The “χ” of the Matter: Testing the Relationship between Paleoenvironments and Three Theropod Clades

The view of spinosaurs as dinosaurs of semi-aquatic habits and strongly associated with marginal and coastal habitats are deeply rooted in both scientific and popular knowledge, but it was never statistically tested. Inspired by a previous analysis of other dinosaur clades and major paleoenvironmental categories, here we present our own statistical evaluation of the association between coastal and terrestrial paleoenvironments and spinosaurids, along with other two theropod taxa: abelisaurids and carcharodontosaurids. We also included a taphonomic perspective and classified the occurrences in categories related to potential biases in order to better address our interpretations. Our main results can be summarized as follows: 1) the taxon with the largest amount of statistical evidence showing it positively associated to coastal paleoenvironments is Spinosauridae; 2) abelisaurids and carcharodontosaurids had more statistical evidence showing them positively associated with terrestrial paleoenvironments; 3) it is likely that spinosaurids also occupied spatially inland areas in a way somehow comparable at least to carcharodontosaurids; 4) abelisaurids may have been more common than the other two taxa in inland habitats.     

保护区的分类系统与标准

保护区是一个泛称,根据建立的目的和本身的特点可以划分不同的类型,以利于管理工作的开展。每一个国家都应制订一个与本国资源和要求相适应的保护区分类系统。本文着重讨论按保护对象和保护区性质划分的保护区类型,以供判断每一个保护区的归属和管理重点。     

On the impoverishment of scientific education

Hannah Arendt, one of the foremost political philosophers of the twentieth century, has argued that it is the responsibility of educators not to leave children in their own world but instead to bring them into the adult world so that, as adults, they can carry civilization forward to whatever challenges it will face by bringing to bear the learning of the past. In the same collection of essays, she discusses the recognition by modern science that Nature is inconceivable in terms of ordinary human conceptual categories - as she writes, ‘unthinkable in terms of pure reason’. Together, these views on scientific education lead to an educational process that transforms children into adults, with a scientific adult being one who has the ability to conceptualize scientific systems independent of ordinary physical intuition. This article begins with Arendt’s basic educational and scientific points and develops from them a critique of current scientific education in conjunction with an appeal to educate young scientists in a manner that allows them to fulfill their potential ‘on the shoulders of giants’. While the article takes a general philosophical perspective, its specifics tend to be directed at biomedical education, in particular, how such education pertains to translational science.     

A career pathway in protein folding: from model peptides to postreductionist protein science

This review discusses the inherent challenge of linking "reductionist" approaches to decipher the information encoded in protein sequences with burgeoning efforts to explore protein folding in native environments-"postreductionist" approaches. Because the invitation to write this article came as a result of my selection to receive the 2010 Dorothy Hodgkin Award of the Protein Society, I use examples from my own work to illustrate the evolution from the reductionist to the postreductionist perspective. I am incredibly honored to receive the Hodgkin Award, but I want to emphasize that it is the combined effort, creativity, and talent of many students, postdoctoral fellows, and collaborators over several years that has led to any accomplishments on which this selection is based. Moreover, I do not claim to have unique insight into the topics discussed here; but this writing opportunity allows me to illustrate some threads in the evolution of protein folding research with my own experiences and to point out to those embarking on careers how the twists and turns in anyone's scientific path are influenced and enriched by the scientific context of our research. The path my own career has taken thus far has been shaped by the timing of discoveries in the field of protein science; together with our contemporaries, we become part of a knowledge evolution. In my own case, this has been an epoch of great discovery in protein folding and I feel very fortunate to have participated in it.     

The System of Interpretance, Naturalizing Meaning as Finality

A materialist construction of semiosis requires system embodiment at particular locales, in order to function as systems of interpretance. I propose that we can use a systemic model of scientific measurement to construct a systems view of semiosis. I further suggest that the categories required to understand that process can be used as templates when generalizing to biosemiosis and beyond. The viewpoint I advance here is that of natural philosophy—which, once granted, incurs no principled block to further generalization all the way to pansemiotics—nearer to Peirce’s own very general perspective. This project requires a hylozooic framework, which I present in the form of a specification hierarchy, whereby physical dynamics subsume all other transactions at more highly developed integrative levels. The upshot of the paper is a proposal that meanings can be assimilated most generally to final causes.     

