Nonvulnerability of ecosystems in unpredictable environments

One way to bracket the effects of a real environment on an ecosystem during a finite time interval is to use the concept of vulnerability. If a deterministic model ecosystem has a good Lyapunov function, it may be possible to derive simple and useful tests for the system to be nonvulnerable. For a subset of Lotka-Volterra models, the system is nonvulnerable if the smallest eigenvalue of a certain matrix is not only positive, but is greater than a positive number, which depends on a priori estimates for the bounds on the unpredictable forcing functions. The bounded but unknown functions which act on the Lotka-Volterra equations also can be interpreted as errors in the system's equations which can be tolerated without a qualitative change in the behaviour of its solutions.     

荧光标记的染色体原位杂交及其在人类基因组研究中的应用

FISH技术是80年代开始发展起来的一种新的定位技术.在人类基因组研究中得到了广泛的应用.通过中期染色体的FISH可以进行SCP,Cosmid和YAC的染色体定位,嵌合克隆的鉴别;通过间期核的FISH可以在50kb的分辨率下进行基因作图;最新的研究进展已可以进行伸展的染色质丝(chromatin fibre)的FISH,直接测量基因的长度,从而达到高精度基因作图的目的.总之,随着FISH技术本身的发展,它将在人类基因组研究中发挥更大的作用.     

Optimal dispatching of multipriority jobs to two heterogeneous workstations

The general problem scenario of this paper is the following: Jobs of various priorities, stationed in a common storage area, are waiting to be dispatched to two non-identical workstations. Any of the waiting jobs can be accessed from the storage at any given time. Each job can be processed on either of the workstations, but once a job has been assigned it may not be preempted. By job priority it is meant that a higher priority job has disptach preference over a lower priority job. The processing time of a job on a given workstation is assumed to be random, the distribution being dependent on the job type and the configuration of the workstation. Specifically, the first problem studied considers only two classes of jobs: (1) “hot” jobs, whose processing is to be expedited and thus have the higher dispatch priority, and (2) “routine” jobs which may be assigned to an available workstation only if the workstation has been rejected by all “hot” jobs. The processing times are assumed to be exponentially distributed with means depending on the job class and workstation. We assume that, on the average, one workstation is faster than the other with regard to processing any job. The dispatching objective for each job class is to minimize its expected flowtime. It is shown that threshold dispatching policies are optimal for this problem. That is, the faster processor should be utilized whenever possible, and for each class there exists an explicit threshold such that when the number of jobs of that class in the buffer exceeds this threshold then a job of that class is dispatched to the slower processor, otherwise these jobs wait for the faster processor to become available. For the higher priority jobs, this threshold is shown to be a function only of the various processing rates of the two workstations. For the lower priority jobs, the threshold also depends on the number of higher priority jobs in the buffer. The results is extended to a system with n priority classes. Again, it is shown that when the processing times are exponentially distributed with different rates and the dispatching objective for each class is to minimize its expected flowtime, the optimal dispatching policies are of threshold type. Explicit thresholds are easily derived.     

The role of bioregenerative life-support systems in a manned future in space

Thus far in the manned space program, human life support has depended on storage of air, water, food, and energy. There are no refrigerators on Shuttle, and fresh foods are limited to what can be stowed in lockers for the first 3 days of a mission, when spoilage becomes a factor. Oxygen is stored, CO2 is scrubbed, and water is stored and treated. As we approach the Space Station era, life support will be a combination of storage and resupply. Duty cycles will be 90 days, and physico-chemical (P/C) systems will be important for recycling oxygen and water. Nutritionists seek a capability for refrigerated storage of fresh food on Station. However, most food still will be thermostabilized, rehydratables that can be stored at room temperature. Present Shuttle food is not much more sophisticated than repackaged camp food, and tends to be high in salt content. Hopefully, menus will be healthier on Station, where dietary countermeasures against biomedical responses to chronic microgravity might be implemented, and certainly need to be studied.     

