PCAtest: testing the statistical significance of Principal Component Analysis in R

Divide (evenly) and conquer (quickly): Spatial exploration behaviors predict navigational learning and differ by sex

The ability to learn new environments is a foundational human skill, yet we know little about how exploration behaviors shape spatial learning. Here, we investigated the relationships between exploration behaviors and spatial memory in healthy young adults, and further related performance to other measures of individual differences. In the present study, 100 healthy young adults (ages 18-37) freely explored a maze in a virtual desktop environment to learn the locations of 9 objects. Participants then navigated from one object to another without feedback, and their accuracy and path efficiency were determined. Interestingly, participant accuracy ranged from near 0 % to 100 %. Correlations and principal component regression revealed that evenness of exploration (i.e., visiting all locations with a similar frequency) and how quickly all objects were found during exploration were related to performance. Indeed, differences in performance become apparent by the time participants found the 6th object (within the first 50 moves), emphasizing the importance of exploration quality over exploration quantity. Perspective taking ability and video game experience were also related to performance. Critically, we found no correlations between performance on matched pairs of active-passive exploration paths, suggesting that experiencing a "good" exploration path does not lead to better performance; instead, the path is more likely a reflection of the navigator's ability. Sex differences were observed, however, a serial mediation analysis revealed that even exploration had a greater explanatory effect on those sex differences compared to video game experience. Our results indicate that exploration behaviors predict navigational performance and highlight the importance of moment-to-moment behaviors exhibited during exploration and learning.

The genetic and environmental composition of socioeconomic status in Norway

Estimating the contributions of genetic and environmental factors is key to understanding differences in socioeconomic status (SES). However, the heritability of SES varies by measure, method, and context. Here, we estimate genetic and environmental sources of variance and commonality in the 'big four' SES indicators. We use high-quality administrative data on educational attainment, occupational prestige, income, and wealth, and employ four family-based and unrelated genotype-based heritability methods, all drawn from the same population-wide cohort of >170,000 Norwegians aged 35-45. By drawing subsamples from a consistent sample and using registry-based data, we reduce differences in estimates due to population characteristics and measurement error. Our results show that genetic variation consistently explains more for educational attainment and occupational prestige. Family-shared environmental contributions explained more for educational attainment and wealth. Our results highlight considerable common influences on the four SES indicators among genetic and shared environmental factors, but not among non-shared environmental factors. Overall, we show how the relative importance of genetic and environmental factors to SES differences in Norway varies by method and type of socioeconomic attainment. This study is a reliable source for comparing heritability methods, and for comparing SES indicators and their genetic and environmental commonality in a social-democratic welfare state.

Cryptic genetic variation in brain gene expression precedes the evolution of cannibalism in spadefoot toad tadpoles

The origins of novel behaviors are poorly understood, despite behavior's hypothesized roles in evolution. One model, "genetic accommodation," proposes that selection on ancestral phenotypic plasticity may precede the evolution of novel traits. A critical assumption of genetic accommodation is that ancestral lineages possess heritable genetic variation for trait plasticity that is revealed in novel environments, thereby providing the raw materials for subsequent refinement of the novel trait in derived lineages. Here, we use a combination of behavioral and RNA-seq approaches to test this assumption in the context of a novel tadpole behavior: predatory cannibalism. Cannibalism evolved in the spadefoot genus Spea, where an invertebrate diet induces a carnivorous tadpole morph capable of consuming live conspecific tadpoles. In contrast, closely related Scaphiopus tadpoles do not induce this carnivorous phenotype. Through species comparisons, we found that ancestral Spea likely expressed behavioral plasticity and harbored latent (i.e., "cryptic") genetic variation in brain gene expression plasticity associated with cannibalism-inducing cues. Further, we found that this cryptic genetic variation includes genes specifically associated with a dietary response and cannibalism in derived Spea. Our results suggest that novel behaviors, alongside novel morphologies, can evolve via the process of genetic accommodation. More generally, our results provide key evidence for the plausibility of genetic accommodation, revealing that cryptic genetic variation-the raw material for the evolution of novel traits-exists in natural populations at the level of gene expression.

