A text mining analysis of the climate change literature in industrial ecology

The literature on climate change research has evolved tremendously since the 1990s. The goal of this study is to use text mining to review the climate change literature and study the evolution of the main trends over time. Specific keywords from articles published in the special issue “ Industrial Ecology for Climate Change Adaptation and Resilience” in the Journal of Industrial Ecology are first selected. Details of over 35,000 publications containing these keywords are downloaded from the Web of Science from 1990 to 2018. The number of publications and co‐occurrence of keywords are analyzed. Moreover, latent Dirichlet allocation (LDA)—a probabilistic approach that can retrieve topics from large and unstructured text documents—is applied on the abstracts to uncover the main topics (consisting of new terms) that naturally emerge from them. The evolution in time of the importance of some emerging topics is then analyzed on the basis of their relative frequency. Overall, a rapid growth in climate change publications is observed. Terms such as “climate change adaptation” appear on the rise, whereas other terms are declining such as “pollution.” Moreover, several terms tend to co‐occur frequently, such as “climate change adaptation” and “resilience.” The database collected and the LiTCoF (Literature Topic Co‐occurrence and Frequency) Python‐based tool developed for this study are also made openly accessible. This article met the requirements for a gold – gold JIE data openness badge described http://jie.click/badges .     

A single aromatic core mutation converts a designed “primitive” protein from halophile to mesophile folding

The halophile environment has a number of compelling aspects with regard to the origin of structured polypeptides (i.e., proteogenesis) and, instead of a curious niche that living systems adapted into, the halophile environment is emerging as a candidate “cradle” for proteogenesis. In this viewpoint, a subsequent halophile‐to‐mesophile transition was a key step in early evolution. Several lines of evidence indicate that aromatic amino acids were a late addition to the codon table and not part of the original “prebiotic” set comprising the earliest polypeptides. We test the hypothesis that the availability of aromatic amino acids could facilitate a halophile‐to‐mesophile transition by hydrophobic core‐packing enhancement. The effects of aromatic amino acid substitutions were evaluated in the core of a “primitive” designed protein enriched for the 10 prebiotic amino acids (A,D,E,G,I,L,P,S,T,V)—having an exclusively prebiotic core and requiring halophilic conditions for folding. The results indicate that a single aromatic amino acid substitution is capable of eliminating the requirement of halophile conditions for folding of a “primitive” polypeptide. Thus, the availability of aromatic amino acids could have facilitated a critical halophile‐to‐mesophile protein folding adaptation—identifying a selective advantage for the incorporation of aromatic amino acids into the codon table.     

Contrasting patterns of density‐dependent selection at different life stages can create more than one fast–slow axis of life‐history variation

There has been much recent research interest in the existence of a major axis of life‐history variation along a fast–slow continuum within almost all major taxonomic groups. Eco‐evolutionary models of density‐dependent selection provide a general explanation for such observations of interspecific variation in the "pace of life." One issue, however, is that some large‐bodied long‐lived “slow” species (e.g., trees and large fish) often show an explosive “fast” type of reproduction with many small offspring, and species with “fast” adult life stages can have comparatively “slow” offspring life stages (e.g., mayflies). We attempt to explain such life‐history evolution using the same eco‐evolutionary modeling approach but with two life stages, separating adult reproductive strategies from offspring survival strategies. When the population dynamics in the two life stages are closely linked and affect each other, density‐dependent selection occurs in parallel on both reproduction and survival, producing the usual one‐dimensional fast–slow continuum (e.g., houseflies to blue whales). However, strong density dependence at either the adult reproduction or offspring survival life stage creates quasi‐independent population dynamics, allowing fast‐type reproduction alongside slow‐type survival (e.g., trees and large fish), or the perhaps rarer slow‐type reproduction alongside fast‐type survival (e.g., mayflies—short‐lived adults producing few long‐lived offspring). Therefore, most types of species life histories in nature can potentially be explained via the eco‐evolutionary consequences of density‐dependent selection given the possible separation of demographic effects at different life stages.     

