Protocols,Toolboxes and Resource papers

In the August 2009 issue of Autophagy, I indicated that we were launching a new category of article, Protocols. At that time, I noted that we would ultimately be placing these articles on a new site online. Well, that time has finally arrived (see www.landesbioscience.com/journals/autophagy/protocols/ for links to these papers). Therefore, it seems appropriate for me to briefly distinguish among three types of community-oriented papers, Protocol, Toolbox and Resource.     

Assessing models of optimal diving

Many birds and mammals forage under water and have to return to the surface to breathe. Models of optimal diving attempt to explain the behaviour of such animals in terms of selection for successful foraging given the constraints imposed by physiology. Several recent papers have questioned the accuracy of both the assumptions and the predictions of these models. Here, I provide a critical review of these papers, arguing that they misrepresent both the models and the data. As a result, they focus on inappropriate tests. I use the debate to suggest various new models and to explore the general relationship between theory and data in behavioural ecology. In particular, I consider the merits of qualitative and quantitative predictions.     

A decade since ”diversification of ruminants”: has our knowledge improved?

In his landmark 1989 paper, R.R. Hofmann classified ruminants into three categories based upon digestive anatomy and preferred forages, and proposed that divergence of feeding strategies among ruminants is a result of morphological evolution of the digestive tract. Because of the hypothetical nature of these views and the ingrained beliefs that they challenged, several papers were published that reported tests of Hofmann’s predictions. The consensus among these papers was that Hofmann’s predictions were inadequate. I describe the experimental evidence that has been put forth in opposition to the ruminant diversification hypothesis and contend that we have failed to adequately test Hofmann’s predictions. Received: 11 October 1999 / Accepted: 6 April 2000     

Global stability results for a generalized Lotka-Volterra system with distributed delays

The paper contains an extension of the general ODE system proposed in previous papers by the same authors, to include distributed time delays in the interaction terms. The new system describes a large class of Lotka-Volterra like population models and epidemic models with continuous time delays. Sufficient conditions for the boundedness of solutions and for the global asymptotic stability of nontrivial equilibrium solutions are given. A detailed analysis of the epidemic system is given with respect to the conditions for global stability. For a relevant subclass of these systems an existence criterion for steady states is also given.Work supported by the Special Program Control of Infectious Diseases, C.N.R. and by the M.P.I., Italy     

How we do business (or, Why does it take other journals so long to review your paper?)

Have you ever wondered why it takes so long to get comments back from reviewers at some journals? After all, how long should it take to review a paper? I suspect most of us have asked this question at one time or another. While recently contemplating this, I thought it was time to tell you a little about how we run Autophagy, and at the same time compare it to the practices at some other journals where I have, on occasion (notably before the start of Autophagy), sent my own papers.     

The Special Column of Primate Behavior

It is a long-term policy to publish SPECIAL COLUMNsin Current Zoology, and I am delighted that thejournal is publishing this special column devoted to thetopic of Primate Behavior. The eight papers in this sectionpresent significant new data and synthesize thesefindings with existing information on sexual selection of     

Trends and themes in African ornithology

Ornithology in Africa has a long history. I review trends in the ornithological literature since 1990 within the context of the 14th Pan-African Ornithological Congress. Using full text searches of papers on PubMed® and abstracts from main ornithological journals I found that most papers referencing African bird species are focused on medical-related research questions. Restricting the literature search to journals African ornithologists are most likely to publish in, I found 2 279 relevant papers. These describe work on 29% of African bird species from 82% of African bird families, in all but two African countries. Overall output has increased slightly over time, with more papers tackling more research topics. Most popular research topics were demography, conservation and climate, with disease ecology, physiology and ecological processes the least researched topics. I found that while many authors with African affiliations publish papers, outside of South Africa very few African-based authors reliably publish in the international research literature, perhaps indicating difficulties in establishing a productive research career in much of Africa. I conclude with a call to overseas ornithologists working in Africa and to organisations funding research in Africa to work together to build capacity outside of the few established research centres.     

How we do business (or,why does it take other journals so long to review your paper?)

Have you ever wondered why it takes so long to get comments back from reviewers at some journals? After all, how long should it take to review a paper? I suspect most of us have asked this question at one time or another. While recently contemplating this question I thought it was time to tell you a little about how we run Autophagy, and at the same time compare it to the practices at some other journals where I have, on occasion (notably before the start of Autophagy), sent my own papers.     