Microbial metabolites associated in stool and left ventricle of heart failure patients revealed by meta-analysis

Heart Failure (HF) impacts approximately 64 million people globally. While overall incidence of HF is relatively stable across countries, the overall number of HF patients is increasing due to aging populations. Many articles examine the microbiome in HF, however, studies from humans have not been analyzed systematically. The aim of this meta-analysis is to bridge this gap by analyzing previously published data on human HF patients with untargeted metabolomics to understand whether microbially-mediated metabolites are consistently important for HF status. A systematic survey of the literature identified 708 articles discussing HF, the microbiome, and metabolomics. Of these, 82 were primary studies of HF patients, 61 studied human adults, 23 included an untargeted metabolomics measure, and 3 studies had data that was usable and publicly accessible. These studies include a GCMS study from stool, NMR of saliva and exhaled breath condensate, and LCMS from left ventricle of HF patients undergoing transplantation and unused donor hearts. Significant differences were observed from PCA between HF and controls for stool and left ventricle, but not saliva or EBC samples. OPLS-DA was conducted for stool and ventricle samples, and further revealed significant group differences. Univariate testing with FDR correction revealed 8 significant microbially-relevant metabolites (p < 0.005 after correction), most notably asparagine from left ventricle and 2-methylbutyryl carnitine from stool. Though there is much discussion of the microbiome in health outcomes in HF, there is limited research from human populations. Some microbial co-metabolites from both stool and heart were significantly associated with HF.

Microphysiological gut-on-chip enables extended in vitro development of Cryptosporidium hominis

Introduction

Cryptosporidium hominis is the dominant Cryptosporidium species infecting humans, but most advances in developing robust in vitro culturing platforms for Cryptosporidium have utilised C. parvum. Consequently, there is relatively little available information specific to the biology and life cycle of C. hominis. The present study utilised a pumpless and tubeless gut-on-chip to generate a physiologically relevant in vitro environment by applying a constant fluid shear stress of 0.02 dyn cm-2 to HCT-8 cells.

Methods

Gut-on-chips were fabricated using standard soft lithography. C. hominis oocysts isolated from human pathology samples were used to infect the human ileocecal colorectal adenocarcinoma (HCT-8) cell line under a constant fluid shear stress of 0.02 dyn cm-2. Parasite growth was assessed using a C. hominis-specific quantitative PCR, a Cryptosporidium genus-specific immunofluorescence assay, and scanning electron microscopy. Differences in the HCT-8 transcriptome with and without fluid shear stress, and the host-parasite interaction, were both assessed using bulk transcriptomics.

Results

Transcriptomic analysis of the HCT-8 cell line cultured within the gut-on-chip demonstrated a metabolic shift towards oxidative phosphorylation when compared to the same cell line cultured under static conditions. Extended C. hominis (subtype IdA15G1) cultures were sustained for up to 10 days within the gut-on-chip as shown by a C. hominis-specific qPCR and a Cryptosporidium genus-specific immunofluorescence assay, which demonstrated ~30-fold amplification in the gut-on-chip over the duration of the experiment. Scanning electron microscopy of infected monolayers identified trophozoites, meronts, merozoites, macrogamonts, microgamonts, and possible gamont-like stages at 48 h post-infection. The potential role of gamonts in the Cryptosporidium life cycle remains unclear and warrants further investigation. Transcriptomes of HCT-8 cells infected with C hominis revealed upregulation of biological processes associated with cell cycle regulation and cell signalling in C. hominis-infected cells under fluid shear stress compared to static culture.

Conclusions

These data demonstrate that bioengineered gut-on-chip models support extended C. hominis growth and can be used to interrogate responses of host cells to infection. Owing to its relative simplicity, the pumpless and tubeless gut-on-chip can be accessible to most laboratories with established HCT-8 infection models for Cryptosporidium culture.

