Occupational Preferences, Childhood Behavior, and Openness: The Role of Sex, Sexual Orientation, and Gender Identity in Iran

Previous research suggests that both same-sex attraction and the personality trait "openness" are associated with sex-atypical preferences and behaviors. Here, we examined the links between adulthood occupational preferences, childhood play behavior, and openness among Iranian cisgender gynephilic males (n = 228), cisgender ambiphilic males (n = 48), cisgender androphilic males (n = 178), transgender androphilic males (n = 58), cisgender androphilic females (n = 226), cisgender ambiphilic females (n = 94), cisgender gynephilic females (n = 31), and transgender gynephilic females (n = 121) from Iran. Cisgender and transgender same-sex attracted males and females exhibited sex-atypical occupational preferences with the latter group showing even more sex-atypicality than the former. The personality trait openness did not differ between cisgender groups. Transgender androphilic males had a significantly higher mean score for openness compared to cisgender androphilic females and transgender gynephilic females, whereas transgender gynephilic females had a significantly lower mean score compared to cisgender androphilic males. In both males and females, childhood sex-atypicality, same-sex attraction, and openness were associated with sex-atypical occupational preferences. Our findings from Iran provides cross-cultural support for interconnectedness of childhood and adulthood sex-atypicality, openness, and same-sex attraction in males and females who are cisgender and transgender.

Reduction of bitter taste receptor gene family in folivorous colobine primates relative to omnivorous cercopithecine primates

Bitter taste perception is important in preventing animals from ingesting potentially toxic compounds. Whole-genome assembly (WGA) data have revealed that bitter taste receptor genes (TAS2Rs) comprise a multigene family with dozens of intact and disrupted genes in primates. However, publicly available WGA data are often incomplete, especially for multigene families. In this study, we employed a targeted capture (TC) approach specifically probing TAS2Rs for ten species of cercopithecid primates with diverse diets, including eight omnivorous cercopithecine species and two folivorous colobine species. We designed RNA probes for all TAS2Rs that we modeled to be intact in the common ancestor of cercopithecids ("ancestral-cercopithecid TAS2R gene set"). The TC was followed by short-read and high-depth massive-parallel sequencing. TC retrieved more intact TAS2R genes than found in WGA databases. We confirmed a large number of gene "births" at the common ancestor of cercopithecids and found that the colobine common ancestor and the cercopithecine common ancestor had contrasting trajectories: four gene "deaths" and three gene births, respectively. The number of intact TAS2R genes was markedly reduced in colobines (25-28 detected via TC and 20-26 detected via WGA analysis) as compared with cercopithecines (27-36 via TC and 19-30 via WGA). Birth or death events occurred at almost every phylogenetic-tree branch, making the composition of intact genes variable among species. These results show that evolutionary change in intact TAS2R genes is a complex process, refute a simple general prediction that herbivory favors more TAS2R genes, and have implications for understanding dietary adaptations and the evolution of detoxification abilities.

Spatiotemporal dynamics in butterfly hybrid zones

Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.

Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions

Protein Protein low complexity regions (LCRs) are compositionally biased amino acid sequences, many of which have significant evolutionary impacts on the proteins which contain them. They are mutationally unstable experiencing higher rates of indels and substitutions than higher complexity regions. LCRs also impact the expression of their proteins, likely through multiple effects along the path from gene transcription, through translation, and eventual protein degradation. It has been observed that proteins which contain LCRs are associated with elevated transcript abundance (TAb), despite having lower protein abundance. We have gathered and integrated human data to investigate the co-evolution of TAb and LCRs through ancestral reconstructions and model inference using an approximate Bayesian calculation based method. We observe that on short evolutionary timescales TAb evolution is significantly impacted by changes in LCR length, with insertions driving TAb down. But in contrast, the observed data is best explained by indel rates in LCRs which are unaffected by shifts in TAb. Our work demonstrates a coupling between LCR and TAb evolution, and the utility of incorporating multiple responses into evolutionary analyses.

Simultaneous catheter and multicriteria optimization for HDR cervical cancer brachytherapy with a complex intracavity/interstitial applicator

BACKGROUND

Complex intracavity and interstitial (IC/IS) applicators, such as the Venezia applicator, can improve the HR-CTV coverage while adequately protecting organs at risk in the treatment of cervical cancer with high-dose-rate (HDR) brachytherapy. Although the Venezia applicator offers more choice for catheter selection, commercially available catheter and dose optimization algorithms are still missing for complex applicators. Moreover, studies on catheter and dose optimization for IC/IS implants in the treatment of cervical cancer are still limited.

PURPOSE

This work aims to combine a GPU-based multi-criteria optimization (gMCO) algorithm with a sparse catheter (SC) optimization algorithm for the Venezia applicator.

METHODS

Fifty-eight cervical cancer patients who received 28 Gy in 4 fx of HDR brachytherapy with the Venezia applicator (combination to external beam radiation therapy) are retrospectively revisited. The modelization of the applicator is done by virtually reconstructing all the IS catheters passing through the ring. Template catheters are reconstructed using an in-house python script. To perform simultaneous MCO and SC optimization (SC+MCO), the objective function includes aggregated dose objectives in a weighted sum and a group sparsity term that individually penalizes the contribution of IS catheters. Plans generated with the SC+MCO algorithm are compared with plans generated with MCO using clinical catheters (CC+MCO) and the clinical plans (CP). The EMBRACE II soft constraints (planning aims) and hard constraints (limits for prescribed dose) are used as plan evaluation criteria.

RESULTS

CC+MCO gives the most important gain with an increase up to 20.7% in meeting all EMBRACE II soft constraints compared with CP. The SC+MCO algorithm (adding catheter optimization to MCO) provides a second order increase (up to 12.1% with total acceptance rate of 60.3% or 35/58) in the acceptance rate versus CC+MCO (total increase of 32.8% vs. CP). Acceptance rate in EMBRACE II hard constraints is 98.3% (57/58) for both CC+MCO and SC+MCO versus 91.4% (53/58) for CP. The median SC+MCO optimization time is 11 s to generate a total of 5000 Pareto-optimal plans with different catheter configurations (position and number) for each fraction.

CONCLUSIONS

Simultaneous catheter and MCO optimization is clinically feasible for HDR cervical cancer brachytherapy using the Venezia applicator. Clinical catheter configurations could be improved and/or the catheter number could be reduced without decreasing plan quality using SC+MCO compared with the CP.

Assessing morphological preservation of gastrointestinal parasites from fecal samples of wild capuchin monkeys (Cebus imitator) stored in ethanol versus formalin

The copromicroscopic identification of gastrointestinal parasites is a common, cost-effective method vital to understanding host-parasite interactions. However, its efficacy depends on effective preservation of the samples. In this study, we compare the preservation of ethanol and formalin preserved gastrointestinal parasites collected from a wild population of Costa Rican capuchin monkeys (Cebus imitator). Fecal samples were collected, halved, and stored in either 10% formalin or 96% ethanol at ambient temperature, then microscopically screened for the presence of parasites. Parasites were morphologically identified and rated based on their preservation using a newly developed rubric. We identified more parasitic morphotypes in formalin-preserved samples but found no difference in the number of parasites per fecal gram (PFG) between mediums. There was no difference in the PFG of two most prevalent parasite morphotypes, Filariopsis barretoi larvae and Strongyle-type eggs, and while Filariopsis larvae were better preserved in formalin, strongyle eggs showed no preservation difference between mediums. Our results support the suitability of both ethanol and formalin for morphological parasite identification in samples stored over 1 year, describe the morphological changes and challenges associated with parasite degradation, and highlight the potential for future studies to use both morphological and molecular methods in non-invasively collected samples.

