bluuebunny/crossref_metadata_2025 huggingface dataset:
Brood Parasitism in a Host Generalist, the Shiny Cowbird: I. The Quality of Different Species as Hosts
Authors: Mason Paul
Published: October 2019

The Shiny Cowbird (Molothrus bonariensis) of South America, Panama, and the West Indies is an obligate brood parasite known to have used 176 species of birds as hosts. This study documents wide variability in the quality of real and potential hosts in terms of response to eggs, nestling diet, and nest survivorship. The eggs of the parasite are either spotted or immaculate in eastern Argentina and neighboring parts of Uruguay and Brazil. Most species accept both morphs of cowbird eggs, two reject both morphs, and one (Chalk-browed Mockinbird, Mimus saturninus) rejects immaculate eggs but accepts spotted ones. No species, via its rejection behavior, protects the Shiny Cowbird from competition with a potential competitor, the sympatric Screaming Cowbird (M. rufoaxillaris). Cross-fostering experiments and natural-history observations indicate that nestling cowbirds require a diet composed of animal protein. Because most passerines provide their nestlings with such food, host selection is little restricted by diet. Species-specific nest survivorship, adjusted to appropriate values of Shiny Cowbird life-history variables, varied by over an order of magnitude. Shiny Cowbirds peck host eggs. This density-dependent source of mortality lowers the survivorship of nests of preferred hosts and creates natural selection for greater generalization. Host quality is sensitive to the natural-history attributes of each host species and to the behavior of cowbirds at nests.
Influence of Resource Abundance on Use of Tree-Fall Gaps by Birds in an Isolated Woodlot
Authors: Blake John G. , Hoppes William G.
Published: October 2019

The occurrence of birds in forest understory and tree-fall gaps during spring and fall migration periods was determined in an isolated woodlot. We used mist-net captures to test the hypothesis that birds are attracted to gaps because of higher resource levels. We captured 1,010 birds (74 species) in spring and 458 (44 species) in fall. Total captures and captures per net were higher (P < 0.001) in gaps during spring and fall. Mean number of species per net was higher in gaps (P < 0.001) during both seasons, but total species in gaps (69 spring, 43 fall) was not significantly higher than in forest understory (60 spring, 28 fall). Of 44 species represented by adequate sample sizes (n > 5) in spring, 9 were significantly (P < 0.05) more common in gaps and 2 were more common in forest understory. Nine of 17 species were captured more often (P < 0.05) in gaps during fall. During spring, flycatchers, ground insectivores, foliage insectivores, and granivore-omnivores were captured more frequently (P < 0.05) in gaps. Flycatchers showed no difference in fall, but other trophic groups, including frugivores, were captured more frequently (P < 0.05) in gaps than in forest understory sites. Bark foragers showed no statistical preference for gaps or forest understory in spring or fall. Total species per net and total captures per net correlated positively (P < 0.05) with density of foliage in the lower canopy and negatively with density of upper canopy foliage in both spring and fall. Total species and captures correlated positively (P < 0.05) with insect abundance in spring and with fruit abundance in fall. Foliage insectivores correlated positively with low canopy foliage and insect abundance in both spring and fall. Captures of frugivores correlated with fruit abundance in fall. These data support the hypothesis that birds are attracted to tree-fall gaps because of higher resource abundance and provide further evidence of the importance of habitat heterogeneity to the structure and composition of bird communities.
Egg Formation in Cassin's Auklet
Authors: Astheimer Lee B.
Published: October 2019

Female Cassin's Auklets (Ptychoramphus aleuticus) were given oral doses of lipophilic and proteophilic dyes during their prelaying period. Yolk ring structure in freshly laid eggs was analyzed to determine the timing of yolk deposition using the dye-stained layer as a date marker within the yolk. Additional information from necropsies of five females killed at specific intervals during the formation of a replacement egg indicated that only a single follicle enlarges in the ovary during a reproductive event and this yolk requires about 8 days to complete rapid yolk deposition (RYD). Once RYD is completed, the egg is not laid for a period of 4.2 ± 1.0 days, an interval termed the lag period (Astheimer et al. 1979). Albumen synthesis appears to begin at, or just before, completion of the yolk and continues until approximately 1 day before oviposition. During this time, however, the yolk remains in the follicle. Replacement eggs are laid 14.5 ± 1.7 days following egg removal or natural loss. Combining the above information with egg composition data, the daily deposition of lipid and protein from the female into the egg was computed. Evidence from the size distribution of small (<5 mm) primordial follicles suggests that the auklet ovary undergoes a cycle of follicular growth and atresia before a single follicle is selected for RYD. Based on these findings, and the correlation between initiation of spring egg laying and decreased sea surface temperatures for Farallon Island auklets, I suggest that the onset of RYD is modulated by environmental conditions.
A Phylogenetic Analysis of Recent Anseriform Genera Using Morphological Characters
Authors: Livezey Bradley C.
Published: October 2019

