Errata

New Phytologist 145 (2000), 1–3
In the January 2000 issue of New Phytologist , we published the forum article entitled 'Cadmium for all meals – plants with an unusual appetite' by U. Krämer. Since its publication, it has been brought to our attention that an error was introduced during typesetting. In the text several instances of concentrations are erroneously presented as mg⁻¹: these should be kg mg⁻¹.
New Phytologist 145 (2000), 367–421
In the March 2000 issue of New Phytologist , we published the Tansley review entitled 'Numerical and physical properties of orchid seeds and their biological implications' by J. Arditti and A. K. A. Ghani. Since its publication, it has been brought to our attention that an error was introduced during typesetting. On p. 391, Eqn 5, the horizontal line above the right side of the equation should form a square root sign.
We apologize to the authors and to our readers for these mistakes.     

On the statistical significance of protein complex

Background: Statistical validation of predicted complexes is a fundamental issue in proteomics and bioinformatics. The target is to measure the statistical significance of each predicted complex in terms of p-values. Surprisingly, this issue has not received much attention in the literature. To our knowledge, only a few research efforts have been made towards this direction. Methods: In this article, we propose a novel method for calculating the p-value of a predicted complex. The null hypothesis is that there is no difference between the number of edges in target protein complex and that in the random null model. In addition, we assume that a true protein complex must be a connected subgraph. Based on this null hypothesis, we present an algorithm to compute the p-value of a given predicted complex. Results: We test our method on five benchmark data sets to evaluate its effectiveness. Conclusions: The experimental results show that our method is superior to the state-of-the-art algorithms on assessing the statistical significance of candidate protein complexes.     

DNA typing and microsatellite associated sequence amplification (MASA) in detecting loss or gain of alleles

Constant exposure of genomic DNA to a variety of damaging agents including radiations poses a major challenge for developing an experimental approach for monitoring such damages. No single approach can be used to address this issue. In the present article, we have provided examples of DNA typing and believe that various approaches may enable to uncover not only loss or gain(s) of the alleles but also reveal subtle changes in the genome. Similarly, our genome analysis of the animal systems provides a method to assess the effects of radiation on domestic animals.     

Fire Severity in the Sierra Nevada Revisited: Conclusions Robust to Further Analysis

In our previous article (Odion and Hanson, Ecosystems 9:1177–89, 2006), we reported that fire severity in the conifer forests of the Sierra Nevada mountains of California, contrary to prevailing assumptions, did not burn with predominately stand-replacing, high severity fire. The reply by Safford and others (Ecosystems, this issue) using a new mapping approach also found this pattern. Their methods identify more high severity fire; however, as we illustrate here, this may be attributed to the different mapping approaches used. We previously also found that condition class based upon fire return interval departure (FRID) was not an effective predictor of fire severity. Safford and others (this issue) concluded that there was a strong correlation between FRID-based condition class and fire severity based upon data from the McNally fire of 2002. The difference between these findings about McNally fire reflects the fact that they combined FRID categories whereas we kept the categories separate. Here, using their fire severity data to evaluate all three fires, we found that severity was not predicted by FRID. Developing a consensus definition of fire severity within the scientific community might help alleviate future contradictions regarding fire effects.     

On the further integration of cooperative breeding and cooperation theory

We present a synopsis about the commentaries to the target article "Integrating cooperative breeding into theoretical concepts of cooperation", in which we attempted to integrate general mechanisms to explain cooperative behaviour among unrelated individuals with classic concepts to explain helping behaviour in cooperative breeders that do not invoke kin-based benefits. Here we (1) summarize the positions of the commentators concerning the main issues we raised in the target article and discuss important criticisms and extensions. (2) We relate our target article to some recent reviews on the evolution of cooperation and, (3) clarify how we use terminology with regard to cooperation and cooperative behaviour. (4) We discuss several aspects that were raised with respect to cooperative interactions including by-product mutualism, generalised reciprocity and multi-level selection and, (5) examine the alternatives to our classification scheme as proposed by some commentaries. (6) Finally, we highlight several aspects that might hinder the application of game theoretical mechanisms of cooperation in cooperatively breeding systems. Although there is broad agreement that cooperative breeding theory should be integrated within the more general concepts of cooperation, there is some debate about how this may be achieved. We conclude that the contributions in this special issue provide a fruitful first step and ample suggestions for future directions with regard to a more unified framework of cooperation in cooperative breeders.     