Effect of snow cover on the off-host survival of Dermacentor variabilis (Acari: Ixodidae) larvae

The geographical range of the American dog tick, Dermacentor variabilis (Say), in Canada continues to expand northwards into areas with colder winter temperatures. Understanding what influences the off-host survival of D. variabilis over winter is important for predicting the northern distributional limit of this species. A field experiment was conducted to determine the effect of snow cover on the off-host survival of unfed D. variabilis larvae from a population situated near the northern distributional limit in Saskatchewan, Canada. Ticks were placed in tubes within 1 of 9 field enclosures (tickaria) in early fall. The 9 tickaria were divided into 3 equal treatment groups: no snow cover, natural snow cover (maximum depth of 25 cm) and extra snow cover (maximum depth of 32 cm). Tick survival was measured in mid-winter and in early spring (i.e., ~17 and ~26 wk after start of experiment). The results showed that snow cover had a significant impact on the relative humidity, but not temperature, in the tickaria. Larvae in tickaria with no snow cover had a higher mortality rate (27%) than larvae in tickaria with natural snow cover (6%) or extra snow cover (4%). Although snow cover enhanced off-host survival, many individuals were able to survive in sub-zero temperatures under leaf litter in the absence of continuous snow cover for a period of 108 days. These findings have implications for the construction of predictive models to determine the northern distributional limits of D. variabilis, a species that is an important vector of several pathogens.

Impact of bacterial admixtures on the compressive and tensile strengths, permeability, and pore structure of ternary mortars: Comparative study of ureolytic and phototrophic bacteria

The addition of bacterial biomass to cementitious materials can improve strength and permeability properties by altering the pore structure. Photoautotrophic bacteria are understudied mortar bio-additives that do not produce unwanted by-products compared to commonly studied ureolytic species. This study directly compares the impact of the addition of heterotrophic Bacillus subtilis to photoautotrophic Synechocystis sp. PCC6803 on mortar properties and microstructure. Cellulose fibers were used as a bacteria carrier. A commercial concrete healing agent composed of dormant bacterial spores was also tested. Strength, water absorption tests, mercury intrusion porosimetry, differential scanning calorimetry, thermogravimetric analysis, and scanning electron microscopy were applied to experimental mortar properties. The photoautotrophic modifications had a stronger positive impact on mortar strength and permeability properties than sporulated heterotrophic modifications due to differences in surface properties and production of exopolysaccharides. The findings provide support for photoautotrophic species as additives for mortars to move away from ammonia-generating species.

Estimating Groundwater Pumping for Irrigation: A Method Comparison

Effective groundwater management is critical to future environmental, ecological, and social sustainability and requires accurate estimates of groundwater withdrawals. Unfortunately, these estimates are not readily available in most areas due to physical, regulatory, and social challenges. Here, we compare four different approaches for estimating groundwater withdrawals for agricultural irrigation. We apply these methods in a groundwater-irrigated region in the state of Kansas, USA, where high-quality groundwater withdrawal data are available for evaluation. The four methods represent a broad spectrum of approaches: (1) the hydrologically-based Water Table Fluctuation method (WTFM); (2) the demand-based SALUS crop model; (3) estimates based on satellite-derived evapotranspiration (ET) data from OpenET; and (4) a landscape hydrology model which integrates hydrologic- and demand-based approaches. The applicability of each approach varies based on data availability, spatial and temporal resolution, and accuracy of predictions. In general, our results indicate that all approaches reasonably estimate groundwater withdrawals in our region, however, the type and amount of data required for accurate estimates and the computational requirements vary among approaches. For example, WTFM requires accurate groundwater levels, specific yield, and recharge data, whereas the SALUS crop model requires adequate information about crop type, land use, and weather. This variability highlights the difficulty in identifying what data, and how much, are necessary for a reasonable groundwater withdrawal estimate, and suggests that data availability should drive the choice of approach. Overall, our findings will help practitioners evaluate the strengths and weaknesses of different approaches and select the appropriate approach for their application.

Biophysical control of plasticity and patterning in regeneration and cancer

Cells and tissues display a remarkable range of plasticity and tissue-patterning activities that are emergent of complex signaling dynamics within their microenvironments. These properties, which when operating normally guide embryogenesis and regeneration, become highly disordered in diseases such as cancer. While morphogens and other molecular factors help determine the shapes of tissues and their patterned cellular organization, the parallel contributions of biophysical control mechanisms must be considered to accurately predict and model important processes such as growth, maturation, injury, repair, and senescence. We now know that mechanical, optical, electric, and electromagnetic signals are integral to cellular plasticity and tissue patterning. Because biophysical modalities underly interactions between cells and their extracellular matrices, including cell cycle, metabolism, migration, and differentiation, their applications as tuning dials for regenerative and anti-cancer therapies are being rapidly exploited. Despite this, the importance of cellular communication through biophysical signaling remains disproportionately underrepresented in the literature. Here, we provide a review of biophysical signaling modalities and known mechanisms that initiate, modulate, or inhibit plasticity and tissue patterning in models of regeneration and cancer. We also discuss current approaches in biomedical engineering that harness biophysical control mechanisms to model, characterize, diagnose, and treat disease states.

Discovery and Visualization of the Hidden Relationships among N-Glycosylation, Disulfide Bonds, and Membrane Topology

Membrane proteins (MPs) are functionally important but structurally complex. In particular, MPs often carry three structural features, i.e., transmembrane domains (TMs), disulfide bonds (SSs), and N-glycosylation (N-GLYCO). All three features have been intensively studied; however, how the three features potentially correlate has been less addressed in the literature. With the growing accuracy from computational prediction, we used publicly available information on SSs and N-GLYCO and analyzed the potential relationships among post-translational modifications (PTMs) and the predicted membrane topology in the human proteome. Our results suggested a very close relationship between SSs and N-GLYCO that behaved similarly, whereas a complementary relation between the TMs and the two PTMs was also revealed, in which the high SS and/or N-GLYCO presence is often accompanied by a low TM occurrence in a protein. Furthermore, the occurrence of SSs and N-GLYCO in a protein heavily relies on the protein length; however, TMs seem not to possess such length dependence. Finally, SSs exhibits larger potential dynamics than N-GLYCO, which is confined by the presence of sequons. The special classes of proteins possessing extreme or unique patterns of the three structural features are comprehensively identified, and their structural features and potential dynamics help to identify their susceptibility to different physiological and pathophysiological insults, which could help drug development and protein engineering.

The fission yeast methyl phosphate capping enzyme Bmc1 guides 2'-O-methylation of the U6 snRNA

Splicing requires the tight coordination of dynamic spliceosomal RNAs and proteins. U6 is the only spliceosomal RNA transcribed by RNA Polymerase III and undergoes an extensive maturation process. In humans and fission yeast, this includes addition of a 5' γ-monomethyl phosphate cap by members of the Bin3/MePCE family as well as snoRNA guided 2'-O-methylation. Previously, we have shown that the Bin3/MePCE homolog Bmc1 is recruited to the S. pombe telomerase holoenzyme by the LARP7 family protein Pof8, where it acts in a catalytic-independent manner to protect the telomerase RNA and facilitate holoenzyme assembly. Here, we show that Bmc1 and Pof8 are required for the formation of a distinct U6 snRNP that promotes 2'-O-methylation of U6, and identify a non-canonical snoRNA that guides this methylation. We also show that the 5' γ-monomethyl phosphate capping activity of Bmc1 is not required for its role in promoting snoRNA guided 2'-O-methylation, and that this role relies on different regions of Pof8 from those required for Pof8 function in telomerase. Our results are consistent with a novel role for Bmc1/MePCE family members in stimulating 2'-O-methylation and a more general role for Bmc1 and Pof8 in guiding noncoding RNP assembly beyond the telomerase RNP.