View-Invariant Visuomotor Processing in Computational Mirror Neuron System for Humanoid

Mirror neurons are visuo-motor neurons found in primates and thought to be significant for imitation learning. The proposition that mirror neurons result from associative learning while the neonate observes his own actions has received noteworthy empirical support. Self-exploration is regarded as a procedure by which infants become perceptually observant to their own body and engage in a perceptual communication with themselves. We assume that crude sense of self is the prerequisite for social interaction. However, the contribution of mirror neurons in encoding the perspective from which the motor acts of others are seen have not been addressed in relation to humanoid robots. In this paper we present a computational model for development of mirror neuron system for humanoid based on the hypothesis that infants acquire MNS by sensorimotor associative learning through self-exploration capable of sustaining early imitation skills. The purpose of our proposed model is to take into account the view-dependency of neurons as a probable outcome of the associative connectivity between motor and visual information. In our experiment, a humanoid robot stands in front of a mirror (represented through self-image using camera) in order to obtain the associative relationship between his own motor generated actions and his own visual body-image. In the learning process the network first forms mapping from each motor representation onto visual representation from the self-exploratory perspective. Afterwards, the representation of the motor commands is learned to be associated with all possible visual perspectives. The complete architecture was evaluated by simulation experiments performed on DARwIn-OP humanoid robot.     

Network-Driven Reputation in Online Scientific Communities

The ever-increasing quantity and complexity of scientific production have made it difficult for researchers to keep track of advances in their own fields. This, together with growing popularity of online scientific communities, calls for the development of effective information filtering tools. We propose here an algorithm which simultaneously computes reputation of users and fitness of papers in a bipartite network representing an online scientific community. Evaluation on artificially-generated data and real data from the Econophysics Forum is used to determine the method''s best-performing variants. We show that when the input data is extended to a multilayer network including users, papers and authors and the algorithm is correspondingly modified, the resulting performance improves on multiple levels. In particular, top papers have higher citation count and top authors have higher h-index than top papers and top authors chosen by other algorithms. We finally show that our algorithm is robust against persistent authors (spammers) which makes the method readily applicable to the existing online scientific communities.     

Restoration and Science: A Practitioner/Scientist's View from Rare Habitat Restoration at a Southern California Preserve

Researchers reexamining the relationship between restoration science and practice report a continuing scientist‐practitioner gap. As a land manager with scientific training, I offer my perspective of the chasm and describe a restoration practice infused with as much science as the realities of limited budget and time allow. The coastal sage scrub (CSS) restoration project at Starr Ranch, a 1,585 ha Audubon preserve in southern California, combines non‐chemical invasive species control, restoration, and applied research. Our practices evolve from modified scientific approaches and the scientific literature. Results from experiments with non‐optimum replication (on effects of seed rates, soil tamping, and timing of planting) nonetheless had value for management decisions. A critical practice came from academic research that encouraged cost‐effective passive restoration. Our passive restoration monitoring data showed 28–100% total native cover after 3–5 years. Another published study found that restoration success in semiarid regions is dependent on rainfall, a finding vital for understanding active restoration monitoring results that showed a range of 0–88% total native cover at the end of the first season. Work progresses through a combination of applied research, a watchful eye on the scientific literature, and “ecological intuition” informed by the scientific literature and our own findings. I suggest that it is less critical for academic scientists to address the basic questions on technique that are helpful to land managers but rather advocate practitioner training in methods to test alternative strategies and long‐term monitoring.     

Malaria and social health determinants: a new heuristic framework from the perspective of Latin American social medicine

Traditionally, malaria research and study have followed the positivist scientific paradigm and its biomedical conception of disease. From this perspective, diverse control actions and strategies have been designed. However, despite a century of scientific experience and the depth and thoroughness achieved in the knowledge of malaria, this has not been translated into a constant and progressive decrease of its epidemiological burden. This essay argues for the need for a change in malaria conception, reconfiguring it as a process of biological and social character, where the geno-phenotypical possibilities of the host-parasite relationship and of the diseases clinical expression are articulated with the historic and social dynamics of the spaces in which they occur. In addition, it proposes rethinking the epidemiological research of this entity on the basis of the visualization of the dynamic, heterogeneous, dialectic and complex character of biosocial organizations that constitute the reality of malaria (from the social structure to the genetic and phenotypic level of parasite individuals, vectors and humans). To achieve this, it is suggested that: 1) the Latin American perspective on the social determinants of health be adopted; 2) new analytical categories (for instance, malaria social territory) and new investigation tools (matrices of critical processes of social determination) be incorporated, and 3) the conventional epidemiological categories of infectious diseases such as the transmission and infectiousness be reinterpreted.     

