The effect of water movement on the distribution of Oligochaeta in lakes

The Oligochaeta are more exposed to disturbance under conditions of intense water movement than other invertebrates, particularly when the substrate is unstable. Furthermore, low mobility of bottom water, which can lead to excessive accumulation of organic matter in sediments, and to the formation of sapropel, can also be limiting to the distribution of oligochaetes. Organic contamination in conditions of low water dynamics can result in the absence of Oligochaeta through oxygen depletion. Dynamic water movement can stimulate the mass development of Oligochaeta in organically polluted areas.     

Dynamics of the interaction of polyreactive immunoglobulins with immobilized antigens]

The kinetic of polyreactive immunoglobulins (PRIG) and immobilized antigen interaction was examined at different temperatures. It was shown that this process can be described by the so-called "competitive" model, and the relatively simple method for the rate constant determination for this process was developed. According to the "competitive" model PRIG molecule could be either in "active" or in "inactive" state and dynamic equilibrium exist between "active" and "inactive" molecules which strongly depend on incubation temperature. Only "active" PRIG can interact with antigens, and this is the reason of strong temperature dependence of PRIG-antigen interaction. The data also show that the mechanism of PRIG-antigen interaction differ from that of antibody-antigen interaction.     

Metal accumulation by fungi: Applications in environmental biotechnology

Summary Fungi can accumulate metal and radionuclide species by physico-chemical and biological mechanisms including extracellular binding by metabolites and biopolymers, binding to specific polypeptides and metabolism-dependent accumulation. Biosorptive processes appear to have the most potential for environmental biotechnology. Biosorption consists of accumulation by predominatly metabolism-independent interactions, such as adsorptive or ion-exchange processes: the biosorptive capacity of the biomass can be manipulated by a range of physical and chemical treatments. Immobilized biomass retains biosorptive properties and possesses a number of advantages for process applications. Native or immobilized biomass can be used in fixed-bed, air-lift or fluidized bed bioreactors; biosorbed metal/radionuclide species can be removed for reclamation and the biomass regenerated by simple chemical treatments.     

Toward consistent definitions for preload and afterload

Significant differences exist among textbook definitions for the terms preload and afterload, leading to confusion and frustration among students and faculty alike. Many faculty also chose to use in their teaching simple terms such as "end-diastolic volume" or "aortic pressure" as common-usage approximations of preload and afterload, respectively, but these are only partial representations of these important concepts. Straightforward definitions both of preload and afterload that are concise yet still comprehensive can be developed using the Law of LaPlace to describe the relationships among chamber pressure, chamber radius, and wall thickness. Within this context, the term "preload" can be defined as all of the factors that contribute to passive ventricular wall stress (or tension) at the end of diastole, and the term "afterload" can be defined as all of the factors that contribute to total myocardial wall stress (or tension) during systolic ejection. The inclusion of "wall stress" in both definitions helps the student appreciate both the complexities of cardiac pathophysiology and the rationale for therapeutic intervention.     

Scope for growth in Gammarus pulex,a freshwater benthic detritivore

Although toxic substances affect the physiological processes of individual organisms, their ecological impacts occur at the population and community levels. However, physiological processes can often be assessed more easily and precisely than population and community ones. Here we argue that scope for growth, the difference between the energy input to an organism from its food and the output from respiratory metabolism, can give a good physiological measure of stress that, at least in principle, is straightforwardly related to population and community processes. We describe, in detail, how scope for growth can be measured in Gammarus pulex (Crustacea, Amphipoda). The results indicate that both zinc and low pH can significantly reduce the scope for growth of individuals and that the most sensitive component of the energy budget is food absorption.     

Confusion and controversy in the stress field.

An attempt is made to further clarify present areas of controversy in the stress field, in response to a two-part article by Dr. John W. Mason which concludes in this issue of the Journal of Human Stress. The author tries to elucidate each source of confusion enumerated by Dr. Mason. The continued use of the word "stress" for the nonspecific response to any demand is deemed most desirable. The once vague term can now be applied in a well-defined sense and is accepted in all foreign languages as well, including those in which no such word existed previously in any sense. Subdivision of the stress concept has become necessary as more recent work has led to such notions as "eustress," "distress," "systemic stress" and "local stress." Confusion between stress as both an agent and a result can be avoided only by the distinction between "stress" and "stressor". It is explained that the stress syndrome is--by definition--nonspecific in its causation. However, depending upon conditioning factors, which can selectively influence the reactivity of certain organs, the same stressor can elicit different manifestations in different individuals.     