The basis for colorless hemolymph and cocoons in the Y-gene recessive Bombyx mori mutants: a defect in the cellular uptake of carotenoids

Bombyx mori is an excellent model for the study of carotenoid-binding proteins (CBP). In previous papers, we identified and molecularly characterized a CBP from the Y-gene dominant mutants. In the present study, we attempted to correlate and establish lipid metabolism and distribution in these mutants. When [3H]-triolein was fed to the mutants, typical patterns of uptake of labeled fatty acids from midgut to hemolymph and subsequent delivery to fat body and silk glands were obtained in all mutants. Further analysis of lipid and carotenoid profiles revealed that the yellow coloration in the hemolymph associated with lipophorin is not attributed to a difference in lipophorin concentrations among the mutants, nor to its lipid composition, but rather to its carotenoid content. Lipophorin of the Y+I mutant exhibited the highest concentration of total carotenoids of 55.8 microg/mg lipophorin compared to 3.1 microg/mg in the +Y+I mutant, 1.2 microg/mg in the YI mutant and 0.5 microg/mg in the +YI mutant. Characteristic retention time in HPLC of the different classes of carotenoids of lipophorin identified the presence of lutein as the major chromophore (62-77%), followed by beta-carotenes (22-38%). Although lutein and beta-carotene content of mutants' lipophorin differed significantly, the ratio of lutein to beta-carotene of 3:1 was not different among mutants. Similarly, lipid compositions of mutant silk glands were not significantly different, but carotenoid contents were. The significantly high concentration of lutein in the Y+I mutant silk gland represented more than 160-fold increase compared to +Y+I mutant (p<0.001). In this report, we conclude that lipid metabolism in the mutants is not defected and that the molecular basis for colorless hemolymph and cocoons is a defect in the cellular uptake of lutein associated with the Y-gene recessive mutants.     

Development of a variational scheme for model inversion of multi-area model of brain. Part I: simulation evaluation

We previously developed an integrated model of the brain within a single cortical area for functional Magnetic Resonance Imaging (fMRI), electroencephalography (EEG), and magnetoencephalography (MEG) using an extended neural mass model (ENMM). We then extended ENMM from a single-area to a multi-area model to develop a neural mass model of the entire brain. To this end, we derived a nonlinear state-space representation of the multi-area model. In Parts I and II of these two companion papers (henceforth called Part I and Part II), we develop and evaluate a variational Bayesian expectation maximization (VBEM) method to estimate parameters of multi-area ENMM (MEN) using E/MEG data. In Part I, we derive a state-space representation of MEN and use VBEM method for model inversion (parameter estimation). We evaluate and validate performance of VBEM method for model inversion of MEN using simulation studies in various signal-to-noise ratios. Details of VBEM method are presented in Part II. The proposed approach provides a useful technique for analyzing effective connectivity using non-invasive EEG and MEG methods.     

The Increasing Importance of Gene-Based Analyses

In recent years, genome and exome sequencing studies have implicated a plethora of new disease genes with rare causal variants. Here, I review 150 exome sequencing studies that claim to have discovered that a disease can be caused by different rare variants in the same gene, and I determine whether their methods followed the current best-practice guidelines in the interpretation of their data. Specifically, I assess whether studies appropriately assess controls for rare variants throughout the entire gene or implicated region as opposed to only investigating the specific rare variants identified in the cases, and I assess whether studies present sufficient co-segregation data for statistically significant linkage. I find that the proportion of studies performing gene-based analyses has increased with time, but that even in 2015 fewer than 40% of the reviewed studies used this method, and only 10% presented statistically significant co-segregation data. Furthermore, I find that the genes reported in these papers are explaining a decreasing proportion of cases as the field moves past most of the low-hanging fruit, with 50% of the genes from studies in 2014 and 2015 having variants in fewer than 5% of cases. As more studies focus on genes explaining relatively few cases, the importance of performing appropriate gene-based analyses is increasing. It is becoming increasingly important for journal editors and reviewers to require stringent gene-based evidence to avoid an avalanche of misleading disease gene discovery papers.     

Solutions to the New Threats to Academic Freedom?

In my commentary on Francesca Minerva's article ‘New Threats to Academic Freedom’, I agree with her contention that the existence of the Internet has given rise to new and very serious threats to academic freedom. I think that it is crucial that we confront those threats, and find ways to eliminate them, which I believe can be done. The threats in question involve both authors and editors. In the case of authors, I argue that the best solution is not anonymous publication, but publication using pseudonyms, and I describe how that would work. In the case of editors, my proposal is a website that a number of journals would have access to, where papers that editors judge to be clearly worthy of publication, but whose publication seems likely to set off a firestorm of public and media protest, could be published without any indication of the journal that had accepted the paper for publication.     