White matter microstructure links with brain, bodily and genetic attributes in adolescence, mid- and late life

Advanced diffusion magnetic resonance imaging (dMRI) allows one to probe and assess brain white matter (WM) organisation and microstructure in vivo. Various dMRI models with different theoretical and practical assumptions have been developed, representing partly overlapping characteristics of the underlying brain biology with potentially complementary value in the cognitive and clinical neurosciences. To which degree the different dMRI metrics relate to clinically relevant geno- and phenotypes is still debated. Hence, we investigate how tract-based and whole WM skeleton parameters from different dMRI approaches associate with clinically relevant and white matter-related phenotypes (sex, age, pulse pressure (PP), body-mass-index (BMI), brain asymmetry) and genetic markers in the UK Biobank (UKB, n=52,140) and the Adolescent Brain Cognitive Development (ABCD) Study (n=5,844). In general, none of the imaging approaches could explain all examined phenotypes, though the approaches were overall similar in explaining variability of the examined phenotypes. Nevertheless, particular diffusion parameters of the used dMRI approaches stood out in explaining some important phenotypes known to correlate with general human health outcomes. A multi-compartment Bayesian dMRI approach provided the strongest WM associations with age, and together with diffusion tensor imaging, the largest accuracy for sex-classifications. We find a similar pattern of metric and tract-dependent asymmetries across datasets, with stronger asymmetries in ABCD data. The magnitude of WM associations with polygenic scores as well as PP depended more on the sample, and likely age, than dMRI metrics. However, kurtosis was most indicative of BMI and potentially of bipolar disorder polygenic scores. We conclude that WM microstructure is differentially associated with clinically relevant pheno- and genotypes at different points in life.

Paternity analysis reveals sexual selection on cognitive performance in mosquitofish

In many animal species, cognitive abilities are under strong natural selection because decisions about foraging, habitat choice and predator avoidance affect fecundity and survival. But how has sexual selection, which is usually stronger on males than females, shaped the evolution of cognitive abilities that influence success when competing for mates or fertilizations? We aimed to investigate potential links between individual differences in male cognitive performance to variation in paternity arising solely from sexual selection. We therefore ran four standard cognitive assays to quantify five measures of cognitive performance by male mosquitofish (Gambusia holbrooki). Males were then assigned to 11 outdoor ponds where they could compete for females. Females mate many times, which leads to intense sperm competition and broods with mixed paternity. We genotyped 2,430 offspring to identify their fathers. Males with greater inhibitory control and better spatial learning abilities sired significantly more offspring, while males with better initial impulse control sired significantly fewer offspring. Associative and reversal learning did not predict a male's share of paternity. In sum, there was sexual selection on several, but not all, aspects of male cognitive performance.

Human disturbance and aridity influence biomass harvesting by leaf-cutting ants with impacts on nutrient dynamics in a Caatinga dry forest

Human activities have converted mature forests into mosaics of successional vegetation and chronically disturbed habitats, altering the patterns of population distribution, foraging ecology and thus, the flow of matter and nutrients through ecosystems. Although the effects of human disturbance are mostly harmful, hyperabundant native generalist species can emerge and increase their populations under disturbance, such as leaf-cutting ants (LCA), prominent herbivores that are considered ecosystem engineers. Here, we examined the population response of two LCA species of the Caatinga dry forest (Acromyrmex balzani and A. rugosus) to increasing levels of chronic anthropogenic disturbance and aridity, and assessed the foraging activity, biomass and nutrients harvested by their colonies. We found that colony densities increased at more disturbed habitats, varying considerably from 0 to 81 nests/ha, but aridity had no effect. The two species exhibited markedly different foraging activities (44.66 ± 28.76 and 294.6 ± 260.53 ants foraging daily), with the foraging rate increasing in more arid conditions for a species with smaller nests, but with no response to disturbance. Biomass consumption varied distinctly between species, ranging from 0 to 4.81 g (7.24 kg ha.year-1, in A. balzani) and from 5.6 to 74 g (174.39 kg ha.year-1, in A. rugosus). Furthermore, there was no effect of disturbance and aridity on the biomass harvesting of individual colonies. However, there was a considerable increase in the biomass harvested by the populations of colonies in the plots (i.e. accounting for colony densities). Moreover, the species A. balzani foraged upon more nutrient-rich material at more disturbed and arid habitats, with plant material containing higher concentrations of N, Ca, S, Sr, Fe and Mn, as well as a lower C:N ratio in these areas. Our results suggest that Acromyrmex species (1) can achieve larger populations in more disturbed habitats, though not directly associated with aridity, (2) operate as a key herbivore able to fit harvesting/diet through the entire environmental gradient and forage complementarily (monocot vs. dicot) and (3) reallocate expressive amount of forest biomass, resulting in temporary nutrient sinks with potential impacts on Caatinga resilience.