A phylogenetic analysis of all Recent genera of the Anseriformes using 120 morphological characters supports much of the current consensus regarding intraordinal relationships. I found that (1) Anseranas should be placed in a monotypic family; (2) Dendrocygna, Thalassornis, geese and swans, and Stictonetta are paraphyletic to the rest of the Anatidae; (3) Cereopsis is the sister group to Anser and Branta, and Coscoroba is the sister group to Cygnus and Olor; (4) Plectropterus is the sister group to the Tadorninae (shelducks) and the Anatinae (typical ducks); (5) the shelducks are monophyletic and include Sarkidiornis (provisionally), Malacorhynchus, Hymenolaimus, Merganetta, and Tachyeres; (6) the tribe "Cairinini" ("perching ducks") is an unnatural, polyphyletic assemblage and is rejected; (7) the dabbling ducks (including the smaller "perching ducks") comprise an unresolved, probably paraphyletic group; (8) tribal monophyly of the pochards (including Marmaronetta and Rhodonessa), sea ducks (including the eiders), and stiff-tailed ducks (including Heteronetta) is confirmed; and (9) the retention of Mergellus and resurrection of Nomonyx are recommended based on clarifications of intratribal relationships. Problematic groups, effects of homoplasy, phenetic comparisons, life-history correlates, biogeographic patterns, and fossil species are discussed, and a phylogenetic classification of Recent genera is proposed.
Female Site Fidelity and Polygyny in the Blackpoll Warbler (Dendroica Striata)
Authors: Eliason Bonita C.
Published: October 2019

From 1980 to 1982, 8-30% of male Blackpoll Warblers (Dendroica striata) studied on Kent Island, New Brunswick, were bigamous each year (x̄ = 16.8%). I tested whether differences in the quality of the breeding situation can give rise to polygynous matings. Five territory parameters and two male parameters were used as measures of quality. Male arrival times were correlated with male mating status and the reproductive success of monogamous females. Territories of bigamous males had more large conifers than did those of monogamous males. Territory parameters did not appear to influence female choices.

Strong site attachment by females may lead them to mate bigamously when few males are available early in the season near the females' former nest sites. The reproductive success of secondary females was not different from that of monogamous females. Any costs of mating bigamously may be offset by increased reproductive success associated with early nest initiation and competitive advantages conferred by site dominance.

Site attachment and return patterns can account for the incidence of polygyny in this population, but probably could not give rise to high levels of polygyny or large harems. More information is needed to evaluate the influence of site fidelity on mating decisions of females in other polygynous passerine species.
Economics of Breeding Territoriality in Male Calliope Hummingbirds
Authors: Armstrong Doug P.
Published: October 2019

Several lines of evidence indicate that the territorial behavior of postbreeding North American hummingbirds can be explained in primarily energetic terms. The territoriality of breeding males, however, may be different in that it may play an important role in courtship. The results of this study on breeding male Calliope Hummingbirds (Stellula calliope) indicated that territoriality could not be explained either directly or indirectly in terms of defense of energy resources. Throughout the 2-month breeding season, flower sampling indicated that males could have obtained energy faster by foraging on nearby undefended areas than by foraging on their territories. In June there were no profitable flowers on the territories, and males did all or nearly all of their foraging away from their territories. In May, when territory nectar availability was fairly high, males did not leave, expand, or shift their territories in response to experimental exclosure of all profitable flowers on those territories. I suggest that males may have preferentially selected territory sites with prominent perches near females' nesting areas, and that these considerations outweighed the potential benefits of defending territories on areas with high-quality nectar resources.
Competitive Interactions within and between Species in a Guild of Avian Scavengers
Authors: Wallace Michael P. , Temple Stanley A.
Published: October 2019

We observed Andean Condors (Vultur gryphus), King Vultures (Sarcoramphus papa), Black Vultures (Coragyps atratus), Turkey Vultures (Cathartes aura), and Crested Caracaras (Polyborus plancus) interacting at 217 animal carcasses at two sites in northern Peru. At 53 carcasses for which we knew order of arrival, Turkey Vultures usually arrived first, Black Vultures second, and condors third. On the basis of our observations of 8,066 aggressive encounters between birds, we constructed dominance hierarchies by calculating the proportion of encounters won by an individual of one species, sex, or age during encounters with an individual of another species, sex, or age. Within each species there was a positive relationship between a bird's dominance and its age. In condors, males dominated females of the same age. Interspecific dominance was correlated positively with body mass. There are convergent similarities between the organizations of guilds of Old and New World vultures.
Incubation Behavior of Emperor Geese Compared with Other Geese: Interactions of Predation, Body Size, and Energetics
Authors: Thompson Steven C. , Raveling Dennis G.
Published: October 2019

The incubation constancy of 11 female Emperor Geese (Chen canagica) was monitored electronically and behavior of both sexes was observed during incubation recesses in 1983 and 1984 at Kokechik Bay, Alaska. Average nest attentiveness of female Emperor Geese was 99.5% during 4,800 h of monitored incubation time. Recesses averaged (±SE) 13.3 ± 0.8 min, and modal recess length was 8 min (n = 107). Recess frequency was 0.54/day. This high degree of nest attentiveness exceeded that reported for any goose species. Nest attentiveness did not vary significantly through the incubation period, but increased in the last 3 days, probably in response to embryo noises and pipping. Most recesses (45%) occurred between 1200 and 1800, the warmest portion of the day. There were no significant differences in recess length at different times of day, however, and recess duration and frequency were not related to differences in daily temperature or wind speed. Females fed for only 14% of the time during their infrequent and brief recesses. Most time (43%) during recesses was spent preening and bathing. Males were alert for 49% of the time females were on recess but were present during only 56% of recesses, reflecting their relative lack of attendance during incubation. Behavior of females during recesses when males were absent did not differ significantly from when males were present.