Estimating position-time relationships in steady-state,one-dimensional growth zones

Two methods are described for estimating position-time relationships (pathlines) in steady, one-dimensional growth zones. Pathlines can be used to provide a time base for spatial data in developmental studies. The methods apply within extension-only zones (zones of growth without cell division) and require data for cell-number densities, or cumulative cell numbers, or mean cell lengths, and for the overall elongation rate of an organ. The first method (continuous-pathline method) can be used to estimate spatial velocity fields within extension-only zones and pathlines can then be obtained by integration of the velocity data. This method is based on the continuity equation for cell-number densities. Pathlines can also be estimated using a simple graphical version of this method. The second method (pathline-coordinate method) is based on the approximation that a cell of mean length remains of mean length as it moves through the extension-only zone, and can be used to estimate the coordinates of wall pathlines at discrete intervals. The methods are illustrated using published data from studies of apical growth in Zea mays L. roots and of intercalary growth in Triticum aestivum L. leaves.     

Effective norm emergence in cell systems under limited communication

Background

The cooperation of cells in biological systems is similar to that of agents in cooperative multi-agent systems. Research findings in multi-agent systems literature can provide valuable inspirations to biological research. The well-coordinated states in cell systems can be viewed as desirable social norms in cooperative multi-agent systems. One important research question is how a norm can rapidly emerge with limited communication resources.

Results

In this work, we propose a learning approach which can trade off the agents’ performance of coordinating on a consistent norm and the communication cost involved. During the learning process, the agents can dynamically adjust their coordination set according to their own observations and pick out the most crucial agents to coordinate with. In this way, our method significantly reduces the coordination dependence among agents.

Conclusion

The experiment results show that our method can efficiently facilitate the social norm emergence among agents, and also scale well to large-scale populations.

     

Attacking the bottlenecks of backfilling schedulers

Backfilling is a simple and effective way of improving the utilization of spacesharing schedulers. Simple firstcomefirstserved approaches are ineffective because large jobs can fragment the available resources. Backfilling schedulers address this problem by allowing jobs to move ahead in the queue, provided that they will not delay subsequent jobs. Previous research has shown that inaccurate estimates of execution times can lead to better backfilling schedules. In the first part of this study, we characterize this effect on several workloads, and show that average slowdowns can be effectively reduced by systematically lengthening estimated execution times. Further, we show that the average job slowdown metric can be addressed directly by sorting jobs by increasing execution time. Finally, we modify our sorting scheduler to ensure that incoming jobs can be given hard guarantees. The resulting scheduler guarantees to avoid starvation, and performs significantly better than previous backfilling schedulers. In the second part of this study, we show how queue randomization and even more a combination of queue randomization and sorting by job length can improve performance. We show that these improvements are better than with queue sorting by job length alone in the simulation with actual estimates of job running times. We investigate the real characteristics of these estimates, and show the wide range of overestimation. To exploit even more randomization and queue sorting, we eliminate guarantees from backfilling algorithm, and show significant improvements. Finally, we show a limited usefulness of these guarantees, and show that queue sorting criteria can be modified to prevent starvation in the modified backfilling algorithm.     

Caspase-1-Mediated Pyroptosis of the Predominance for Driving CD4$$^{}$$ T Cells Death: A Nonlocal Spatial Mathematical Model

Caspase-1-mediated pyroptosis is the predominance for driving CD4\(^{+}\) T cells death. Dying infected CD4\(^{+}\) T cells can release inflammatory signals which attract more uninfected CD4\(^{+}\) T cells to die. This paper is devoted to developing a diffusive mathematical model which can make useful contributions to understanding caspase-1-mediated pyroptosis by inflammatory cytokines IL-1\(\beta \) released from infected cells in the within-host environment. The well-posedness of solutions, basic reproduction number, threshold dynamics are investigated for spatially heterogeneous infection. Travelling wave solutions for spatially homogeneous infection are studied. Numerical computations reveal that the spatially heterogeneous infection can make \(\mathscr {R}_0>1\), that is, it can induce the persistence of virus compared to the spatially homogeneous infection. We also find that the random movements of virus have no effect on basic reproduction number for the spatially homogeneous model, while it may result in less infection risk for the spatially heterogeneous model, under some suitable parameters. Further, the death of infected CD4\(^{+}\) cells which are caused by pyroptosis can make \(\mathscr {R}_0<1\), that is, it can induce the extinction of virus, regardless of whether or not the parameters are spatially dependent.     

