Cost of departure from optimality in arterial branching

Measurements of branching angles in the arterial tree have in the past indicated a great deal of scatter away from what is expected to be optimum on theoretical grounds. In this study the cost penalty of nonoptimum branching angles is calculated for the first time to determine how far from optimum these angles are. The results lead to the remarkable conclusion that while the scatter of the measured branching angles is fairly large, they represent deviations from optimum angles which correspond to only 2% or so penalty in cost.     

The branching angles in computer-generated optimized models of arterial trees

The structure of a complex arterial tree model is generated on the computer using the newly developed method of "constrained constructive optimization." The model tree is grown step by step, at each stage of development fulfilling invariant boundary conditions for pressures and flows. The development of structure is governed by adopting minimum volume inside the vessels as target function. The resulting model tree is analyzed regarding the relations between branching angles and segment radii. Results show good agreement with morphometric measurements on corrosion casts of human coronary arteries reported in the literature.     

On the principles of the vascular network branching

We propose an explanation of Murray's law without applying the minimality principles. The model deals with a "delivering" artery system of an organ that is characterized, first, by the space-filling embedding into the organ tissue and, second, by the uniform distribution of the blood pressure drop over it. The latter assumption is justified using the available physiological data and the idea about conditions needed for perfect self-regulation. Based on the two statements we get Murray's law, and so, demonstrate that it can be also regarded as a direct consequence of the organism's capacity for controlling finely the blood flow redistribution over peripheral vascular networks.     

Medical ethics: four principles plus attention to scope.

The "four principles plus scope" approach provides a simple, accessible, and culturally neutral approach to thinking about ethical issues in health care. The approach, developed in the United States, is based on four common, basic prima facie moral commitments--respect for autonomy, beneficence, nonmaleficence, and justice--plus concern for their scope of application. It offers a common, basic moral analytical framework and a common, basic moral language. Although they do not provide ordered rules, these principles can help doctors and other health care workers to make decisions when reflecting on moral issues that arise at work.     

Predictions of protein backbone bond distances and angles from first principles

A procedure is described, based on a spline-function representation of ab initio peptide conformational geometry maps, that allows one to predict backbone bond distances and angles of proteins as functions of the peptide ?(N-C^α)/Ψ(C^α-C′) torsions with an accuracy comparable to that of high-resolution protein crystallography. For example, for the more than 40 residues of crambin, the rms deviation between predicted and crystallographic values of N-C^α-C′ is 1.9° for the 1.5 Å resolution structure and 1.9° for the 0.83 Å resolution structure, compared with angle variations of < 10°. Accurate information on protein backbone geometries is important for establishing dictionaries of flexible geometry functions for use in empirical peptide and protein modeling. © 1995 John Wiley & Sons, Inc.     

在生理学研究中如何严格遵循试验设计四原则

目的：为从事生理学研究的科研工作者严格遵循试验设计四原则（以下简称四原则）提供一些有效的技术方法。方法：通过简单介绍"四原则的概念"、举例阐述"生理学研究中在落实四原则方面出现的常见错误和案例"和简单介绍"生理学研究中如何遵循四原则"来阐述遵循四原则的具体做法。结果：需要根据实际情况,选择合适的随机化方法,分层随机化是常用的好方法;应力求设置合理的对照组,才能真正体现出对照原则的价值;有根据地给出每个小组合适的样本含量,是试验结果具有重现性的基本保证;严格遵循随机、对照和重复原则,最终才能实现对比组之间达到极好的均衡效果,这说明均衡原则是一个把关的原则。结论：在生理学科研中,严格遵循四原则对保证生理学研究结果准确可靠至关重要。     

A two-phase growth strategy in cultured neuronal networks as reflected by the distribution of neurite branching angles

Neurite outgrowth and branching patterns are instrumental in dictating the wiring diagram of developing neuronal networks. We study the self-organization of single cultured neurons into complex networks focusing on factors governing the branching of a neurite into its daughter branches. Neurite branching angles of insect ganglion neurons in vitro were comparatively measured in two neuronal categories: neurons in dense cultures that bifurcated under the presence of extrinsic (cellular environment) cues versus neurons in practical isolation that developed their neurites following predominantly intrinsic cues. Our experimental results were complemented by theoretical modeling and computer simulations. A preferred regime of branching angles was found in isolated neurons. A model based on biophysical constraints predicted a preferred bifurcation angle that was consistent with this range shown by our real neurons. In order to examine the origin of the preferred regime of angles we constructed simulations of neurite outgrowth in a developing network and compared the simulated developing neurons with our experimental results. We tested cost functions for neuronal growth that would be optimized at a specific regime of angles. Our results suggest two phases in the process of neuronal development. In the first, reflected by our isolated neurons, neurons are tuned to make first contact with a target cell as soon as possible, to minimize the time of growth. After contact is made, that is, after neuronal interconnections are formed, a second branching strategy is adopted, favoring higher efficiency in neurite length and volume. The two-phase development theory is discussed in relation to previous results.     

