Physiological significance of the structure and components of the apoplast canal system for water absorption in plants

The non-linear differential equation that describes the coupling between water transport and solute transport in the apoplast canal system in plants was proposed by Katou and Furumoto in 1986. In the present paper, we analytically solved the equation in order to find the law describing the canal system. In the canal system, water transport is regulated linearly by solute transport under physiological conditions. The approximate solution of the differential equations defines the conditions of the structure and components of the apoplast canal for optimal water absorption. Water absorption during cell elongation in plants requires that the apoplast canal be composed of a cell wall with an appropriate diffusion coefficient for solute.     

Structure-approximating inverse protein folding problem in the 2D HP model.

The inverse protein folding problem is that of designing an amino acid sequence which has a particular native protein fold. This problem arises in drug design where a particular structure is necessary to ensure proper protein-protein interactions. In this paper, we show that in the 2D HP model of Dill it is possible to solve this problem for a broad class of structures. These structures can be used to closely approximate any given structure. One of the most important properties of a good protein (in drug design) is its stability--the aptitude not to fold simultaneously into other structures. We show that for a number of basic structures, our sequences have a unique fold.     

Endodontic considerations in the elderly

Tooth retention has increased significantly in older adults, and dentists are now challenged by the need to preserve critical teeth. There will be a need to consider endodontic therapy, and this paper describes how successful endodontics can be provided for elderly patients. Strategic treatment planning is essential, and preservation of key teeth will facilitate satisfactory oral function for elderly patients. These teeth may be important in achieving and maintaining an intact anterior dental arch, for removable partial denture retention or preservation of alveolar bone. In some cases, this can only be achieved if endodontic procedures are undertaken. When infection of a root canal is present, there is no reason why good quality endodontic therapy should not work in a healthy elderly patient. Elimination of infection can be challenging in narrow root canals, and a systematic approach for improving access into and negotiating these canals is outlined.     

分数阶微分方程边值问题正解的唯一性

分数阶微分方程在生物科学和其他领域发挥着重要作用.考虑来类分数阶微分方程边值问题正解的这来性,得到的结证不仅可以保证正解的存在这来,而且可以用于构造迭代序列来逼近这个解.     

Electron-magnetohydrodynamic description of a steady-state current flow in a plasma with a three-dimensional localized density perturbation

The problem of a steady-state current flow through a localized density perturbation is analyzed in the framework of electron magnetohydrodynamics. It is examined how the degree of localization of such a flow depends on the plasma magnetization parameter and the geometric characteristics of the density perturbation. Corrections to the unperturbed current field are found by the iteration method. It is shown that the first-order correction to the current can be determined for an arbitrary perturbation. In the case of perfectly conducting plasma, the second-order correction can be found only for dipole perturbations, for which the integral change in the density is zero. In this case, the first-order correction to the current is localized, which makes possible the existence of the second-order correction. The finite plasma conductivity also assists current localization; therefore, for sufficiently small values of the plasma magnetization parameter, both first- and second-order steady-state corrections to the current can be obtained for any moderate plasma density perturbation.     

RhoGEF2 and the formin Dia control the formation of the furrow canal by directed actin assembly during Drosophila cellularisation

The physical interaction of the plasma membrane with the associated cortical cytoskeleton is important in many morphogenetic processes during development. At the end of the syncytial blastoderm of Drosophila the plasma membrane begins to fold in and forms the furrow canals in a regular hexagonal pattern. Every furrow canal leads the invagination of membrane between adjacent nuclei. Concomitantly with furrow canal formation, actin filaments are assembled at the furrow canal. It is not known how the regular pattern of membrane invagination and the morphology of the furrow canal is determined and whether actin filaments are important for furrow canal formation. We show that both the guanyl-nucleotide exchange factor RhoGEF2 and the formin Diaphanous (Dia) are required for furrow canal formation. In embryos from RhoGEF2 or dia germline clones, furrow canals do not form at all or are considerably enlarged and contain cytoplasmic blebs. Both Dia and RhoGEF2 proteins are localised at the invagination site prior to formation of the furrow canal. Whereas they localise independently of F-actin, Dia localisation requires RhoGEF2. The amount of F-actin at the furrow canal is reduced in dia and RhoGEF2 mutants, suggesting that RhoGEF2 and Dia are necessary for the correct assembly of actin filaments at the forming furrow canal. Biochemical analysis shows that Rho1 interacts with both RhoGEF2 and Dia, and that Dia nucleates actin filaments. Our results support a model in which RhoGEF2 and dia control position, shape and stability of the forming furrow canal by spatially restricted assembly of actin filaments required for the proper infolding of the plasma membrane.     