Raw material criticality assessment as a complement to environmental life cycle assessment: Examining methods for product‐level supply risk assessment

The diversity of raw materials used in modern products, compounded by the risk of supply disruptions—due to uneven geological distribution of resources, along with socioeconomic factors like production concentration and political (in)stability of raw material producing countries—has drawn attention to the subject of raw material “criticality.” In this article, we review the state of the art regarding the integration of criticality assessment, herein termed “product‐level supply risk assessment,” as a complement to environmental life cycle assessment. We describe and compare three methods explicitly developed for this purpose—Geopolitical Supply Risk (GeoPolRisk), Economic Scarcity Potential (ESP), and the Integrated Method to Assess Resource Efficiency (ESSENZ)—based on a set of criteria including considerations of data sources, uncertainties, and other contentious methodological aspects. We test the methods on a case study of a European‐manufactured electric vehicle, and conclude with guidance for appropriate application and interpretation, along with opportunities for further methodological development. Although the GeoPolRisk, ESP, and ESSENZ methods have several limitations, they can be useful for preliminary assessments of the potential impacts of raw material supply risks on a product system (i.e., “outside‐in” impacts) alongside the impacts of a product system on the environment (i.e., “inside‐out” impacts). Care is needed to not overlook critical raw materials used in small amounts but nonetheless important to product functionality. Further methodological development could address regional and firm‐level supply risks, multiple supply‐chain stages, and material recycling, while improving coverage of supply risk characterization factors.     

Aspects of the Phænogamic Vegetation of Rodriguez,with Descriptions of new Plants from the Island.

As regards the history of its flora, the island of Rodriguez bears a striking resemblance to St. Helena. We read of the latter island that fire, goats, and finally introduced foreign plants well nigh exterminated the indigenous flora; and the same causes have operated and, I regret to say, are still operating in Rodriguez. The result is that the primitive vegetation has been in great part destroyed, leaving the island a field for the rank and rapid growth of common tropical weeds. The old and luxuriant vegetation of two hundred years ago—thus quaintly described by Leguat*, “We could hardly take our eyes off from the little mountains of which the island entirely consists; they are so richly spread with great and tall trees,” and, again, “‘Tis as I have hinted, composed of lovely hills covered all with fine trees whose perpetual verdure is entirely charming”—has now, to a large extent, disappeared, and is represented by only a few species, many of which are confined to the more unfrequented and less accessible places. It is indeed difficult to recognize in the barren and arid Rodriguez of the present day the “little Eden,”“lovely isle,”“earthly paradise” of Leguat. The flora, as it now exists, is an exceedingly fragmentary one; it is therefore a matter of some difficulty to determine its exact limits and to draw conclusions as to its affinities with the floras of other oceanic islands and of adjacent continents. This is the more to be regretted, as, from the geographical position of the island and the physical condition of climate to which it is subject, its flora might be expected, whether taken singly or as part of that of the Mascarene group, to contribute very important data towards the solution of the problem of the distribution of plant‐life in that region. The following general statements may, however, be made:—     

Govindjee,an institution,at his 80th (really 81st) birthday in Třeboň in October, 2013: a pictorial essay

Govindjee (one name only), who himself is an institution, has been recognized and honored by many in the past for he is a true ambassador of “Photosynthesis Research” to the World. He has been called “Mr. Photosynthesis”, and compared to the Great Wall of China. To us in T?eboň, he has been a great research collaborator in our understanding of chlorophyll a fluorescence in algae and in cyanobacteria, and more than that a friend of the Czech “Photosynthesis” group, from the time of Ivan ?etlík (1928–2009) and of Zdeněk ?esták (1932–2008). Govindjee’s 80th (really 81st) birthday was celebrated by the Institute of Microbiology, Laboratory of Photosynthesis, by toasting him with an appropriate drink of a suspension of green algae grown at the institute itself. After my presentation, on October 23, 2013, of Govindjee’s contributions to photosynthesis, and his intimate association with the photosynthetikers (in Jack Myers’s words) of the Czech Republic, Govindjee gave us his story of how he began research in photosynthesis in the late 1950s. This was followed by a talk on October 25 by him on “Photosynthesis: Stories of the Past.” Everyone enjoyed his animated talk—it was full of life and enjoyment. Here, I present a brief pictorial essay on Govindjee at his 80th (really 81st) birthday in T?eboň during October 23–25, 2013.     

