Aboriginal hunting buffers climate-driven fire-size variability in Australia's spinifex grasslands

Across diverse ecosystems, greater climatic variability tends to increase wildfire size, particularly in Australia, where alternating wet-dry cycles increase vegetation growth, only to leave a dry overgrown landscape highly susceptible to fire spread. Aboriginal Australian hunting fires have been hypothesized to buffer such variability, mitigating mortality on small-mammal populations, which have suffered declines and extinctions in the arid zone coincident with Aboriginal depopulation. We test the hypothesis that the relationship between climate and fire size is buffered through the maintenance of an anthropogenic, fine-grained fire regime by comparing the effect of climatic variability on landscapes dominated by Martu Aboriginal hunting fires with those dominated by lightning fires. We show that Aboriginal fires are smaller, more tightly clustered, and remain small even when climate variation causes huge fires in the lightning region. As these effects likely benefit threatened small-mammal species, Aboriginal hunters should be considered trophic facilitators, and policies aimed at reducing the risk of large fires should promote land-management strategies consistent with Aboriginal burning regimes.     

From the Cover: The skeleton of tropical intraseasonal oscillations

The Madden–Julian oscillation (MJO) is the dominant mode of variability in the tropical atmosphere on intraseasonal timescales and planetary spatial scales. Despite the primary importance of the MJO and the decades of research progress since its original discovery, a generally accepted theory for its essential mechanisms has remained elusive. Here, we present a minimal dynamical model for the MJO that recovers robustly its fundamental features (i.e., its “skeleton”) on intraseasonal/planetary scales: (i) the peculiar dispersion relation of dω/dk ≈ 0, (ii) the slow phase speed of ≈5 m/s, and (iii) the horizontal quadrupole vortex structure. This is accomplished here in a model that is neutrally stable on planetary scales; i.e., it is tacitly assumed that the primary instabilities occur on synoptic scales. The key premise of the model is that modulations of synoptic scale wave activity are induced by low-level moisture preconditioning on planetary scales, and they drive the “skeleton” of the MJO through modulated heating. The “muscle” of the MJO—including tilts, vertical structure, etc.—is contributed by other potential upscale transport effects from the synoptic scales.     

Tropical islands of the Anthropocene: Deep histories of anthropogenic terrestrial–marine entanglement in the Pacific and Caribbean

Islands are useful model systems for examining human–environmental interactions. While many anthropogenic effects visible in the archaeological and paleoecological records are terrestrial in nature (e.g., clearance of tropical forests for agriculture and settlement; introduction of nonnative flora and fauna), native peoples also relied heavily on marine environments for their subsistence and livelihood. Here we use two island case studies—Palau (Micronesia) and the Lesser Antilles (Caribbean)—and approach their long-term settlement history through a “ridge-to-reef” perspective to assess the role that human activity played in land- and seascape change over deep time. In particular, we examine the entanglement of terrestrial and marine ecosystems resulting from anthropogenic effects and cultural responses to socio-environmental feedback. We suggest that on the humanized tropical islands of the Anthropocene, mangroves, near shore and littoral areas, and coral reefs were major sites of terrestrial–marine interface chronicling and modulating anthropogenic effects.     

Reducing abrupt climate change risk using the Montreal Protocol and other regulatory actions to complement cuts in CO2 emissions

Current emissions of anthropogenic greenhouse gases (GHGs) have already committed the planet to an increase in average surface temperature by the end of the century that may be above the critical threshold for tipping elements of the climate system into abrupt change with potentially irreversible and unmanageable consequences. This would mean that the climate system is close to entering if not already within the zone of “dangerous anthropogenic interference” (DAI). Scientific and policy literature refers to the need for “early,” “urgent,” “rapid,” and “fast-action” mitigation to help avoid DAI and abrupt climate changes. We define “fast-action” to include regulatory measures that can begin within 2–3 years, be substantially implemented in 5–10 years, and produce a climate response within decades. We discuss strategies for short-lived non-CO₂ GHGs and particles, where existing agreements can be used to accomplish mitigation objectives. Policy makers can amend the Montreal Protocol to phase down the production and consumption of hydrofluorocarbons (HFCs) with high global warming potential. Other fast-action strategies can reduce emissions of black carbon particles and precursor gases that lead to ozone formation in the lower atmosphere, and increase biosequestration, including through biochar. These and other fast-action strategies may reduce the risk of abrupt climate change in the next few decades by complementing cuts in CO₂ emissions.     

