Music notation: a new method for visualizing social interaction in animals and humans

Background

Researchers have developed a variety of techniques for the visual presentation of quantitative data. These techniques can help to reveal trends and regularities that would be difficult to see if the data were left in raw form. Such techniques can be of great help in exploratory data analysis, making apparent the organization of data sets, developing new hypotheses, and in selecting effects to be tested by statistical analysis. Researchers studying social interaction in groups of animals and humans, however, have few tools to present their raw data visually, and it can be especially difficult to perceive patterns in these data. In this paper I introduce a new graphical method for the visual display of interaction records in human and animal groups, and I illustrate this method using data taken on chickens forming dominance hierarchies.

Results

This new method presents data in a way that can help researchers immediately to see patterns and connections in long, detailed records of interaction. I show a variety of ways in which this new technique can be used: (1) to explore trends in the formation of both group social structures and individual relationships; (2) to compare interaction records across groups of real animals and between real animals and computer-simulated animal interactions; (3) to search for and discover new types of small-scale interaction sequences; and (4) to examine how interaction patterns in larger groups might emerge from those in component subgroups. In addition, I discuss how this method can be modified and extended for visualizing a variety of different kinds of social interaction in both humans and animals.

Conclusion

This method can help researchers develop new insights into the structure and organization of social interaction. Such insights can make it easier for researchers to explain behavioural processes, to select aspects of data for statistical analysis, to design further studies, and to formulate appropriate mathematical models and computer simulations.     

利用基于Normal矩阵的谱平分法挖掘酵母蛋白质相互作用网络中的社团

蛋白质-蛋白质相互作用(protein-protein interaction,PPI)网络是生物网络的重要组成部分,也是后基因组时代的热点研究问题。揭示PPI网络中的社团结构,对于理解其复杂相互作用的结构和动态特征,了解活体细胞的结构和功能都有很大作用。但目前对于PPI网络结构的分析带有很强的试探性,还没有成熟可靠的方法。传统的谱平分法需要预先知道社团的个数,为了克服这一缺点,在无向无权的PPI网络中使用改进后的基于Normal矩阵的谱平分法,得到了55个有生物学意义的社团。实验结果表明:尽管PPI网络中的社团结构不是很明显,基于Normal矩阵的谱平分法依然可以有效地挖掘出其中具有生物学意义的社团结构。     

在电子耳蜗CIS方案中语音增强算法的实现

目的：电子耳蜗是一个帮助聋人恢复听觉的装置。它根据人耳的仿生学原理,用有限个电极刺激神经以恢复聋人听觉。目前实际应用的电子耳蜗技术已经能够在安静环境下帮助聋人恢复一定的听觉。本文在使用GIS方案的基础上,采取了频谱增强的方法,以提高电子耳蜗的在噪声环境下的性能。另外采用计算机仿真及声音合成的方法,以评估耳蜗植入者听到的声音。本实验获得了比较好的试听效果。其中提出的方法对耳子耳蜗的研究和工程现实具有一定的意义。     

Identification of large-scale genomic variation in cancer genomes using in silico reference models

Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.     

星座图聚类分析在小麦品种资源分类中的应用

根据星座图聚类分析的原理和方法,对濮阳市农科所从各地引进的20个小麦品种进行分析,分成3类,分析结果与田间表现相吻合。为育种者进行亲本选择和小麦品种资源分类提供了依据。     

Robustness and balance in the mixed model

When balanced data are analyzed by a robust method, different weights are applied to data points depending on their apparent status as outliers. This results in the effective unbalancing of the data. Concepts developed for the analysis of unbalanced data can help to suggest robust methods of analysis for balanced data.     

A dose-rate effect in single-particle electron microscopy

A low beam intensity, low electron dose imaging method has been developed for single-particle electron cryo-microscopy (cryo-EM). Experiments indicate that the new technique can reduce beam-induced specimen movement and secondary radiolytic effects, such as "bubbling". The improvement in image quality, especially for multiple-exposure data collection, will help single-particle cryo-EM to reach higher resolution.     

Protein identification in DNA databases by peptide mass fingerprinting.

Proteins can be identified using a set of peptide fragment weights produced by a specific digestion to search a protein database in which sequences have been replaced by fragment weights calculated for various cleavage methods. We present a method using multidimensional searches that greatly increases the confidence level for identification, allowing DNA sequence databases to be examined. This method provides a link between 2-dimensional gel electrophoresis protein databases and genome sequencing projects. Moreover, the increased confidence level allows unknown proteins to be matched to expressed sequence tags, potentially eliminating the need to obtain sequence information for cloning. Database searching from a mass profile is offered as a free service by an automatic server at the ETH, Zürich. For information, send an electronic message to the address cbrg/inf.ethz.ch with the line: help mass search, or help all.     

提高植物学实验教学质量的一些体会

实验是植物学教学的重要环节.针对植物学传统实验教学中的实际情况,进行了实验方法力求多样化、变部分过程性实验为过程性实验、增加综合性实验和研究性实验等尝试,进而充分发挥教师和学生在实验教学中的作用,培养学生的创造能力.     

蛋白质检测的方法学研究概述

蛋白质作为生命活动中起重要作用的生物大分子,与一切揭开生命奥秘的重大研究课题都有密切的关系.蛋白质的分离与检测是蛋白质研究的主要技术之一.我们就蛋白质检测的常规方法、电化学检测方法、分子生物学检测方法、电泳法和质谱法等进行了简要综述.     