Investigation of Camera-Free Eye-Tracking Glasses Compared to a Video-Based System

Technological advances in eye-tracking have resulted in lightweight, portable solutions that are capable of capturing eye movements beyond laboratory settings. Eye-tracking devices have typically relied on heavier, video-based systems to detect pupil and corneal reflections. Advances in mobile eye-tracking technology could facilitate research and its application in ecological settings; more traditional laboratory research methods are able to be modified and transferred to real-world scenarios. One recent technology, the AdHawk MindLink, introduced a novel camera-free system embedded in typical eyeglass frames. This paper evaluates the AdHawk MindLink by comparing the eye-tracking recordings with a research "gold standard", the EyeLink II. By concurrently capturing data from both eyes, we compare the capability of each eye tracker to quantify metrics from fixation, saccade, and smooth pursuit tasks-typical elements in eye movement research-across a sample of 13 adults. The MindLink system was capable of capturing fixation stability within a radius of less than 0.5∘, estimating horizontal saccade amplitudes with an accuracy of 0.04∘± 2.3∘, vertical saccade amplitudes with an accuracy of 0.32∘± 2.3∘, and smooth pursuit speeds with an accuracy of 0.5 to 3∘s, depending on the pursuit speed. While the performance of the MindLink system in measuring fixation stability, saccade amplitude, and smooth pursuit eye movements were slightly inferior to the video-based system, MindLink provides sufficient gaze-tracking capabilities for dynamic settings and experiments.

Gene Expression in Cord Blood and Tuberculosis in Early Childhood: A Nested Case-Control Study in a South African Birth Cohort

BACKGROUND

Transcriptomic profiling of adults with tuberculosis (TB) has become increasingly common, predominantly for diagnostic and risk prediction purposes. However, few studies have evaluated signatures in children, particularly in identifying those at risk for developing TB disease. We investigated the relationship between gene expression obtained from umbilical cord blood and both tuberculin skin test conversion and incident TB disease through the first 5 years of life.

METHODS

We conducted a nested case-control study in the Drakenstein Child Health Study, a longitudinal, population-based birth cohort in South Africa. We applied transcriptome-wide screens to umbilical cord blood samples from neonates born to a subset of selected mothers (N = 131). Signatures identifying tuberculin conversion and risk of subsequent TB disease were identified from genome-wide analysis of RNA expression.

RESULTS

Gene expression signatures revealed clear differences predictive of tuberculin conversion (n = 26) and TB disease (n = 10); 114 genes were associated with tuberculin conversion and 30 genes were associated with the progression to TB disease among children with early infection. Coexpression network analysis revealed 6 modules associated with risk of TB infection or disease, including a module associated with neutrophil activation in immune response (P < .0001) and defense response to bacterium (P < .0001).

CONCLUSIONS

These findings suggest multiple detectable differences in gene expression at birth that were associated with risk of TB infection or disease throughout early childhood. Such measures may provide novel insights into TB pathogenesis and susceptibility.

Characterization of Proteus mirabilis and associated plasmids isolated from anaerobic dairy cattle manure digesters

Proteus mirabilis is an opportunistic pathogen associated with a variety of human infections, including urinary tract infections. The prevalence of P. mirabilis in foods of animal origin and in the manure by-products created in animal production is not well documented. Further, the prevalence and persistence of extended-spectrum cephalosporin (ESC) resistant P. mirabilis is largely unknown. In this study, we characterized ESC-resistant P. mirabilis recovered from various stages of dairy manure anaerobic digestion. Isolates were screened by PCR for blaCTX-M, blaCMY and blaSHV, and antimicrobial susceptibility testing was performed. Fifty-six P. mirabilis carrying CTX-M were sequenced with short and long read sequencing technologies, and the assembled chromosomes and plasmids were compared. ESC-resistant Proteus was found in four of the six manure digesters, an indication that not all digesters were colonized with resistant strains. Both CTX-M-1 and CTX-M-15 plasmids were found in P. mirabilis isolates. Transfer of plasmid DNA by conjugation was also explored, with ESC-resistance plasmids able to transfer to Escherichia coli at high frequency. We concluded that P. mirabilis can harbour and transfer ESC-resistance genes and plasmids, and may be an overlooked reservoir of antimicrobial resistance.

A novel machine learning system for identifying sleep-wake states in mice

Research into sleep-wake behaviors relies on scoring sleep states, normally done by manual inspection of electroencephalogram (EEG) and electromyogram (EMG) recordings. This is a highly time-consuming process prone to inter-rater variability. When studying relationships between sleep and motor function, analyzing arousal states under a four-state system of active wake (AW), quiet wake (QW), nonrapid-eye-movement (NREM) sleep, and rapid-eye-movement (REM) sleep provides greater precision in behavioral analysis but is a more complex model for classification than the traditional three-state identification (wake, NREM, and REM sleep) usually used in rodent models. Characteristic features between sleep-wake states provide potential for the use of machine learning to automate classification. Here, we devised SleepEns, which uses a novel ensemble architecture, the time-series ensemble. SleepEns achieved 90% accuracy to the source expert, which was statistically similar to the performance of two other human experts. Considering the capacity for classification disagreements that are still physiologically reasonable, SleepEns had an acceptable performance of 99% accuracy, as determined blindly by the source expert. Classifications given by SleepEns also maintained similar sleep-wake characteristics compared to expert classifications, some of which were essential for sleep-wake identification. Hence, our approach achieves results comparable to human ability in a fraction of the time. This new machine-learning ensemble will significantly impact the ability of sleep researcher to detect and study sleep-wake behaviors in mice and potentially in humans.

Minimal Kidney Disease Phenotype in Shroom3 Heterozygous Null Mice

Background

Shroom family member 3 (SHROOM3) encodes an actin-associated protein that regulates epithelial morphology during development. Several genome-wide association studies (GWAS) have identified genetic variances primarily in the 5' region of SHROOM3, associated with chronic kidney disease (CKD) and poor transplant outcomes. These genetic variants are associated with alterations in Shroom3 expression.

Objective

Characterize the phenotypic abnormalities associated with reduced Shroom3 expression in postnatal day 3-, 1-month and 3-month-old mice.

Methods

The Shroom3 protein expression pattern was determined by immunofluorescence. We generated Shroom3 heterozygous null mice (Shroom3Gt/+) and performed comparative analyses with wild type littermates based on somatic and kidney growth, gross renal anatomy, renal histology, renal function at postnatal day 3, 1 month, and 3 months.

Results

The Shroom3 protein expression localized to the apical regions of medullary and cortical tubular epithelium in postnatal wild type kidneys. Co-immunofluorescence studies confirmed protein expression localized to the apical side of the tubular epithelium in proximal convoluted tubules, distal convoluted tubules, and collecting ducts. While Shroom3 heterozygous null mice exhibited reduced Shroom3 protein expression, no differences in somatic and kidney growth were observed when compared to wild type mice. Although, rare cases of unilateral hypoplasia of the right kidney were observed at postnatal 1 month in Shroom3 heterozygotes. Yet renal histological analysis did not reveal any overt abnormalities in overall kidney structure or in glomerular and tubular organization in Shroom3 heterozygous null mice when compared to wild type mice. Analysis of the apical-basolateral orientation of the tubule epithelium demonstrated alterations in the proximal convoluted tubules and modest disorganization in the distal convoluted tubules at 3 months in Shroom3 heterozygotes. Additionally, these modest abnormalities were not accompanied by tubular injury or physiological defects in renal and cardiovascular function.

