Avian diversity and function across the world's most populous cities

Understanding the composition of urban wildlife communities is crucial to promote biodiversity, ecosystem function and links between nature and people. Using crowdsourced data from over five million eBird checklists, we examined the influence of urban characteristics on avian richness and function at 8443 sites within and across 137 global cities. Under half of the species from regional pools were recorded in cities, and we found a significant phylogenetic signal for urban tolerance. Site-level avian richness was positively influenced by the extent of open forest, cultivation and wetlands and avian functional diversity by wetlands. Functional diversity co-declined with richness, but groups including granivores and aquatic birds occurred even at species-poor sites. Cities in arid areas held a higher percentage of regional species richness. Our results indicate commonalities in the influence of habitat on richness and function, as well as lower niche availability, and phylogenetic diversity across the world's cities.     

Escherichia coli K12 does not colonize the gastrointestinal tract of Fischer-344 rats

Summary The colonizing potential ofEscherichia coli K12 containing a vector coding for somidobove (bovine somatotropin) was determined. Treated male and female Fischer-344 rats were given a single oral gavage inoculum of sucrose with/without tetracycline (15 g/ml). Untreated control animals received similar drinking water regimes. All animals survived until termination. There were no clinical signs of toxicity observed and no treatment-related effect upon body weight, food consumption, or efficiency of food utilization. Fresh fecal samples were collected from each rat every 24 h following inoculation and the population of the marked strain was quantitated until no bacterial colonies were observed for two consecutive days. While all inoculated rats were positive at 24 h, by 72 and 96 h all had become negative for the test (marked) strain, as were the corresponding control group throughout the test. The frozen stock of the marked strain used as the positive control demonstrated that the agar plates were selective for the test strain. Fourteen days following inoculation, all groups of rats were killed and the gastrointestinal tracts removed and treated to recover the marked strain. There was no evidence of the marked strain in the gastrointestinal tract of any rat from any group. Thus, theE. coli K12 host/vector system used in this experiment does not colonize the gastrointestinal tract of Fischer-344 rats.     

Estradiol regulation of secretory component: Expression by rat uterine epithelial cells

Sex hormones are known to play an important role in the regulation of mucosal immunity in the female reproductive tract. The purpose of this study was to examine the effect of estradiol (E₂) on secretory component (SC) expression by epithelial cells in the rat uterus and to determine whether SC mRNA is present in uterine tissues and is under hormonal control. When ovariectomized rats treated with E₂ for 3 days and sacrificed 12 h after the last injection, expression of SC on luminal and glandular epithelial cells, as determined by immunohistochemistry, was elevated when compared to control animals. To determine whether E₂ regulation of SC involves mRNA synthesis, uterine RNA was extracted and analyzed by Northern blot. These experiments demonstrated that SC RNA is present in uteri from intact rats and markedly increased when ovariectomized animals are treated with E₂. In other studies, uterine epithelial cells from adult rats were isolated and grown on permeable membranes for 5 to 10 days. Under these conditions, isolated epithelial cells grow to confluence, form tight junctions, and preferentially secrete SC into the apical medium. These studies identify epithelial cells as a key target cell in the uterus for the regulation of mucosal immunity by E₂, which we postulate will play an important role in studies to prevent and/or control the spread of sexually transmitted diseases.     

Coherent modeling of longitudinal causal effects on binary outcomes

Analyses of biomedical studies often necessitate modeling longitudinal causal effects. The current focus on personalized medicine and effect heterogeneity makes this task even more challenging. Toward this end, structural nested mean models (SNMMs) are fundamental tools for studying heterogeneous treatment effects in longitudinal studies. However, when outcomes are binary, current methods for estimating multiplicative and additive SNMM parameters suffer from variation dependence between the causal parameters and the noncausal nuisance parameters. This leads to a series of difficulties in interpretation, estimation, and computation. These difficulties have hindered the uptake of SNMMs in biomedical practice, where binary outcomes are very common. We solve the variation dependence problem for the binary multiplicative SNMM via a reparameterization of the noncausal nuisance parameters. Our novel nuisance parameters are variation independent of the causal parameters, and hence allow for coherent modeling of heterogeneous effects from longitudinal studies with binary outcomes. Our parameterization also provides a key building block for flexible doubly robust estimation of the causal parameters. Along the way, we prove that an additive SNMM with binary outcomes does not admit a variation independent parameterization, thereby justifying the restriction to multiplicative SNMMs.     

Ecomorphological constraints imposed by the kidney component measurements in honeyeater birds inhabiting different environments

The histological renal anatomy of 10 species of honeyeaters was examined quantitatively, using stereology. The kidneys of five species of predominantly wet zone inhabiting birds: the western spinebill Acanthorhynchus superciliosus , White-checked honeyeater Phylidonyris nigra . New Holland honeyeater Phylidonyris novaehollandiae , little wattlebird anthochaera chrysoptera and red wattlebird Anthochaera carunculata , were compared to five predominantly arid zone inhabiting birds: the grey-fronted honeyeater Meliphaga plumula , white-plumed honeyeater Meliphaga penicillata , white-fronted honeyeater Phylidonyris albifrons , spiny-checked honeyeater Acanthogenys rufogularis and yellow-throated miner Manorina flarigula. The kidneys were asymmetrical, with the left kidney being larger than the right kidney. Kidney mass was directly proportional to body mass (coefficient of correlation, r =+0·95), as was kidney volume to kidney mass (r =+1·0). Wet zone honeyeaters generally and a higher percentage and absolute volume of renal cortex, whilst arid zone honeyeaters generally had a significantly higher percentage and absolute volume of renal medulla. There were few differences between species, in either the percentage or absolute volume or luminal surface area of nephron components within the cortex. Within the medulla, wet zone honeyeaters generally had a higher percentage and absolute luminal surface area of collecting ducts, whilst arid zone honeyeaters had a higher percentage and absolute surface area of capillaries. This may be due to factors such as variations in diet and climate between habitats resulting in differences in honeyeater renal morphology which enable arid zone birds to conserve water and wet zone birds to conserve ions more efficiently.     

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.     

POLLEN REMOVAL AND POLLEN DEPOSITION AFFECT THE DURATION OF THE STAMINATE AND PISTILLATE PHASES IN CAMPANULA RAPUNCULOIDES

We examined factors affecting the duration of the staminate and pistillate phases in the protandrous flowers of Campanula rapunculoides L. (Campanulaceae). Under conditions of natural pollinator visitation, flowers experiencing low rates of pollen removal lasted significantly longer than flowers that had faster rates of pollen removal. Experimental manipulations showed that low levels of pollen removal resulted in extension of the staminate phase. Hand-pollinations in which we varied the amount and source of pollen showed that when the number of fertilized ovules within an ovary is low, senescence of the flower is delayed, resulting in extension of the pistillate phase. We also report on pollinator foraging patterns within the vertical inflorescences of C. rapunculoides and the limiting factor for seed set in this population. The results are relevent to recent suggestions that floral characters often serve to reduce interference between the sexual functions in cosexual plants.