From the Cover: Setting cumulative emissions targets to reduce the risk of dangerous climate change

Avoiding “dangerous anthropogenic interference with the climate system” requires stabilization of atmospheric greenhouse gas concentrations and substantial reductions in anthropogenic emissions. Here, we present an inverse approach to coupled climate-carbon cycle modeling, which allows us to estimate the probability that any given level of carbon dioxide (CO₂) emissions will exceed specified long-term global mean temperature targets for “dangerous anthropogenic interference,” taking into consideration uncertainties in climate sensitivity and the carbon cycle response to climate change. We show that to stabilize global mean temperature increase at 2 °C above preindustrial levels with a probability of at least 0.66, cumulative CO₂ emissions from 2000 to 2500 must not exceed a median estimate of 590 petagrams of carbon (PgC) (range, 200 to 950 PgC). If the 2 °C temperature stabilization target is to be met with a probability of at least 0.9, median total allowable CO₂ emissions are 170 PgC (range, −220 to 700 PgC). Furthermore, these estimates of cumulative CO₂ emissions, compatible with a specified temperature stabilization target, are independent of the path taken to stabilization. Our analysis therefore supports an international policy framework aimed at avoiding dangerous anthropogenic interference formulated on the basis of total allowable greenhouse gas emissions.     

A Comparison of Microtensile Bond Strength,Film Thickness,and Microhardness of Photo-Polymerized Luting Composites

The aim of this study was to evaluate the effect of CAD/CAM composite thickness on micro-tensile bond strength (µTBS), microhardness (HV), and film thickness (FT) of different luting composites. Composite blocks (6.8 mm × 6.8 mm) were divided into 12 groups according to: CAD/CAM thickness and luting composite. For each group, 21 rods (1 mm × 1 mm) were tested in tension at crosshead speed of 1 mm/min. Fracture modes were categorized as adhesive, mixed, and cohesive. Microhardness (n = 5/group) was assessed using microhardness tester. Film thickness (12-rods/group) was evaluated using a stereomicroscope (×40). Data were analyzed using the two-way ANOVA/Tukey’s HSD test (p = 0.05). Parameters “thickness”, “cement”, and “thickness x cement” showed significant difference on µTBS and HV (p < 0.05). At 2 mm, heated x-tra fil composite showed the highest µTBS (45.0 ± 8.5 MPa), while at 4 mm thickness, Grandio Flow revealed the lowest µTBS (33.3 ± 6.3 MPa). Adhesive, mixed, and cohesive failures were reported. The HV of all composites decreased when photo-polymerized through 4 mm thickness (p < 0.05). Regardless of CAD/CAM thickness, photo-polymerized composites can be successfully used for luting CAD/CAM composite.     

Neophobia in the foraging-site selection of a neotropical migrant bird: An experimental study

I hand-raised chestnut-sided warblers (Dendroica pensylvanica) in a room with eight experimental microhabitats; the microhabitats were removed after 6 weeks. I then measured the response of the warblers to the eight “natal” and eight “novel” microhabitats in two experiments conducted 2 and 4 months after removal. Chestnut-sided warblers responded with decreased feeding latency (neophobia) and a greater preference for foraging at the natal microhabitats. I suggest that an ontogenetic increase in neophobia restricts chestnut-sided warblers to foraging at microhabitats most similar to those experienced as juveniles.     