Conclusion

Taken together, our results describe a mild kidney disease phenotype in adult Shroom3 heterozygous null mice, suggesting that Shroom3 expression and function may be required for proper structure and maintenance of the various tubular epithelial parenchyma of the kidney.

MicroRNAs in tear fluids predict underlying molecular changes associated with Alzheimer's disease

Extracellular circulating microRNAs (miRNAs) have been discussed as potential biomarkers for Alzheimer's disease (AD) diagnosis. As the retina is a part of the CNS, we hypothesize that miRNAs expression levels in the brain, particularly neocortex-hippocampus, eye tissues, and tear fluids are similar at different stages of AD progression. Ten miRNA candidates were systematically investigated in transgenic APP-PS1 mice, noncarrier siblings, and C57BL/6J wild-type controls at young and old ages. Relative expression levels of tested miRNAs revealed a similar pattern in both APP-PS1 mice and noncarrier siblings when compared with age- and sex-matched wild-type controls. However, the differences seen in expression levels between APP-PS1 mice and noncarrier siblings could possibly have resulted from underlying molecular etiology of AD. Importantly, miRNAs associated with amyloid beta (Aβ) production (-101a, -15a, and -342) and proinflammation (-125b, -146a, and -34a) showed significant up-regulations in the tear fluids with disease progression, as tracked by cortical Aβ load and reactive astrogliosis. Overall, for the first time, the translational potential of up-regulated tear fluid miRNAs associated with AD pathogenesis was comprehensively demonstrated.

Parsimonious methodology for synthesis of silver and copper functionalized cellulose

Metal nanomaterials, such as silver and copper, are often incorporated into commercial textiles to take advantage of their Antibacterial and antiviral properties. The goal of this study was to identify the most parsimonious method for the synthesis of silver, copper, or silver/copper bimetallic treated textiles. To accomplish this eight different methods were employed to synthesize silver, copper, and silver/copper functionalized cotton batting textiles. Using silver and copper nitrate as precursors, different reagents were used to initiate/catalyze the deposition of metal, including: (1) no additive, (2) sodium bicarbonate, (3) green tea, (4) sodium hydroxide, (5) ammonia, (6, 7) sodium hydroxide/ammonia at a 1:2 and 1:4 ratio, and (8) sodium borohydride. The use of sodium bicarbonate as a reagent to reduce silver onto cotton has not been used previously in literature and was compared to established methods. All synthesis methods were performed at 80 °C for one hour following textile addition to the solutions. The products were characterized by x-ray fluorescence (XRF) analysis for quantitative determination of the metal content and x-ray absorption near edge structure (XANES) analysis for silver and copper speciation on the textile. Scanning electron microscopy (SEM) with energy dispersive x-ray (EDX) and size distribution inductively coupled plasma mass spectrometry (ICP-MS) were used to further characterize the products of the sodium bicarbonate, sodium hydroxide, and sodium borohydride synthesis methods following ashing of the textile. For the silver treatment methods (1 mM Ag +), sodium bicarbonate and sodium hydroxide resulted in the highest amounts of silver on the textile (8900 mg Ag/kg textile and 7600 mg Ag/kg textile) and for copper treatment (1 mM Cu +) the sodium hydroxide and sodium hydroxide/ammonium hydroxide resulted in the highest amounts of copper on the textile (3800 mg Ag/kg textile and 2500 mg Ag/kg textile). Formation of copper oxide was dependent on the pH of the solution, with 4 mM ammonia and other high pH solutions resulting in majority of the copper on the textile existing as copper oxide, with smaller amounts of ionic-bound copper. The identified parsimonious methods will lend themselves to the efficient manufacturing of antibacterial and antiviral textiles, or the development of multifunctionalized smart textiles.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10570-023-05099-7.

Musicians and non-musicians show different preference profiles for single chords of varying harmonic complexity

The inverted U hypothesis in music predicts that listeners prefer intermediate levels of complexity. However, the shape of the liking response to harmonic complexity and the effect of musicianship remains unclear. Here, we tested whether the relationship between liking and harmonic complexity in single chords shows an inverted U shape and whether this U shape is different for musicians and non-musicians. We recorded these groups' liking ratings for four levels of harmonic complexity, indexed by their level of acoustic roughness, as well as several measures of inter-individual difference. Results showed that there is an inverted U-shaped relationship between harmonic complexity and liking in both musicians and non-musicians, but that the shape of the U is different for the two groups. Non-musicians' U is more left-skewed, with peak liking for low harmonic complexity, while musicians' U is more right-skewed, with highest ratings for medium and low complexity. Furthermore, musicians who showed greater liking for medium compared to low complexity chords reported higher levels of active musical engagement and higher levels of openness to experience. This suggests that a combination of practical musical experience and personality is reflected in musicians' inverted U-shaped preference response to harmonic complexity in chords.

Toward a data infrastructure for the Plant Cell Atlas

We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European Bioinformatics Institute has developed a Single Cell Expression Atlas, that currently houses several plant data sets. We discuss issues related to appropriate ontologies for describing a plant single cell experiment. We imagine how such an infrastructure will enable biologists and data scientists to glean new insights into plant biology in the coming decades, as long as such data are made accessible to the community in an open manner.

Central-place foraging poses variable constraints year-round in a neotropical migrant

BACKGROUND

"Central-place foragers" are constrained in their habitat selection and foraging range by the frequency with which they need to return to a central place. For example, chick-rearing songbirds that must feed their offspring hourly might be expected to have smaller foraging ranges compared to non-breeding songbirds that return nightly to a roost.

METHODS

We used GPS units to compare the foraging behaviour of an aerial insectivorous bird, the purple martin (Progne subis), during the breeding season in three regions across North America, as well as the non-breeding season in South America. Specifically, we tested foraging range size and habitat selection.

RESULTS

Foraging range did not vary among regions during breeding (14.0 ± 39.2 km²) and was larger during the nonbreeding period (8840 ± 8150 km²). Purple martins strongly preferred aquatic habitats to other available habitats year-round and in the Amazon commuted from night roosts in low productivity sediment-poor water, where risk of predation was probably low, to daytime foraging sites in productive sediment-rich water sites.

CONCLUSIONS

We provide the first estimates for foraging range size in purple martins and demonstrate foraging preference for aquatic habitats throughout two stages of the annual cycle. Understanding foraging constraints and habitat of aerial insectivores may help plan conservation actions throughout their annual cycle. Future research should quantify foraging behaviour during the post-breeding period and during migration.

Successive climate crises in the deep past drove the early evolution and radiation of reptiles

Climate change-induced mass extinctions provide unique opportunities to explore the impacts of global environmental disturbances on organismal evolution. However, their influence on terrestrial ecosystems remains poorly understood. Here, we provide a new time tree for the early evolution of reptiles and their closest relatives to reconstruct how the Permian-Triassic climatic crises shaped their long-term evolutionary trajectory. By combining rates of phenotypic evolution, mode of selection, body size, and global temperature data, we reveal an intimate association between reptile evolutionary dynamics and climate change in the deep past. We show that the origin and phenotypic radiation of reptiles was not solely driven by ecological opportunity following the end-Permian extinction as previously thought but also the result of multiple adaptive responses to climatic shifts spanning 57 million years.

Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada

Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in Canada in the first two waves of 2020 and early 2021. Maximum likelihood phylogenetic trees were used to infer viruses' geographic origins, enabling identification of 2263 (95% confidence interval: 2159-2366) introductions, including 680 (658-703) Canadian sublineages, which are international introductions resulting in sampled Canadian descendants, and 1582 (1501-1663) singletons, introductions with no sampled descendants. Of the sublineages seeded during the first wave, 49% (46-52%) originated from the USA and were primarily introduced into Quebec (39%) and Ontario (36%), while in the second wave, the USA was still the predominant source (43%), alongside a larger contribution from India (16%) and the UK (7%). Following implementation of restrictions on the entry of foreign nationals on 21 March 2020, importations declined from 58.5 (50.4-66.5) sublineages per week to 10.3-fold (8.3-15.0) lower within 4 weeks. Despite the drastic reduction in viral importations following travel restrictions, newly seeded sublineages in summer and fall 2020 contributed to the persistence of COVID-19 cases in the second wave, highlighting the importance of sustained interventions to reduce transmission. Importations rebounded further in November, bringing newly emergent variants of concern (VOCs). By the end of February 2021, there had been an estimated 30 (19-41) B.1.1.7 sublineages imported into Canada, which increasingly displaced previously circulating sublineages by the end of the second wave.Although viral importations are nearly inevitable when global prevalence is high, with fewer importations there are fewer opportunities for novel variants to spark outbreaks or outcompete previously circulating lineages.

Identification of quantitative trait loci associated with seed quality traits between Canadian and Ukrainian mega-environments using genome-wide association study

KEY MESSAGE

Identifying QTL associated with soybean seed quality traits from a diverse GWAS panel cultivated in Canadian and Ukrainian mega-environments may facilitate future cultivar development for foreign markets. Understanding the complex genetic basis of seed quality traits for soybean in the mega-environments (MEs) is critical for developing a marker-assisted selection program that will lead to breeding superior cultivars adapted to specific regions. This study aimed to analyze the accumulation of 14 soybean seed quality traits in Canadian ME and two seed quality traits in Ukrainian ME and identify associated ME specific quantitative trait loci (QTLSP) and ME universal QTL (QTLU) for protein and oil using a genome-wide association study (GWAS) panel consisting of 184 soybean genotypes. The panel was planted in three locations in Canada and two locations in Ukraine in 2018 and 2019. Genotype plus genotype-by-environment biplot analysis was conducted to assess the accumulation of individual seed compounds across different locations. The protein accumulation was high in the Canadian ME and low in the Ukrainian ME, whereas the oil concentration showed the opposite trends between the two MEs. No QTLU were identified across the MEs for protein and oil concentrations. In contrast, nine Canadian QTLSP for protein were identified on various chromosomes, which were co-located with QTL controlling other traits identified in the Canadian ME. The lack of common QTLU for protein and oil suggests that it may be necessary to use QTLSP associated with these traits separately for the Canadian and Ukrainian ME. Additional Ukrainian data for seed compounds other than oil and protein are required to identify novel QTLSP and QTLU for such traits for the individual or combined Canadian and Ukrainian MEs.

Sufficient principal component regression for pattern discovery in transcriptomic data

Motivation

Methods for the global measurement of transcript abundance such as microarrays and RNA-Seq generate datasets in which the number of measured features far exceeds the number of observations. Extracting biologically meaningful and experimentally tractable insights from such data therefore requires high-dimensional prediction. Existing sparse linear approaches to this challenge have been stunningly successful, but some important issues remain. These methods can fail to select the correct features, predict poorly relative to non-sparse alternatives or ignore any unknown grouping structures for the features.

Results

We propose a method called SuffPCR that yields improved predictions in high-dimensional tasks including regression and classification, especially in the typical context of omics with correlated features. SuffPCR first estimates sparse principal components and then estimates a linear model on the recovered subspace. Because the estimated subspace is sparse in the features, the resulting predictions will depend on only a small subset of genes. SuffPCR works well on a variety of simulated and experimental transcriptomic data, performing nearly optimally when the model assumptions are satisfied. We also demonstrate near-optimal theoretical guarantees.

Availability and implementation

Code and raw data are freely available at https://github.com/dajmcdon/suffpcr. Package documentation may be viewed at https://dajmcdon.github.io/suffpcr.

Contact

daniel@stat.ubc.ca.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Implication of synaptotagmins 4 and 7 in activity-dependent somatodendritic dopamine release in the ventral midbrain

Dopamine (DA) neurons can release DA not just from axon terminals, but also from their somatodendritic (STD) compartment through a mechanism that is still incompletely understood. Using voltammetry in mouse mesencephalic brain slices, we find that STD DA release has low capacity and shows a calcium sensitivity that is comparable to that of axonal release. We find that the molecular mechanism of STD DA release differs from axonal release with regard to the implication of synaptotagmin (Syt) calcium sensors. While individual constitutive knockout of Syt4 or Syt7 is not sufficient to reduce STD DA release, the removal of both isoforms reduces this release by approximately 50%, leaving axonal release unimpaired. Our work unveils clear differences in the mechanisms of STD and axonal DA release.

Methane removal and the proportional reductions in surface temperature and ozone

Mitigating climate change requires a diverse portfolio of technologies and approaches, including negative emissions or removal of greenhouse gases. Previous literature focuses primarily on carbon dioxide removal, but methane removal may be an important complement to future efforts. Methane removal has at least two key benefits: reducing temperature more rapidly than carbon dioxide removal and improving air quality by reducing surface ozone concentration. While some removal technologies are being developed, modelling of their impacts is limited. Here, we conduct the first simulations using a methane emissions-driven Earth System Model to quantify the climate and air quality co-benefits of methane removal, including different rates and timings of removal. We define a novel metric, the effective cumulative removal, and use it to show that each effective petagram of methane removed causes a mean global surface temperature reduction of 0.21 ± 0.04°C and a mean global surface ozone reduction of 1.0 ± 0.2 parts per billion. Our results demonstrate the effectiveness of methane removal in delaying warming thresholds and reducing peak temperatures, and also allow for direct comparisons between the impacts of methane and carbon dioxide removal that could guide future research and climate policy. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 1)'.

Rhythm and timing as vulnerabilities in neurodevelopmental disorders

Millions of children are impacted by neurodevelopmental disorders (NDDs), which unfold early in life, have varying genetic etiologies and can involve a variety of specific or generalized impairments in social, cognitive and motor functioning requiring potentially lifelong specialized supports. While specific disorders vary in their domain of primary deficit (e.g. autism spectrum disorder (social), attention-deficit/hyperactivity disorder (attention), developmental coordination disorder (motor) and developmental language disorder (language)), comorbidities between NDDs are common. Intriguingly, many NDDs are associated with difficulties in skills related to rhythm, timing and synchrony though specific profiles of rhythm/timing impairments vary across disorders. Impairments in rhythm/timing may instantiate vulnerabilities for a variety of NDDs and may contribute to both the primary symptoms of each disorder as well as the high levels of comorbidities across disorders. Drawing upon genetic, neural, behavioural and interpersonal constructs across disorders, we consider how disrupted rhythm and timing skills early in life may contribute to atypical developmental cascades that involve overlapping symptoms within the context of a disorder's primary deficits. Consideration of the developmental context, as well as common and unique aspects of the phenotypes of different NDDs, will inform experimental designs to test this hypothesis including via potential mechanistic intervention approaches. This article is part of the theme issue 'Synchrony and rhythm interaction: from the brain to behavioural ecology'.

Enhanced medium-range order in vapor-deposited germania glasses at elevated temperatures

Glasses are nonequilibrium solids with properties highly dependent on their method of preparation. In vapor-deposited molecular glasses, structural organization could be readily tuned with deposition rate and substrate temperature. Here, we show that the atomic arrangement of strong network-forming GeO₂ glass is modified at medium range (<2 nm) through vapor deposition at elevated temperatures. Raman spectral signatures distinctively show that the population of six-membered GeO₄ rings increases at elevated substrate temperatures. Deposition near the glass transition temperature is more efficient than postgrowth annealing in modifying atomic structure at medium range. The enhanced medium-range organization correlates with reduction of the room temperature internal friction. Identifying the microscopic origin of room temperature internal friction in amorphous oxides is paramount to design the next-generation interference coatings for mirrors of the end test masses of gravitational wave interferometers, in which the room temperature internal friction is a main source of noise limiting their sensitivity.