Phylogeny,natural groups and nemertean classification

Contemporary practice in the classification of nemerteans (phylum Nemertea) is critically discussed. It is argued that basing higher taxa on the existence of a unique combination of characters in a species (or genus) is unlikely to lead to monophyletic taxa, and that this approach should be abandoned in favour of a classification based on explicit hypotheses of phylogeny. These hypotheses should be based on all available characters and characters should not be excluded before the analysis. The classification should be based on a reconstruction of the phylogeny and reflect this phylogeny in an unambiquous way.     

Primary malignant melanoma of uterine cervix: a rare entity diagnosed on fine needle aspiration cytology – report of a case

Primary malignant melanoma of uterine cervix is a rare neoplasm. Its diagnosis on cervical fine needle aspiration cytology, a first of its kind in the literature, has been reported. Although cervix is a rare site for melanoma, cytopathologists should be familiar with it and be able to diagnose this entity on cervical cytology when pigment containing tumour cells are present. In a patient with visible growth on cervix, fine needle aspiration cytology may prove to be a useful diagnostic tool, especially when cervical smear/scrape cytology is non-diagnostic.     

Possibility of analytical application of the partition in aqueous biphasic polymeric systems technique

The partition behaviour of a number of ionic and nonionic surface-active substances in the dextran-polyethylene glycol system was examined. The strictly linear dependence of the logarithm of the partition coefficient on the alkyl chain length for a homologous series of nonionic surfactants provides a measure of the difference in the relative hydrophobicity between the two phases of the system, in terms of the free energy of transfer of a CH₂ group from the bottom phase to the top phase of the system. This difference is found to be altered in the presence of NaCl or KCl depending on the salt concentration. It is concluded that the influence of the salt composition of the system on the distributed solutes' behaviour may be due to the effect of the ions on the hydrophobicity difference between the phases.The partition of ionic amphiphiles is found to be dependent on the relative hydrophobicity of the compounds as well as on their charge. It is shown that at salt concentrations up to about 0.1 M NaCl the charged solute partition is determined by its charge as well as its relative hydrophobicity, in the presence of 0.1–0.2 M NaCl the substance distribution is highly dependent on its charge and slightly on its lipophility. At the salt concentrations above 0.2 M the solute partition is determined just by its hydrophobic character and seems to be totally independent of its charge. It is concluded that the partition technique can be used for analytical purposes. The method seems to be unique in providing quantitative information on the amphiphilic surface properties of the solutes being partitioned.     

Molecular evolution of synonymous codon usage in <Emphasis Type="Italic">Populus</Emphasis>

Background  

Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes.     

The beta-geometric distribution applied to comparative fecundability studies

A convenient measure of fecundability is time (number of menstrual cycles) required to achieve pregnancy. Couples attempting pregnancy are heterogeneous in their per-cycle probability of success. If success probabilities vary among couples according to a beta distribution, then cycles to pregnancy will have a beta-geometric distribution. Under this model, the inverse of the cycle-specific conception rate is a linear function of time. Data on cycles to pregnancy can be used to estimate the beta parameters by maximum likelihood in a straightforward manner with a package such as GLIM. The likelihood ratio test can thus be employed in studies of exposures that may impair fecundability. Covariates are incorporated in a natural way. The model is illustrated by applying it to data on cycles to pregnancy in smokers and nonsmokers, with adjustment for covariates. For a cross-sectional study, when length-biased sampling is taken into account, the pre-interview attempt time is shown to follow a beta-geometric distribution, so that the same methods of analysis can be applied even though all of the available data are right-censored. For a cohort followed prospectively, there will be some couples enrolled whose fecundability is effectively 0, and for such applications, the beta could be considered to be contaminated by a distribution degenerate at 0. The mixing parameter (proportion sterile) can be estimated by application of the expectation-maximization (EM) algorithm. This, too, can be carried out using GLIM.     

Image segmentation using a neural network

An object extraction problem based on the Gibbs Random Field model is discussed. The Maximum a'posteriori probability (MAP) estimate of a scene based on a noise-corrupted realization is found to be computationally exponential in nature. A neural network, which is a modified version of that of Hopfield, is suggested for solving the problem. A single neuron is assigned to every pixel. Each neuron is supposed to be connected only to all of its nearest neighbours. The energy function of the network is designed in such a way that its minimum value corresponds to the MAP estimate of the scene. The dynamics of the network are described. A possible hardware realization of a neuron is also suggested. The technique is implemented on a set of noisy images and found to be highly robust and immune to noise.     