Forelimb reduction and digit loss were evolutionarily decoupled in oviraptorosaurian theropod dinosaurs

Theropod forelimbs exhibit wide morphological disparity, from the elongated wings of birds to the diminutive arms of T. rex. A wealth of work has sought to understand the evolution of bird flight via arm elongation, but despite widespread occurrences of forelimb reduction and digit loss throughout theropod dinosaurs, the evolutionary drivers behind these patterns are poorly understood. Previous studies demonstrate broad allometric trends that can account for some instances of forelimb reduction, but the repeated loss of digits, and their hypothesized link to forelimb shortening, has received less attention. Here, we evaluate evolutionary associations between digit loss and forelimb reduction in an iconic and data-rich theropod clade, Oviraptorosauria. Unexpectedly, we find that the evolution of digit III and the rest of the forelimb are decoupled. Support for different evolutionary models and a lower phylogenetic signal in digit III than the rest of the forelimb suggests these segments were subject to different evolutionary processes leading to independent morphological change. Oviraptorosaurs exhibit four distinct forelimb morphotypes, but these do not exactly correspond to patterns of dietary niche partitioning. Overall, forelimb evolution in oviraptorosaurs is more complex than anticipated, potentially as a result of an evolutionary radiation they underwent in the Late Cretaceous.

Assessing spatial and temporal patterns of benthic bacterial communities in response to different sediment conditions

Benthic bacterial communities are sensitive to habitat condition and present a fast response to environmental stressors, which makes them powerful ecological indicators of estuarine environments. The aim of this work is to study the spatial-temporal patterns of benthic bacterial communities in response to contrasting environmental conditions and assess their potential as ecological indicators of estuarine sediments. We characterized the diversity of bacterial communities in three contrasting sites on Sado Estuary (SW Coast, Portugal) and 4 sampling occasions, using 16S metagenomic approach. Based on previous studies, we hypothesized that diversity patterns of bacterial communities will be distinct between sites and across sampling occasions. Bacterial communities were more influenced by each site conditions than by temporal variations in the sediments. The main drivers of bacterial distribution were sediments' composition, organic contents, and hydrodynamic activity. This work provided an important baseline dataset from Sado estuary to explore bacterial networks concerning benthic ecosystem functioning.

Normal-Weight Offspring of Parents With Diet-Induced Obesity Display Altered Gene Expression Profiles

Objective

A Western diet is associated with obesity, and the link between parental and offsprings' obesity is unclear. Among mice, this study examined how parents' Western diets affect their male offspring's obesity risk. This study further explored whether early exposure to obesogenic diets from either parent influences offsprings' long-term weight gain.

Methods

Three-week-old C57BL6/NTac mice were assigned to a Western diet (WD) or control diet (CD), given from six to 14 weeks old. Adults from these dietary groups were then mated to create four breeding combinations: CD/CD, CD/WD, WD/CD, and WD/WD. Weight gain trajectories were studied in parents (P) and offspring (F1), along with gene expression in four tissues of male offspring. Non-linear mixed effect modeling and q-mode PCA were used to assess the influence of sex, litter size, and parental diet on gene expression, before describing gene expression in more detail.

Results

Offsprings' weight gain was mainly influenced by sex and litter size, with no significant impact from parental diet. At the same time, gene expression differences among offspring, particularly between WD/WD and CD/CD offspring, were linked to genes associated with inflammation, stress response, and other obesity-relevant processes.

Conclusions

Obegenesic diet of two parents with obesity, rather than only one, likely alters the risks of metabolic disease in male mice even at normal weights.