Mechanisms underlying leaf photosynthetic acclimation to warming and elevated CO2 as inferred from least‐cost optimality theory

The mechanisms responsible for photosynthetic acclimation are not well understood, effectively limiting predictability under future conditions. Least‐cost optimality theory can be used to predict the acclimation of photosynthetic capacity based on the assumption that plants maximize carbon uptake while minimizing the associated costs. Here, we use this theory as a null model in combination with multiple datasets of C₃ plant photosynthetic traits to elucidate the mechanisms underlying photosynthetic acclimation to elevated temperature and carbon dioxide (CO₂). The model‐data comparison showed that leaves decrease the ratio of the maximum rate of electron transport to the maximum rate of Rubisco carboxylation (J_max/V_cmax) under higher temperatures. The comparison also indicated that resources used for Rubisco and electron transport are reduced under both elevated temperature and CO₂. Finally, our analysis suggested that plants underinvest in electron transport relative to carboxylation under elevated CO₂, limiting potential leaf‐level photosynthesis under future CO₂ concentrations. Altogether, our results show that acclimation to temperature and CO₂ is primarily related to resource conservation at the leaf level. Under future, warmer, high CO₂ conditions, plants are therefore likely to use less nutrients for leaf‐level photosynthesis, which may impact whole‐plant to ecosystem functioning.     

Bayesian profiling for cost with zeros to decompose total cost into probability of cost and mean nonzero cost

Cost of health care can vary substantially across hospitals, centers, or providers. Data from electronic health records provide information for studying patterns of cost variation and identifying high or low cost centers. Cost data often include zero values when patients receive no care, and joint two-part models have been developed for clustered cost data with zeros. Standard methods for center comparisons, sometimes called profiling, can use these methods to incorporate zero values into total cost. However, zero costs also provide opportunities to further examine sources of cost variation and outliers. For example, a hospital may have high (or low) cost due to frequency of nonzero cost, amount of nonzero cost, or a combination of those. We give methods for decomposing hospital differences in total cost with zeros into components for probability of use (i.e., of nonzero cost) and for cost of use (mean of nonzero cost). The components multiply to total cost and quantify components on the same easily interpreted multiplicative scales. The methods are based on Bayesian hierarchical models and counterfactual arguments, with Markov chain Monte Carlo estimation. We used simulated data to illustrate use, interpretation, and visualization of the methods in diverse situations, and applied the methods to 30,024 patients at 57 US Veterans Administration hospitals to characterize outlier hospitals in one year cost of inpatient care following a cardiac procedure. Twenty eight percent of patients had zero cost. These methods are useful in providing insight into cost variation and outliers for planning future studies or interventions.     

Biological optimality: Comparison of generalized feasibility and optimality conditions for linear,error-minimizing systems

An attempt is made to compare the conditions for the general error-optimality of linear systems developed by Kalman with the conditions for feasibility of linear models of neuromuscular and physiological control systems. Models of three actual physiological systems are tested for both the above criteria. Theoretical analysis presented here shows that there are no simple relationships between the two sets of conditions. Analysis carried out on the physiological systems models suggests the need for a general set of conditions for other optimality criteria, such as time and energy minimization, similar to Kalman's condition for error minimization.     

An optimality criterion to determine areas of endemism

A formal method was developed to determine areas of endemism. The study region is divided into cells, and the number of species that can be considered as endemic is counted for a given set of cells (= area). Thus, the areas with the maximum number of species considered endemic are preferred. This is the first method for the identification of areas of endemism that implements an optimality criterion directly based on considering the aspects of species distribution that are relevant to endemism. The method is implemented in two computer programs, NDM and VNDM, available from the authors.     

Beyond hectares: four principles to guide reforestation in the context of tropical forest and landscape restoration

New climate change agreements emerging from the 21st Conference of the Parties and ambitious international commitments to implement forest and landscape restoration (FLR) are generating unprecedented political awareness and financial mobilization to restore forests at large scales on deforested or degraded land. Restoration interventions aim to increase functionality and resilience of landscapes, conserve biodiversity, store carbon, and mitigate effects of global climate change. We propose four principles to guide tree planting schemes focused on carbon storage and commercial forestry in the tropics in the context of FLR. These principles support activities and land uses that increase tree cover in human‐modified landscapes, while also achieving positive socioecological outcomes at local scales, in an appropriate contextualization: (1) restoration interventions should enhance and diversify local livelihoods; (2) afforestation should not replace native tropical grasslands or savanna ecosystems; (3) reforestation approaches should promote landscape heterogeneity and biological diversity; and (4) residual carbon stocks should be quantitatively and qualitatively distinguished from newly established carbon stocks. The emerging global restoration movement and its growing international support provide strong momentum for increasing tree and forest cover in mosaic landscapes. The proposed principles help to establish a platform for FLR implementation and monitoring based on a broad set of socioenvironmental benefits including, but not solely restricted, to carbon mitigation and wood production.     

