The Exploration-Exploitation Dilemma: A Multidisciplinary Framework

The trade-off between the need to obtain new knowledge and the need to use that knowledge to improve performance is one of the most basic trade-offs in nature, and optimal performance usually requires some balance between exploratory and exploitative behaviors. Researchers in many disciplines have been searching for the optimal solution to this dilemma. Here we present a novel model in which the exploration strategy itself is dynamic and varies with time in order to optimize a definite goal, such as the acquisition of energy, money, or prestige. Our model produced four very distinct phases: Knowledge establishment, Knowledge accumulation, Knowledge maintenance, and Knowledge exploitation, giving rise to a multidisciplinary framework that applies equally to humans, animals, and organizations. The framework can be used to explain a multitude of phenomena in various disciplines, such as the movement of animals in novel landscapes, the most efficient resource allocation for a start-up company, or the effects of old age on knowledge acquisition in humans.     

基于知识图谱的肿瘤MDT研究可视化分析

目的 梳理肿瘤多学科诊疗团队研究关键主题,分析研究热点和趋势。方法 应用CiteSpace对肿瘤多学科诊疗团队研究进行可视化分析。结果 相关文献共2 160篇,关键文献10篇,主要主题聚类15个,突现术语29个。结论 肿瘤MDT研究主要集中于多学科诊疗团队的构建及运行、推行情况、效果评价,研究前沿如提高实施效率、成本—效果分析、随机对照研究等,为中国肿瘤多学科诊疗团队研究和发展提供了新视角。     

Knowledge Integration and Good Marine Governance: A Multidisciplinary Analysis and Critical Synopsis

Human Ecology - Our research addresses knowledge integration for the good governance of the environment and the oceans: (a) through a comprehensive legal, political science, and anthropological...     

A Framework to Link International Clinical Research to the Promotion of Justice in Global Health

How international research might contribute to justice in global health has not been substantively addressed by bioethics. Theories of justice from political philosophy establish obligations for parties from high‐income countries owed to parties from low and middle‐income countries. We have developed a new framework that is based on Jennifer Ruger's health capability paradigm to strengthen the link between international clinical research and justice in global health. The ‘research for health justice’ framework provides direction on three aspects of international clinical research: the research target, research capacity strengthening, and post‐trial benefits. It identifies the obligations of justice owed by national governments, research funders, research sponsors, and investigators to trial participants and host communities. These obligations vary from those currently articulated in international research ethics guidelines. Ethical requirements of a different kind are needed if international clinical research is to advance global health equity.     

GO-PCA: An Unsupervised Method to Explore Gene Expression Data Using Prior Knowledge

Method

Genome-wide expression profiling is a widely used approach for characterizing heterogeneous populations of cells, tissues, biopsies, or other biological specimen. The exploratory analysis of such data typically relies on generic unsupervised methods, e.g. principal component analysis (PCA) or hierarchical clustering. However, generic methods fail to exploit prior knowledge about the molecular functions of genes. Here, I introduce GO-PCA, an unsupervised method that combines PCA with nonparametric GO enrichment analysis, in order to systematically search for sets of genes that are both strongly correlated and closely functionally related. These gene sets are then used to automatically generate expression signatures with functional labels, which collectively aim to provide a readily interpretable representation of biologically relevant similarities and differences. The robustness of the results obtained can be assessed by bootstrapping.

Results

I first applied GO-PCA to datasets containing diverse hematopoietic cell types from human and mouse, respectively. In both cases, GO-PCA generated a small number of signatures that represented the majority of lineages present, and whose labels reflected their respective biological characteristics. I then applied GO-PCA to human glioblastoma (GBM) data, and recovered signatures associated with four out of five previously defined GBM subtypes. My results demonstrate that GO-PCA is a powerful and versatile exploratory method that reduces an expression matrix containing thousands of genes to a much smaller set of interpretable signatures. In this way, GO-PCA aims to facilitate hypothesis generation, design of further analyses, and functional comparisons across datasets.     

RNA干扰技术在几项研究领域的应用

作为一项新的反向遗传学技术 ,RNA干扰技术正在越来越多地应用于包括鉴定基因功能、疾病治疗、植物病毒抗性研究在内的多项研究领域。在鉴定基因功能研究中 ,由于该技术的操作简便性 ,使得在基因组水平进行大范围的基因功能鉴定成为可能 ;而针对致病相关基因、致病病毒基因组进行RNA干扰 ,可以有效抑制病情恶化 ,有可能成为未来疾病治疗的重要手段 ;同时 ,将RNA干扰技术应用于植物抗病毒研究 ,为工程化植物抗病毒遗传育种提供了一个高效、特异的抗性获得手段。对RNA干扰技术在上述三个研究领域的应用作简要综述 ,并对应用过程中需注意的问题进行了探讨 。     

A Spatial Framework for Understanding Population Structure and Admixture

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build “geogenetic maps,” which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.     

