Improve survival prediction using principal components of gene expression data

The purpose of many microarray studies is to find the association between gene expression and sample characteristics such as treatment type or sample phenotype. There has been a surge of efforts developing different methods for delineating the association. Aside from the high dimensionality of microarray data, one well recognized challenge is the fact that genes could be complicatedly inter-related, thus making many statistical methods inappropriate to use directly on the expression data. Multivariate methods such as principal component analysis （PCA） and clustering are often used as a part of the effort to capture the gene correlation, and the derived components or clusters are used to describe the association between gene expression and sample phenotype. We propose a method for patient population dichotomization using maximally selected test statistics in combination with the PCA method, which shows favorable results. The proposed method is compared with a currently well-recognized method.     

A Bionic Approach for Topology Optimization for Tension-only or Compression-only Design

##正## A new bionic approach is presented to find the optimal topologies of a structure with tension-only or compression-onlymaterial based on bone remodelling theory.By traditional methods,the computational cost of topology optimization of thestructure is high due to material nonlinearity.To improve the efficiency of optimization,the reference-interval with material-replacement method is presented.In the method,firstly,the optimization process of a structure is considered as bone remodellingprocess under the same loading conditions.A reference interval of Strain Energy Density (SED),corresponding to thedead zone or lazy zone in bone mechanics,is adopted to control the update of the design variables.Secondly,a material-replacement scheme is used to simplify the Finite Element Analysis (FEA) of structure in optimization.In the operation ofmaterial-replacement,the original tension-only or compression-only material in design domain is replaced with a new isotropicmaterial and the Effective Strain Energy Density (ESED) of each element can be obtained.Finally,the update of design variablesis determined by comparing the local ESED and the current reference interval of SED,e.g.,the increment of a relativedensity is nonzero if the local ESED is out of the current reference interval.Numerical results validate the method.     

The nest architecture of the ant, Pheidole oxyops Forel, 1908 （Hymenoptera： Formicidae）

Pheidole oxyops builds subterranean nests, with an external architecture that is distinctive and easily recognizable by its wide and specific entrance hole, measuring up to 12.2 cm in diameter, denoting a pitfall-trap. In order to study the nests＇ internal architecture, seven nests were excavated; four were identified with neutral talc, while the others were cast in cement and then excavated. Measurements were made in order to gain a better understand- ing of their structures, and a photographic documentation was obtained as well. The excavations revealed that the nests are perpendicular relative to the ground, beginning with a cylindrical channel with a mean length of 13.5 cm, containing irregular formations, and whose diameter becomes progressively narrower until the first chamber is formed. As the channel continues, dish-like chambers appear, interconnected by channels that become progressively narrower and longer, while the chambers are arranged at greater distances from each other as nest depth increases. Both channels and chambers are located on the vertical projection of the entrance hole. Nests may reach a depth of up to 5.09 m, with a number of chambers ranging between 4 and 14.     

Pattern analysis in landscape ecology: progress, challenges and outlook

Landscape pattern indices or landscape metrics, an important means in landscape pattern analysis, has resulted in the prosperity of landscape ecology. However, landscape pattern analysis was criticized recently for its poor correlation with ecological processes. In this paper, the current situation and challenges in landscape pattern analysis was elaborated, and the future of landscape pattern analysis was discussed. We believe that the landscape metrics is still the main method in spatial pattern analysis, and is important for landscape ecology. However, there are 3 challenges in landscape pattern analysis: (1) how to develop new methods by integrating explicit ecological sense in landscape pattern analysis? (2) How to link landscape pattern and ecological processes? (3) How to apply the theory of “matrix-patch-corridor” to practice? In future, 5 issues are to be addressed: (1) to develop a methodology to describe landscape pattern in a dynamic manner; (2) to explore the ecological sense of landscape pattern using a series of landscape metrics; (3) to develop new methods for landscape pattern analysis related to ecological processes; (4) to conduct landscape pattern analysis at multi-dimensions; (5) to explain the relationship between landscape pattern and ecological processes by multi-scale pattern analysis.     