Biosynthesis of the Novel Endogenous 15-Lipoxygenase Metabolites N-13-Hydroxy-octodecadienoyl-ethanolamine and 13-Hydroxy-octodecadienoyl-glycerol by Human Neutrophils and Eosinophils

The endocannabinoids 2-arachidonoyl-glycerol and N-arachidonoyl-ethanolamine are lipids regulating many physiological processes, notably inflammation. Endocannabinoid hydrolysis inhibitors are now being investigated as potential anti-inflammatory agents. In addition to 2-arachidonoyl-glycerol and N-arachidonoyl-ethanolamine, the endocannabinoidome also includes other monoacylglycerols and N-acyl-ethanolamines such as 1-linoleoyl-glycerol (1-LG) and N-linoleoyl-ethanolamine (LEA). By increasing monoacylglycerols and/or N-acyl-ethanolamine levels, endocannabinoid hydrolysis inhibitors will likely increase the levels of their metabolites. Herein, we investigated whether 1-LG and LEA were substrates for the 15-lipoxygenase pathway, given that both possess a 1Z,4Z-pentadiene motif, near their omega end. We thus assessed how human eosinophils and neutrophils biosynthesized the 15-lipoxygenase metabolites of 1-LG and LEA. Linoleic acid (LA), a well-documented substrate of 15-lipoxygenases, was used as positive control. N-13-hydroxy-octodecadienoyl-ethanolamine (13-HODE-EA) and 13-hydroxy-octodecadienoyl-glycerol (13-HODE-G), the 15-lipoxygenase metabolites of LEA and 1-LG, were synthesized using Novozym 435 and soybean lipoxygenase. Eosinophils, which express the 15-lipoxygenase-1, metabolized LA, 1-LG, and LEA into their 13-hydroxy derivatives. This was almost complete after five minutes. Substrate preference of eosinophils was LA > LEA > 1-LG in presence of 13-HODE-G hydrolysis inhibition with methyl-arachidonoyl-fluorophosphonate. Human neutrophils also metabolized LA, 1-LG, and LEA into their 13-hydroxy derivatives. This was maximal after 15-30 s. Substrate preference was LA ≫ 1-LG > LEA. Importantly, 13-HODE-G was found in humans and mouse tissue samples. In conclusion, our data show that human eosinophils and neutrophils metabolize 1-LG and LEA into the novel endogenous 15-lipoxygenase metabolites 13-HODE-G and 13-HODE-EA. The full biological importance of 13-HODE-G and 13-HODE-EA remains to be explored.

In Situ Collection of Nanoparticles during Femtosecond Laser Machining in Air

Nanoparticles generated during laser material processing are often seen as annoying side products, yet they might find useful application upon proper collection. We present a parametric study to identify the dominant factors in nanoparticle removal and collection with the goal of establishing an in situ removal method during femtosecond laser machining. Several target materials of different electrical resistivity, such as Cu, Ti, and Si were laser machined at a relatively high laser fluence. Machining was performed under three different charge conditions, i.e., machining without an externally applied charge (alike atmospheric pulsed laser deposition (PLD)) was compared to machining with a floating potential and with an applied field. Thereby, we investigated the influence of three different charge conditions on the behavior of laser-generated nanoparticles, in particular considering plume deflection, nanoparticle accumulation on a collector plate and their redeposition onto the target. We found that both strategies, machining under a floating potential or under an applied field, were effective for collecting laser-generated nanoparticles. The applied field condition led to the strongest confinement of the nanoparticle plume and tightest resulting nanoparticle collection pattern. Raster-scanning direction was found to influence the nanoparticle collection pattern and ablation depth. However, the laser-processed target surface remained unaffected by the chosen nanoparticle collection strategy. We conclude that machining under a floating potential or an applied field is a promising setup for removing and collecting nanoparticles during the machining process, and thus provides an outlook to circular waste-free laser process design.

Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus)

Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24-35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.

Identification of ancestry proportions in admixed groups across the Americas using clinical pharmacogenomic SNP panels

We evaluated the performance of three PGx panels to estimate biogeographical ancestry: the DMET panel, and the VIP and Preemptive PGx panels described in the literature. Our analysis indicate that the three panels capture quite well the individual variation in admixture proportions observed in recently admixed populations throughout the Americas, with the Preemptive PGx and DMET panels performing better than the VIP panel. We show that these panels provide reliable information about biogeographic ancestry and can be used to guide the implementation of PGx clinical decision-support (CDS) tools. We also report that using these panels it is possible to control for the effects of population stratification in association studies in recently admixed populations, as exemplified with a warfarin dosing GWA study in a sample from Brazil.

Fractal structures arising from interfacial instabilities in bio-oil atomization

The intriguing multi-scale fractal patterns ubiquitously observed in nature similarly emerge as fascinating structures in two-phase fluid flows of bio-oil breakup and atomization processes. High-resolution microscopy of the two-phase flows under 15 flow conditions (cases of different flow rates of the liquid and co-flowing air streams as well as different degrees of liquid preheating) reveal that the geometrical complexities evolve under the competing/combined action of the instability mechanisms such as Kelvin-Helmholtz, Rayleigh-Taylor and Rayleigh-Plateau leading into the transition from break-up to atomization. A thorough analysis of the higher order moments of statistics evaluated based on the probability density functions from 15,000 fractal dimension samples suggest that a single-value analysis is not sufficient to describe the complex reshaping mechanisms in two-phase flows. Consistently positive skewness of the statistics reveal the role of abrupt two-phase mechanisms such as liquid column rupture, ligament disintegration, liquid sheet bursting and droplet distortions in a hierarchical geometrical entanglement. Further, large kurtosis values at increased flow inertia are found associated with turbulence-induced intermittent geometrical reshaping. Interestingly, the proposed power-law correlation reveals that the global droplet size obtained from laser-diffraction measurements declines as the two-phase geometrical complexity increases.

Quantitative UV-C dose validation with photochromic indicators for informed N95 emergency decontamination

With COVID-19 N95 shortages, frontline medical personnel are forced to reuse this disposable-but sophisticated-multilayer respirator. Widely used to decontaminate nonporous surfaces, UV-C light has demonstrated germicidal efficacy on porous, non-planar N95 respirators when all surfaces receive ≥1.0 J/cm2 dose. Of utmost importance across disciplines, translation of empirical evidence to implementation relies upon UV-C measurements frequently confounded by radiometer complexities. To enable rigorous on-respirator measurements, we introduce a photochromic indicator dose quantification technique for: (1) UV-C treatment design and (2) in-process UV-C dose validation. While addressing outstanding indicator limitations of qualitative readout and insufficient dynamic range, our methodology establishes that color-changing dosimetry can achieve the necessary accuracy (>90%), uncertainty (<10%), and UV-C specificity (>95%) required for UV-C dose measurements. In a measurement infeasible with radiometers, we observe a striking ~20× dose variation over N95s within one decontamination system. Furthermore, we adapt consumer electronics for accessible quantitative readout and use optical attenuators to extend indicator dynamic range >10× to quantify doses relevant for N95 decontamination. By transforming photochromic indicators into quantitative dosimeters, we illuminate critical considerations for both photochromic indicators themselves and UV-C decontamination processes.