基于科学知识图谱的生态足迹研究演进、框架与前沿中外比较

生态足迹是评估人类活动下生态可持续性的有效工具。基于1999-2020年CNKI中文核心期刊与1994-2020年Web of Science核心合集有关生态足迹研究文献共5104篇,运用CiteSpace可视化软件,绘制中外研究高频词时区、关键词聚类及突现词时间分布科学知识图谱,梳理中外生态足迹相关研究演进路径、基本理论框架与动态前沿。研究结果表明:(1)中外生态足迹研究演进路径均可分为三个阶段,但演进方式有所差异,且国内研究较国外相对滞后;(2)中外生态足迹研究均已形成以生态足迹模型方法为工具、以足迹测算为基础、以生态安全为落脚点、以促进人与生态协调发展为目标的基础框架体系,国外侧重基础框架构建、宏观尺度研究与微观机制分析,国内侧重模型和方法优化与外部环境分析;(3)当前国外前沿方向为环境库兹涅茨曲线假设验证研究与生态网络分析,国内为碳足迹和水资源足迹的测算、三维生态足迹模型下的自然资本评估以及生态补偿问题。     

A Sero-epidemiological Approach to Explore Transmission of Mycobacterium ulcerans

The debilitating skin disease Buruli ulcer (BU) is caused by infection with Mycobacterium ulcerans. While various hypotheses on potential reservoirs and vectors of M. ulcerans exist, the mode of transmission has remained unclear. Epidemiological studies have indicated that children below the age of four are less exposed to the pathogen and at lower risk of developing BU than older children. In the present study we compared the age at which children begin to develop antibody responses against M. ulcerans with the age pattern of responses to other pathogens transmitted by various mechanisms. A total of 1,352 sera from individuals living in the BU endemic Offin river valley of Ghana were included in the study. While first serological responses to the mosquito transmitted malaria parasite Plasmodium falciparum and to soil transmitted Strongyloides helminths emerged around the age of one and two years, sero-conversion for M. ulcerans and for the water transmitted trematode Schistosoma mansoni occurred at around four and five years, respectively. Our data suggest that exposure to M. ulcerans intensifies strongly at the age when children start to have more intense contact with the environment, outside the small movement range of young children. Further results from our serological investigations in the Offin river valley also indicate ongoing transmission of Treponema pallidum, the causative agent of yaws.     

A Framework for Managing Core Facilities within the Research Enterprise

Core facilities represent increasingly important operational and strategic components of institutions'' research enterprises, especially in biomolecular science and engineering disciplines. With this realization, many research institutions are placing more attention on effectively managing core facilities within the research enterprise. A framework is presented for organizing the questions, challenges, and opportunities facing core facilities and the academic units and institutions in which they operate. This framework is intended to assist in guiding core facility management discussions in the context of a portfolio of facilities and within the overall institutional research enterprise.     

外泌体：探究微生物感染机制的新视角

外泌体是细胞外囊泡的一种,由多囊泡体和细胞膜融合后释放到细胞外。外泌体能递送有功能的分子,包括蛋白质、脂质和核酸给受体细胞,参与细胞间通讯,影响细胞的各种生理与病理功能。近年来,越来越多研究发现,外泌体在病原微生物感染性疾病发病机制中也发挥重要作用。在慢性感染中,外泌体能传播感染性蛋白质和病毒RNA,并改变未感染细胞的功能。同时,这些具有极强免疫原性的蛋白质可向免疫系统递送病原信息,激活免疫系统。本文就外泌体在慢性病原体感染中的相关研究进展进行综述。研究这些机制,可为慢性感染的诊断和治疗提供新的思路。     

用ELISA方法检测稻田捕食者对摇蚊的捕食作用

应用酶联免疫吸附（ELISA）双抗体夹心法,研究了稻田19种常见捕食性天敌对中性昆虫摇蚊的捕食作用。用摇蚊作抗原免疫雄性大白兔获得抗血清,用中和法、双向琼脂扩散实验及交叉反应对所制备的抗血清作特异性检测,抗体反应表明制备的抗血清对摇蚊抗原具有较高的特异性。测定了19种捕食者捕食摇蚊的临界吸收值。在检测的19种捕食者中,有13种捕食了摇蚊,占被检测捕食者种数的67.89％。ELISA阳性反应率最高的是在早稻前期采集的褶管巢蛛,阳性率高达50％,其次是晚稻中期采集的拟水狼蛛,其阳性率为40％。ELISA方法敏感,能快速检测捕食者对猎物的捕食作用及确定节肢类捕食者如蜘蛛对水稻害早控制作用大小,作为一种有效实验工具,可有助于发展水稻害虫综合管理理论。     

Microbiome Structure and Function: A New Framework for Interpreting Data

A distinction between different notions of “structure” and “function” is suggested for interpreting the overwhelming amount of data on microbiome structure and function. Sequence data, biochemical agents, interaction networks, taxonomic communities, and their dynamics can be linked to potential or actual biochemical activities, causal roles, and selected effects, respectively. This conceptual clarification has important methodological consequences for how to interpret existing data and approach open questions in contemporary microbiome research practice. In particular, the field will have to start thinking about notions of function more directly. Also see the video abstract here https://youtu.be/j5pq5uGld1k .     

Voices of Our Past: Using Oral History to Explore Funds of Knowledge within a Puerto Rican Family

This article presents an educational rationale for using oral history to teach students that there are multiple sources of knowledge and ways to seek valid information. A case study to explore the funds of knowledge within an extended Puerto Rican family is used illustratively. The study describes the leadership role played by one grandmother as the family participated in multiple migrations, describes creative ways employed by her and other women to reestablish the community, and challenges some stereotypes of Latinas.     

Ethnobotanical Knowledge and Crop Diversity in Swidden Fields: A Study in a Native Amazonian Society

Crop diversity protects food consumption in poor households within developing nations. Here we estimate the association between crop diversity on swidden fields and ethnobotanical knowledge. We conducted research among 215 male household heads from a native Amazonian society. Using multivariate regressions, we found higher crop diversity among households that depend on agricultural production for household consumption. We also found a statistically significant and positive, but low, association between the ethnobotanical knowledge of the male household head and crop diversity. Doubling the stock of ethnobotanical knowledge of the male household head is associated with a 9% increase in the number of crops sown by a household. The association remained after we controlled for the household level of market exposure, but vanished after we controlled for the social capital of the male household head. Future research should compare the association between ethnobotanical knowledge and crop diversity across different agricultural systems (i.e., home gardens, fallow fields).