Design and Kinematic Analysis of a Novel Humanoid Robot Eye Using Pneumatic Artificial Muscles

This paper proposed a novel humanoid robot eye, which is driven by six Pneumatic Artificial Muscles （PAMs） and rotates with 3 Degree of Freedom （DOF）. The design of the mechanism and motion type of the robot eye are inspired by that of human eyes. The model of humanoid robot eye is established as a parallel mechanism, and the inverse-kinematic problem of this flexible tendons driving parallel system is solved by the analytical geometry method. As an extension, the simulation result for saccadic movement is presented under three conditions. The design and kinematic analysis of the prototype could be a sig- nificant step towards the goal of building an autonomous humanoid robot eye with the movement and especially the visual functions similar to that of human.     

Brainnetome and related projects

<正>The brain is organized as a hierarchy of complex networks on different temporal and spatial scales.The complex connectivities within the brain are presented in the anatomical architecture as well as dynamic activity.There have long been efforts to make a connection map of the brain[1],and this has now been achieved with the establishment of the     

The Novel Mechanical Property of Tongue of a Woodpecker

Biomaterials such as bone,teeth,nacre and silk are known to have superior mechanical properties due to their specificnanocomposite structures.Here we report that the woodpecker’s tongue exhibits a novel strength and flexibility due to its specialcomposite micro/nanostructure.The tongue consists of a flexible cartilage-and-bone skeleton covered with a thin layer tissue ofhigh strength and elasticity.At the interface between the cartilage-and-bone skeleton and the tissue layer,there is a hierarchicalfiber-typed connection.It is this special design of the tongue that makes the woodpeckers efficient in catching the insects insidetrees.The special micro/nanostructures of the woodpecker’s tongue show us a potential method to enhance the interfacialconnection between soft and hard material layers for bio-inspired composite system designs.     

Foraging site recursion by forest elephants Elephas maximus borneensis

Recursion by herbivores is the repeated use of the same site or plants. Recursion by wild animals is rarely investigated but may be ubiquitous. Optimal foraging theory predicts site recursion as a function of the quality of the site, extent of its last use, and time since its last use because these influence site resource status and recovery. We used GPS collars, behaviour and site sampling to investigate recursion to foraging sites for two elephant Elephas maximus borneensis herds in the Lower Kinabatangan Wildlife Sanctuary, Borneo, over a 12 month period. Recursion occurred to 48 out of 87 foraging sites and was most common within 48 hours or between 151-250 days, indicating two different types ofrecursion. Recursion was more likely to occur if the site had previously been occupied for longer. Moreover, the time spent at a site at recursion was the same as the time spent at the site on the first occasion. The number of days that had passed between the first visit and recursion was also positively correlated with how much time was spent at the site at recursion. Habitat type also influenced the intensity of site-use, with more time spent at recursion within riverine/open grass areas along forest margins compared to other habitat types. Recursion is a common behaviour used by the elephants and its pattern suggests it may be a foraging strategy for revisiting areas of greater value. The qualities of recursion sites might usefully be incorporated into landscape management strategies for elephant conservation in the area [Current Zoology 60 （4）： 551-559, 2014].     

Landscape changes have greater effects than climate changes on six insect pests in China

In recent years, global changes are the major causes of frequent, widespread outbreaks of pests in mosaic landscapes, which have received substantial attention worldwide. We collected data on global changes(landscape and climate) and economic damage caused by six main insect pests during 1951–2010 in China. Landscape changes had significant effects on all six insect pests. Pest damage increased significantly with increasing arable land area in agricultural landscapes. However, climate changes had no effect on damage caused by pests, except for the rice leaf roller(Cnaphalocrocis medinalis Guenee) and armyworm(Mythimna separate(Walker)), which caused less damage to crops with increasing mean temperature. Our results indicate that there is slight evidence of possible offset effects of climate changes on the increasing damage from these two agricultural pests. Landscape changes have caused serious outbreaks of several species, which suggests the possibility of the use of landscape design for the control of pest populations through habitat rearrangement. Landscape manipulation may be used as a green method to achieve sustainable pest management with minimal use of insecticides and herbicides.     