The high incubation constancy, loss of body mass during incubation (20.7%), and relatively large average clutch size (5.2) indicate that Emperor Geese arrive on nesting grounds with an extremely high level of endogenous reserves relative to other geese. Clutch size and incubation behavior also represent trade-offs in energy investment related to body size, egg size, food availability, and feeding needs during incubation. Generally, larger species or subspecies of geese depend more on endogenous reserves than do smaller forms. We believe, however, that this relationship is not satisfactorily explained just by energetic constraints related to body size because Emperor Geese were more attentive to incubation than even larger goose species. Emperor Geese usually can defend their nests from arctic foxes (Alopex lagopus) but, when on incubation recesses, are apparently less efficient in defense against avian predators than sympatric-nesting smaller geese. These smaller species are more vulnerable to foxes but more agile and effective against avian predators. The incubation constancy of geese results from an interaction of predation pressures related to body size and defense capabilities.
Signaling Subordinate and Female Status: Two Hypotheses for the Adaptive Significance of Subadult Plumage in Female Tree Swallows
Authors: Stutchbury Bridget J. , Robertson Raleigh J.
Published: October 2019

Delayed plumage maturation in males is relatively common among North American passerines, but the Tree Swallow (Tachycineta bicolor) is one of few species in which 1-yr-old females have a distinct subadult plumage. Although they are reproductively mature, most subadult females do not breed in their first year because of intense intrasexual competition for nesting sites. Early in the season, subadult female floaters explore for recently vacated nest sites. The subadult plumage of young females could be adaptive by communicating their low threat to residents, thereby decreasing the cost of this exploration.

To determine whether resident aggression depends on intruder color, we observed live intrusions and conducted model presentations. When the resident female was out of sight or did not respond to intruders, resident males were significantly less aggressive toward subadult females than toward adult intruders in both the nest-building/egg-laying and incubation stages. Early in the season, resident females were equally aggressive toward subadult female and adult intruders. When presented simultaneously with adult and subadult female models, resident males were always more aggressive toward the adult model, whereas females were aggressive toward either model.

We propose two hypotheses for the adaptive significance of subadult plumage in female Tree Swallows: subordinance signaling and sex signaling. Our results suggest that subadult females may reduce resident aggression by signaling their female status to resident males, rather than by signaling their subordinate status to resident females.
The Function of Delayed Plumage Maturation in Male Black-Headed Grosbeaks
Authors: Hill Geoffrey E.
Published: October 2019

I used data from two breeding populations of Black-headed Grosbeaks (Pheucticus melanocephalus) in central New Mexico to test alternative hypotheses regarding the function of delayed plumage maturation in male passerines. Yearling male grosbeaks displayed a wide range of subadult plumage types, but most individuals were intermediate in appearance between adult males and females. Subadult male grosbeaks arrived on the study sites about 2 weeks after adult males, with no tendency for individuals with brighter or duller plumage to arrive first. Only a few of the most brightly plumaged subadult males defended territories and attracted females; most were nonterritorial floaters. All territories of subadult males were positioned outside clusters of adult male territories with few total neighbors. When I removed adult males from their territories, the territories remained empty. These results are not consistent with predictions of the female-mimicry hypothesis, but they are in accord with those of the cryptic hypothesis.
Male Parental Care and Extrapair Copulations in the Indigo Bunting
Authors: Westneat David F.
Published: October 2019

Levels of parental care by male Indigo Buntings (Passerina cyanea) were predicted to be lower and the tendency to pursue extrapair matings greater when (1) the opportunity of additional matings (extrapair copulations) was high, (2) the male was cuckolded, and (3) the clutch or brood size was small. Observations of male care revealed that approximately 10% of all males fed nestlings at least once, whereas more than 30% fed fledglings. Males in their first breeding season were never seen feeding young. Males made more trips off their territories when females were fertilizable on nearby territories, but other measures of parental care (feeding young and time spent within 10 m of nest) were not affected. Cuckolded males (known through genetic analyses of parents and offspring) tended to feed young less often, but forayed off their territories significantly less than apparently uncuckolded males. Finally, males with small clutches or broods gave slightly, but not significantly, less care than males with large clutches or broods. These results suggest that the relationship between mating effort and parental effort is complicated by the presence of extrapair copulations as a type of mating effort, and that factors not included in current theory on parental care might influence a male's parental care.
The Beached-bird Assemblage of a Highly Saline Lake and Its Relevance for Reconstructing Paleoenvironments
Authors: Jehl Joseph R.
Published: October 2019