THE CONTRIBUTION OF GENE MOVEMENT TO THE “TWO RULES OF SPECIATION”

The two “rules of speciation”—the Large X‐effect and Haldane's rule—hold throughout the animal kingdom, but the underlying genetic mechanisms that cause them are still unclear. Two predominant explanations—the “dominance theory” and faster male evolution—both have some empirical support, suggesting that the genetic basis of these rules is likely multifarious. We revisit one historical explanation for these rules, based on dysfunctional genetic interactions involving genes recently moved between chromosomes. We suggest that gene movement specifically off or onto the X chromosome is another mechanism that could contribute to the two rules, especially as X chromosome movements can be subject to unique sex‐specific and sex chromosome specific consequences in hybrids. Our hypothesis is supported by patterns emerging from comparative genomic data, including a strong bias in interchromosomal gene movements involving the X and an overrepresentation of male reproductive functions among chromosomally relocated genes. In addition, our model indicates that the contribution of gene movement to the two rules in any specific group will depend upon key developmental and reproductive parameters that are taxon specific. We provide several testable predictions that can be used to assess the importance of gene movement as a contributor to these rules in the future.     

Sequential parallel comparison design for “gold standard” noninferiority trials with a prespecified margin

Three‐arm noninferiority trials (involving an experimental treatment, a reference treatment, and a placebo)—called the “gold standard” noninferiority trials—are conducted in patients with mental disorders whenever feasible, but often fail to show superiority of the experimental treatment and/or the reference treatment over the placebo. One possible reason is that some of the patients receiving the placebo show apparent improvement in the clinical condition. An approach to addressing this problem is the use of the sequential parallel comparison design (SPCD). Nonetheless, the SPCD has not yet been discussed in relation to gold standard noninferiority trials. In this article, our aim was to develop a hypothesis‐testing method and its corresponding sample size calculation method for gold standard noninferiority trials with the SPCD. In a simulation, we show that the proposed hypothesis‐testing method achieves the nominal type I error rate and power and that the proposed sample size calculation method has adequate power accuracy.     

Comparison of five different scoring methods in the evaluation of inflammatory infiltration (tumor‐infiltrating lymphocytes) in superficial spreading and nodular melanoma

The objective of our study was to compare the five different scoring methods of tumor‐infiltrating lymphocytes (TILs) assessment in a group of 213 cases of superficial spreading and nodular melanoma. The scoring methods include (a) Clark scoring; (b) Melanoma Institute Australia system; (c) scoring system used in the study of Saldanha et al.; (d) scoring system used in the TCGA study and modified by Park et al.; and (e) the system recently proposed by the “International Immuno‐Oncology Biomarker Working Group” for TILs scoring in all solid tumors. Prediction of survival with three main outcomes—disease‐specific‐free survival, local recurrence‐free survival, and distant metastasis‐free survival—was evaluated. The prognostic value of TILs showed statistical significance in univariate analysis regarding all three of the outcomes only for three of the five evaluated methods; the Clark scoring, the Melanoma Institute Australia system, and the system proposed by the “International Immuno‐Oncology Biomarker Working Group”. However, in multivariate analysis with covariants including Breslow thickness, type of melanoma, location, sex, and age, we did not find TILs to be an independent prognostic factor.     