Microstructure-based Finite Element Modelling and Characterisation of Bovine Trabecular Bone

1 Introduction The mechanical behaviour of trabecular bone is dependent on both the properties of individual trabeculae as well as the three-dimensional architecture into which they are arranged. Hence, a comprehensive study of trabecular bone requires the consideration of microscopic as well as macroscopic length scales. Nanoindentation is a technique particularly suited to the mechanical characterisation of single trabecula[1?3] owing to the impracticalities of isolating individual tra- becu…     

应用创造酶切位点法检测单碱基突变

应用引物错配技术结合单碱基突变位点而配合成一个酶切位点,使之成为可用PCR-RFLP方法分析的突变位点,是对单碱基突变位点进行基因型鉴定的有效而简捷的手段。本文以鸡胞外脂肪酸结合蛋白(Extracelluar fatty acid binding protein,EX-FABP)基因单碱基突变的基因型检测为例,探讨了应用创造酶切位点PCR（Created Restriction Site PCR,CRS-PCR）检测单碱基突变基因型的思路、方法和策略。 Abstract:Created Restriction Site PCR (CRS-PCR) is a simple and efficient method to identify SNP genotypes.One or more mismatch bases are used in a primer to create a restriction site by combining SNP site after PCR.The CRS-PCR products can be genotyped with a way the same as PCR-RFLP.In the study,Extracelluar fatty acid binding protein (EX-FABP)　gene was served as an example for establishing the CRS-PCR method.Strategy of CRS-PCR was also discussed.     

Transfer of Natural Micro Structures to Bionic Lightweight Design Proposals

The abstraction of complex biological lightweight structure features into a producible technical component is a funda- mental step within the transfer of design principles from nature to technical lightweight solutions. A major obstacle for the transfer of natural lightweight structures to technical solutions is their peculiar geometry. Since natural lightweight structures possess irregularities and often have extremely complex forms due to elaborate growth processes, it is usually necessary to simplify their design principles. This step of simplification/abstraction has been used in different biomimetic methods, but so far, it has an arbitrary component, i.e. it crucially depends on the competence of the person who executes the abstraction. This paper describes a new method for abstraction and specialization of natural micro structures for technical lightweight compo- nents. The new method generates stable lightweight design principles by using topology optimization within a design space of preselected biological archetypes such as diatoms or radiolarian. The resulting solutions are adapted to the technical load cases and production processes, can be created in a large variety, and may be further optimized e.g. by using parametric optimization.     

The Methodology of Probe Design with Better Resolution and Less Resistive Donut Probe to Achieve the Best Performance

Probes are the interface between microsystems and bio-cells.The ideal interface is one-to-one interface.Though variousresearch groups have been able to establish some sort of interfaces after many years of research,they are very crude.Neurons aremillions in numbers,whereas the prostheses successfully built so far have only a few hundred probes at best.Creating an ef-fective interface is still far away.Though we have micro-and nano-technologies,we couldn’t build a prosthesis with an effectiveresolution.Main reasons behind it are the type of probe being used and the poor design of the probe.To address this problem,wedeveloped a methodology to design a probe and an array of probes with better resolution and less resistive donut probe.Thismethodology helps us to design a probe optimizing all the parameters.We presented our methodology through a design that iscapable of 70 μm penetration inside the tissue.The tissue heating by our designed probe is only 0.411 °C.We also characterizedthe donut probe,which could be used by any research group to design a donut probe of their specific need.     