The beached-bird deposits of saline (80-90%) Mono Lake, California, are dominated by Eared Grebes (Podiceps nigricollis) and California Gulls (Larus californicus), which together comprise 95% of the specimens. Nevertheless, the diversity of waterbirds in these deposits is high (31 species), because mortality is high among migratory species that are poorly adapted to saline environments. The composition of the Mono Lake assemblage differs markedly from local Pleistocene faunas that accumulated in fresh or slightly saline habitats.
Site Fidelity and Survival Differences between Two Groups of New World Red Knots (Calidris canutus)
Authors: Harrington Brian A. , Hagan John M. , Leddy Linda E.
Published: October 2019

During the boreal winter, New World Red Knots (Calidris canutus rufa) principally occupy two areas widely separated in latitude. The larger group of approximately 100,000 birds is distributed along the Patagonian Atlantic coast, the smaller group of about 10,000 along Florida's Gulf coast. Resightings of banded individuals showed no interchange between these groups. The annual survival rate of knots marked in Florida is twice that of marked knots that winter in Patagonia. During northward migration Florida knots were sighted significantly less often at a major New Jersey stopover site than knots marked in Argentina. Whether this segregation is maintained during the breeding season is unknown. Wing and culmen lengths did not differ between the groups. The higher survival of individuals from the smaller Florida group, which presumably migrates a much shorter distance than the Argentina birds, runs counter to current evolutionary theories on the benefits of migration.
Forelimb Joint Mobility and the Evolution of Wing-Propelled Diving in Birds
Authors: Raikow Robert J. , Bicanovsky Lesley , Bledsoe Anthony H.
Published: October 2019

We measured wing joint mobility in penguins, alcids, diving-petrels, and non-diving fliers. Great reduction in mobility of the intrinsic wing joints was found in penguins, but not in alcids or diving-petrels. This reduction is correlated with simplification of the intrinsic wing musculature. In contrast, alcids and diving-petrels, which use their wings in both air and water, retain the full functional capacities for flight. Movement through the air probably requires a capability for subtle and varied motions, forces, and shape changes that preclude stiffening and simplification of the wing. Hence, the conversion of an aerial wing to a flipper, as in penguins, must be possible only after the evolutionary loss of flight.
An Early Condor-Like Vulture from North America
Authors: Emslie Steven D.
Published: October 2019

A new genus and species of condor-like vulture (Ciconiiformes: Vulturidae) is described from the middle Miocene (Barstovian) of North America and is the earliest condor now known in the New World. The fossil record at present indicates that the Vulturidae originated in the Old World, but diversified in the New World. Large body size in vultures developed in North America at least 4 million years (Ma) earlier than thought previously, and the condors probably evolved in North America. Condors were most diverse in the late Pleistocene but are now near extinction.
Reproductive Success of Hand-Reared vs. Parent-Reared Cockatiels (Nymphicus hollandicus)
Authors: Myers S. A. , Millam J. R. , Roudybush T. E. , Grau C. R.
Published: October 2019

We studied the influence of early rearing experience on the reproductive success of Cockatiels (Nymphicus hollandicus) by force-pairing somatically mature birds that had been either hand-reared (H) or parent-reared (P) from hatch to 6 weeks of age. Pairs of H-males and H-females, H-males and P-females, P-males and P-females, or P-males and H-females were encouraged to breed by providing nest-boxes and exposing pairs to a sexually stimulatory environment. Hand-rearing produced gender-specific effects that greatly affected reproductive success. Pairs containing H-females were more likely to lay eggs and laid more eggs than pairs with P-females but often laid them on the cage floor rather than in nest-boxes, reducing hatching success. Pairs containing H-males were less likely than pairs with P-males to produce fertile eggs, inspect nest-boxes, or lay eggs in nest-boxes. Fledging occurred only in pairs containing P-males. Early rearing experience is important for males to learn characteristics of the opposite sex, and for males and females to learn characteristics of nest-sites.
Distribution and Dispersal in the Piping Plover
Authors: Haig Susan M. , Oring Lewis W.
Published: October 2019

Individually marked Piping Plovers (Charadrius melodus) were studied from 1981-1987 in Manitoba and Minnesota relative to dispersal patterns of age and sex classes. Unlike monogamous passerines, males returned to former breeding sites only slightly more often than females. Dispersal distances did not differ between the sexes. Across North America, 24-69% of adults exhibited breeding-site fidelity, a variability equivalent to that among species of migratory shorebirds. Distribution of Piping Plover habitat across the species range accounts for some of this variability: birds used local sites if they were available, rather than disperse long distances. Similar to most migratory shorebirds, few (1.6-23%) Piping Plover chicks returned to natal sites to breed. No difference was found in return patterns between first-year males and females, nor in distances either sex dispersed from natal sites. First-year birds were found in the vicinity of their natal sites when habitat was available. During winter, birds from the Northern Great Plains and Great Lakes were seen primarily in mixed population flocks on the Gulf of Mexico. Piping Plovers from Atlantic coast breeding areas wintered further south on the Atlantic.
Seed Handling Ability, Bill Structure, and the Cost of Specialization for Crossbills
Authors: Benkman Craig W.
Published: October 2019