The approximability of the String Barcoding problem

The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given strings represent a set of known viruses, while the substrings can be used as probes for an hybridization experiment via microarray. Eventually, one aims at the classification of new strings (unknown viruses) through the result of the hybridization experiment. In this paper we show that SBC is as hard to approximate as Set Cover. Furthermore, we show that the constrained version of SBC (with probes of bounded length) is also hard to approximate. These negative results are tight.     

Correction of low-set ear: superoposterior mobilization of the ear as a transposition flap pivoted on the ear canal with burring of the superoposterior canal wall

In a number of congenital, developmental, and postoperative conditions, many patients have a difference in the vertical and anteroposterior position of the ears. On correction of this deformity, the most difficult problem is the low and anterior location of the external auditory canal. To overcome this unyielding limitation, the authors perform superoposterior transposition of the low-set ear pivoted on the ear canal after making a new path for the canal by burring of the thick superoposterior canal wall. A mastoid hairline incision is followed by three-quarters circumferential subpericranial dissection around the bony ear canal posteriorly. A preauricular incision is followed by subcutaneous dissection anteriorly. By using the natural deformability of the cartilaginous ear canal, the S-shaped canal can be straightened through a new path made by burring of the thick superoposterior wall. Then the low-set ear can be mobilized superoposteriorly as a transposition flap pivoted on the ear canal with minimal tension by straightening of the canal. The corrected auricular position can be maintained by (1) several permanent sutures between the cavum conchae and the mastoid and deep temporal fascia, (2) a suspensory temporoparietal fascial loop, and (3) a skin support provided by the repair in an elevated position and V-Y-plasty or Z-plasty on the lower pole of the ear. From December of 1997 to October of 1998, three cases with a maximum follow-up of 15 months were examined. Symmetric ear position was achieved and maintained on both frontal and lateral views after the operation in all cases. This new technique for correction of low-set ear produces symmetric ear position in both vertical and anteroposterior dimensions for a long time. In addition, it can be performed with various other surgical procedures safely and simultaneously in a variety of pathologic conditions.     

The Effect of Incentives and Meta-incentives on the Evolution of Cooperation

Although positive incentives for cooperators and/or negative incentives for free-riders in social dilemmas play an important role in maintaining cooperation, there is still the outstanding issue of who should pay the cost of incentives. The second-order free-rider problem, in which players who do not provide the incentives dominate in a game, is a well-known academic challenge. In order to meet this challenge, we devise and analyze a meta-incentive game that integrates positive incentives (rewards) and negative incentives (punishments) with second-order incentives, which are incentives for other players’ incentives. The critical assumption of our model is that players who tend to provide incentives to other players for their cooperative or non-cooperative behavior also tend to provide incentives to their incentive behaviors. In this paper, we solve the replicator dynamics for a simple version of the game and analytically categorize the game types into four groups. We find that the second-order free-rider problem is completely resolved without any third-order or higher (meta) incentive under the assumption. To do so, a second-order costly incentive, which is given individually (peer-to-peer) after playing donation games, is needed. The paper concludes that (1) second-order incentives for first-order reward are necessary for cooperative regimes, (2) a system without first-order rewards cannot maintain a cooperative regime, (3) a system with first-order rewards and no incentives for rewards is the worst because it never reaches cooperation, and (4) a system with rewards for incentives is more likely to be a cooperative regime than a system with punishments for incentives when the cost-effect ratio of incentives is sufficiently large. This solution is general and strong in the sense that the game does not need any centralized institution or proactive system for incentives.     