Offline perception: an introduction

Experiences that are self-generated and independent of sensory stimulations permeate our whole life. This theme issue examines their similarities and differences, systematizes the literature from an integrative perspective, critically discusses state-of-the-art empirical findings and proposes new theoretical approaches. The aim of the theme issue is to foster interaction between the different disciplines and research directions involved and to explore the prospects of a unificatory account of offline perception in general.This article is part of the theme issue ‘Offline perception: voluntary and spontaneous perceptual experiences without matching external stimulation’.     

Issues impacting genetic network reverse engineering algorithm validation using small networks

Genetic network reverse engineering has been an area of intensive research within the systems biology community during the last decade. With many techniques currently available, the task of validating them and choosing the best one for a certain problem is a complex issue. Current practice has been to validate an approach on in-silico synthetic data sets, and, wherever possible, on real data sets with known ground-truth. In this study, we highlight a major issue that the validation of reverse engineering algorithms on small benchmark networks very often results in networks which are not statistically better than a randomly picked network. Another important issue highlighted is that with short time series, a small variation in the pre-processing procedure might yield large differences in the inferred networks. To demonstrate these issues, we have selected as our case study the IRMA in-vivo synthetic yeast network recently published in Cell. Using Fisher's exact test, we show that many results reported in the literature on reverse-engineering this network are not significantly better than random. The discussion is further extended to some other networks commonly used for validation purposes in the literature. The results presented in this study emphasize that studies carried out using small genetic networks are likely to be trivial, making it imperative that larger real networks be used for validating and benchmarking purposes. If smaller networks are considered, then the results should be interpreted carefully to avoid over confidence. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction.     

The essential role of chemokines in the selective regulation of lymphocyte homing

Knowledge of lymphocyte migration has become a major issue in our understanding of acquired immunity. The selective migration of na?ve, effector, memory and regulatory T-cells is a multiple step process regulated by a specific arrangement of cytokines, chemokines and adhesion receptors that guide these cells to specific locations. Recent research has outlined two major pathways of lymphocyte trafficking under homeostatic and inflammatory conditions, one concerning tropism to cutaneous tissue and a second one related to mucosal-associated sites. In this article we will outline our present understanding of the role of cytokines and chemokines as regulators of lymphocyte migration through tissues.     

Reply to comment on “Mantle plume: the invisible serial killer — Application to the Permian–Triassic boundary mass extinction” by E. Heydari, N. Arzani and J. Hassanzadeh [Palaeogeography, Palaeoclimatology, Palaeoecology 264 (2008) 147–162]

