clearing methods CUBIC and iDISCO+ were used to clear opaque specimens so that they would become more transparent, after which the specimens were imaged with a two‐photon microscope. The 3D analysis methods showed specimens at a large spatial scale at cell‐level resolution and had overwhelming advantages in comparison to the 2D methods. Furthermore, in 3D, heterogeneity in terms of cell stemness, the microvasculature, and immune cell infiltration within GBM was comprehensively observed and analysed. Overall, we propose that 2D and 3D analysis methods should be combined to provide much greater detail to increase the understanding of GBM spatial heterogeneity.     

High‐dimensional data analysis: Selection of variables,data compression and graphics – Application to gene expression

The paper presents effective and mathematically exact procedures for selection of variables which are applicable in cases with a very high dimension as, for example, in gene expression analysis. Choosing sets of variables is an important method to increase the power of the statistical conclusions and to facilitate the biological interpretation. For the construction of sets, each single variable is considered as the centre of potential sets of variables. Testing for significance is carried out by means of the Westfall‐Young principle based on resampling or by the parametric method of spherical tests. The particular requirements for statistical stability are taken into account; each kind of overfitting is avoided. Thus, high power is attained and the familywise type I error can be kept in spite of the large dimension. To obtain graphical representations by heat maps and curves, a specific data compression technique is applied. Gene expression data from B‐cell lymphoma patients serve for the demonstration of the procedures.     

Linkage mechanisms in the vertebrate skull: Structure and function of three‐dimensional,parallel transmission systems

Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two‐dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four‐bar linkages. Here, we present new, three‐dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure–function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single‐chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing geometries and configurations, enabling novel interpretations of the mechanics of force transmission across a diversity of vertebrate feeding mechanisms and enhancing our understanding of musculoskeletal function and evolution. J. Morphol. 277:1570–1583, 2016. © 2016 Wiley Periodicals, Inc.     

Getting a grip on the evolution of grasping in musteloid carnivorans: a three‐dimensional analysis of forelimb shape

The ability to grasp and manipulate is often considered a hallmark of hominins and associated with the evolution of their bipedal locomotion and tool use. Yet, many other mammals use their forelimbs to grasp and manipulate objects. Previous investigations have suggested that grasping may be derived from digging behaviour, arboreal locomotion or hunting behaviour. Here, we test the arboreal origin of grasping and investigate whether an arboreal lifestyle could confer a greater grasping ability in musteloid carnivorans. Moreover, we investigate the morphological adaptations related to grasping and the differences between arboreal species with different grasping abilities. We predict that if grasping is derived from an arboreal lifestyle, then the anatomical specializations of the forelimb for arboreality must be similar to those involved in grasping. We further predict that arboreal species with a well‐developed manipulation ability will have articulations that facilitate radio‐ulnar rotation. We use ancestral character state reconstructions of lifestyle and grasping ability to understand the evolution of both traits. Finally, we use a surface sliding semi‐landmark approach capable of quantifying the articulations in their full complexity. Our results largely confirm our predictions, demonstrating that musteloids with greater grasping skills differ markedly from others in the shape of their forelimb bones. These analyses further suggest that the evolution of an arboreal lifestyle likely preceded the development of enhanced grasping ability.     

Craniometric variation of some Mediterranean and Atlantic populations of Stenella coeruleoalba (Mammalia,Delphinidae): A three‐dimensional geometric morphometric analysis

The variability of cranial features of Atlantic and Mediterranean samples of Stenella coeruleoalba was examined using a three‐dimensional geometric morphometric approach. Data were collected on 79 skulls from the upper and middle Mediterranean Sea, the Atlantic French coasts, and Scotland. Three‐dimensional x, y, and z coordinates of 27 landmarks were recorded on each left half skull using a Microscribe 3‐D digitizer. All configurations were rotated, centered, and scaled, and residuals from the mean configuration were analyzed through multivariate analyses of variance. Mahalanobis distances among populations were used to evaluate phenetic relationships. Consensus configurations were compared to visualize shape differences among samples. Analyses revealed significant differences among populations, a clear distinction of the Scottish coasts dolphins from the other samples, and a closer relationship of the dolphins from the French coasts to the Mediterranean populations than to the Scottish one. Shape differences are mainly concentrated in the rostral and in the occipital regions of the skull. Phylogenetic and adaptive factors were invoked as possible causes of the variation patterns.     