Urimem,a membrane that can store urinary proteins simply and economically,makes the large-scale storage of clinical samples possible

By nature,biomarker is the measurable change associated with a physiological or pathophysiological process.Unlike blood which has mechanisms to minimize changes and to keep the internal environment homeostatic,urine is more likely to reflect changes of the body and is a better biomarker source.Because of its potential in biomarker discovery,urinary proteins should be preserved comprehensively as the duration of the patients’corresponding medical records.Here,we propose a method to adsorb urinary proteins onto a membrane we named Urimem.This simple and inexpensive method requires minimal sample handling,uses no organic solvents,and is environmentally friendly.Urine samples were filtered through the membrane,and urinary proteins were adsorbed onto the membrane.The proteins on the membrane were dried and stored in a vacuum bag,which keeps the protein pattern faithfully preserved.The membrane may even permit storage at room temperature for weeks.Using this simple and inexpensive method,it is possible to begin preserving urine samples from all consenting people.Thus,medical research especially biomarker research can be conducted more economically.Even more objective large-scale prospective studies will be possible.This method has the potential to change the landscape of medical research and medical practice.     

High-Lift Effect of Bionic Slat Based on Owl Wing

A slat without a cove is built on the basis of a bionic airfoil （i.e. stowed multi-element airfoil）, which is extracted from a long-eared owl wing. The three-dimensional models with a deployed slat and a stowed slat are measured in a low-turbulence wind tunnel. The results are used to characterize high-lift effect： compared with the stowed slat, the deployed slat works more like a spoiler at low angles of attack, but like a conventional slat or slot at high angles of attack. In addition, it can also increase stall angle and maximum lift coefficient, and postpone the decrease in the gradient of the lift coefficient. At the same time, the flow field visualized around both three-dimensional models suggests the leading-edge separation associated with the decrease in the gradient of the lift coefficient, Furthermore, the related two-dimensional simulation well agrees with the analysis of the lift coefficient, as the complement to the experiment. The bionic slat may be used as reference in the design of leading-edge slats without a cove.     

A Procedure for the Design of Novel Assisting Devices for the Sit-to-Stand

The Sit-to-Stand （STS） is an activity most people perform numerous times daily. Standing up deals with the transition from two stabilized postures, namely seated to standing, with movement of all body segments except the feet. During the STS the body＇s Center of Gravity （COG） is moved upward from a sitting position to a standing position without losing balance and requiring a good coordination of many muscles. Three main phases of the STS movement can be recognized. One begins to stand up by inclining the upper body forward, which moves body mass toward the feet in order to maintain balance after lift-off. Prior to leaving the chair, hip and knee extensor muscles are activated to provide antigravity support for these joints, this action is commonly referred to as ＂weight shift＂. Finally; after leaving the chair, the leg and trunk joints are straightened to achieve upright stance. The STS task can be considered of major importance for impaired and elderly people to achieve minimal mo- bility and independence. In this paper we detail a procedure for the design of assisting devices to be used for the STS. In par- ticular, an experimental procedure is described firstly to track and record point trajectories and the orientation of the trunk during the STS. This analysis is then used to get information for the design of assisting devices. A proposal and simulation results are presented for a novel mechatronic system. In particular, for the case under study experimental tests are used to drive the actua- tion system for the reported simulation. A functional mechatronic scheme is then proposed to control the device during its operation.     

Initial Development of a Novel Amphibious Robot with Transformable Fin-Leg Composite Propulsion Mechanisms