In a recent article, Heydari et al. (2008) suggested that the perturbation at the Permian–Triassic boundary (PTB) was initiated by processes associated with an end-Permian mantle plume including igneous intrusions and uplift. These events resulted in the massive release of CH₄ primarily from the dissociation of marine gas hydrates, and secondarily from maturation of organic-rich sediments and fracturing of petroleum reservoirs. Injection of CH₄ into the ocean changed seawater composition (the acid-bath ocean) leading to marine mass extinction. Transfer of CO₂ and CH₄ from the ocean to the atmosphere created a hot climate (the end-Permian inferno) which caused the terrestrial mass extinction. We suggested that the Siberian trap volcanism and marine anoxia played little role in this catastrophe.Wignall and Racki (2009-this issue) have raised three criticisms to our article. The first is that our interpretation has been previously advocated by others. Our re-evaluation indicates that our interpretation was in fact opposite of those considered by Wignall and Racki (2009-this issue) to have presented scenarios similar to ours.The second, Wignall and Racki (2009-this issue) also suggest that our proposed change in carbonate mineralogy across the PTB did not occur because such a change “should produce a large positive excursion rather than the observed negative excursion”. Wignall and Racki (2009-this issue) have made a basic mathematical error in evaluating the effect of carbonate mineralogy on δ¹³C values. Therefore, they have reached two wrong conclusions: one about the validity of a change in carbonate mineralogy and the other regarding its effect on the shift in δ¹³C values at the PTB. A change in carbonate mineralogy produced a larger negative excursion rather than a positive shift.The third, Wignall and Racki (2009-this issue) indicate that the PTB ocean was anoxic to the rim. This criticism is not supported by the rock record because highly bioturbated strata were deposited in environments ranging from shallow shelves to deep waters under oxygenated water column at the time of the PTB mass extinction. If the ocean were totally stratified for 20 Ma, and if anoxia extended all the way to the shoreline, and if the ocean were anoxic to the rim and H₂S were oozing out of it, then we should see at least 100 m of organic-rich, varved-laminated strata in areas ranging from the abyssal plain to the shoreline environments. Such strata have not yet been found.     

Latent splice sites and stop codons revisited

The accuracy of the data we reported in an RNA Letter to the Editor earlier this year on the possible relationship between stop codons and splicing is questioned by Miriami et al. (this issue). We reply here that we see no inaccuracy in our data presentation and offer a possible explanation for their interpretation.     

Time-dependent spatial specificity of high-resolution fMRI: insights into mesoscopic neurovascular coupling

High-resolution functional magnetic resonance imaging (fMRI) is becoming increasingly popular because of the growing availability of ultra-high magnetic fields which are capable of improving sensitivity and spatial resolution. However, it is debatable whether increased spatial resolutions for haemodynamic-based techniques, like fMRI, can accurately detect the true location of neuronal activity. We have addressed this issue in functional columns and layers of animals with haemoglobin-based optical imaging and different fMRI contrasts, such as blood oxygenation level-dependent, cerebral blood flow and cerebral blood volume fMRI. In this review, we describe empirical evidence primarily from our own studies on how well these fMRI signals are spatially specific to the neuronally active site and discuss insights into neurovascular coupling at the mesoscale.This article is part of the theme issue ‘Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity’.     

Plankton dynamics under different climate conditions in tropical freshwater systems (a reply to the comment by Sarmento,Amado & Descy, )

相似文献   

What is being done in biological physics in the United Kingdom

In an earlier issue of this journal (Volume 1, number 2) we outlined current research projects and graduate training programs in American universities. This article is similar in that it includes relevant data for British universities.     

The African development dilemma revisited: Theoretical and empirical explorations

This article considers the issue of ethnic diversity in black Africa. In the first part of the article we discuss the various implications and possible consequences of the extensive ethnic diversity that characterizes most African countries, paying special attention to the relationship between the multi‐ethnic state and socio‐economic development. In the second part of the article we delve more deeply into the nature of ethnic diversity in contemporary Africa by examining in detail the cultural differences between two particular ethnic groups, the Kipsigis and Kikuyu of Kenya. Our empirical analyses indicate that some of the historic differences between these groups disappeared during the course of modernization. However, our findings also show that certain traditional aspects of both Kipsigis and Kikuyu culture remain. We conclude by noting the persisting importance of ethnicity as African states continue to struggle with the ‘development dilemma’.     

Introduction: Have hunter-gatherers ever lived in tropical rain forest independently of agriculture?

It has often been assumed that peoples living today as foragers in tropical rain forests are remnants of paleolithic populations that have been subsisting in their forest habitats for millennia and have only recently come into contact with sources of domesticated plants and animals. Independently, the two of us have published articles that challenge this view and propose the hypothesis that hunter- gatherers could never have lived in tropical rain forest without direct or indirect access to cultivated foods. This article serves as an introduction to six articles in this issue of Human Ecology, all devoted to this hypothesis. To provide background for this journal's readers, we summarize here our original articles.     