Aphelion clustering of "new" comets: Star tracks through Oort's cloud

An explanation is proposed for the observed and often discussed clustering of long-period comet aphelia on the sky. Poisson and several multinomial distributions are applied to the most conspicuous cluster, considering only the 80 “new” and 59 “intermediate” comets with the best-determined orbits. The observed number of aphelion points in adjacent areas in two tests with 24 and 36 equal sky areas, respectively, shows a large deviation from a random distribution. The expected probability frequency for this to happen by chance is <0.1% for the “new” comets alone; it is further reduced when “new” and “intermediate” comets are combined. When these comets are analyzed separately from others, it is found that the clustering is the result of perturbations of their original orbits by the passage of a star, or a stellar system, through Oort's cloud a few million years ago. Because the statistical effect on the change of a comet's angular momentum about the sun is proportional to the square of the ratio of the mass to the velocity of a star relative to the sun, it is a priori probable that passages by a few stars should produce clustering of the aphelia, as is discussed in detail.     

Indigenous knowledge and the shackles of wilderness

The environmental crises currently gripping the Earth have been codified in a new proposed geological epoch: the Anthropocene. This epoch, according to the Anthropocene Working Group, began in the mid-20th century and reflects the “great acceleration” that began with industrialization in Europe [J. Zalasiewicz et al., Anthropocene 19, 55–60 (2017)]. Ironically, European ideals of protecting a pristine “wilderness,” free from the damaging role of humans, is still often heralded as the antidote to this human-induced crisis [J. E. M. Watson et al., Nature, 563, 27–30 (2018)]. Despite decades of critical engagement by Indigenous and non-Indigenous observers, large international nongovernmental organizations, philanthropists, global institutions, and nation-states continue to uphold the notion of pristine landscapes as wilderness in conservation ideals and practices. In doing so, dominant global conservation policy and public perceptions still fail to recognize that Indigenous and local peoples have long valued, used, and shaped “high-value” biodiverse landscapes. Moreover, the exclusion of people from many of these places under the guise of wilderness protection has degraded their ecological condition and is hastening the demise of a number of highly valued systems. Rather than denying Indigenous and local peoples’ agency, access rights, and knowledge in conserving their territories, we draw upon a series of case studies to argue that wilderness is an inappropriate and dehumanizing construct, and that Indigenous and community conservation areas must be legally recognized and supported to enable socially just, empowering, and sustainable conservation across scale.     

Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems

Sorghum is a drought-tolerant crop with a vital role in the livelihoods of millions of people in marginal areas. We examined genetic structure in this diverse crop in Africa. On the continent-wide scale, we identified three major sorghum populations (Central, Southern, and Northern) that are associated with the distribution of ethnolinguistic groups on the continent. The codistribution of the Central sorghum population and the Nilo-Saharan language family supports a proposed hypothesis about a close and causal relationship between the distribution of sorghum and languages in the region between the Chari and the Nile rivers. The Southern sorghum population is associated with the Bantu languages of the Niger-Congo language family, in agreement with the farming-language codispersal hypothesis as it has been related to the Bantu expansion. The Northern sorghum population is distributed across early Niger-Congo and Afro-Asiatic language family areas with dry agroclimatic conditions. At a finer geographic scale, the genetic substructure within the Central sorghum population is associated with language-group expansions within the Nilo-Saharan language family. A case study of the seed system of the Pari people, a Western-Nilotic ethnolinguistic group, provides a window into the social and cultural factors involved in generating and maintaining the continent-wide diversity patterns. The age-grade system, a cultural institution important for the expansive success of this ethnolinguistic group in the past, plays a central role in the management of sorghum landraces and continues to underpin the resilience of their traditional seed system.Sorghum [Sorghum bicolor (L.) Moench] is a drought-tolerant C₄ crop of major importance for food security in Africa (1, 2). The grain crop has played a fundamental role in adaptation to environmental change in the Sahel since the early Holocene, when the Sahara desert was a green homeland for Nilo-Saharan groups pursuing livelihoods based on hunting or herding of cattle and wild grain collecting (3, 4). The earliest archaeological evidence of human sorghum use is dated 9100–8900 B.P., and the seeds were excavated together with cattle bones, lithic artifacts, and pottery from a site close to the current border between Egypt and Sudan (5, 6). The timing of the domestication of cattle and sorghum remains contested due to limited archaeological evidence, but, at some point, the livelihoods in this region transformed from hunting and gathering into agropastoralism. Sorghum cultivation in combination with cattle herding was a successful livelihood adaptation to the dry grassland ecology, and, eventually, as the climate changed and the Sahel moved south, the agropastoral adaptation spread over large parts of the Central African steppes (7).Recent molecular work on sorghum diversity (8–13) stands on the shoulders of J. R. Harlan and others’ work from the 1960s–1980s. Diversity of sorghum types, varieties, and races has been related to movement of people, disruptive selection, geographic isolation, gene flow from wild to cultivated plants, and recombination of these types in different environments (2, 14, 15). On the basis of morphology, Harlan and de Wet (16) classified sorghum into five basic and 10 intermediary botanical races (16). The race “bicolor” has small elongated grains, and, because of the “primitive” morphology, it is considered the progenitor of more derived races (16, 17). The race “guinea” has open panicles well adapted to high rainfall areas, and it is proposed that the “guinea margaritiferum” type from West Africa represents an independent domestication (10, 12). The race “kafir” is associated with the Bantu agricultural tradition, and the race “durra” is considered well-adapted to the dryland agricultural areas along the Arabic trade routes from West Africa to India (14). The fifth race, “caudatum,” is characterized by “turtle-backed” grains, and Stemler et al. (ref. 17, p. 182) proposed that “the distribution of caudatum sorghums and Chari-Nile–speaking peoples coincide so closely that a causal relationship seems probable.” This hypothesis is considered plausible on the basis of historical linguistics, but it remains to be tested by independent evidence (3). The hypothesis is a specific version of the interdisciplinary “farming-language codispersal hypothesis,” which proposes that farming and language families have moved together through population growth and migration (18, 19).The role of cultural selection and adaptation has been documented in many studies of domestication and translocation of crops (20, 21). The literature on the role of farmers’ management in maintaining and enhancing genetic resources (22–26) is relevant to understanding how patterns of diversity visible at large spatial scales are caused by evolutionary processes operating at finer scales. On-farm management of crop varieties and cultural boundaries influencing the diffusion of seeds, practices, and knowledge are important local-scale explanatory factors behind patterns of regional and continental scale associations between ethnolinguistic groups and crop genetic structure (27–30).Knowledge on the role of social, cultural, and environmental factors in structuring crop diversity is important to assess the resilience of rural livelihoods in the face of global environmental change. Impact studies project that anthropogenic climate change will negatively affect sorghum yields in Sub-Saharan Africa (31, 32). Such projections pose questions about the availability of appropriate genetic resources and the ability of both breeding programs and local seed systems to develop the required adaptations in a timely manner (33, 34). Insight in local seed systems can contribute to more sustainable development assistance efforts aimed at building resilience in African agriculture in the face of climate change and human insecurity (25, 35).Here, we present a study of geographic patterns in African sorghum diversity and its associations with the distribution of ethnolinguistic groups. First, we evaluate the proposed farming-language codispersal hypothesis by genotyping sorghum accessions from a continent-wide diversity panel (36). Second, to elucidate the local level mechanisms involved in generating and maintaining this diversity, we present a case study of the sorghum seed system of a group of descendants of the first Nilo-Saharan sorghum cultivators, the Pari people in South Sudan. By comparing accessions collected in 1983 with seeds sampled from the same villages in 2010 and 2013, we assess the resilience of the traditional Pari seed system during a period of civil war and climatic stress. We draw on environmental, linguistic, and anthropological evidence to understand the role of geographic, ecological, historical, and cultural factors in shaping sorghum genetic structure.     

Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme,TYW2

S-adenosylmethionine (AdoMet) is a methyl donor used by a wide variety of methyltransferases, and it is also used as the source of an α-amino-α-carboxypropyl (“acp”) group by several enzymes. tRNA-yW synthesizing enzyme-2 (TYW2) is involved in the biogenesis of a hypermodified nucleotide, wybutosine (yW), and it catalyzes the transfer of the “acp” group from AdoMet to the C7 position of the imG-14 base, a yW precursor. This modified nucleoside yW is exclusively located at position 37 of eukaryotic tRNA^Phe, and it ensures the anticodon-codon pairing on the ribosomal decoding site. Although this “acp” group has a significant role in preventing decoding frame shifts, the mechanism of the “acp” group transfer by TYW2 remains unresolved. Here we report the crystal structures and functional analyses of two archaeal homologs of TYW2 from Pyrococcus horikoshii and Methanococcus jannaschii. The in vitro mass spectrometric and radioisotope-labeling analyses confirmed that these archaeal TYW2 homologues have the same activity as yeast TYW2. The crystal structures verified that the archaeal TYW2 contains a canonical class-I methyltransferase (MTase) fold. However, their AdoMet-bound structures revealed distinctive AdoMet-binding modes, in which the “acp” group, instead of the methyl group, of AdoMet is directed to the substrate binding pocket. Our findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the “acp” group, and not the methyl group, from AdoMet to the nucleobase.     

Large-scale reconstruction and phylogenetic analysis of metabolic environments

The topology of metabolic networks may provide important insights not only into the metabolic capacity of species, but also into the habitats in which they evolved. Here we introduce the concept of a metabolic network's “seed set”—the set of compounds that, based on the network topology, are exogenously acquired—and provide a methodological framework to computationally infer the seed set of a given network. Such seed sets form ecological “interfaces” between metabolic networks and their surroundings, approximating the effective biochemical environment of each species. Analyzing the metabolic networks of 478 species and identifying the seed set of each species, we present a comprehensive large-scale reconstruction of such predicted metabolic environments. The seed sets' composition significantly correlates with several basic properties characterizing the species' environments and agrees with biological observations concerning major adaptations. Species whose environments are highly predictable (e.g., obligate parasites) tend to have smaller seed sets than species living in variable environments. Phylogenetic analysis of the seed sets reveals the complex dynamics governing gain and loss of seeds across the phylogenetic tree and the process of transition between seed and non-seed compounds. Our findings suggest that the seed state is transient and that seeds tend either to be dropped completely from the network or to become non-seed compounds relatively fast. The seed sets also permit a successful reconstruction of a phylogenetic tree of life. The “reverse ecology” approach presented lays the foundations for studying the evolutionary interplay between organisms and their habitats on a large scale.     

Leaf assemblages across the Cretaceous-Tertiary boundary in the Raton Basin, New Mexico and Colorado

Analyses of leaf megafossil and dispersed leaf cuticle assemblages indicate that major ecologic disruption and high rates of extinction occurred in plant communities at the Cretaceous-Tertiary boundary in the Raton Basin. In diversity increase, the early Paleocene vegetational sequence mimics normal short-term ecologic succession, but on a far longer time scale. No difference can be detected between latest Cretaceous and early Paleocene temperatures, but precipitation markedly increased at the boundary. Higher survival rate of deciduous versus evergreen taxa supports occurrence of a brief cold interval (<1 year), as predicted in models of an “impact winter.”     

Reoperation in an adult female with "right-sided" Hirschsprung's disease complicated by refractory hypertension and cough

