Reconstructing gene regulatory networks with a memetic-neural hybrid based on fuzzy cognitive maps

Reconstructing gene regulatory networks (GRNs) plays an important role in identifying the complicated regulatory relationships, uncovering regulatory patterns in cells, and gaining a systematic view for biological processes. In order to reconstruct large-scale GRNs accurately, in this paper, we first use fuzzy cognitive maps (FCMs), which are a kind of cognition fuzzy influence graphs based on fuzzy logic and neural networks, to model GRNs. Then, a novel hybrid method is proposed to reconstruct GRNs from time series expression profiles using memetic algorithm (MA) combined with neural network (NN), which is labeled as MANN_FCM-GRN. In MANN_FCM-GRN, the MA is used to determine regulatory connections in GRNs and the NN is used to determine the interaction strength of the regulatory connections. In the experiments, the performance of MANN_FCM-GRN is validated on both synthetic data and the benchmark dataset DREAM3 and DREAM4. The experimental results demonstrate the efficacy of MANN_FCM-GRN and show that MANN_FCM-GRN can reconstruct GRNs with high accuracy without expert knowledge. The comparison with existing algorithms also shows that MANN_FCM-GRN outperforms ant colony optimization, non-linear Hebbian learning, and real-coded genetic algorithms.

     

烟道流量计量标准装置

为了解决我国烟道流量计的量值溯源问题,中国计量科学研究院建立了烟道流量计量标准装置。装置使用可溯源至标准转盘的激光多普勒测速仪作为原级标准器,采用激光多普勒流速剖面扫描和超声流量计波动修正的方式测量标准流量,经校准的8声道超声流量计为工作级标准表,具备了908~104840m3/h的测量能力,扩展不确定度为0.62%(k=2),可对最大口径为1m的流量计进行校准。装置下游测试段包括圆形管段和矩形管段,能够开展烟道流量计测量性能的研究。     

Visual Detection of Adenosine Triphosphate by Taylor Rising: A Simple Point-of-Care Testing Method Based on Rolling Circle Amplification

Rapid and sensitive point-of-care testing (POCT) is an extremely critical mission in practical applications, especially for rigorous military medicine, home health care, and in the third world. Here, we report a visual POCT method for adenosine triphosphate (ATP) detection based on Taylor rising in the corner of quadratic geometries between two rod surfaces. We discuss the principle of Taylor rising, demonstrating that it is significantly influenced by contact angle, surface tension, and density of the sample, which are controlled by ATP-dependent rolling circle amplification (RCA). In the presence of ATP, RCA reaction effectively suppresses Taylor-rising behavior, due to the increased contact angle, density, and decreased surface tension. Without addition of ATP, untriggered RCA reaction is favorable for Taylor rising, resulting in a significant height. With this proposed method, visual sensitive detection of ATP without the aid of other instruments is realized with only a 5 μL droplet, which has good selectivity and a low detection limit (17 nM). Importantly, this visual method provides a promising POCT tool for user-friendly molecular diagnostics.     

Modified hippocampal long-term potentiation in PKC gamma-mutant mice

Calcium-phospholipid-dependent protein kinase (PKC) has long been suggested to play an important role in modulating synaptic efficacy. We have created a strain of mice that lacks the gamma subtype of PKC to evaluate the significance of this brain-specific PKC isozyme in synaptic plasticity. Mutant mice are viable, develop normally, and have synaptic transmission that is indistinguishable from wild-type mice. Long-term potentiation (LTP), however, is greatly diminished in mutant animals, while two other forms of synaptic plasticity, long-term depression and paired-pulse facilitation, are normal. Surprisingly, when tetanus to evoke LTP was preceded by a low frequency stimulation, mutant animals displayed apparently normal LTP. We propose that PKC gamma is not part of the molecular machinery that produces LTP but is a key regulatory component.     