Is affordable and cost-effective assisted reproductive technology in low-income countries possible? What should we know to answer the question?

¹ Correspondence address. E-mail: j.d.f.habbema{at}erasmusmc.nl Decision making on infertility treatment in low-income countries(LIC) assumes answers to quite a few questions: how should theinfertility problem be defined? How often does infertility occur?What is the burden-of-disease of infertility? What is the incomein LIC, and what can be spend on health care? How cheap shouldIVF be in order to be accessible to a considerable part of thepopulation? With what alternative health interventions shouldinfertility treatment be compared? How cost-effective shouldIVF be in order to compete with those other interventions? Thesequestions will be discussed. The emphasis is on the situationin Sub-Saharan Africa (SSA). It is concluded that a place forART in a health care package is not straightforward. Many ofthe questions are not or only partially answered. Moreover,cheap and effective ART has yet to be developed and tested.From the limited evidence available for each of the questions,it could be calculated that an IVF cycle should cost between50 and 75 dollar in order to be a candidate for the inclusionin a health package in SSA. This estimate can easily changeconsiderably when in the future the calculations will be basedon thorough research. Thus, a targeted research programme foranswering the open questions, especially on quality-of-lifeimplications of infertility in different societies, is the preferredoption for facilitating the future evaluation of ART in LIC.     

高密度基因芯片探针布局方法

为了提高基因芯片制备质量和检测的准确性,提出两种基因芯片布局方法,一是分子印章凸点优化布局方法,另一种是基于探针杂交解链温度的梯度场布局方法。利用上述两种方法对所设计的高密度基因芯片进行控针布局实验,结果表明,第一种方法能够使制备基因芯片的分子印章上凸点均匀分布,解决误压印问题,从而提高基因芯片的制备质量;而第二种方法能够使基因芯片上的探针按照杂交解链温度有序地组织起来,从而提高基因芯片对碱基错配的辨别力。     

ClaMS: A Classifier for Metagenomic Sequences

ClaMS - "Classifier for Metagenomic Sequences" - is a Java application for binning assembled contigs in metagenomes using user-specified training sets and initial parameters. Since ClaMS trains on sequence composition-based genomic signatures, it is much faster than binning tools that rely on alignments to homologs; ClaMS can bin ~20,000 sequences in 3 minutes on a laptop with a 2.4 GH× Intel Core 2 Duo processor and 2 GB RAM. ClaMS is meant to be a desktop application for biologists and can be run on any machine under any Operating System on which the Java Runtime Environment can be installed.     

Modulation of respiration during brain hypoxia

This review is a summary of the effects of brain hypoxia on respiration with a particular emphasis on those studies relevant to understanding the cellular basis of these effects. Special attention is given to mechanisms that may be responsible for the respiratory depression that appears to be the primary sequela of brain hypoxia in animal models. Although a variety of potential mechanisms for hypoxic respiratory depression are considered, emphasis is placed on changes in the neuromodulator constituency of the respiratory neuron microenvironment during hypoxia as the primary cause of this phenomenon. Hypoxia is accompanied by a net increase in neuronal inhibition due to both decreased excitatory and increased inhibitory neuromodulator levels. A survey of hypoxia-tolerant cellular systems and organisms suggests that hypoxic respiratory depression may be a manifestation of the depression of cellular metabolism, which appears to be a major adaptation to limited oxygen availability in these systems.     