Hirschsprung’s disease (HD) is an intestinal malformation caused by the innate absence of ganglion cells in the neural plexus of the colorectal wall, and is most common in male infants. It is rare in adult, and is usually left-sided. Herein we reported based on the CARE guidelines a case of a 47-year-old adult female suffering from “right-sided” HD complicated by refractory hypertension and cough. The patient with a history of cesarean section and with digestive unfitness (abdominal pain, distention, and constipation) only since 20 years old had recurrence of HD after initial surgery due to the incomplete removal of the HD-affected bowel based on a diagnosis of “chronic ileus”, leading to the relapse of the digestive symptoms and the emergence of some intractable circulatory and respiratory complications which could be hardly controlled by conservative treatment. During the long interval before coming to our department for help, she had been re-hospitalized for several times with various misdiagnoses and supplied merely with symptomatic treatment which could only achieve temporary symptomatic relief. At her admission to our department, the imaging examinations strongly indicated recurrent HD which was further supported by pathological examinations, and right hemi-colectomy was performed to remove the remnant aganglionic intestinal segment. Intraoperative and postoperative pathology supported the completeness of the definitive resection. Post-operation, the patient’s bowel motility significantly improved, and interestingly, the complications disappeared. For adult patients with long-term constipation combined with cough and hypertension, rare diseases like HD which requires definite surgery and which could be “right-sided” should not be overlooked. It is vital to diagnose and cure HD patients in childhood. Through the comparison of the two surgeries, it is noteworthy that for diagnosed HD, sufficient removal of the non-functional intestine confirmed by intraoperative pathology is essential.     

Effects of land use on bird populations and pest control services on coffee farms