A new use for synchrotron X‐ray microtomography: three‐dimensional biomechanical modeling of chelicerate mouthparts and calculation of theoretical bite forces

Abstract. We present the first report on the use of the non‐invasive method of synchrotron X‐ray microtomography to model the dynamics and theoretical bite forces of arthropod mouthparts. The nature of the data allowed us to include precise measurements of muscle areas and the spatial geometry of muscle origins and insertions into a biomechanical model of a morphological microstructure. We investigated the functional morphology of the chelicera in the oribatid mite Archegozetes longisetosus (Acari, Oribatida), a model organism for Chelicerata. The chelicera represents a first‐class lever; the intrinsic muscular system consists of a feather‐shaped depressor with six muscle bundles and a bouquet‐shaped levator with 16 bundles. The relative bite forces, as compared with body mass (force/mass^2/3), are 390 N kg^?1 and lie within those known for vertebrates (≤260 N kg^?1) and decapod chelae (≤915 N kg^?1). The dynamics of force transmission and bite forces during the movement of the apotele are calculated. The conserved organization of cheliceral musculature allows broad adaptation of the model to other chelicerate taxa.     

Comparison of design strategies for a three‐arm clinical trial with time‐to‐event endpoint: Power,time‐to‐analysis,and operational aspects

To optimize resources, randomized clinical trials with multiple arms can be an attractive option to simultaneously test various treatment regimens in pharmaceutical drug development. The motivation for this work was the successful conduct and positive final outcome of a three‐arm randomized clinical trial primarily assessing whether obinutuzumab plus chlorambucil in patients with chronic lympocytic lymphoma and coexisting conditions is superior to chlorambucil alone based on a time‐to‐event endpoint. The inference strategy of this trial was based on a closed testing procedure. We compare this strategy to three potential alternatives to run a three‐arm clinical trial with a time‐to‐event endpoint. The primary goal is to quantify the differences between these strategies in terms of the time it takes until the first analysis and thus potential approval of a new drug, number of required events, and power. Operational aspects of implementing the various strategies are discussed. In conclusion, using a closed testing procedure results in the shortest time to the first analysis with a minimal loss in power. Therefore, closed testing procedures should be part of the statistician's standard clinical trials toolbox when planning multiarm clinical trials.     

Three‐dimensional analysis of sexual dimorphism in human thoracic vertebrae: Implications for the respiratory system and spine morphology

Research suggests that nonmaternal caregivers (allomothers) offer essential assistance through caregiving and provisioning, helping to support lengthy child development. Here, we examine the role of allomothers and the broader social and sharing network on Aka forager children's anthropometrics. We hypothesize that nonmaternal investors strategically target their assistance when it is most needed and when it will have the greatest effect. We evaluate children's nutritional status using WHO standards [weight‐for‐age (WAZ), height‐for‐age (HAZ), and weight‐for‐height (WHZ)] during four periods of child development [early infancy (birth to <9 months), mobility to weaning (9 to <36 months), early childhood (36 to <72 months), and middle childhood (72 to <120 months); N = 127]. We explore the effects of allomothers and the social network across these different risk periods and examine whether the broader social network buffers the loss of a primary allomother. ANOVA results suggest that girls may be experiencing some growth faltering, while boys start smaller and remain small across these stages. We used OLS multiple regression models to evaluate the effects of sex, camp composition, risk periods, and allomothers' presence on WAZ, HAZ, and WHZ. Grandmothers are the most influential allomother, with their effect most evident during the 9 to <36 month period. Camp size was also associated with greater WAZ, suggesting that children residing in small camps may be disadvantaged. Our findings also indicate that, under specific residence patterns, cooperative child rearing networks buffer the loss of a grandmother. Overall, our results suggest the importance of social networks to children's nutritional status and that individuals target investment to critical phases. Am J Phys Anthropol 153:513–525, 2014. © 2014 Wiley Periodicals, Inc.     