Crossbills (Loxia) are specialized to extract and handle seeds from conifer cones. I evaluated the ability of crossbills to handle nonconifer seeds by comparing seed handling efficiencies with other cardueline finches. For all seed sizes, crossbills required seed encounter rates or seed abundances 2-3 times greater than other species to meet their daily energy requirements. Consequently, crossbills may suffer high mortality during conifer cone failures. Crossbills are inefficient at meeting their energy demands on nonconifer seeds because of their narrow mandibles, lowered horny palate, and large body size. The narrow mandibles enable crossbills to efficiently extract seeds from conifer cones and the lowered palate enables them to handle small seeds rapidly. Crossbills have evolved larger bills, and associated musculature and body mass, to provide the power necessary to separate cone scales. Some of the increase in body mass, however, may counterbalance the large bills to improve predator evasion.
3D genome organisation in Drosophila
Authors: Moretti Charlotte , Stévant Isabelle , Ghavi-Helm Yad
Published: October 2019

Ever since Thomas Hunt Morgan’s discovery of the chromosomal basis of inheritance by using Drosophila melanogaster as a model organism, the fruit fly has remained an essential model system in studies of genome biology, including chromatin organisation. Very much as in vertebrates, in Drosophila, the genome is organised in territories, compartments and topologically associating domains (TADs). However, these domains might be formed through a slightly different mechanism than in vertebrates due to the presence of a large and potentially redundant set of insulator proteins and the minor role of dCTCF in TAD boundary formation. Here, we review the different levels of chromatin organisation in Drosophila and discuss mechanisms and factors that might be involved in TAD formation. The dynamics of TADs and enhancer–promoter interactions in the context of transcription are covered in the light of currently conflicting results. Finally, we illustrate the value of polymer modelling approaches to infer the principles governing the three-dimensional organisation of the Drosophila genome.
NMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data
Authors: Jiménez-Sánchez Daniel , Ariz Mikel , Morgado José Mário , Cortés-Domínguez Iván , Ortiz-de-Solórzano Carlos
Published: October 2019

Motivation

Recent advances in multiplex immunostaining and multispectral cytometry have opened the door to simultaneously visualizing an unprecedented number of biomarkers both in liquid and solid samples. Properly unmixing fluorescent emissions is a challenging task, which normally requires the characterization of the individual fluorochromes from control samples. As the number of fluorochromes increases, the cost in time and use of reagents becomes prohibitively high. Here, we present a fully unsupervised blind spectral unmixing method for the separation of fluorescent emissions in highly mixed spectral data, without the need for control samples. To this end, we extend an existing method based on non-negative Matrix Factorization, and introduce several critical improvements: initialization based on the theoretical spectra, automated selection of ‘sparse’ data and use of a re-initialized multilayer optimizer.

Results

Our algorithm is exhaustively tested using synthetic data to study its robustness against different levels of colocalization, signal to noise ratio, spectral resolution and the effect of errors in the initialization of the algorithm. Then, we compare the performance of our method to that of traditional spectral unmixing algorithms using novel multispectral flow and image cytometry systems. In all cases, we show that our blind unmixing algorithm performs robust unmixing of highly spatially and spectrally mixed data with an unprecedently low computational cost. In summary, we present the first use of a blind unmixing method in multispectral flow and image cytometry, opening the door to the widespread use of our method to efficiently pre-process multiplex immunostaining samples without the need of experimental controls.

Availability and implementation

https://github.com/djimenezsanchez/Blind_Unmixing_NMF_RI/ contains the source code and all datasets used in this manuscript.

Supplementary information

Supplementary data are available at Bioinformatics online.
Historical, Ethical, and (Extra)legal Perspectives on Culpability in Accidental Species Introductions
Authors: Perry Gad , Curzer Howard , Farmer Michael , Gore Meredith L , Simberloff Daniel
Published: October 2019

Some nonnative species benefit humans, but many become invasive, with high economic, cultural, and ecological costs. Although many introductions are considered accidental, inadvertent, or unintentional, this terminology often cannot be justified. Prevention policies have been proposed or implemented, and a diversity of proven control methods is available, but invasion problems grow, largely because feasible policy and management approaches are not implemented. The lack of action reflects willful myopia, a decision not to act because of negligence by policymakers, managers, and individuals. We explore the multidimensional ethical implications of this view and propose a continuum of ethical hazard. We relate the ethical dimensions to legal aspects of culpability and suggest a possible cutoff for legal liability. Finally, we identify four components of a desired policy response: It must ensure legal authority for action, base policy response on market forces, assure that more than simplistic economic considerations underpin decisions, and better engage the public.
Traversing the Wasteland: A Framework for Assessing Ecological Threats to Drylands
Authors: Hoover David L , Bestelmeyer Brandon , Grimm Nancy B , Huxman Travis E , Reed Sasha C , Sala Osvaldo , Seastedt Timothy R , Wilmer Hailey , Ferrenberg Scott
Published: October 2019