The other cooperation problem: generating benefit

Understanding how cooperation evolves is central to explaining some core features of our biological world. Many important evolutionary events, such as the arrival of multicellularity or the origins of eusociality, are cooperative ventures between formerly solitary individuals. Explanations of the evolution of cooperation have primarily involved showing how cooperation can be maintained in the face of free-riding individuals whose success gradually undermines cooperation. In this paper I argue that there is a second, distinct, and less well explored, problem of cooperation that I call the generation of benefit. Focusing on how benefit is generated within a group poses a different problem: how is it that individuals in a group can (at least in principle) do better than those who remain solitary? I present several different ways that benefit may be generated, each with different implications for how cooperation might be initiated, how it might further evolve, and how it might interact with different ways of maintaining cooperation. I argue that in some cases of cooperation, the most important underlying “problem” of cooperation may be how to generate benefit, rather than how to reduce conflict or prevent free-riding.     

Management of textile wastewater for improving growth and yield of field mustard (Brassica campestris L.)

Disposal of industrial wastewater is a current issue of urbanization. However, this problem can be sorted out by using wastewater as an alternate source of irrigation after the addition of some amendment. In this way, the problem of disposal of wastewater not only will be resolved but also scarcity of irrigation water can be kept off in the future. The current research study was performed to evaluate the influence of different concentrations of wastewater along with canal water for enhancing growth and yield of field mustard. Plants were irrigated with different mixtures of canal water and wastewater (75:25, 50:50, 25:75, and 00:100) in addition to canal water as control. The results revealed that application of 50:50% waste and canal water improved plant height, the number of pods plant^?1, pod length, root length, root dry weight, shoot dry weight, 100 grain weight, grain and biomass yield plant^?1, and nitrogen, phosphorus, and potassium concentration in grain and straw up to 16%, 15%, 17%, 29%, 15%, 56%, 25%, 41%, 35%, 20%, 52%, 45%, 20%, 44%, and 42%, respectively, over positive control treatment. While, nutrient uptakes and agronomic efficiency of fertilizers also improved by the application of 50:50% canal and wastewater compared to positive control treatment. Furthermore, the concentration of heavy metals, predominantly Cr, Cu, Cd, and Pb, was reduced in grains by application of 50% canal water and 50% wastewater. The outcomes suggest that wastewater utilization along with canal water mixing might be an effective approach for enhancing growth and yield of field mustard.     

Effect of pooling samples on the efficiency of comparative studies using microarrays

MOTIVATION: Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray experiments for detecting differentially expressed genes, recent publications have addressed the problem of the efficiency of sample pooling, and some approximate formulas were provided for the power and sample size calculations. It is desirable to have exact formulas for these calculations and have the approximate results checked against the exact ones. We show that the difference between the approximate and the exact results can be large. RESULTS: In this study, we have characterized quantitatively the effect of pooling samples on the efficiency of microarray experiments for the detection of differential gene expression between two classes. We present exact formulas for calculating the power of microarray experimental designs involving sample pooling and technical replications. The formulas can be used to determine the total number of arrays and biological subjects required in an experiment to achieve the desired power at a given significance level. The conditions under which pooled design becomes preferable to non-pooled design can then be derived given the unit cost associated with a microarray and that with a biological subject. This paper thus serves to provide guidance on sample pooling and cost-effectiveness. The formulation in this paper is outlined in the context of performing microarray comparative studies, but its applicability is not limited to microarray experiments. It is also applicable to a wide range of biomedical comparative studies where sample pooling may be involved.     

Symmetries of S-systems.

An S-system is a set of first-order nonlinear differential equations that all have the same structure: The derivative of a variable is equal to the difference of two products of power-law functions. S-systems have been used as models for a variety of problems, primarily in biology. In addition, S-systems possess the interesting property that large classes of differential equations can be recast exactly as S-systems, a feature that has been proven useful in statistics and numerical analysis. Here, simple criteria are introduced that determine whether an S-system possesses certain types of symmetries and how the underlying transformation groups can be constructed. If a transformation group exists, families of solutions can be characterized, the number of S-system equations necessary for solution can be reduced, and some boundary value problems can be reduced to initial value problems.     