基于信息化平台的临床科室精准管理探索

精准医学时代,临床科室的“精准管理”是应用高度结构化、自动化、精准化的信息管理平台进行科室的全面监管和预警,能够通过精准预测,精准监督,精准定位来提高预测准确性和预测能力,制定合理有效的计划目标,规范医疗诊疗行为,改进医疗服务流程,提高科研效率质量以及有针对性地进行人才培养和个性化教学管理,在医院的科室管理中具有较好的临床应用性及推广价值。     

Biohumanities: rethinking the relationship between biosciences, philosophy and history of science, and society

We argue that philosophical and historical research can constitute a "Biohumanities" that deepens our understanding of biology itself engages in constructive "science criticism," helps formulate new "visions of biology," and facilitates "critical science communication." We illustrate these ideas with two recent "experimental philosophy" studies of the concept of the gene and of the concept of innateness conducted by ourselves and collaborators. We conclude that the complex and often troubled relations between science and society are critical to both parties, and argue that the philosophy and history of science can help to make this relationship work.     

Biological chromatology. The laws of colour and design in nature

Summary Biochromatology can be defined as the study of the relationships between colours, and between colours and design in nature. Certain laws concerning biochromatics can be formulated in the terminology of the Colour Circle. One of them is that planes in warm colours and planes in cold colours never adjoin. Another law is that design is never polychromatic. It seems that the observed biochromatical facts can be explained with the help of the principle optimal manifestation of colour, which in turn is based on the formative principles of matter itself.     

THE EVOLUTION OF REVERSIBLE SWITCHES IN THE PRESENCE OF IRREVERSIBLE MIMICS

Reversible phenotypic switching can be caused by a number of different mechanisms including epigenetic inheritance systems and DNA-based contingency loci. Previous work has shown that reversible switching systems may be favored by natural selection. Many switches can be characterized as "on/off" where the "off" state constitutes a temporary and reversible loss of function. Loss-of-function phenotypes corresponding to the "off" state can be produced in many different ways, all yielding identical fitness in the short term. In the long term, however, a switch-induced loss of function can be reversed, whereas many loss-of-function mutations, especially deletions, cannot. We refer to these loss-of-function mutations as "irreversible mimics" of the reversible switch. Here, we develop a model in which a reversible switch evolves in the presence of both irreversible mimics and metapopulation structure. We calculate that when the rate of appearance of irreversible mimics exceeds the migration rate, the evolved reversible switching rate will exceed the bet-hedging rate predicted by panmictic models.     

Originator dynamics

We study the origin of evolution. Evolution is based on replication, mutation, and selection. But how does evolution begin? When do chemical kinetics turn into evolutionary dynamics? We propose "prelife" and "prevolution" as the logical precursors of life and evolution. Prelife generates sequences of variable length. Prelife is a generative chemistry that proliferates information and produces diversity without replication. The resulting "prevolutionary dynamics" have mutation and selection. We propose an equation that allows us to investigate the origin of evolution. In one limit, this "originator equation" gives the classical selection equation. In the other limit, we obtain "prelife." There is competition between life and prelife and there can be selection for or against replication. Simple prelife equations with uniform rate constants have the property that longer sequences are exponentially less frequent than shorter ones. But replication can reverse such an ordering. As the replication rate increases, some longer sequences can become more frequent than shorter ones. Thus, replication can lead to "reversals" in the equilibrium portraits. We study these reversals, which mark the transition from prelife to life in our model. If the replication potential exceeds a critical value, then life replicates into existence.     

"DIROM"--an interactive system for planning experiments on directed mutagenesis and design of artificial genes]

We present a computer system "DIROM" for oligonucleotide-directed mutagenesis and artificial gene design experiments planning and support. "DIROM" allows to search for optimal oligonucleotides according to such parameters as sufficient energy of oligonucleotide-target hybridization, secondary structure of oligonucleotide and target DNA, presence of alternative attachment sites in target DNA, terminal G/C pairs presence. Both single-stranded and double-stranded vector mutagenesis methods are implemented. It can be also used for optimal primer selection for polymerase chain reaction, sequencing etc. "DIROM" can search for both existent and potential carry out vector+target sequence construction. Both amino acid and nucleotide sequences can be operated.     