Identification of Escherichia coli Host Genes That Influence the Bacteriophage Lambda (λ) T4rII Exclusion (Rex) Phenotype

The T4rII exclusion (Rex) phenotype is the inability of T4rII mutant bacteriophage to propagate in hosts (Escherichia coli) lysogenized by bacteriophage lambda (λ). The Rex phenotype, triggered by T4rII infection of a rex+ λ lysogen, results in rapid membrane depolarization imposing a harsh cellular environment that resembles stationary phase. Rex "activation" has been proposed as an altruistic cell death system to protect the λ prophage and its host from T4rII superinfection. Although well studied for over 60 years, the mechanism behind Rex still remains unclear. We have identified key nonessential genes involved in this enigmatic exclusion system by examining T4rII infection across a collection of rex+ single-gene knockouts. We further developed a system for rapid, one-step isolation of host mutations that could attenuate/abrogate the Rex phenotype. For the first time, we identified host mutations that influence Rex activity and rex+ host sensitivity to T4rII infection. Among others, notable genes include tolA, ompA, ompF, ompW, ompX, ompT, lpp, mglC, and rpoS They are critical players in cellular osmotic balance and are part of the stationary phase and/or membrane distress regulons. Based on these findings, we propose a new model that connects Rex to the σS, σE regulons and key membrane proteins.

Personality affects dynamics of an experimental pathogen in little brown bats

Host behaviour can affect host-pathogen dynamics and theory predicts that certain individuals disproportionately infect conspecifics during an epidemic. Consistent individual differences in behaviour, or personality, could influence this variation with the most exploratory or sociable individuals most likely to spread pathogens. We quantified exploration and sociability in little brown bats (Myotis lucifugus) and then experimentally manipulated exposure to a proxy pathogen (i.e. ultraviolet (UV) fluorescent powder) to test two related hypotheses: (i) more sociable and more exploratory individuals would be more likely to transmit infections to other individuals, and (ii) more sociable and more exploratory individuals uninfected with an invading pathogen would be more likely to acquire infections. We captured 10 groups of 16 bats at a time and held each group in an outdoor flight tent equipped with roosting-boxes. We used hole-board and Y-maze tests to quantify exploration and sociability of each bat and randomly selected one individual from each group for 'infection' with non-toxic, UV fluorescent powder. Each group of 10 bats was released into the flight tent for 24 h, which represented an experimental infection trial. After 24 h, we removed bats from the trial, photographed each individual under UV light and quantified infection intensity from digital photographs. As predicted, the exploratory behaviour of the experimentally infected individual was positively correlated with infection intensity in their group-mates, while more exploratory females had higher pathogen acquisition. Our results highlight the potential influence of host personality and sex on pathogen dynamics in wildlife populations.

Submaximal exercise cardiac output is increased by 4 weeks of sprint interval training in young healthy males with low initial Q̇-V̇O2: Importance of cardiac response phenotype

Cardiovascular adaptations to exercise, particularly at the individual level, remain poorly understood. Previous group level research suggests the relationship between cardiac output and oxygen consumption (Q˙-V˙O2) is unaffected by training as submaximal Q˙ is unchanged. We recently identified substantial inter-individual variation in the exercise Q˙-V˙O2 relationship that was correlated to stroke volume (SV) as opposed to arterial oxygen content. Therefore we explored the effects of sprint interval training (SIT) on modulating Q˙-V˙O2 given an individual’s specific Q˙-V˙O2 relationship. 22 (21±2 yrs) healthy, recreationally active males participated in a 4-week SIT (8, 20 second sprints; 4x/week, 170% of the work rate at V˙O2 peak) study with progressive exercise tests (PET) until exhaustion. Cardiac output (Q˙ L/min; inert gas rebreathe, Finometer Modelflow™), oxygen consumption (V˙O2 L/min; breath-by-breath pulmonary gas exchange), quadriceps oxygenation (near infrared spectroscopy) and exercise tolerance (6–20; Borg Scale RPE) were measured throughout PET both before and after training. Data are mean Δ from bsl±SD. Higher Q˙ (HQ˙) and lower Q˙ (LQ˙) responders were identified post hoc (n = 8/group). SIT increased the Q˙-V˙O2 post-training in LQ˙ (3.8±0.2 vs. 4.7±0.2; P = 0.02) while HQ˙ was unaffected (5.8±0.1 vs. 5.3±0.6; P = 0.5). ΔQ˙ was elevated beyond 80 watts in LQ˙ due to a greater increase in SV (all P<0.04). Peak V˙O2 (ml/kg/min) was increased in LQ˙ (39.7±6.7 vs. 44.5±7.3; P = 0.015) and HQ˙ (47.2±4.4 vs. 52.4±6.0; P = 0.009) following SIT, with HQ˙ having a greater peak V˙O2 both pre (P = 0.02) and post (P = 0.03) training. Quadriceps muscle oxygenation and RPE were not different between groups (all P>0.1). In contrast to HQ˙, LQ˙ responders are capable of improving submaximal Q˙-V˙O2 in response to SIT via increased SV. However, the increased submaximal exercise Q˙ does not benefit exercising muscle oxygenation.

A type 2 diabetes disease module with a high collective influence for Cdk2 and PTPLAD1 is localized in endosomes

Despite the identification of many susceptibility genes our knowledge of the underlying mechanisms responsible for complex disease remains limited. Here, we identified a type 2 diabetes disease module in endosomes, and validate it for functional relevance on selected nodes. Using hepatic Golgi/endosomes fractions, we established a proteome of insulin receptor-containing endosomes that allowed the study of physical protein interaction networks on a type 2 diabetes background. The resulting collated network is formed by 313 nodes and 1147 edges with a topology organized around a few major hubs with Cdk2 displaying the highest collective influence. Overall, 88% of the nodes are associated with the type 2 diabetes genetic risk, including 101 new candidates. The Type 2 diabetes module is enriched with cytoskeleton and luminal acidification–dependent processes that are shared with secretion-related mechanisms. We identified new signaling pathways driven by Cdk2 and PTPLAD1 whose expression affects the association of the insulin receptor with TUBA, TUBB, the actin component ACTB and the endosomal sorting markers Rab5c and Rab11a. Therefore, the interactome of internalized insulin receptors reveals the presence of a type 2 diabetes disease module enriched in new layers of feedback loops required for insulin signaling, clearance and islet biology.

Detection and Characterization of Antibiotic-Resistant Bacteria Using Surface-Enhanced Raman Spectroscopy

This mini-review summarizes the most recent progress concerning the use of surface-enhanced Raman spectroscopy (SERS) for the detection and characterization of antibiotic-resistant bacteria. We first discussed the design and synthesis of various types of nanomaterials that can be used as the SERS-active substrates for biosensing trace levels of antibiotic-resistant bacteria. We then reviewed the tandem-SERS strategy of integrating a separation element/platform with SERS sensing to achieve the detection of antibiotic-resistant bacteria in the environmental, agri-food, and clinical samples. Finally, we demonstrated the application of using SERS to investigate bacterial antibiotic resistance and susceptibility as well as the working mechanism of antibiotics based on spectral fingerprinting of the whole cells.

Characterization of normative hand movements during two functional upper limb tasks

Background

Dexterous hand function is crucial for completing activities of daily living (ADLs), which typically require precise hand-object interactions. Kinematic analyses of hand trajectory, hand velocity, and grip aperture provide valuable mechanistic insights into task performance, but there is a need for standardized tasks representative of ADLs that are amenable to motion capture and show consistent performance in non-disabled individuals. Our objective was to develop two standardized functional upper limb tasks and to quantitatively characterize the kinematics of normative hand movement.

Methods

Twenty non-disabled participants were recruited to perform two tasks: the Pasta Box Task and Cup Transfer Task. A 12-camera motion capture system was used to collect kinematic data from which hand movement and grip aperture measures were calculated. Measures reported for reach-grasp and transport-release segments were hand distance travelled, hand trajectory variability, movement time, peak and percent-to-peak hand velocity, number of movement units, peak and percent-to-peak grip aperture, and percent-to-peak hand deceleration. A between-session repeatability analysis was conducted on 10 participants.