Plasticity‐led evolution: A survey of developmental mechanisms and empirical tests

Recent years have witnessed increased interest in evaluating whether phenotypic plasticity can precede, facilitate, and possibly even bias adaptive evolution. Despite accumulating evidence for “plasticity‐led evolution” (i.e., “PLE”), critical gaps remain, such as: how different developmental mechanisms influence PLE; whether some types of traits and taxa are especially prone to experience PLE; and what studies are needed to drive the field forward. Here, we begin to address these shortcomings by first speculating about how various features of development—modularity, flexible regulation, and exploratory mechanisms—might impact and/or bias whether and how PLE unfolds. We then review and categorize the traits and taxa used to investigate PLE. We do so both to identify systems that may be well‐suited for studying developmental mechanisms in a PLE context and to highlight any mismatches between PLE theory and existing empirical tests of this theory. We conclude by providing additional suggestions for future research. Our overarching goal is to stimulate additional work on PLE and thereby evaluate plasticity's role in evolution.     

Assessing the “Short Mental Distance” in Eco‐Industrial Networks

Like many economic exchanges, industrial symbiosis (IS) is thought to be influenced by social relationships and shared norms among actors in a network. While many implicit references to social characteristics exist throughout the literature, there have been few explicit attempts to operationalize and measure the concepts. The “short mental distance,”“trust,”“openness,” and “communication” recorded among managers in Kalundborg, Denmark, set a precedent for examining and encouraging social interactions among key personnel in the dozens of eco‐industrial networks around the world. In this article we explore the relationships among various aspects of social embeddedness, social capital, and IS. We develop a conceptual framework and an approach using quantitative and qualitative methods to identify and measure these social characteristics, including social network structure, communication, and similarities in norms and conceptions of waste, and apply them in an industrial network in Nanjangud, South India. The findings suggest that there is a fairly high level of shared norms about dealing with waste—the “short mental distance”—in this network, but by‐product transactions are only weakly correlated with the structure and content of communication among managers. Replication of this approach can increase the understanding and comparability of the role of social characteristics in eco‐industrial activities around the world.     

Exergy‐Based Population Dynamics

This article discusses whether “sustainability” has a physical meaning in applied thermodynamics. If it has, then it should be possible to derive general principles and rules for devising “sustainable systems.” If not, then other sides of the issue retain their relevance, but thermodynamic laws are not appropriate by themselves to decide whether a system or a scenario is sustainable. Here, we make use of a single axiom: that final consumption (material or immaterial) can be quantified solely in terms of equivalent primary exergy flows. On this basis, we develop a system theory that shows that if “simple” systems are based solely on the exploitation of fossil resources, they cannot be thermodynamically “sustainable.” But as renewable resources are brought into the picture and the system complexity grows, there are thresholds below or beyond which the system exhibits an ability to maintain itself (perhaps through fluctuations), in a self‐preserving (i.e., a sustainable) state. It appears that both complexity and the degree of nonlinearity of the transfer functions of the systems play a major role and—even for some of the simplest cases—lead to nontrivial solutions in phase space. Therefore, even if the examples presented in the article can be considered rather crude approximations to real, complex systems at best, the results show a trend that is worth further consideration.     

Transcriptome analysis reveals the difference between “healthy” and “common” aging and their connection with age‐related diseases

A key goal of aging research was to understand mechanisms underlying healthy aging and develop methods to promote the human healthspan. One approach is to identify gene regulations unique to healthy aging compared with aging in the general population (i.e., “common” aging). Here, we leveraged Genotype‐Tissue Expression (GTEx) project data to investigate “healthy” and “common” aging gene expression regulations at a tissue level in humans and their interconnection with diseases. Using GTEx donors' disease annotations, we defined a “healthy” aging cohort for each tissue. We then compared the age‐associated genes derived from this cohort with age‐associated genes from the “common” aging cohort which included all GTEx donors; we also compared the “healthy” and “common” aging gene expressions with various disease‐associated gene expressions to elucidate the relationships among “healthy,” “common” aging and disease. Our analyses showed that 1. GTEx “healthy” and “common” aging shared a large number of gene regulations; 2. Despite the substantial commonality, “healthy” and “common” aging genes also showed distinct function enrichment, and “common” aging genes had a higher enrichment for disease genes; 3. Disease‐associated gene regulations were overall different from aging gene regulations. However, for genes regulated by both, their regulation directions were largely consistent, implying some aging processes could increase the susceptibility to disease development; and 4. Possible protective mechanisms were associated with some “healthy” aging gene regulations. In summary, our work highlights several unique features of GTEx “healthy” aging program. This new knowledge could potentially be used to develop interventions to promote the human healthspan.     