Systematic Differences in Impact across Publication Tracks at PNAS

Background

Citation data can be used to evaluate the editorial policies and procedures of scientific journals. Here we investigate citation counts for the three different publication tracks of the Proceedings of the National Academy of Sciences of the United States of America (PNAS). This analysis explores the consequences of differences in editor and referee selection, while controlling for the prestige of the journal in which the papers appear.

Methodology/Principal Findings

We find that papers authored and “Contributed” by NAS members (Track III) are on average cited less often than papers that are “Communicated” for others by NAS members (Track I) or submitted directly via the standard peer review process (Track II). However, we also find that the variance in the citation count of Contributed papers, and to a lesser extent Communicated papers, is larger than for direct submissions. Therefore when examining the 10% most-cited papers from each track, Contributed papers receive the most citations, followed by Communicated papers, while Direct submissions receive the least citations.

Conclusion/Significance

Our findings suggest that PNAS “Contributed” papers, in which NAS–member authors select their own reviewers, balance an overall lower impact with an increased probability of publishing exceptional papers. This analysis demonstrates that different editorial procedures are associated with different levels of impact, even within the same prominent journal, and raises interesting questions about the most appropriate metrics for judging an editorial policy''s success.     

Afterword: Dark Anthropology in Papua New Guinea?

Ranging from colonial modernism to postcolonial disappointment, the papers in this collection explore the possibilities of Dark Anthropology and an Anthropology of the Good in Papua New Guinea. With these two prospects in mind, I consider what these papers tell us about the situations of rural people on the peripheries of large resource projects and those in ‘Last Places’ bypassed by development and the State. In all of these cases, difficult predicaments entail hardship or suffering, but are also met with responses seeking to realise varying versions of the good. This, in turn, prompts further questions about which and whose good are at issue amid a plurality of values. I conclude by suggesting that the ensemble of papers offers a retrospective on local versions of modernity as possibility contends with experience.     

More reliable protein NMR peak assignment via improved 2-interval scheduling.

Protein NMR peak assignment refers to the process of assigning a group of "spin systems" obtained experimentally to a protein sequence of amino acids. The automation of this process is still an unsolved and challenging problem in NMR protein structure determination. Recently, protein NMR peak assignment has been formulated as an interval scheduling problem (ISP), where a protein sequence P of amino acids is viewed as a discrete time interval I (the amino acids on P one-to-one correspond to the time units of I), each subset S of spin systems that are known to originate from consecutive amino acids from P is viewed as a "job" j(s), the preference of assigning S to a subsequence P of consecutive amino acids on P is viewed as the profit of executing job j(s) in the subinterval of I corresponding to P, and the goal is to maximize the total profit of executing the jobs (on a single machine) during I. The interval scheduling problem is max SNP-hard in general; but in the real practice of protein NMR peak assignment, each job j(s) usually requires at most 10 consecutive time units, and typically the jobs that require one or two consecutive time units are the most difficult to assign/schedule. In order to solve these most difficult assignments, we present an efficient 13/7-approximation algorithm for the special case of the interval scheduling problem where each job takes one or two consecutive time units. Combining this algorithm with a greedy filtering strategy for handling long jobs (i.e., jobs that need more than two consecutive time units), we obtain a new efficient heuristic for protein NMR peak assignment. Our experimental study shows that the new heuristic produces the best peak assignment in most of the cases, compared with the NMR peak assignment algorithms in the recent literature. The above algorithm is also the first approximation algorithm for a nontrivial case of the well-known interval scheduling problem that breaks the ratio 2 barrier.     

Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics

The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the second in a series of papers devoted to the analysis and comparison of metrics for tree-child time consistent phylogenetic networks on the same set of taxa. In this paper, we generalize to phylogenetic networks two metrics that have already been introduced in the literature for phylogenetic trees: the nodal distance and the triplets distance. We prove that they are metrics on any class of tree-child time consistent phylogenetic networks on the same set of taxa, as well as some basic properties for them. To prove these results, we introduce a reduction/expansion procedure that can be used not only to establish properties of tree-child time consistent phylogenetic networks by induction, but also to generate all tree-child time consistent phylogenetic networks with a given number of leaves.