A two‐phase growth strategy in cultured neuronal networks as reflected by the distribution of neurite branching angles

Neurite outgrowth and branching patterns are instrumental in dictating the wiring diagram of developing neuronal networks. We study the self‐organization of single cultured neurons into complex networks focusing on factors governing the branching of a neurite into its daughter branches. Neurite branching angles of insect ganglion neurons in vitro were comparatively measured in two neuronal categories: neurons in dense cultures that bifurcated under the presence of extrinsic (cellular environment) cues versus neurons in practical isolation that developed their neurites following predominantly intrinsic cues. Our experimental results were complemented by theoretical modeling and computer simulations. A preferred regime of branching angles was found in isolated neurons. A model based on biophysical constraints predicted a preferred bifurcation angle that was consistent with this range shown by our real neurons. In order to examine the origin of the preferred regime of angles we constructed simulations of neurite outgrowth in a developing network and compared the simulated developing neurons with our experimental results. We tested cost functions for neuronal growth that would be optimized at a specific regime of angles. Our results suggest two phases in the process of neuronal development. In the first, reflected by our isolated neurons, neurons are tuned to make first contact with a target cell as soon as possible, to minimize the time of growth. After contact is made, that is, after neuronal interconnections are formed, a second branching strategy is adopted, favoring higher efficiency in neurite length and volume. The two‐phase development theory is discussed in relation to previous results. © 2004 Wiley Periodicals, Inc. J Neurobiol, 2005     

Developmental anatomy and branching of roots of four Zeylanidium species (podostemaceae), with implications for evolution of foliose roots

Podostemaceae have markedly specialized and diverse roots that are adapted to extreme habitats, such as seasonally submerged or exposed rocks in waterfalls and rapids. This paper describes the developmental anatomy of roots of four species of Zeylanidium, with emphasis on the unusual association between root branching and root-borne adventitious shoots. In Z. subulatum and Z. lichenoides with subcylindrical or ribbon-like roots, the apical meristem distal (exterior) to a shoot that is initiated within the meristem area reduces and loses meristematic activity. This results in a splitting into two meristems that separate the parental root and lateral root (anisotomous dichotomy). In Z. olivaceum with lobed foliose roots, shoots are initiated in the innermost zone of the marginal meristem, and similar, but delayed, meristem reduction usually occurs, producing a parenchyma exterior to shoots located between root lobes. In some extreme cases, due to meristem recovery, root lobing does not occur, so the margin is entire. In Z. maheshwarii with foliose roots, shoots are initiated proximal to the marginal meristem and there is no shoot-root lobe association. Results suggest that during evolution from subcylindrical or ribbon-like roots to foliose roots, reduction of meristem exterior to a shoot was delayed and then arrested as a result of inward shifting of the sites of shoot initiation. The evolutionary reappearance of a protective tissue or root cap in Z. olivaceum and Z. maheshwarii in the Zeylanidium clade is implied, taking into account the reported molecular phylogeny and root-cap development in Hydrobryum.     

Bisexual branching processes to model extinction conditions for Y-linked genes

In a two-sex monogamic population, the evolution of the number of carriers of the two alleles of a Y-linked gene is considered. To this end, a multitype bisexual branching model is presented in which it is assumed that the gene has no influence on the mating process. It is deduced from this model that the average numbers of female and male descendants per mating unit constitute the key to determining the extinction or survival of each allele. Moreover, the destiny of each allele in the population is found not to depend on the behavior of the other.     

An equivalence result for integral equations with application to branching processes

A theorem is proved, concerning expected values of a multitype branching process in a varying environment. The consequence of the theorem is that the branching process can be treated (in the sense of expected values) as a dynamical system with control terms. This is of importance in situations where the process serves as an abstract model of the dynamics of malignant cells for use in chemotherapy. A simple example of this kind is given. Work supported by the Polish Academy of Sciences Research Problem No. 10.4.3.01.4.     

On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices

Statistical and biochemical studies have revealed non-random patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslation errors and point mutations, since it is known that when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, using altered forms of the fitness functions used in the prior studies, we have optimized the parameters involved in the calculation of the error minimizing property of the genetic code so that the genetic code outscores the random codes as much as possible. This work also compares two prominent matrices, the Mutation Matrix and Point Accepted Mutations 74-100 (PAM(74-100)). It has been resulted that the hypothetical properties of the coevolution theory of the genetic code are already considered in PAM(74-100), giving more evidence on the existence of bias towards the genetic code in this matrix. Furthermore, our results indicate that PAM(74-100) is biased towards the single base mistranslation occurrences in second codon position as well as the frequency of amino acids. Thus PAM(74-100) is not a suitable substitution matrix for the studies conducted on the evolution of the genetic code.