Preferences Predict Food Intake From 5 to 11 Years,but Not in Girls With Higher Weight Concerns,Dietary Restraint,and %Body Fat

Food preferences (FP) predict food intake in childhood; however, the predictive power of FP may decline among girls as weight concerns (WC) and dietary restraint (DR) increase during preadolescence. To examine longitudinal change in the preference‐intake (P‐I) relation and assess whether this relation weakens among non‐Hispanic white girls (n = 197) with a history of WC and DR from age 5 to 11. Girls' preferences for and intake (kcal) of 10 palatable snack foods were assessed biennially. Height, weight, percent body fat (%BF), WC, and DR were measured. Individual correlation coefficients were calculated per girl to capture within‐person P‐I correlations at each time of measurement. Overall, FP predicted girls' snack food calorie intakes between 5 and 11 years, but latent profile analysis (LPA) revealed three distinct patterns of change in P‐I correlations over time: “strong/stable” P‐I correlations were relatively high and became stronger with age; “increasing/later null” P‐I correlations were initially weak and became stronger between 5 and 9 years, but dropped to near 0 at 11 years; “initially weak/later strong” P‐I correlations were initially null and increased with age. Mixed models revealed that the “increasing/later null” group had greater increases in %BF, and higher WC, DR, and BMI percentiles from 5 to 11 years, compared to the other groups. In summary, FP predicted snack food calorie intake among most girls during childhood, but waned as a predictor of calorie intake at age 11 for a subset of girls with increasing %BF, and higher WC, DR, and BMIs.     

A Review of “Maritime Power and the Law of the Sea: Expeditionary Operations in World Politics”

Abstract

The purpose of the London Dumping Convention (LDC) is the protection of the marine environment including its seabed and subsoil. The preamble, articles, and annexes of the LDC make clear that the Convention must be interpreted in a manner which ensures that this responsibility is met. As a partial response to that mandate, the LDC prohibits the dumping at sea of certain wastes, including high‐level radioactive wastes. Disposal of high‐level wastes in seabed sediments is the subject of ongoing technical, environmental, and engineering feasibility studies by several countries. In the LDC's definition of dumping, the phrase “disposal at sea”; could be interpreted narrowly to mean the final resting place of wastes—with seabed disposal excluded from coverage because those wastes are not in direct contact with “marine waters.”; Given the LDC's object and purpose, though, the only harmonious and reasonable interpretation is that which defines “disposal at sea”; to mean the place where the dumping activities occur. Other international agreements also support this object and purpose‐based interpretation which concludes that seabed disposal is covered and prohibited. In addition, this approach is preferred because it contributes to the continued effectiveness of the LDC.     

Tropicality and abjection: What do we really mean by “Neglected Tropical Diseases”?

Neglected tropical diseases are defined operationally as diseases that prevail in “tropical” regions and are under‐researched, under‐funded, and under‐treated compared with their disease burden. By analysing the adjectives “tropical” and “neglected,” I expose and interrogate the discourses within which the term “neglected tropical disease” derives its meaning. First, I argue that the term “tropical” conjures the notion of “tropicality,” a form of Othering which erroneously explains the disease‐prevalence of “tropical” regions by reference to environmental determinism, rather than colonialism and neocolonialism. Second, I examine the way in which this Othering enables the abjection of tropical regions and their peoples, leading to neglect. I recommend that the term “neglected tropical diseases” be more carefully contextualised within health scholarship, education, and policy.     