Origin of translation: The hypothesis of permanently attached adaptors

A mechanism for prebiotic translation is proposed in which primeval transfer-RNA (adaptors) are assumed to be permanently associated with messenger nucleic acid molecules. Residual fossil evidences are found to be present within the base sequences of contemporary tRNAs, suggesting the existence of inter-primal-tRNA interactions necessary for the mechanism. The structure of proposed primal-tRNA is such that it can not only choose its own amino acid in the absence of aminoacyl synthetase, but can also associate nonspecifically with adjacent primal-tRNA molecules attached to the neighbouring codons. Such associations can give rise, through cooperative binding between message and adaptors to the static template surfaces which can direct translation of nucleotide sequences into those of amino acids. The origins of ribosomes and contemporary genetic code are suggested by this hypothesis. Proposed structures and processes are thermodynamically compatible. The approximate date of occurence of the proposed system is calculated, which is consistent with the period of occurence of the earliest organisms with ribosomes.     

The Endolysosomal System in Cell Death and Survival

The endocytic pathway is a system specialized for the uptake of compounds from the cell microenvironment for their degradation. It contains an arsenal of hydrolases, including proteases, which are normally enclosed in membrane-bound organelles, but if released to the cytosol can initiate apoptosis signaling pathways. Endogenous and exogenous compounds have been identified that can mediate destabilization of lysosomal membranes, and it was shown that lysosomal proteases are not only able to initiate apoptotic signaling but can also amplify the apoptotic pathways initiated in other cellular compartments. The endocytic pathway also receives cargo destined for degradation via the autophagic pathway. By recycling energy and biosynthetic substrates, and by degrading damaged organelles and molecules, the endocytic system assists the autophagic system in resisting apoptotic stimuli. Steps leading to lysosomal membrane permeabilization and subsequent triggering of cell death as well as the therapeutic potential of intervention in lysosomal membrane permeabilization will be discussed.Since the discovery of lysosomes in 1950s (de Duve et al. 1955), the concept of the endocytic pathway has changed. Although there has been huge progress in understanding the molecular mechanisms of targeting and fusion of organelles, several conceptual dilemmas have not been completely resolved. The primary function of the endocytic pathway is bulk degradation and recycling of the internalized material and redundant cellular components. Over the years, additional functions have been associated with it. Endosomes and lysosomes can fuse with the plasma membrane to repair it and to release the accumulated nondegradable material (Medina et al. 2011). Intraluminal vesicles are the source of exosomes, which have multiple functions, especially for the immune system (Ludwig and Giebel 2012). Endosomes have numerous functions in fighting infections: they can signal the presence of pathogens through Toll-like receptors, they are the site of antigenic peptide generation and their assembly with major histocompatibility complex class II molecules, and they can also kill residing pathogens (Gruenberg and van der Goot 2006). Because of a high content of proteases, de Duve (1959) coined the figurative term “suicide bags” for lysosomes, a concept since supported by a wealth of experimental reports (de Duve 1959). Perhaps the best examples of this concept are natural killer cells and cytotoxic T cells. Both have specialized lysosome-related organelles, secretory granules, that contain perforin and granzyme B, which can mediate apoptosis in the target cell (Blott and Griffiths 2002; Trapani and Smyth 2002). However, every cell can potentially become a victim of its own lysosomal hydrolases, especially if lysosomal membranes are destabilized so that the enzymes can escape into the cytosol. These offer great potential to exploit scenarios for therapy for certain diseases, most importantly cancer. On the other hand, by enabling degradation of the material sequestered by autophagy, the endocytic pathway can assist autophagy in counteracting apoptosis when cells are challenged with an apoptotic stimulus (Repnik and Turk 2010; Hafner Česen et al. 2012; Repnik et al. 2012).     

Random perturbations of spiking activity in a pair of coupled neurons

We examine the effects of stochastic input currents on the firing behaviour of two coupled Type 1 or Type 2 neurons. In Hodgkin–Huxley model neurons with standard parameters, which are Type 2, in the bistable regime, synaptic transmission can initiate oscillatory joint spiking, but white noise can terminate it. In Type 1 cells (models), typified by a quadratic integrate and fire model, synaptic coupling can cause oscillatory behaviour in excitatory cells, but Gaussian white noise can again terminate it. We locally determine an approximate basin of attraction, of the periodic orbit and explain the firing behaviour in terms of the effects of noise on the probability of escape of trajectories from