A direction‐selective local‐thresholding method,DSLT, in combination with a dye‐based method for automated three‐dimensional segmentation of cells and airspaces in developing leaves

Quantifying the anatomical data acquired from three‐dimensional (3D) images has become increasingly important in recent years. Visualization and image segmentation are essential for acquiring accurate and detailed anatomical data from images; however, plant tissues such as leaves are difficult to image by confocal or multi‐photon laser scanning microscopy because their airspaces generate optical aberrations. To overcome this problem, we established a staining method based on Nile Red in silicone‐oil solution. Our staining method enables color differentiation between lipid bilayer membranes and airspaces, while minimizing any damage to leaf development. By repeated applications of our staining method we performed time‐lapse imaging of a leaf over 5 days. To counteract the drastic decline in signal‐to‐noise ratio at greater tissue depths, we also developed a local thresholding method (direction‐selective local thresholding, DSLT) and an automated iterative segmentation algorithm. The segmentation algorithm uses the DSLT to extract the anatomical structures. Using the proposed methods, we accurately segmented 3D images of intact leaves to single‐cell resolution, and measured the airspace volumes in intact leaves.     

The origin of novel features by changes in developmental mechanisms: ontogeny and three‐dimensional microanatomy of polyodontode scales of two early osteichthyans

Recent advances in synchrotron imaging allow us to study the three‐dimensional (3D) histology of vertebrate fossils, including microfossils (e.g. teeth and scales) of early jawed vertebrates. These microfossils can often be scanned at submicron resolution (<1 µm) because of their small size. The resulting voxel (3D pixel) stacks can be processed into virtual thin sections revealing almost every internal detail of the samples, comparable to traditional thin sections. In addition, 3D models of the internal microanatomical structures, such as embedded odontodes and vasculature, can be assembled and examined in situ. Scales of two early osteichthyans, Psarolepis romeri from the Early Devonian of China and Andreolepis hedei from the Late Silurian of Sweden, were scanned using propagation phase‐contrast synchrotron X‐ray microtomography (PPC‐SRµCT), and 3D models of internal canal systems and buried odontodes were created from the scans. Based on these new data, we review the evolutionary origin of cosmine and its associated pore‐canal system, which has been long recognized as a synapomorphy of sarcopterygians. The first odontode that appeared during growth shows almost identical morphology in the two scales, but the second odontode of the Psarolepis scale shows a distinctive morphology with several pores on the surface. It is suggested that a shift from ridge‐like odontode to pore‐bearing odontode was the key step in the origin of cosmine, which was then elaborated further in more‐derived sarcopterygians. We perform a detailed comparison between the two scales and propose a primary homology framework to generate microanatomical characters, which can be used in the phylogenetic analysis of early osteichthyans when more 3D data become available. Our results highlight the importance of 3D data for the study of histology and ontogeny of the dermal skeleton of early jawed vertebrates, especially scales of the polyodontode type. The traditional microvertebrate collection is not only useful for biostratigraphic studies, but also preserves invaluable biological information about the growth of vertebrate hard tissues. Today, we are only beginning to understand the biological meaning of the new 3D data. The increasing availability of such data will enable, and indeed require, a complete revision of traditional palaeohistological studies on early vertebrates.     

Exponential model for a two-ligand,regulatory enzyme. Part 1: Computer programs for the determination of the model constants from initial velocity data

The exponential model for a regulatory enzyme with two ligands (either two substrates or one substrate and an effector) provides an expression for the initial velocity of the catalysed reaction in terms of the fractional saturation of the enzyme by each ligand. This paper describes a program which determines the constants of the model from velocity data, measured with respect to the concentrations of the two ligands, when the corresponding fractional saturations are unknown. Listings of the essential routines, written in BASIC, are provided.     

Cranial ontogeny in the Puma lineage,Puma concolor,Herpailurus yagouaroundi,and Acinonyx jubatus (Carnivora: Felidae): a three‐dimensional geometric morphometric approach

The Puma lineage is a monophyletic group that includes three living species: Puma concolor, Herpailurus yagouaroundi, and Acinonyx jubatus. It has been analysed from ecological and taxonomic perspectives, but their cranial ontogeny has been poorly studied. In this study, we assessed the cranial shape and size variation through three‐dimensional geometric morphometric techniques, and explored the acquisition of definitive shape and size in relation to key life‐history events. Each species occupied different locations in the shape morphospace: A. jubatus and P. concolor showed shorter and wider skulls, with more expanded zygomatic arches, than H. yagouaroundi, which presented the most divergent pattern of change. Ontogeny was more similar between P. concolor and A. jubatus than between the closely related P. concolor and H. yagouaroundi. The evolution of ontogenetic change in the lineage seems to be more influenced by size. Changes detected between juvenile and adult skulls enhanced predatory skills, coincident with the change from a diet of milk to a carnivorous diet. Change patterns suggest that the skull is not morphologically conservative in the lineage, in contrast with other carnivores such as canids and hyaenids. The enlargement of the rostrum observed in some canids and the reinforcement of the bite mechanism of hyaenids were not detected in this group. © 2013 The Linnean Society of London     