Autoimmunity and the microbiome: T‐cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts

I propose a T‐cell receptor (TcR)‐based mechanism by which immunity mediates both “genetic self” and “microbial self” thereby, connecting microbiome disease with autoimmunity. The hypothesis is based on simple principles. First, TcR are selected to avoid strong cross‐reactivity with “self,” resulting in selection for a TcR repertoire mimicking “genetic self.” Second, evolution has selected for a “microbial self” that mimics “genetic self” so as to share tolerance. In consequence, our TcR repertoire also mimics microbiome antigenicity, providing a novel mechanism for modulating tolerance to it. Also, the microbiome mimics the TcR repertoire, acting as a secondary immune system. I call this TcR‐microbiome mimicry “holoimmunity” to denote immune tolerance to the “holobiont self.” Logically, microbiome‐host mimicry means that autoimmunity directed at host antigens will also attack components of the microbiome, and conversely, an immunological attack on the microbiome may cross‐react with host antigens producing “holoautoimmunity.”

     

Disability and <Emphasis Type="Italic">Depression</Emphasis>

Here, Ann Cvetkovich, interviewed by Abby Wilkerson, brings Cvetkovich’s influential cultural studies analysis of depression explicitly into conversation with disability studies. Cvetkovich understands “feeling bad” (a term she prefers to “depression”) as a defining affective state under neoliberalism. Drawing on a distinctive historical/cultural archive, she challenges the atomism of the neoliberal medical model that frames depression and affective distress more generally as the result of faulty brain chemistry—individual organisms gone awry. Instead, she traces these common experiences to sociopolitical phenomena ranging from current neoliberal demands for productivity as exemplified in university life, to histories of colonization, slavery, and displacement. The conversation considers the value of disability frameworks for understanding mental health diagnoses and the intersections of social institutions, bodily practices, and everyday affective life.     

“Making coin” and the networker: Masculine self‐making in the Australian professional managerial class

In this article I unpack the labour of “networking” to understand the changes in sociality and worker identity that have occurred in the Australian professional managerial class workforce under post‐Fordism. Drawing on fieldwork undertaken at the interface of the pubic service and private consultancy firms in Canberra, I break from dominant readings of intimacy in post‐Fordism which preference either a downwards imposition of “ways of being” from capital to worker, or a reactive self‐regulation in line with objective external structures. Networking, I argue, is as much about being recognised as patron as it is about any tangible economic benefits. The intimate relations and self‐fashioning of networking constitute attempts to embody particular classed, sexualised, gendered fantasies of the figure of “the networker” in post‐Fordist Australian business culture. This interpretation does not necessitate overlooking the tangible results of networking, and I discuss too, how masculine fantasy structures the topography of workplaces.     

Biological Pathway Specificity in the Cell—Does Molecular Diversity Matter?

Biology arises from the crowded molecular environment of the cell, rendering it a challenge to understand biological pathways based on the reductionist, low‐concentration in vitro conditions generally employed for mechanistic studies. Recent evidence suggests that low‐affinity interactions between cellular biopolymers abound, with still poorly defined effects on the complex interaction networks that lead to the emergent properties and plasticity of life. Mass‐action considerations are used here to underscore that the sheer number of weak interactions expected from the complex mixture of cellular components significantly shapes biological pathway specificity. In particular, on‐pathway—i.e., “functional”—become those interactions thermodynamically and kinetically stable enough to survive the incessant onslaught of the many off‐pathway (“nonfunctional”) interactions. Consequently, to better understand the molecular biology of the cell a further paradigm shift is needed toward mechanistic experimental and computational approaches that probe intracellular diversity and complexity more directly. Also see the video abstract here https://youtu.be/T19X_zYaBzg .