Drylands cover 41% of the Earth's terrestrial surface, play a critical role in global ecosystem function, and are home to over two billion people. Like other biomes, drylands face increasing pressure from global change, but many of these ecosystems are close to tipping points, which, if crossed, can lead to abrupt transitions and persistent degraded states. Their limited but variable precipitation, low soil fertility, and low productivity have given rise to a perception that drylands are wastelands, needing societal intervention to bring value to them. Negative perceptions of drylands synergistically combine with conflicting sociocultural values regarding what constitutes a threat to these ecosystems. In the present article, we propose a framework for assessing threats to dryland ecosystems and suggest we must also combat the negative perceptions of drylands in order to preserve the ecosystem services that they offer.
Conceptual Risk Framework: Integrating Ecological Risk of Introduced Species with Recipient Ecosystems
Authors: Probert Anna F , Ward Darren F , Beggs Jacqueline R , Lin Sheng-Lin , Stanley Margaret C
Published: October 2019

Global changes are predicted to facilitate the introduction, establishment, and spread of species into new environments leading to potential negative impacts on local biodiversity. Evaluating the risk associated with introduced species with a high likelihood of arrival, or species that have already been introduced, is therefore increasingly important. In the present article, we outline an operational framework to provide a basis for assessing the ecological risk of introduced species in order to facilitate justifiable management decisions. The framework integrates information based on both the species and the (potential) recipient ecosystems, using existing tools to guide pest managers through the stepwise process. This enables the prediction of high-risk species and the identification of those ecosystems most vulnerable to invasion, and facilitates understanding of the potential mechanisms and magnitude of pest impacts. The framework can be applied to different invasion scenarios to evaluate the risks and impacts of species.
Machine learning in the estimation of causal effects: targeted minimum loss-based estimation and double/debiased machine learning
Authors: Díaz Iván
Published: October 2019

In recent decades, the fields of statistical and machine learning have seen a revolution in the development of data-adaptive regression methods that have optimal performance under flexible, sometimes minimal, assumptions on the true regression functions. These developments have impacted all areas of applied and theoretical statistics and have allowed data analysts to avoid the biases incurred under the pervasive practice of parametric model misspecification. In this commentary, I discuss issues around the use of data-adaptive regression in estimation of causal inference parameters. To ground ideas, I focus on two estimation approaches with roots in semi-parametric estimation theory: targeted minimum loss-based estimation (TMLE; van der Laan and Rubin, 2006) and double/debiased machine learning (DML; Chernozhukov and others, 2018). This commentary is not comprehensive, the literature on these topics is rich, and there are many subtleties and developments which I do not address. These two frameworks represent only a small fraction of an increasingly large number of methods for causal inference using machine learning. To my knowledge, they are the only methods grounded in statistical semi-parametric theory that also allow unrestricted use of data-adaptive regression techniques.
Genetic variants in m6A modification genes are associated with colorectal cancer risk
Authors: Meng Yixuan , Li Shuwei , Gu Dongying , Xu Kaili , Du Mulong , Zhu Lingjun , Chu Haiyan , Zhang Zhengdong , Wu Yuan , Fu Zan , Wang Meilin
Published: October 2019

The N6-methyladenosine (m6A) modification plays important regulatory roles in gene expression, cancer occurrence and metastasis. Herein, we aimed to explore the association between genetic variants in m6A modification genes and susceptibility to colorectal cancer. We used logistic regression models to investigate the associations between candidate single-nucleotide polymorphisms (SNPs) in 20 m6A modification genes and colorectal cancer risk. The false discovery rate (FDR) method was used for multiple comparisons. Dual luciferase assays and RNA m6A quantifications were applied to assess transcriptional activity and measure m6A levels, respectively. We found that SND1 rs118049207 was significantly associated with colorectal cancer risk in a Nanjing population (odds ratio (OR) = 1.69, 95% confidence interval (95% CI) = 1.31–2.18, P = 6.51 × 10−6). This finding was further replicated in an independent Beijing population (OR = 1.36, 95% CI = 1.04–1.79, P = 2.41 × 10−2) and in a combined analysis (OR = 1.52, 95% CI = 1.27–1.84, P = 8.75 × 10−6). Stratification and interaction analyses showed that SND1 rs118049207 multiplicatively interacted with the sex and drinking status of the patients to enhance their colorectal cancer risk (P = 1.56 × 10−3 and 1.41 × 10−2, respectively). Furthermore, rs118049207 served as an intronic enhancer on SND1 driven by DMRT3. SND1 mRNA expression was markedly increased in colorectal tumour tissues compared with adjacent normal tissues. The colorimetric m6A quantification strategy revealed that SND1 could alter m6A levels in colorectal cancer cell lines. Our findings indicated that genetic variants in m6A modification genes might be promising predictors of colorectal cancer risk.
Reinstatement of Event Details during Episodic Simulation in the Hippocampus
Authors: Thakral Preston P , Madore Kevin P , Addis Donna Rose , Schacter Daniel L
Published: October 2019