Amphibious robots are very attractive for their broad applications in resource exploration, disaster rescue, and recon- naissance. However, it is very challenging to develop the robots for their complex, amphibious working environments. In the complex amphibious environment, amphibious robots should possess multi-capabilities to walk on rough ground, maneuver underwater, and pass through transitional zones such as sandy and muddy terrain. These capabilities require a high-performance propulsion mechanism for the robots. To tackle a complex task, a novel amphibious robot （AmphiHex-I） with,transformable fin-leg composite propulsion mechanisms is developed. With the fin-leg composite propulsions, AmphiHex-I can walk on rough and soft substrates and swim in water with many maneuvers. This paper presents the structural design of the transformable fin-leg propulsion mechanism and its driving module. A hybrid model is used to explore the dynamics between the trans- formable legs and transitional environment such as granular medium. The locomotion performances of legs with various ellip- tical shapes are analyzed, which is verified by the coincidence between the model predictions and the simulation results. Further, an orthogonal experiment is conducted to study the locomotion performance of a two-legged platform walking with an asyn- chronous gait in the sandy and muddy terrain. Finally, initial experiments of AmphiHex-I walking on various lands and swimming in water are implemented. These results verify that the transformable fin-leg mechanisms enable the amphibious robot to pass through a complex, amphibious working environment.     

Structural features and molecular evolution of Bowman-Birk protease inhibitors and their potential application

The Bowman-Birk inhibitors (BBIs) are well-studied serine protease inhibitors that are abundant in dicotyledonous and monocotyledonous plants. BBIs from dicots usually have a molecular weight of 8k and are double-headed with two reactive sites, whereas those from monocots can be divided into two classes, one approximately 8 kDa in size with one reactive site (another reactive site was lost) and the other approximately 16 kDa in size with two reactive sites. The reactive site is located at unique exposed surfaces formed by a disulfide-linked β-sheet loop that is highly conserved, rigid and mostly composed of nine residues. The structural features and molecular evolution of inhibitors are described, focusing on the conserved disulfide bridges. The sunflower trypsin inhibitor-1 (SFTI-1), with 14 amino acid residues, is a recently discovered bicyclic inhibitor, and is the most small and potent naturally occurring Bowman-Birk inhibitor.Recently, BBIs have become a hot topic because of their potential applications. BBIs are now used for defense against pathogens and insects in transgenic plants, which has advantages over using toxic and polluting insecticides. BBIs could also be applied in the prevention of cancer, Dengue fever, and inflammatory and allergic disorders, because of their inhibitory activity with respect to the serine proteases that play apivotal role in the development and pathogenesis of these diseases. The canonical nine-residue loop of BBIs/STH-1 provides an ideal template for drug design of specific inhibitors to target their respective proteases.     

Using Echo Ultrasound from Schooling Fish to Detect and Classify Fish Types

Fish finders have already been widely available in the fishing market for a number of years.However,the sizes of these fishfinders are too big and their prices are expensive to suit for the research of robotic fish or mini-submarine.The goal of thisresearch is to propose a low-cost fish detector and classifier which suits for underwater robot or submarine as a proximity sensor.With some pre-condition in hardware and algorithms,the experimental results show that the proposed design has good per-formance,with a detection rate of 100 % and a classification rate of 94 %.Both the existing type of fish and the group behaviorcan be revealed by statistical interpretations such as hovering passion and sparse swimming mode.     

Eco-service enhancement in peri-urban area of coal mining city of Huaibei in East China

After 50 years of coal mining, Huaibei Mine, located at 50 km southeast of Xuzhou City in East China, has grown to a middle-size city of 600,000 people from a small village of 2000 farmers. The Zhahe Valley, with 400 km² of a built-up area and more than 100 km² of subsided peri-urban wetland at the city center, is surrounded by eight exhausted old mines and communities. In cooperation with the local city government, an ecological landuse change assessment and eco-city planning project has been carried out with a focus on the assessment, restoration and enhancement of the wetland as an eco-service to the community. The assessment includes relationships to Green House Gas emissions and heat island effects, as well as measures for a livable, workable, affordable and sustainable human settlement development through industrial transition, landscape design and capacity building. This paper will briefly introduce the main ecological approaches and results of the assessment, including measures such as changing the car-dominated transportation network to a rail-dominated network, transforming the coal-oriented high-carbon industry to a service-oriented low-carbon industry, the C-shape urban form to an O-shape with a green–blue core at the center, and the fragmentized collapsed land to integrative eco-service land.