Global increases in both agriculture and biodiversity awareness raise a key question: Should cropland and biodiversity habitat be separated, or integrated in mixed land uses? Ecosystem services by wildlife make this question more complex. For example, birds benefit agriculture by preying on pest insects, but other habitat is needed to maintain the birds. Resulting land use questions include what areas and arrangements of habitat support sufficient birds to control pests, whether this pest control offsets the reduced cropland, and the comparative benefits of “land sharing” (i.e., mixed cropland and habitat) vs. “land sparing” (i.e., separate areas of intensive agriculture and habitat). Such questions are difficult to answer using field studies alone, so we use a simulation model of Jamaican coffee farms, where songbirds suppress the coffee berry borer (CBB). Simulated birds select habitat and prey in five habitat types: intact forest, trees (including forest fragments), shade coffee, sun coffee, and unsuitable habitat. The trees habitat type appears to be especially important, providing efficient foraging and roosting sites near coffee plots. Small areas of trees (but not forest alone) could support a sufficient number of birds to suppress CBB in sun coffee; the degree to which trees are dispersed within coffee had little effect. In simulations without trees, shade coffee supported sufficient birds to offset its lower yield. High areas of both trees and shade coffee reduced pest control because CBB was less often profitable prey. Because of the pest control service provided by birds, land sharing was predicted to be more beneficial than land sparing in this system.Agricultural demand is expected to double by 2050 (1), making integration of efficient agricultural production with biodiversity conservation a global challenge (2, 3). This challenge has sparked a debate over contrasting land use approaches, summarized as “land sparing” (i.e., maximizing agricultural yield in some areas and sparing others for nature) vs. “land sharing” (i.e., wildlife-friendly farming, with lower yields and more area under cultivation to meet demand) (4, 5). To date, empirical evidence suggests that land sparing may be better for crop production and wildlife, especially for forest species (6, 7). However, previous work has not adequately considered the capacity for wildlife to provide ecosystem services that boost yield (5). A more complete understanding of the complex relationships among crop yield, biodiversity conservation, and ecosystem services is needed to enable more effective allocation of land use (8). For mobile wildlife, these relationships are even more complex, given that biodiversity and ecosystem services are affected by the spatial arrangement as well as the variety of different land uses (9–11).The recent discovery that birds provide important pest control services on coffee farms (11–13) illustrates the interactions of land use, conservation, and agricultural production. Coffee farms are an example agricultural system in which mobile predators provide insect pest control, but pest insect populations are too variable over time and space to support predator populations by themselves. Coffee production is often a mix of monoculture and diverse agriculture, with monoculture having higher crop yield but little wildlife habitat and often higher pest insect infestation rates. These characteristics make coffee farms excellent model systems for studying key questions of how land use decisions affect wildlife populations, the pest control services that wildlife provide, and agricultural production.Is it economically beneficial to preserve prey-rich habitat for birds so they provide pest control? If so, how much habitat should be conserved? Is prey-rich habitat more beneficial when it is less fragmented (likely better for bird foraging) or more dispersed among the crops (perhaps making birds more likely to find and consume pests)? More generally, which is better for birds or for agriculture: separate large areas of intensive monoculture and large natural habitat or a mosaic of diverse agriculture and habitat patches? Such questions epitomize the land sparing vs. land sharing debate (4, 6, 14, 15).We address the foregoing questions in the coffee farm system. The world’s most economically damaging insect pest in coffee is Hypothenemus hampei, the coffee berry borer (CBB). Gravid adult females of this tiny (<3 mm) beetle bore into a coffee berry, where they lay a brood of 30–120 eggs. The larvae mature and mate with their siblings inside the berry, and gravid adult females emerge 23–28 d later to disperse to another berry (16). Field research in Jamaica has confirmed that migratory insect-eating warblers (family Parulidae) consume CBB in amounts sufficient to diminish pest abundance and crop damage, and provide a substantial economic benefit (12, 13). Native forest birds also consume CBB in Costa Rican plantations where CBB has recently invaded, and provide a substantial economic benefit (11). CBB by themselves cannot sustain bird populations, owing to their small size and episodic availability. Our observations from Jamaican coffee farms indicate that CBB make up <10% of the warbler diet. Thus, habitat that produces other prey is necessary to sustain bird populations if the birds are to control CBB outbreaks. Such habitat includes intact forest, trees and forest fragments (referred to herein as “trees”), and shade coffee (i.e., coffee grown under tree canopy that has habitat value but a lower average coffee yield).The interactions among land use types and arrangements, bird populations, and pest control are impossible to understand via field experiments alone, owing to the number and complexity of interactions and difficulty of controlling such variables as the number of birds arriving from migration and pest outbreak timing and intensity. Thus, modeling is essential. To make our study tractable while still capturing complexities of real systems, we used an individual-based model of insect-eating birds and CBB closely based on field studies conducted on Jamaican coffee farms (17).The model simulates foraging of individual birds in landscapes that are artificial (allowing manipulation of the areas of various habitat types) while capturing essential characteristics (e.g., habitat types, patch sizes) of real landscapes (Fig. 1). Prey availability and foraging success rates vary among habitat types and between CBB and other prey. Model birds continually move to any adjacent patch offering higher food intake and consume either CBB or other prey, thereby depleting the prey. The model represents prey availability and bird foraging, and also addresses processes (e.g., spatial arrangement of habitat, foraging behavior, prey depletion, competition) that are clearly important but would make a mathematical model very complex.Open in a separate windowFig. 1.Example landscapes. Model landscapes were generated stochastically but represent the general land use characteristics of real farms. (Top) 500 × 500 m of a typical Jamaican coffee farm, with patches of forest (f), sun (monoculture) coffee (n), shade coffee (d), and pasture (u), with trees and forest fragments (t) throughout. (Source: 18°20''19.28”N, 77°54''41.30”W; Google Earth image dated January 7, 2011, accessed January 9, 2014.) (Middle) The model’s 1,000 × 1,000 m synthetic landscape with the baseline habitat areas (10, 18, 19), provide services to humans. In particular, the issue of alternative foraging habitat and prey availability are inevitable in systems where birds—which require reliable food sources because of their rapid metabolism and limited ability to store energy—consume agricultural pest insects, which are of episodic abundance by nature. This study provides an example of the use of spatially explicit, theory-based modeling to address such questions.     

Lambl's Excrescence,Migrainous Headaches,and “Tiger Stripes”: Puzzling Findings in One Patient

Lambl''s excrescences are mobile, thin, filiform structures that occur at sites of valve closure. Even though many clinicians consider them to be part of the normal aging process, evidence suggests an association between Lambl''s excrescences and ischemic stroke, migrainous headaches, and acute coronary syndromes. As a thin filamentous structure, a Lambl''s excrescence is better detected and characterized with transesophageal than with transthoracic echocardiography. Intracardiac oscillatory structures can also be seen as “tiger stripes” on spectral pulsed Doppler echocardiographic recordings. Herein, we present the case of a 68-year-old woman who had 3 concurrent enigmatic findings with unclear correlation: migrainous headaches, Lambl''s excrescences, and the uncommon finding of “tiger stripes” on spectral Doppler echocardiography. We discuss the possible correlation between these 3 findings and review the available literature on Lambl''s excrescences and tiger stripes.     