According to the constructive episodic simulation hypothesis, episodic simulation (i.e., imagining specific novel future episodes) draws on some of the same neurocognitive processes that support episodic memory (i.e., recalling specific past episodes). Episodic retrieval supports the ability to simulate future experiences by providing access to episodic details (e.g., the people and locations that comprise memories) that can be recombined in new ways. In the current functional neuroimaging study, we test this hypothesis by examining whether the hippocampus, a region implicated in the reinstatement of episodic information during memory, supports reinstatement of episodic information during simulation. Employing a multivoxel pattern similarity analysis, we interrogated the similarity between hippocampal neural patterns during memory and simulation at the level of individual event details. Our findings indicate that the hippocampus supports the reinstatement of detail-specific information from episodic memory during simulation, with the level of reinstatement contributing to the subjective experience of simulated details.
Cell atlas of the foetal human heart and implications for autoimmune-mediated congenital heart block
Authors: Suryawanshi Hemant , Clancy Robert , Morozov Pavel , Halushka Marc K , Buyon Jill P , Tuschl Thomas
Published: October 2019

Aims

Investigating human heart development and applying this to deviations resulting in disease is incomplete without molecular characterization of the cell types required for normal functioning. We investigated foetal human heart single-cell transcriptomes from mid-gestational healthy and anti-SSA/Ro associated congenital heart block (CHB) samples.

Methods and results

Three healthy foetal human hearts (19th to 22nd week of gestation) and one foetal heart affected by autoimmune-associated CHB (21st week of gestation) were subjected to enzymatic dissociation using the Langendorff preparation to obtain single-cell suspensions followed by 10× Genomics- and Illumina-based single-cell RNA-sequencing (scRNA-seq). In addition to the myocytes, fibroblasts, immune cells, and other minor cell types, previously uncharacterized diverse sub-populations of endothelial cells were identified in the human heart. Differential gene expression analysis revealed increased and heterogeneous interferon responses in varied cell types of the CHB heart compared with the healthy controls. In addition, we also identified matrisome transcripts enriched in CHB stromal cells that potentially contribute to extracellular matrix deposition and subsequent fibrosis.

Conclusion

These data provide an information-rich resource to further our understanding of human heart development, which, as illustrated by comparison to a heart exposed to a maternal autoimmune environment, can be leveraged to provide insight into the pathogenesis of disease.
Physician adherence to clinical guidelines in euthanasia and assisted suicide in the Netherlands: a qualitative study
Authors: Riley Sean R , Overbeek Anouk , van der Heide Agnes
Published: October 2019

Background

Euthanasia and assisted suicide laws in the Netherlands require physicians meet clinical guidelines when performing the practice to ensure death is peaceful and painless. Despite oversight by the regional review committees over each case, little research exists into the frequency of guideline deviation and the reasons for nonadherence.

Methods

Cases reported and reviewed between 2012 and 2017 that did not meet due medical care were analysed for thematic content. Semistructured interviews were conducted with 11 Dutch physicians on their experience with the clinical and pharmacological elements of euthanasia and assisted suicide, their interaction and comportment with the recommended guidelines, and reasons why guideline deviation might occur. Reported case reviews and interviews were used to obtain themes and subthemes to understand how and why deviations from clinical guidelines happened.

Results

Violations of due medical care were found in 42 (0.07%) of reported cases. The regional review committees found physicians in violation of due medical care mostly for inadequate confirmation of coma-induction and deviations from recommended drug dosages. Physicians reported that they rarely deviated from the guidelines, with the most common reasons being concern for the patient’s family, concern over the drug efficacy, mistrust in the provided guidelines, or relying on the poor advice of pharmacists or hospital administrators.

Conclusions

Deviations from the guidelines and violations of due medical care are rare, but should nonetheless be monitored and prevented. A few areas for improvement include skills training for physicians, consistency between review committee rulings, and further clarity on dosage recommendations.
Dynamics of the microbial community during growth of the house dust mite Dermatophagoides farinae in culture
Authors: Klimov Pavel , Molva Vit , Nesvorna Marta , Pekar Stano , Shcherbachenko Elena , Erban Tomas , Hubert Jan
Published: October 2019

The variation in house dust mite microbial communities is important because various microorganisms modulate the production of allergens by their mite hosts and/or contaminate immunotherapeutic extracts. Temporal changes in mite microbiomes and the mite culture environment occurring at different stages of mite culture development are particularly understudied in this system. Here, we analyzed the dynamics of microbial communities during the culture growth of Dermatophagoides farinae. Changes in microbiomes were related to three key variables: the mite population density, microbial microcosm respiration and concentration of guanine (the mite nitrogenous waste metabolite). Mite populations exhibited the following phases: exponential growth, plateau and exponential decline. The intracellular bacterium Cardinium and the yeast Saccharomyces cerevisiae prevailed in the internal mite microbiomes, and the bacterium Lactobacillus fermentum was prevalent in the mite diet. The reduction in the mite population size during the late phases of culture development was related to the changes in their microbial profiles: the intracellular bacterium Cardinium was replaced by Staphylococcus, Oceanobacillus and Virgibacillus, and S. cerevisiae was replaced by the antagonistic fungi Aspergillus penicillioides and Candida. Increases in the guanine content were positively correlated with increases in the Staphylococcus and A. penicillioides profiles in the culture environment. Our results show that the mite microbiome exhibits strong, dynamic alterations in its profiles across different mite culture growth stages.
A screening system using minimal media identifies a flavin-competing inhibitor of Porphyromonas gingivalis growth
Authors: Saiki Keitarou , Urano-Tashiro Yumiko , Konishi Kiyoshi , Takahashi Yukihiro
Published: October 2019