拟南芥与叶际微生物组的互作遗传机制——基于网络作图理论

叶际微生物组对植物的生长发育至关重要,但植物与其定殖微生物组相互作用机制尚不明确。目前植物与微生物互作研究多集中于根际微生物组,对叶际微生物组的研究较少,且这些研究未能从微生物互作的角度探究植物与微生物的相互作用机理。基于网络作图理论,将拟南芥基因组SNP （Single Nucleotide Polymorphisms）分子标记数据与微生物组网络特征值相关联,挖掘影响叶际微生物组网络结构的枢纽基因,以探究拟南芥塑造叶际微生物组网络结构的遗传机制。通过对188株拟南芥及其叶际微生物组数据的分析,识别出四种关系下的中心节点微生物,筛选到622个显著SNP位点。进一步构建了贝叶斯遗传网络,获得26个枢纽基因,这些基因可能参与了植物抗病、激素分泌和生长发育相关的分子途径。本研究从全基因组角度探究植物调控自身微生物组的遗传机制,揭示植物与微生物组如何互作促进植物健康,将为精准分子育种提供理论基础和遗传资源,并为合成菌群用于创制新型菌剂提供数据支持,具有重要的科学意义和应用价值。     

Biometry, biometrics, biostatistics, bioinformatics,..., bio-X

Recent scientific evolutions force us to rethink our profession's position on the scientific map, in relation to our neighboring professions, the ones with which we traditionally have strong collaborative links as well as the newly emerging fields, but also within our own, diverse professional group. We will show that great inspiration can be drawn from our own history, in fact from the early days of the Society. A recent inspiring example has been set by the late Rob Kempton, who died suddenly just months before he was to become President of the International Biometric Society.     

The olfactory system of crustaceans as a model for ecologo-toxicological studies

Based on our own studies and on literature data, there are considered peculiarities of structural-functional organization of the crustacean olfactory system and effects of pollutants on it. The behavioral reaction changes based on chemoreception in the polluted aquatic environment are described. Usefulness of study of the crustacean olfactory system is substantiated as a perspective object of ecologo-toxicological investigations.     

Prediction of protein functions with gene ontology and interspecies protein homology data

Accurate computational prediction of protein functions increasingly relies on network-inspired models for the protein function transfer. This task can become challenging for proteins isolated in their own network or those with poor or uncharacterized neighborhoods. Here, we present a novel probabilistic chain-graph-based approach for predicting protein functions that builds on connecting networks of two (or more) different species by links of high interspecies sequence homology. In this way, proteins are able to "exchange" functional information with their neighbors-homologs from a different species. The knowledge of interspecies relationships, such as the sequence homology, can become crucial in cases of limited information from other sources of data, including the protein-protein interactions or cellular locations of proteins. We further enhance our model to account for the Gene Ontology dependencies by linking multiple but related functional ontology categories within and across multiple species. The resulting networks are of significantly higher complexity than most traditional protein network models. We comprehensively benchmark our method by applying it to two largest protein networks, the Yeast and the Fly. The joint Fly-Yeast network provides substantial improvements in precision, accuracy, and false positive rate over networks that consider either of the sources in isolation. At the same time, the new model retains the computational efficiency similar to that of the simpler networks.     

基于网络群组特征的生态管理分区——以武汉市为例

生态管理分区是维持区域生态安全、实现城市生态差异化治理的重要手段。然而现有分区方法侧重生态功能属性,较少考虑生态斑块之间联系强度差异,忽视了斑块的群组结构。以武汉市为例构建生态网络,从生态系统结构和功能的视角,结合斑块空间组织和斑块联系强弱,运用凝聚子群方法,提取联系紧密的生态组分,将网络划分为异质性群组,基于网络群组特征和生态景观辐射范围进行分区覆盖分析,并进行分区评价。结果表明：(1)86条生态廊道连接研究区34处生态斑块,进一步形成8个生态群组;(2)多数群组内部连通性较好,北部群组之间联系较强,南部群组之间联系相对较弱;(3)依据群组结构功能特征,形成6大网络群组分区,通过与武汉市经济发展规划分区对比,两者具有较高的一致性;(4)城市外围的分区网络稳定性较好,中部稳定性较差,识别分区内13个重要斑块和16条重要廊道,作为重点发展保护对象;(5)综合分区特征将6大分区确立为生态屏障区、生态控制区、生态改善区、生态修复区、生态开发区以及生态保育区,并提出生态发展差异化保护措施。研究将生态功能属性和空间结构属性进行有机关联并制定分区策略,为区域生态管理分区、生态保护规划提供新视角。     

End-to-end pest detection on an improved deformable DETR with multihead criss cross attention

In the ecological environment, pest infestation seriously affects the ecological balance; therefore, pest control is both necessary and urgent. However, most popular pest detection methods require various handcrafted components, which further limits the improvement of their pest detection performance. This study attempts to overcome this challenge from a new perspective by achieving an end-to-end network that eliminates the introduction of handcrafted components and effectively detects pests by combining residual networks and transformers. First, a squeeze-and-excitation module was introduced to assist the residual network fully extracting pest features. Second, a novel multihead criss cross attention module was designed to fully obtain the mutual relations between object queries with minimal computational cost. Third, data augmentation was incorporated to balance the sample categories. Finally, our model performance was evaluated based on a public pest dataset consisting of 25,378 images and 24 categories, and an average accuracy of 72.5% was achieved. The experimental results demonstrate that our method outperforms state-of-the-art methods. In addition to its excellent detection performance, this method demonstrates promising potential as an effective means of detecting other targets with similar characteristics. Therefore, it can be be effectively applied to practice and provide a new pest detection solution.     

