0-1整数规划问题的半自动化DNA计算模型

对一般的0—1整数规划问题提出了一种半自动化的DNA计算模型。首先产生所给定的0—1整数规划问题的所有可能解,然后设置对应于0—1整数规划问题的约束不等式的探针,利用这些探针设计半自动化装置对所有可能解进行自动分离,最终找出0—1整数规划问题的解。该模型的最大优点在于具有自动化的特点;同时,从理论上来讲,该模型适合含有任意变量的任意0—1整数规划问题的求解。     

Reconstructing recombination network from sequence data: the small parsimony problem

The small parsimony problem is studied for reconstructing recombination networks from sequence data. The small parsimony problem is polynomial-time solvable for phylogenetic trees. However, the problem is proved NP-hard even for galled recombination networks. A dynamic programming algorithm is also developed to solve the small parsimony problem. It takes O(dn2(3h)) time on an input recombination network over length-d sequences in which there are h recombination and n - h tree nodes.     

On the number of phenotype structures in genetic systems

Phenotype structures in genetic systems are carefully defined in an abstract setting so that a considerable amount of enumerative theory can be brought to bear on the problem of enumerating them. Recent results can be used to simplify the computations, and a natural correspondence is suggested which changes the problem of finding the number of phenotype structures to the problem of determining the numbers of certain graphs with colored points. Work supported in part by a grant from the National Science Foundation. Work supported in part by Grant 73-2502 from the Air Force Scientific Research.     

When correlation implies causation in multisensory integration

Inferring which signals have a common underlying cause, and hence should be integrated, represents a primary challenge for a perceptual system dealing with multiple sensory inputs [1-3]. This challenge is often referred to as the correspondence problem or causal inference. Previous research has demonstrated that spatiotemporal cues, along with prior knowledge, are exploited by the human brain to solve this problem [4-9]. Here we explore the role of correlation between the fine temporal structure of auditory and visual signals in causal inference. Specifically, we investigated whether correlated signals are inferred to originate from the same distal event and hence are integrated optimally [10]. In a localization task with visual, auditory, and combined audiovisual targets, the improvement in precision for combined relative to unimodal targets was statistically optimal only when audiovisual signals were correlated. This result demonstrates that humans use the similarity in the temporal structure of multisensory signals to solve the correspondence problem, hence inferring causation from correlation.     

Sparse inverse covariance estimation with the graphical lasso

We consider the problem of estimating sparse graphs by a lasso penalty applied to the inverse covariance matrix. Using a coordinate descent procedure for the lasso, we develop a simple algorithm--the graphical lasso--that is remarkably fast: It solves a 1000-node problem ( approximately 500,000 parameters) in at most a minute and is 30-4000 times faster than competing methods. It also provides a conceptual link between the exact problem and the approximation suggested by Meinshausen and Bühlmann (2006). We illustrate the method on some cell-signaling data from proteomics.     

Assessment of polyethylene degradation by biosurfactant producing ligninolytic bacterium

Biodegradation - Accumulation of plastic waste has become an environmental threat and a global problem. In this research, polyethylene degrading ligninolytic bacteria were isolated from plastic...     

Enhanced production of succinic acid from methanol–organosolv pretreated Strophanthus preussii by recombinant Escherichia coli

Bioprocess and Biosystems Engineering - A biorefinery process for high yield production of succinic acid from biomass sugars was investigated using recombinant Escherichia coli. The major problem...     

Pilot-scale process development for low-cost production of a thermostable biodiesel refining enzyme in Escherichia coli

Bioprocess and Biosystems Engineering - Biodiesels produced from vegetable oils have a major quality problem due to the presence of steryl glucosides (SGs), which form precipitates that clog...     

Design of an Epitope-Based Peptide Vaccine Against the Major Allergen Amb a 11 Using Immunoinformatic Approaches

The Protein Journal - Allergic diseases are a socially significant problem of global importance. The number of people suffering from pollen allergies has increased dramatically in recent decades....     

Children’s Respiratory Health After an Efficient Biomass Stove (Patsari) Intervention

EcoHealth - Household use of fuelwood represents a socio-ecological condition with important health effects mainly in rural areas from developing countries. One approach to tackle this problem has...     