提高植物学实验教学质量的一些体会

实验是植物学教学的重要环节。针对植物学传统实验教学中的实际情况, 进行了实验方法力求多样化、变部分过程性实验为过程性实验、增加综合性实验和研究性实验等尝试, 进而充分发挥教师和学生在实验教学中的作用, 培养学生的创造能力。     

A wireless sensor network to monitor and protect tigers in the wild

This paper investigates the possibility to efficiently use a wireless sensor network (WSN) to help preventing poaching in tiger habitats and to identify tigers’ movement patterns that later on can provide valuable information about their territorial behavior, hunting and reproduction. The same method can be successfully applied to track other mammals in the wild. We concluded that these objectives can be achieved in a 2000 sq. km area with only 2000 module sensors that work in the ZigBee standard, that operates on the IEEE 802.15.4 physical radio specification.     

Empirical mode decomposition method for investigating the structure of large-scale MHD instabilities in a tokamak

A new approach to the processing of experimental data from MHD diagnostics is developed for the purpose of investigating the spatial structure of large-scale MHD instabilities in a tokamak. The empirical mode decomposition method is applied to expand a multimode MHD perturbation in individual modes, which are then identified by constructing a spatial analytic signal with the help of the Hilbert transform. The method can be used to analyze the structure of the tearing instability and of the resistive wall modes.     

医学遗传学实验教学中实施研究性教学的探索实践

我们根据我校实际情况在医学遗传学实验教学中实施开放式研究性教学手段,培养学生具有自主建构的学习能力,掌握现代医学遗传学的基本理论和遗传性疾病诊断的实验方法,培养学员的综合实践能力,启发创造性思维,促进实验教学的改革。     

医学遗传学实验教学中实施研究性教学的探索实践

我们根据我校实际情况在医学遗传学实验教学中实施开放式研究性教学手段,培养学生具有自主建构的学习能力,掌握现代医学遗传学的基本理论和遗传性疾病诊断的实验方法,培养学员的综合实践能力,启发创造性思维,促进实验教学的改革。     

PBL教学法与批判性思维在医学本科生胸外科临床教学中的应用研究

目的:对比研究以问题为中心教学法(PBL)与基于课堂的学习法(LBL),观察批判性思维在医学本科生胸外科临床教学中的作用。方法:随机选取我院本科临床专业学生160名,随机分为PBL教学组及LBL教学组各80人。在学习结束时,采用不记名问卷调查,进行批判性思维能力和教学效果、教学模式的评价。结果:结果显示PBL教学法在批判性思维培养方面优于LBL教学法,且教学效果及教学模式也更受支持。结论:采用PBL教学法有助于提高学生的批判性思维,可有效提高学习效果。     

Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions

Recent advances in functional genomics have helped generate large-scale high-throughput protein interaction data. Such networks, though extremely valuable towards molecular level understanding of cells, do not provide any direct information about the regions (domains) in the proteins that mediate the interaction. Here, we performed co-evolutionary analysis of domains in interacting proteins in order to understand the degree of co-evolution of interacting and non-interacting domains. Using a combination of sequence and structural analysis, we analyzed protein-protein interactions in F1-ATPase, Sec23p/Sec24p, DNA-directed RNA polymerase and nuclear pore complexes, and found that interacting domain pair(s) for a given interaction exhibits higher level of co-evolution than the non-interacting domain pairs. Motivated by this finding, we developed a computational method to test the generality of the observed trend, and to predict large-scale domain-domain interactions. Given a protein-protein interaction, the proposed method predicts the domain pair(s) that is most likely to mediate the protein interaction. We applied this method on the yeast interactome to predict domain-domain interactions, and used known domain-domain interactions found in PDB crystal structures to validate our predictions. Our results show that the prediction accuracy of the proposed method is statistically significant. Comparison of our prediction results with those from two other methods reveals that only a fraction of predictions are shared by all the three methods, indicating that the proposed method can detect known interactions missed by other methods. We believe that the proposed method can be used with other methods to help identify previously unrecognized domain-domain interactions on a genome scale, and could potentially help reduce the search space for identifying interaction sites.     

Method to Estimate Activity of Subcutaneous Thermogenic Structures on Exposure to Stimuli of Different Modalities

A method to estimate activity of subcutaneous thermogenic structures was developed on the basis of dynamical infrared thermography. The gist is comparing the dynamics of skin temperature changes for different body sites on exposure to factors evoking metabolic responses. The method can be used for investigating the mechanisms of changes in body temperature in response to various disturbing factors and, in certain cases, can help to differentiate metabolic and vascular responses.     

A statistical method for detecting regions with different evolutionary dynamics in multialigned sequences.

We describe a stochastic method for tracing the evolutionary pattern of multialigned sequences. This method allows us to detect gene regions with distinct evolutionary dynamics, e.g., regions that significantly deviate from the expected behavior. Accurate detection of hypervariable or hyperconstrained regions may provide useful information on the structure/function relationship of biosequences. This information can help localize functional constraints. In addition, the selection of distinct evolutionary dynamics may assist in the correct use of biosequences as reliable molecular clocks.     

小组学习促进《植物检疫》课程教学效果的探讨

本文介绍了一种小组学习方式提高《植物检疫》教学效果的方法。试验于2010-2014年在本科生中进行,每届学生被分为两批进行比较试验。借助互联网辅助小组学习和文献研读小组学习两种方式对学习效果的影响进行了研究。结果表明,两种教学方式均有效提高了学生的测验成绩,反馈问卷显示两种教学方式受到学生的欢迎并有助于激发他们的学习兴趣。小组学习的方式可作为《植物检疫》课程教学的重要辅助方式。