Results

Movement times were longer for transport-release compared to reach-grasp for every movement. Hand and grip aperture measures had low variability, with 55 out of 63 measures showing good repeatability (ICC > 0.75). Cross-body movements in the Pasta Box Task had longer movement times and reduced percent-to-peak hand velocity values. The Cup Transfer Task showed decoupling of peak grip aperture and peak hand deceleration for all movements. Movements requiring the clearing of an obstacle while transporting an object displayed a double velocity peak and typically a longer deceleration phase.

Discussion

Normative hand kinematics for two standardized functional tasks challenging various aspects of hand-object interactions important for ADLs showed excellent repeatability. The consistency in normative task performance across a variety of task demands shows promise as a potential outcome assessment for populations with upper limb impairment.

Lifetime occupational exposure to metals and welding fumes, and risk of glioma: a 7-country population-based case-control study

BACKGROUND

Brain tumor etiology is poorly understood. Based on their ability to pass through the blood-brain barrier, it has been hypothesized that exposure to metals may increase the risk of brain cancer. Results from the few epidemiological studies on this issue are limited and inconsistent.

METHODS

We investigated the relationship between glioma risk and occupational exposure to five metals - lead, cadmium, nickel, chromium and iron- as well as to welding fumes, using data from the seven-country INTEROCC study. A total of 1800 incident glioma cases and 5160 controls aged 30-69 years were included in the analysis. Lifetime occupational exposure to the agents was assessed using the INTEROCC JEM, a modified version of the Finnish job exposure matrix FINJEM.

RESULTS

In general, cases had a slightly higher prevalence of exposure to the various metals and welding fumes than did controls, with the prevalence among ever exposed ranging between 1.7 and 2.2% for cadmium to 10.2 and 13.6% for iron among controls and cases, respectively. However, in multivariable logistic regression analyses, there was no association between ever exposure to any of the agents and risk of glioma with odds ratios (95% confidence intervals) ranging from 0.8 (0.7-1.0) for lead to 1.1 (0.7-1.6) for cadmium. Results were consistent across models considering cumulative exposure or duration, as well as in all sensitivity analyses conducted.

CONCLUSIONS

Findings from this large-scale international study provide no evidence for an association between occupational exposure to any of the metals under scrutiny or welding fumes, and risk of glioma.

Handedness is a biomarker of variation in anal sex role behavior and Recalled Childhood Gender Nonconformity among gay men

Developmental theories of the biological basis of sexual orientation suggest that sexually differentiated psychological and behavioural traits should be linked with sexual orientation. Subgroups of gay men delineated by anal sex roles differ according to at least one such trait: gender expression. The present study assessed the hypothesis that handedness, a biologically determined sexually differentiated trait, corresponds to differences in subgroups of gay men based on anal sex role. Furthermore, it assessed whether handedness mediates the association between gender nonconformity and male sexual orientation. Straight and gay men (N = 333) completed the Edinburgh Inventory of Handedness and the Recalled Childhood Gender Nonconformity Scale. Gay men also completed measures of anal sex role preference. As in previous studies, gay men showed greater non-right-handedness and gender nonconformity than straight men. Also, among gay men, bottoms/versatiles (i.e., gay men who take a receptive anal sex role, or who take on both a receptive and insertive anal sex role) were more gender-nonconforming than tops (i.e., gay men who take an insertive anal sex role). In support of the hypothesis, bottoms/versatiles were more non-right-handed than tops and handedness mediated the male sexual orientation and anal sex role differences in Recalled Childhood Gender Nonconformity. Together, these findings suggest that developmental processes linked to handedness underpin variation among men in sexual orientation and gender nonconformity as well as variation among subgroups of gay men that are delineated by anal sex roles.

Cellular and neurochemical basis of sleep stages in the thalamocortical network

The link between the combined action of neuromodulators in the brain and global brain states remains a mystery. In this study, using biophysically realistic models of the thalamocortical network, we identified the critical intrinsic and synaptic mechanisms, associated with the putative action of acetylcholine (ACh), GABA and monoamines, which lead to transitions between primary brain vigilance states (waking, non-rapid eye movement sleep [NREM] and REM sleep) within an ultradian cycle. Using ECoG recordings from humans and LFP recordings from cats and mice, we found that during NREM sleep the power of spindle and delta oscillations is negatively correlated in humans and positively correlated in animal recordings. We explained this discrepancy by the differences in the relative level of ACh. Overall, our study revealed the critical intrinsic and synaptic mechanisms through which different neuromodulators acting in combination result in characteristic brain EEG rhythms and transitions between sleep stages.

A Lightweight Social Computing Approach to Emergency Management Policy Selection

In order to select effective policies for emergency management in a timely manner, this paper proposes an agile and lightweight social computing approach to facilitating policy selection, evaluation, and adjustment relative to emergency management in both quantitative and qualitative ways. The approach consists of three components represented as PZE: 1) (P) emergency management policy selecting; 2) (Z) modeling artificial societies with the zombie-city model (a general and formal artificial society model); and 3) (E) policy evaluation. The formal specification of the zombie-city model and rigorous expressions of scenarios enable rigorous description and formal reasoning of an artificial society. A feedback loop of this approach supports the iterative adjustment of emergency management policies and the creation of more effective policies. This approach is verified by applying it to a case of an infectious disease transmission with quantitative evaluations, qualitative reasoning and analysis, and iterative adjustments. Results indicate effective emergency management policies can be established with the approach in an iterative way. In contrast with existing research, our proposed approach offers the benefits of being simple, general, rapidly adaptive to changes, and low cost.

The Interleukin-17 Induced Activation and Increased Survival of Equine Neutrophils Is Insensitive to Glucocorticoids

Background

Glucocorticoids (GCs) are the most effective drugs for the treatment of human asthma. However, a subgroup of asthmatic patients with neutrophilic airway inflammation is insensitive to GCs. Interleukin-17 (IL-17), a cytokine upregulated in the airways of a subset of human asthmatic patients, contributes to the recruitment of neutrophils and induces a glucocorticoid resistance in human airway epithelial cells. We hypothesized that IL-17 similarly activates neutrophils and contributes to their persistence in the asthmatic airways in spite of glucocorticoid therapy.

Objective

To determine whether IL-17 directly activates neutrophils and whether this response is attenuated by GCs.

Methods

Neutrophils were isolated from the blood of horses and incubated in the presence of recombinant equine IL-17, LPS and dexamethasone. mRNA and protein expression of IL-17 receptors (IL-17RA/IL-17RC) were assessed by qPCR and immunoblot, respectively. Pro-inflammatory cytokine expression, cell viability and apoptosis were determined by qPCR, Trypan Blue exclusion test, and flow cytometry, respectively.

Results

Equine neutrophils express both IL-17RA and IL-17RC at the mRNA and protein levels. Neutrophil stimulation with IL-17 increases the mRNA expression of IL-8, which is not attenuated by dexamethasone (p = 0.409). Also, neutrophil viability is significantly increased (p<0.0001) by IL-17 in the presence of LPS when compared to LPS alone. Flow cytometry and light microscopy revealed that LPS-induced apoptosis is decreased by IL-17 (p = 0.02 and p = 0.006 respectively).

Conclusion

These results indicate that IL-17 directly activates equine neutrophils at 24 hours, and that the expression of IL-8 thus induced is not attenuated by GCs. Additionally, IL-17 increases neutrophil viability and decreases apoptosis. These findings suggest an important role of IL-17 in pulmonary persistence of neutrophils in the asthmatic airways.