Are faecal markers good indicators of mucosal healing in inflammatory bowel disease?

AIM: To review the published literature concerning the accuracy of faecal inflammatory markers for identifying mucosal healing. METHODS: Bibliographical searches were performed in MEDLINE electronic database up to February 2015,using the following terms: "inflammatory bowel disease","Crohn′s disease","ulcerative colitis","faecal markers","calprotectin","lactoferrin","S100A12","endoscop*","mucosal healing","remission". In addition,relevant references from these studies were also included. Data were extracted from the published papers including odds ratios with 95%CI,P values and correlation coefficients. Data were grouped together according to each faecal marker,Crohn's disease or ulcerative colitis,and paediatric compared with adult study populations. Studies included in this review assessed mucosal inflammation by endoscopic and/or histological means and compared these findings to faecal marker concentrations in inflammatory bowel diseases(IBD) patient cohorts. Articles had to be published between 1990 and February 2015 and written in English. Papers excluded from the review were those where the faecal biomarker concentration was compared between patients with IBD and controls or other disease groups,those where serum biomarkers were used,those with a heterogeneous study population and those only assessing post-operative disease. RESULTS: The available studies show that faecal markers,such as calprotectin and lactoferrin,are promising non-invasive indicators of mucosal healing. However,due to wide variability in study design,especially with regard to the definition of mucosal healing and evaluation of marker cut offs,the available data do not yet indicate the optimal roles of these markers. Thirty-six studies published between 1990 and 2014 were included. Studies comprised variable numbers of study participants,considered CD(15-164 participants) or UC(12-152 participants) separately or as a combined group(11-252 participants). Eight reports included paediatric patients. Several indices were used to document mucosal inflammation,encompassing elevenendoscopic and eight histologic grading systems. The majority of the available reports focused on faecal calprotectin(33 studies),whilst others assessed faecal lactoferrin(13 studies) and one study assessed S100A12. Across all of the biomarkers,there is a wide range of correlation describing the association between faecal markers and endoscopic disease activity(r values ranging from 0.32 to 0.87,P values ranging from 0.0001 to 0.7815). Correlation coefficients are described in almost all studies and are used more commonly than outcome measures such as sensitivity,specificity,PPV and/or NPV. Overall,the studies that have evaluated faecal calprotectin and/or faecal lactoferrin and their relationship with endoscopic disease activity show inconsistent results. CONCLUSION: Future studies should report the results of faecal inflammatory markers in the context of mucosal healing with clear validated cut offs.     

Evolutionary selection between alternative modes of gene regulation

Microorganisms employ a wealth of gene regulatory mechanisms to adjust their growth programs to variations in the environment. It was pointed out long ago [Savageau M (1977) Proc Natl Acad Sci USA 74: 5647–5651] that the particular mode of gene regulation employed may be correlated with the “demand” on the regulated gene, i.e., how frequently the gene product is needed in its natural habitat. An evolutionary “use-it-or-lose-it” principle was proposed to govern the choice of gene regulatory strategies. Here, we examine quantitatively the forces selecting for and against two opposing modes of gene regulation, in the context of an evolutionary model that takes genetic drift, mutation, and time-dependent selection into account. We consider the effect of time-dependent selection, with periods of strong selection alternating with periods of neutral evolution. Using a variety of analytical methods, we find the effective population size and the typical time scale of environmental variations to be key parameters determining the fitness advantage of the different modes of regulation. Our results support Savageau''s use-it-or-lose-it principle for small populations with long time scales of environmental variations and support a complementary “wear-and-tear” principle for the opposite situation.