Continuous measurement of cardiac output by the Fick principle in infants and children: comparison with the thermodilution method

OBJECTIVE: To compare a system that continuously monitors cardiac output by the Fick principle with measurements by the thermodilution technique in pediatric patients. DESIGN: Prospective direct comparison of the above two techniques. SETTING: Pediatric intensive care unit of a university hospital. PATIENTS: 25 infants and children, aged 1 week to 17 years (median 10 months), who had undergone open heart surgery were studied. Only patients without an endotracheal tube leak and without a residual shunt were included. METHODS: The system based on the Fick principle uses measurements of oxygen consumption taken by a metabolic monitor and of arterial and mixed venous oxygen saturation taken by pulse- and fiberoptic oximetry to calculate cardiac output every 20s. INTERVENTIONS: In every patient one pair of measurements was taken. Continuous Fick and thermodilution cardiac output measurements were performed simultaneously, with the examiners remaining ignorant of the results of the other method. RESULTS: Cardiac output measurements ranged from 0.21 to 4.55 l/min. A good correlation coefficient was found: r2 = 0.98; P < 0.001; SEE = 0.41 l/min. The bias is absolute values and in percent of average cardiac output was - 0.05 l/min or - 4.4% with a precision of 0.32 l/min or 21.3% at 2 SD, respectively. The difference was most marked in a neonate with low cardiac output. CONCLUSION: Continuous measurement of cardiac output by the Fick principle offers a convenient method for the hemodynamic monitoring of unstable infants and children.     

Battery-Aware Routing for Streaming Data Transmissions in Wireless Sensor Networks

Recent technological advances have made it possible to support long lifetime and large volume streaming data transmissions in sensor networks. A major challenge is to maximize the lifetime of battery-powered sensors to support such transmissions. Battery, as the power provider of the sensors, therefore emerges as the key factor for achieving high performance in such applications. Recent study in battery technology reveals that the behavior of battery discharging is more complex than we used to think. Battery powered sensors might waste a huge amount of energy if we do not carefully schedule and budget their discharging. In this paper we study the effect of battery behavior on routing for streaming data transmissions in wireless sensor networks. We first give an on-line computable energy model to mathematically model battery discharge behavior. We show that the model can capture and describe battery behavior accurately at low computational complexity and thus is suitable for on-line battery capacity computation. Based on this battery model we then present a battery-aware routing (BAR) protocol to schedule the routing in wireless sensor networks. The routing protocol is sensitive to the battery status of routing nodes and avoids energy loss. We use the battery data from actual sensors to evaluate the performance of our protocol. The results show that the battery-aware protocol proposed in this paper performs well and can save a significant amount of energy compared to existing routing protocols for streaming data transmissions. Network lifetime is also prolonged with maximum data throughput. As far as we know, this is the first work considering battery-awareness with an accurate analytical on-line computable battery model in sensor network routing. We believe the battery model can be used to explore other energy efficient schemes for wireless networks as well.     

Ozonation of CI Reactive Black 5 using rotating packed bed and stirred tank reactor

This study investigates the ozonation of CI Reactive Black 5 (RB5) by using the rotating packed bed (RPB) and completely stirred tank reactor (CSTR) as ozone contactors. The RPB, which provides high gravitational force by adjusting the rotational speed, was employed as a novel ozone contactor. The same ozone dosage was separately introduced into either the RPB or the CSTR for the investigation, while the experimental solution was continuously circulated within the apparatus consisting of the RPB and CSTR. The decolorization and mineralization efficiencies of RB5 in the course of ozonation are compared for these two methods. Moreover, the dissolved and off‐gas ozone concentrations were simultaneously monitored for the further analysis. As a result, the ozone mass transfer rate per unit volume of the RPB was significantly higher because of its higher mass transfer coefficient and gas–liquid concentration driving force. Furthermore, ozonation kinetics was found to be independent of the gravitational magnitude of an ozone gas–liquid contactor. Therefore, the results suggest employing RPBs as ozone‐contacting devices with the advantage of volume reduction. The experimental results, which can be used for further modeling of the ozonation process in the RPB, also show the requirement of correct design for the RPB. Consequently, the present study is useful for the understanding of practical application of RPBs. Copyright © 2004 Society of Chemical Industry