Inside FlyBase: Biocuration as a career

As research in the biological sciences continues to advance at a rapid pace, it is increasingly important that the data be captured, standardized, organized, and made accessible to the scientific community. This is the job of a biocurator. Here we describe the process of biocuration from our perspective as FlyBase curators.     

Ongoing Processes in a Fitness Network Model under Restricted Resources

In real networks, the resources that make up the nodes and edges are finite. This constraint poses a serious problem for network modeling, namely, the compatibility between robustness and efficiency. However, these concepts are generally in conflict with each other. In this study, we propose a new fitness-driven network model for finite resources. In our model, each individual has its own fitness, which it tries to increase. The main assumption in fitness-driven networks is that incomplete estimation of fitness results in a dynamical growing network. By taking into account these internal dynamics, nodes and edges emerge as a result of exchanges between finite resources. We show that our network model exhibits exponential distributions in the in- and out-degree distributions and a power law distribution of edge weights. Furthermore, our network model resolves the trade-off relationship between robustness and efficiency. Our result suggests that growing and anti-growing networks are the result of resolving the trade-off problem itself.     

Nomenclature and guideline to express the amount of a membrane protein synthesized in animal cells in view of bioprocess optimization and production monitoring

Studies of a bioprocess optimization and monitoring for protein synthesis in animal cells face a challenge on how to express in quantitative terms the system performance. It is possible to have a panel of calculated variables that fits more or less appropriately the intended goal. Each mathematical expression approach translates different quantitative aspects. We can basically separate them into two categories: those used for the evaluation of cell physiology in terms of product synthesis, which can be for bioprocess improvement or optimization, and those used for production unit sizing and for bioprocess operation. With these perspectives and based on our own data of kinetic S2 cells growth and metabolism, as well as on their synthesis of the transmembrane recombinant rabies virus glycoprotein, here indicated as P, we show and discuss the main characteristics of calculated variables and their recommended use. Mainly applied to a bioprocess improvement/optimization and that mainly used for operation definition and to design the production unit, we expect these definitions/recommendations would improve the quality of data produced in this field and lead to more standardized procedures. In turn, it would allow a better and easier comprehension of scientific and technological communications for specialized readers.     

Effects of Context on Visuomotor Interference Depends on the Perspective of Observed Actions

Visuomotor interference occurs when the execution of an action is facilitated by the concurrent observation of the same action and hindered by the concurrent observation of a different action. There is evidence that visuomotor interference can be modulated top-down by higher cognitive functions, depending on whether own performed actions or observed actions are selectively attended. Here, we studied whether these effects of cognitive context on visuomotor interference are also dependent on the point-of-view of the observed action. We employed a delayed go/no-go task known to induce visuomotor interference. Static images of hand gestures in either egocentric or allocentric perspective were presented as “go” stimuli after participants were pre-cued to prepare either a matching (congruent) or non-matching (incongruent) action. Participants performed this task in two different cognitive contexts: In one, they focused on the visual image of the hand gesture shown as the go stimulus (image context), whereas in the other they focused on the hand gesture they performed (action context). We analyzed reaction times to initiate the prepared action upon presentation of the gesture image and found evidence of visuomotor interference in both contexts and for both perspectives. Strikingly, results show that the effect of cognitive context on visuomotor interference also depends on the perspective of observed actions. When focusing on own-actions, visuomotor interference was significantly less for gesture images in allocentric perspective than in egocentric perspective; when focusing on observed actions, visuomotor interference was present regardless of the perspective of the gesture image. Overall these data suggest that visuomotor interference may be modulated by higher cognitive processes, so that when we are specifically attending to our own actions, images depicting others’ actions (allocentric perspective) have much less interference on our own actions.     

国外韧性城市形态研究述评

面对突发的自然和人为灾害,城市表现出极大的脆弱性。韧性城市形态被认为是化解城市脆弱性的关键得到关注,梳理国外研究成果对应对我国快速城市化进程中的不确定灾害风险具有重要意义。以韧性城市形态为主题,从概念与特征、形态要素韧性表现、评估及韧性设计等方面追踪国外研究进展。研究结果表明:国外文献重点探讨了形态与自然灾害的关联;韧性城市形态的概念尚未达成一致意见;从宏观、中观、微观空间层次视角探讨城市形态要素韧性表现成果较多;形态要素韧性评估集中于道路网络要素的韧性表现;形态要素韧性设计关键在于空间异质性。基于分析结果可知,我国未来研究重点应集中在全方位构建韧性城市形态研究框架、丰富并拓展形态要素韧性评估方法与技术、重视形态要素空间异质性等方面。