Chronic periodontitis is caused by dysbiosis of human oral commensals and especially by increase in Porphyromonas gingivalis. Inhibitors of P. gingivalis growth are expected to serve as effective drugs for the periodontal therapy. In the present study, we isolated new growth inhibitors of P. gingivalis using minimal media for P. gingivalis. The minimal media included the previously reported Globulin–Albumin (GA) and the newly developed Lactalbumin-Ferric chloride (LF) and Globulin-Calcium chloride (GC); all supported growth of the wild-type strain of P. gingivalis but did not support the growth of a mutant defective for a type IX secretion system. GC contains CaCl2, indicating that P. gingivalis requires a calcium ion for growth. Using LF and GA, we screened about 100 000 compounds and identified 73 that strongly inhibited the growth of P. gingivalis. More than half of these candidates would not have been obtained if these minimal media had not been used in our screen. One of our candidate inhibitors was diphenyleneiodonium chloride (DPIC), which showed strong bactericidal activity against P. gingivalis. Excess amounts of flavin adenine dinucleotide or flavin mononucleotide suppressed the inhibitory activity of DPIC, suggesting that DPIC would be a novel potent growth inhibitor.
Is Aging Biology Ageist?
Authors: Cohen Alan A , Levasseur Mélanie , Raina Parminder , Fried Linda P , Fülöp Tamàs
Published: October 2019

The scientific questions we pursue are shaped by our cultural assumptions and biases, often in ways we are unaware. Here, we argue that modern biases against older adults (ageism) have unconsciously led aging biologists to assume that traits of older individuals are negative and those of younger individuals positive. We illustrate this bias with the example of how a medieval Chinese scholar might have approached the task of understanding aging biology. In particular, aging biologists have tended to emphasize functional declines during aging, rather than biological adaptation and population selection or composition processes; the reality is certainly that all these processes interact. Failure to make these distinctions could lead to interventions that improve superficial markers of aging while harming underlying health, particularly as the health priorities of older adults (autonomy, function, freedom from suffering, etc.) are often quite different from the goals of aging biologists (reducing disease, prolonging life). One approach to disentangling positive, negative, and neutral changes is to map trajectories of change across the life course of an individual (physiobiography). We emphasize that our goal is not to criticize our colleagues—we have been guilty too—but rather to help us all improve our science.
CLEC3B p.S106G Mutant in a Caucasian Population of Successful Neurological Aging
Authors: Kolicheski Ana , Walton Ronald L , Soto-Beasley Alexandra I , Heckman Michael G , Uitti Ryan J , Parfitt Francine , Graff-Radford Michelle R , Wszolek Zbigniew K , Graff-Radford Neill R , Ross Owen A
Published: October 2019

A number of efforts are underway to better understand the role of genetic variation in successful aging and longevity. However, to date, only two genes have been consistently associated with longevity in humans: APOE and FOXO3, with the APOE ɛ2 allele also protective against dementia. Recently, using an exome-wide SNP array approach, a missense variant CLEC3B c.316G>A (rs13963 p.S106G) was reported to associate with longevity in two independent cohorts of Japanese and Chinese participants. Interestingly, CLEC3B p.S106G is more frequent in Caucasian populations. Herein, we examined the frequency of CLEC3B p.S106G in a Caucasian series of 1,483 neurologically healthy individuals with a specific subset >80 years of age. Although our findings do not support an association between CLEC3B p.S106G and aging without neurological disease (p = .89), we confirmed the association between the APOE ε2 allele and better survival without neurological disease (p = .001). Further assessment of healthy aged cohorts that retain intact neurological function will be critical to understand the etiology of neurodegenerative disease and the role of age at risk.
Testing Proposed Quantifications of Biological Aging in Taiwanese Older Adults
Authors: Gaydosh Lauren , Belsky Daniel W , Glei Dana A , Goldman Noreen
Published: October 2019

Quantification of biological aging is of interest in gerontology as a means to surveil aging rates in the population and to evaluate the effects of interventions to increase healthy life span. Analysis of proposed methods to quantify biological aging has focused on samples of midlife or mixed-age adults in the West. Research is needed to test whether quantifications of biological aging can differentiate aging rates among older adults and if quantifications of biological aging developed in Western samples can differentiate aging rates in non-Western populations. We conducted analysis of Klemera-Doubal method (KDM) Biological Age and homeostatic dysregulation measures of biological aging developed in the U.S. NHANES and tested in a sample of older Taiwanese adults in the Social Environment and Biomarkers of Aging Study. We conducted analysis of physical and cognitive function and mortality, comparing quantifications of biological aging to a biomarker index based on norms within our analysis sample and to participants’ ratings of their own health. Results showed that quantifications of biological aging (a) predicted differences in physical and cognitive function and in mortality risk among Taiwanese older adults and (b) performed as well as a traditional biomarker index and participant self-rated health for prediction of these outcomes.