Nonlinear pulse wave reflection at an arterial stenosis

A simple model is presented to analyze the effect of stenoses of different severities in a long elastic tube or artery on the pressure and flow-rate wave forms incident upon them. Wave propagation in the undisturbed tube is taken to be linear; nonlinearity arises from the quadratic dependence of stenosis pressure drop on flow rate. Before the model can be applied in practice, important physiological questions must be answered; e.g.: (a) Can the incident wave form and mean proximal pressure be regarded as given input? (b) is the mean flow rate given, or does the peripheral resistance remain constant? Results are given on the assumption that the answer to (a) is yes. The principal conclusion is that the input impedance spectrum of a stenosed artery depends strongly on the incident wave form, as well as on the severity of the stenosis and on the distance from it at which measurements are made. There is good qualitative agreement with the results of experiments and of other models.     

A hierarchical method for molecular docking using cloud computing

Discovering small molecules that interact with protein targets will be a key part of future drug discovery efforts. Molecular docking of drug-like molecules is likely to be valuable in this field; however, the great number of such molecules makes the potential size of this task enormous. In this paper, a method to screen small molecular databases using cloud computing is proposed. This method is called the hierarchical method for molecular docking and can be completed in a relatively short period of time. In this method, the optimization of molecular docking is divided into two subproblems based on the different effects on the protein–ligand interaction energy. An adaptive genetic algorithm is developed to solve the optimization problem and a new docking program (FlexGAsDock) based on the hierarchical docking method has been developed. The implementation of docking on a cloud computing platform is then discussed. The docking results show that this method can be conveniently used for the efficient molecular design of drugs.     

Postrhinoplasty "red nose": differential diagnosis and treatment by laser

Prior to anticipated nasal surgery, the nasal and facial skin should be examined for any vascular lesions. The skin type should be ascertained. A history of any prior nasal surgery, particularly on the nasal dorsum, should be noted. If rosacea is a clinical possibility, a trial of 1.5 to 2.0 gm q.d. of tetracycline for 6 to 8 weeks is warranted. If, after rhinoplasty, a diffuse "redness" on the nasal dorsum results and one can exclude other diagnoses, then argon laser therapy should be considered. A 3-mm punch biopsy should be obtained to see whether superficial ectatic vessels are present, a finding that would be indicative of a good result from laser therapy.     

Finite-state models in the alignment of macromolecules

Summary Minimum message length encoding is a technique of inductive inference with theoretical and practical advantages. It allows the posterior odds-ratio of two theories or hypotheses to be calculated. Here it is applied to problems of aligning or relating two strings, in particular two biological macromolecules. We compare the r-theory, that the strings are related, with the null-theory, that they are not related. If they are related, the probabilities of the various alignments can be calculated. This is done for one-, three-, and five-state models of relation or mutation. These correspond to linear and piecewise linear cost functions on runs of insertions and deletions. We describe how to estimate parameters of a model. The validity of a model is itself an hypothesis and can be objectively tested. This is done on real DNA strings and on artificial data. The tests on artificial data indicate limits on what can be inferred in various situations. The tests on real DNA support either the three- or five-state models over the one-state model. Finally, a fast, approximate minimum message length string comparison algorithm is described.Offprint requests to: L. Allison     

Trichophyton fischeri sp. nov.: a saprophyte resembling Trichophyton rubrum

A new species Trichophyton fischeri was isolated as a contaminant on blood agar plates. This fungus is believed to be a saprophyte. It may be confused with T. rubrum. On peptone dextrose agar plate, the growth is white and velvety to cottony. It occasionally forms furrows. The underside of the mature colony is brownish red. Clavate microaleuriospores are common. Trichophyton-type macroaleuriospores are produced occasionally on blood agar and potato dextrose agar. Erythritol does not stimulate T. fischeri to produce a red color on casamino erythritol albumen agar. Closterospore-like projections may be produced on the main filaments on peptone dextrose and potato dextrose agar.     

Method allowing biological and biochemical studies of vacuum-exposed bacteria

A method is described which allows quantitative biological and biochemical studies of the vacuum effect on bacteria. Quantitative studies can only be performed if vacuum-exposed bacteria can be removed completely from their support. This is achieved by exposing bacteria to vacuum on a polyvinylalcohol film. After vacuum exposure this film is dissolved in buffer, leading to a quantitative release of bacteria into the buffer. This suspension of vacuum-exposed bacteria can then be used for quantitative biological and biochemical studies of the vaccum effect on bacteria.