A penetration-based finite element method for hyperelastic 3D biphasic tissues in contact. Part II: finite element simulations

The penetration method allows for the efficient finite element simulation of contact between soft hydrated biphasic tissues in diarthrodial joints. Efficiency of the method is achieved by separating the intrinsically nonlinear contact problem into a pair of linked biphasic finite element analyses, in which an approximate, spatially and temporally varying contact traction is applied to each of the contacting tissues. In Part I of this study, we extended the penetration method to contact involving nonlinear biphasic tissue layers, and demonstrated how to derive the approximate contact traction boundary conditions. The traction derivation involves time and space dependent natural boundary conditions, and requires special numerical treatment. This paper (Part II) describes how we obtain an efficient nonlinear finite element procedure to solve for the biphasic response of the individual contacting layers. In particular, alternate linearization of the nonlinear weak form, as well as both velocity-pressure, v-p, and displacement-pressure, u-p, mixed formulations are considered. We conclude that the u-p approach, with linearization of both the material law and the deformation gradients, performs best for the problem at hand. The nonlinear biphasic contact solution will be demonstrated for the motion of the glenohumeral joint of the human shoulder joint.     

On the variation in maternal birth canal in vivo viscoelastic properties and their effect on the predicted length of active second stage and levator ani tears

The pubovisceral muscles (PVM) help form the distal maternal birth canal. It is not known why 13% of vaginal deliveries end in PVM tears, so insights are needed to better prevent them because their sequelae can lead to pelvic organ prolapse later in life. In this paper we provide the first quantification of the variation in in vivo viscoelastic properties of the intact distal birth canal in healthy nulliparous women using Fung’s Quasilinear Viscoelastic Theory and a secondary analysis of data from a clinical trial of constant force birth canal dilation to 8 cm diameter in the first stage of labor in 26 nullipara. We hypothesized that no significant inter-individual variation would be found in the long time constant, τ_2, which characterizes how long it takes the birth canal to be dilated by the fetal head. That hypothesis was rejected because τ₂ values ranged 20-fold above and below the median value. These data were input to a biomechanical model to calculate how such variations affect the predicted length of the active second stage of labor as well as PVM tear risk. The results show there was a 100-fold change in the predicted length of active second stage for the shortest and longest τ₂ values, with a noticeable increase for τ₂ values over 1000 s. The correlation coefficent between predicted and observed second stage durations was 0.51. We conclude that τ₂ is a strong theoretical contributor to the time a mother has to push in order to deliver a fetal head larger than her birth canal, and a weak predictor of PVM tear risk.     

Solving the set cover problem and the problem of exact cover by 3-sets in the Adleman-Lipton model

Adleman wrote the first paper in which it is shown that deoxyribonucleic acid (DNA) strands could be employed towards calculating solutions to an instance of the NP-complete Hamiltonian path problem (HPP). Lipton also demonstrated that Adleman's techniques could be used to solve the NP-complete satisfiability (SAT) problem (the first NP-complete problem). In this paper, it is proved how the DNA operations presented by Adleman and Lipton can be used for developing DNA algorithms to resolving the set cover problem and the problem of exact cover by 3-sets.     

Homogenization techniques for population dynamics in strongly heterogeneous landscapes

An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction–diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic environment. We find that population persistence and the large-scale population carrying capacity is influenced by patch residence times that depend on patch preference, as well as movement rates in adjacent patches. The forms of the homogenized coefficients yield key theoretical insights into how large-scale dynamics arise from the small-scale features.     

Characterizing fluorescence recovery curves for nuclear proteins undergoing binding events

Fluorescence recovery after photobleaching (FRAP) is an experimental technique used to measure the mobility of proteins within the cell nucleus. After proteins of interest are fluorescently tagged for their visualization and monitoring, a small region of the nucleus is photobleached. The experimental FRAP data are obtained by recording the recovery of the fluorescence in this region over time. In this paper, we characterize the fluorescence recovery curves for diffusing nuclear proteins undergoing binding events with an approximate spatially homogeneous structure. We analyze two mathematical models for interpreting the experimental FRAP data, namely a reaction-diffusionmodel and a compartmental model. Perturbation analysis leads to a clear explanation of two important limiting dynamical types of behavior exhibited by experimental recovery curves, namely, (1) a reduced diffusive recovery, and (2) a biphasic recovery characterized by a fast phase and a slow phase. We show how the two models, describing the same type of dynamics using different approaches, relate and share common ground. The results can be used to interpret experimental FRAP data in terms of protein dynamics and to simplify the task of parameter estimation. Application of the results is demonstrated for nuclear actin and type H1 histone.