Moral Horizons of Land and Place

ABSTRACT

A recent ‘moral turn’ in anthropology has cast new light on morality as a subject of ethnographic inquiry, and on the making of moral meaning and judgment. This article, and the special issue it prefaces, contribute to this emergent literature through foregrounding and examining the moral dimensions of land and place. Taking up Didier Fassin’s injunction for a critical moral anthropology – rather than an anthropology of morality – we look to land and place as groundings for moral challenges and practices that are nevertheless not place-bound. A critical moral anthropology of land and place should be directed, we argue, to the interplay of mobility and emplacement, to the dynamics of landscape and ‘dwelling’, and to the multiplicities of expectation and meaning that surround the making and exploitation of resources. In contexts of global and local change, land and place offer productive grounds from which to consider the moral horizons – both spatial and temporal – of our world and our discipline.     

Addiction,Heroin‐Assisted Treatment and the Idea of Abstinence: A reply to Henden

In our previous article on the question whether heroin addicts are able to give informed consent voluntarily to research on heroin‐assisted treatment, we criticized the ongoing bioethical discussion of a flawed conceptualization of heroin addicts' options. As a participant in this discussion, Edmund Henden defends the conceptualization as sufficient for determining whether heroin addicts are able to give informed consent to the research on heroin‐assisted treatment voluntarily. This discussion on research on heroin‐assisted treatment seems to go astray in several respects. In his reply to our article Henden maintains some of the biases, such as the necessity of abstinence in recovery, that seem to prevail in addiction research on a more general level as well. These biases run the danger of having implausible ethical implications on stakeholders in addiction research and treatment. In our reply to him, we will further clarify and discuss the importance of describing the relevant issues in plausible terms that do justice to the realities of the cases of informed consent in research on heroin‐assisted treatment and also raise a wider issue of the ethics of wording as well as of the narrow scope, or ‘tunnel vision’, in addiction research as currently conducted.     

The Impacts of Household Consumption and Options for Change

This introductory article situates the contributions that comprise this special issue within the field of sustainable consumption and production (SCP) studies. After a brief review of the policy history surrounding SCP, we organize our discussion and the subsequent collection of articles into two groups. The first suite of articles views the environmental impacts associated with household consumption from the perspectives of different consumer groups, income levels, and geographic areas. This work confirms and refines several insights that have been developing over the past several years, namely that food and beverages, mobility, housing, and energy-using products are the most critical consumption domains from the standpoint of environmental sustainability and that higher household income leads to greater (but less than proportional) impacts. The second subset of articles analyzes the potential for mitigating these impacts through behavioral changes and innovation strategies. Although the contributions to this special issue describe several noteworthy examples of information- and team-based initiatives to catalyze behavioral changes, the state of knowledge pertaining to this aspect of the consumption problem is much more inchoate. Research on the formulation and implementation of effective "change management for sustainable consumption" should be treated as an area of priority attention for industrial ecologists.     

Mini Review: Immune Response to Myelin-Derived Sulfatide and CNS-Demyelination

Here we briefly review our understanding of the immune response to myelin-derived glycolipids during an inflammatory autoimmune response in the central nervous system (CNS). We focus primarily on the recognition of the self-glycolipid sulfatide by a distinct population of non-invariant NK T cells. The results of studies we have obtained so far in investigating the presentation of sulfatide by CNS-resident cells including microglia and their interactions with T cells indicate that this pathway might be successfully targeted for the treatment of autoimmune demyelination in multiple sclerosis. Special issue of the Journal dedicated to Drs. Anthony T. Campagnoni and Celia W. Campagnoni. It is a privilege to contribute an article for this special occasion. It was highly rewarding for me to participate in the Journal Club meetings at UCLA initiated by Tony in which experts in Neurochemistry, Neurosciences and Immunology would discuss and learn from each other with passion. I personally enjoyed and benefited both from these meetings and especially from the get-togethers at their lovely home overlooking the Santa Monica hills. I will always treasure my association and friendship with Tony and Celia.