Residue-rotamer-reduction algorithm for the protein side-chain conformation problem

MOTIVATION: The protein side-chain conformation problem is a central problem in proteomics with wide applications in protein structure prediction and design. Computational complexity results show that the problem is hard to solve. Yet, instances from realistic applications are large and demand fast and reliable algorithms. RESULTS: We propose a new global optimization algorithm, which for the first time integrates residue reduction and rotamer reduction techniques previously developed for the protein side-chain conformation problem. We show that the proposed approach simplifies dramatically the topology of the underlining residue graph. Computations show that our algorithm solves problems using only 1-10% of the time required by the mixed-integer linear programming approach available in the literature. In addition, on a set of hard side-chain conformation problems, our algorithm runs 2-78 times faster than SCWRL 3.0, which is widely used for solving these problems. AVAILABILITY: The implementation is available as an online server at http://eudoxus.scs.uiuc.edu/r3.html     

DNA computation model to solve 0-1 programming problem

0-1 programming problem is an important problem in opsearch with very widespread applications. In this paper, a new DNA computation model utilizing solution-based and surface-based methods is presented to solve the 0-1 programming problem. This model contains the major benefits of both solution-based and surface-based methods; including vast parallelism, extraordinary information density and ease of operation. The result, verified by biological experimentation, revealed the potential of DNA computation in solving complex programming problem.     

Butanol fermentation liquor production and separation by reverse osmosis

The problem of dilute solvent concentration in butanol-acetone fermentations can be solved by using reverse osmosis to dewater the fermentation liquor. Polyamide membranes have a potential application in a butanol-acetone fermentation and exhibited rejection rates as high as 98%. Optimum rejection of butanol in the fermentation liquor occurred at recoveries of 20-45%. Flux ranged from 0.05 to 0.6 L m(-2) min(-1).     

Emotion Recognition from Physiological Signals Using Parallel Stacked Autoencoders

Neurophysiology - The problem of recognition of emotions in humans is still open from a few aspects. In our study, we used a deep learning method named stacked autoencoder to classify regions of...     

Ant colony optimization for multicasting in static wireless ad-hoc networks

Nodes of wireless ad-hoc networks are generally equipped with batteries. This makes energy a scarce resource. Therefore, power consumption of network operations is critical and subject to optimization. One of the fundamental problems in ad-hoc networks is multicasting. In this work, we consider the so-called minimum energy multicast (MEM) problem in static ad-hoc networks. This problem can be stated as a combinatorial optimization problem. We develop an ant colony optimization algorithm for networks with omni-directional as well as directional antennas. The results show that our algorithm consistently outperforms existing techniques. This work was supported by grant TIN2007-66523 (FORMALISM) of the Spanish Government, and by the EU project FRONTS (FP7-ICT-2007-1) funded by the European Commission under the FET Proactive Initiative Pervasive Adaptation. In addition, Christian Blum acknowledges support from the Ramón y Cajal program of the Spanish Ministry of Science and Innovation, and Hugo Hernández acknowledges support from the Catalan Government through an FI grant.     

Pseudoreplication in ecological research: the problem overlooked by Russian scientists

The use of differential statistics to test for treatment effect with data from experiments where either treatments were not replicated (though samples may be) or replicates are not statistically independent leads to serious methodological problem. This problem, discovered by Hurbert (1984), is called pseudoreplication. Due to unknown reasons, pseudoreplication issue was completely overlooked by the Russian ecologists, in spite of the fact that the international scientific community is aware of pseudoreplication for almost twenty years. As the result, up to 47% of the experimental ecological papers, published in six Russian academic journals (Botanicheskij zhurnal, Ekologia, Izvestija RAN Ser. Biol., Lesovedenie, Zhurnal Obshchei Biologii, Zooligicheskij zhurnal) in 1998-2001, are pseudoreplicated; this proportion is nearly twice as high as the proportion of pseudoreplicated studies in international journals during 1960-1980, e.g. before the problem was discovered by Hurlbert (1984). This situation is alarming, especially because a substantial part of pseudoreplication arise from incorrect use of statistics, not from incorrect designing of experiments. By using several examples from the recent papers of Russian ecologists I shortly review the situations where pseudoreplication may occur and discuss some aspects of the experimental design, which are critical for correct processing and interpretation of ecological data.     