Structural requirements essential for elastin coacervation: favorable spatial arrangements of valine ridges on the three‐dimensional structure of elastin‐derived polypeptide (VPGVG)n

The elastin precursor tropoelastin possesses a number of polymeric peptides with repeating 3–9 mer sequences. One of these is the pentapeptide Val‐Pro‐Gly‐Val‐Gly (VPGVG) present in almost all animal species, and its polymer (VPGVG)n coacervates just as does tropoelastin. In the present study, in order to explore the structural requirements essential for coacervation, (VPGVG)n and its shortened repeat analogs (VPGV)n, (VPG)n, and (PGVG)n were synthesized and their structural properties were investigated. In our turbidity measurements, (VPGVG)n demonstrated complete reversible coacervation in agreement with previous findings. The Gly⁵‐deleted polymer (VPGV)n also achieved self‐association, though the onset of self‐association occurred at a lower temperature. However, the dissociation of (VPGV)n upon temperature lowering was found to occur in a three‐step process; the Val_i⁴‐Val_i+1¹ structure arising in the VPGV polypeptide appeared to perturb the dissociation. No self‐association was observed for (VPG)n or (PGVG)n repeats. Spectroscopic measurements by CD, FT‐IR, and ¹H‐NMR showed that the (VPGV)n and (VPG)n both assumed ordered structures similar to that of (VPGVG)n. These results demonstrated that VPGVG is a structural element essential to achieving the β‐spiral structure required for self‐association followed by coacervation, probably due to the ideal spatial arrangement of the hydrophobic Val residues. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

genecap: a program for analysis of multilocus genotype data for non‐invasive sampling and capture‐recapture population estimation

We created genecap to facilitate analysis of multilocus genotype data for use in non‐invasive DNA sampling and genetic capture‐recapture studies. genecap is a Microsoft excel macro that uses multilocus genetic data to match samples with identical genotypes, calculate frequency of alleles, identify sample genotypes that differ by one and two alleles, calculate probabilities of identity, and match probabilities for matching samples. genecap allows the user to include background data and samples with missing genotypes for multiple loci. Capture histories for each user‐defined sampling period are output in formats consistent with commonly employed population estimation programs.     

Combining Multiregional Input‐Output Analysis with a World Trade Model for Evaluating Scenarios for Sustainable Use of Global Resources,Part I: Conceptual Framework

Consumption in a particular country often entails resource extraction, production, and environmental degradation in remote locations. This fact has stimulated a growing body of empirical analysis using input‐output (I‐O) databases and techniques to reveal and quantify the underlying linkages. Two lines of research rooted in I‐O economics, multiregional input‐output (MRIO) analysis and I‐O modeling of the world economy, describe and analyze these relationships, the first for the past, increasingly in the form of footprints and the underlying pathways, and the latter under alternative scenarios about possible courses of action in the future. The article shows how organizing such scenario outcomes into an MRIO database can extend the reach of MRIO analysis to the future while simultaneously supplementing the capabilities of the world trade modeling framework. We describe the compilation of an MRIO database from the results of scenario analysis using the world trade model (WTM) in a companion article (Part II, Implementation); the subsequent application of MRIO techniques to this database permits the evaluation of prospects for the future. We also address several overlooked challenges, namely, the need to include factor endowments and distances between potential trade partners in an MRIO database, the representation of sectors providing transport of internationally traded goods, and the manipulation of mixed physical and money units when both quantities and prices are endogenous.     

Protein–protein‐interactions in a multiplexed,miniaturized format a functional analysis of Rho GTPase activation and inhibition

A miniaturized, bead‐based protein–protein‐interaction assay was developed to study the interaction of Rho GTPases with regulatory proteins. The setup, which uses only minute amounts of sample, was used to analyze small molecules that inhibit the interaction between Rho GTPases and RhoGDIα. Prenylcysteine analogues and the replacement of GDP by non‐hydrolysable GTP analogues prevented the formation of Rho GTPase‐RhoGDIα complexes in a concentration‐dependent manner.