Use of a modified oxygen microelectrode and laser-Doppler flowmetry to monitor changes in oxygen tension and microcirculation in a flap

Flap failure is a clinical problem in free tissue transfer, and there is no reliable device for monitoring the tissue. Differentiating between an arterial occlusion and venous congestion is also a problem. A study was undertaken to monitor viability in a pedicled groin flap and to compare two different monitoring methods. The oxygen tension in the flap, measured with a modified Clark-type microelectrode (tip diameter = 3 to 8 microm; 90 percent response within 2.6 +/- 0.5 seconds), was compared with changes in blood flow in the flap, measured with a laser-Doppler probe. In 11 Sprague-Dawley rats, the changes in oxygen tension and blood flow in the pedicled groin flap were studied after clamping and subsequent reperfusion of the artery or vein. After occlusion of the artery to the flap, oxygen tension decreased to a stable value (i.e., the recording level remained unchanged for 30 seconds), from 19.7 +/- 1.8 to 0.3 +/- 0.1 mmHg, after 193 +/-25 seconds; blood flow decreased to a stable value, from 117 +/- 21 to 54 +/- 18 perfusion units, after 26 +/- 6 seconds. Clamping of the vein resulted in a decrease in oxygen tension, from 17.1 +/- 1.8 to 1.4 +/- 0.7 mmHg, after 416 +/- 67 seconds, and blood flow decreased to a stable value, from 90 +/- 14 to 35 +/- 6 perfusion units, after 107 +/- 27 seconds. The results of this study show that there is a difference in oxygen tension and blood flow responses between arterial and venous occlusion and that it may be possible with both methods to distinguish arterial from venous occlusion. However, although oxygen tension measurements are slightly slower in response than laser-Doppler measurements, the values are more reliable as a diagnostic tool for interpretation of a vessel occlusion.     

Malaria in the whole world and in Romania

Malaria is the world's most important tropical parasitic disease. Malaria is a public health problem today in more than 90 countries. Worldwide prevalence of the disease is estimated to be in the order of 300-500 million clinical cases each year. Malaria is endemic in a total of 101 countries and territories. In Romania, malaria does not represent an important public health problem. In 1999, there were reported a total number of 32 malaria cases in Romanian people. 78% from these recognized as etiological agent Pl. falciparum. The malaria cases imported from Turkey (5) have had as etiological agent Pl. vivax. The most affected age group is between 21-50 years and a distribution by profession shows that sailor personnel accounts for 65.6% of all cases. Africa remains the most important endemic region from where the malaria cases in Romanian people are imported. An adequate chemoprophylaxis is not, yet, easy to obtain for Romanian people who are travelling abroad in endemic countries because of the lack of specific drugs (especially for resistant forms of Pl. falciparum). Even if the Romanian Ministry of Health had elaborated orders regarding malaria and Cloroquine is the usual drug administered, as chemoprophylaxis, to Romanian people who travel abroad, in each year in our country appears around 30-60 imported malaria cases. That is the cause why Romanian Ministry of Health wants to solve this problem which is the major cause of the malaria cases in Romanian people.     

Reversed phase high performance liquid chromatography of adrenocorticotropin 1-39 and its fragments in the native and oxidized forms

This paper reports HPLC separations of human ACTH 1-39 and its fragments (ACTH 1-10, 4-10, 11-24) making use of original gradient systems. Both H2O2 or chloramine T were demonstrated to oxidize the Met 4 present in ACTH 1-39, 1-10, and 4-10; the oxidized forms were HPLC separated from the corresponding native polypeptides, indicating that this method is suitable for the identification in biological fluid of ACTH, its fragment and their methionine-sulphoxide derivatives with possible relevance to the problem of ageing and inactivation of active polypeptide.     

Frontiers in metabolic reconstruction and modeling of plant genomes

A major goal of post-genomic biology is to reconstruct and model in silico the metabolic networks of entire organisms. Work on bacteria is well advanced, and is now under way for plants and other eukaryotes. Genome-scale modelling in plants is much more challenging than in bacteria. The challenges come from features characteristic of higher organisms (subcellular compartmentation, tissue differentiation) and also from the particular severity in plants of a general problem: genome content whose functions remain undiscovered. This problem results in thousands of genes for which no function is known ('undiscovered genome content') and hundreds of enzymatic and transport functions for which no gene is yet identified. The severity of the undiscovered genome content problem in plants reflects their genome size and complexity. To bring the challenges of plant genome-scale modelling into focus, we first summarize the current status of plant genome-scale models. We then highlight the challenges - and ways to address them - in three areas: identifying genes for missing processes, modelling tissues as opposed to single cells, and finding metabolic functions encoded by undiscovered genome content. We also discuss the emerging view that a significant fraction of undiscovered genome content encodes functions that counter damage to metabolites inflicted by spontaneous chemical reactions or enzymatic mistakes.