Long-term impact of embryonic exposure to ethinylestradiol and clotrimazole on behavior and neuroplasticity in zebrafish (Danio rerio)

Estrogen receptors (ER) are widely expressed in the brain of many species and experimental results highlighted the role of estradiol in neuronal plasticity and behavior. Consequently, the brain is therefore a prime target for endocrine disrupting chemicals (EDCs) interacting with estrogen signaling. Very little is known about the late effects of early disruption of estrogen signaling by EDCs. We focused on: ethinylestradiol (EE2; ER agonist) and clotrimazole (inhibitor of key steroidogenesis enzymes, including aromatases). Zebrafish eleutheroembryos were exposed (0-5 days) and then raised normally until adulthood. Several behavioral tests were performed in adults, then cell proliferation and dopaminergic neurons were quantified in several brain regions using immunostaining. Overall, a developmental exposure to EDCs stimulates cell proliferation in the dorsal telencephalon. At environmentally-relevant concentrations, male fish exposed to EE2 exhibited increased activity levels and decreased social behavior, posing a potential risk to population balance and health.

Putting seedlings on the map: Trade-offs in demographic rates between ontogenetic size classes in five tropical forests

All species must partition resources among the processes that underly growth, survival, and reproduction. The resulting demographic trade-offs constrain the range of viable life-history strategies and are hypothesized to promote local coexistence. Tropical forests pose ideal systems to study demographic trade-offs as they have a high diversity of coexisting tree species whose life-history strategies tend to align along two orthogonal axes of variation: a growth-survival trade-off that separates species with fast growth from species with high survival and a stature-recruitment trade-off that separates species that achieve large stature from species with high recruitment. As these trade-offs have typically been explored for trees ≥1 cm dbh, it is unclear how species' growth and survival during earliest seedling stages are related to the trade-offs for trees ≥1 cm dbh. Here, we used principal components and correlation analyses to (1) determine the main demographic trade-offs among seed-to-seedling transition rates and growth and survival rates from the seedling to overstory size classes of 1188 tree species from large-scale forest dynamics plots in Panama, Puerto Rico, Ecuador, Taiwan, and Malaysia and (2) quantify the predictive power of maximum dbh, wood density, seed mass, and specific leaf area for species' position along these demographic trade-off gradients. In four out of five forests, the growth-survival trade-off was the most important demographic trade-off and encompassed growth and survival of both seedlings and trees ≥1 cm dbh. The second most important trade-off separated species with relatively fast growth and high survival at the seedling stage from species with relatively fast growth and high survival ≥1 cm dbh. The relationship between seed-to-seedling transition rates and these two trade-off aces differed between sites. All four traits were significant predictors for species' position along the two trade-off gradients, albeit with varying importance. We concluded that, after accounting for the species' position along the growth-survival trade-off, tree species tend to trade off growth and survival at the seedling with later life stages. This ontogenetic trade-off offers a mechanistic explanation for the stature-recruitment trade-off that constitutes an additional ontogenetic dimension of life-history variation in species-rich ecosystems.

Impact of foliar application of phyllosphere yeast strains combined with soil fertilizer application on rice growth and yield

BACKGROUND

The application of beneficial microbes in agriculture is gaining increasing attention as a means to reduce reliance on chemical fertilizers. This approach can potentially mitigate negative impacts on soil, animal, and human health, as well as decrease climate-changing factors. Among these microbes, yeast has been the least explored, particularly within the phyllosphere compartment. This study addresses this knowledge gap by investigating the potential of phyllosphere yeast to improve rice yield while reducing fertilizer dosage.

RESULTS

From fifty-two rice yeast phyllosphere isolates, we identified three yeast strains-Rhodotorula paludigena Y1, Pseudozyma sp. Y71, and Cryptococcus sp. Y72-that could thrive at 36 °C and possessed significant multifarious plant growth-promoting traits, enhancing rice root and shoot length upon seed inoculation. These three strains demonstrated favorable compatibility, leading to the creation of a yeast consortium. We assessed the combined effect of foliar application of this yeast consortium and individual strains with two distinct recommended doses of chemical fertilizers (RDCFs) (75 and 100%), as well as RDCFs alone (75 and 100%), in rice maintained in pot-culture and field experiments. The pot-culture experiment investigated the leaf microbial community, plant biochemicals, root and shoot length during the stem elongation, flowering, and dough phases, and yield-related parameters at harvest. The field experiment determined the actual yield. Integrated results from both experiments revealed that the yeast consortium with 75% RDCFs was more effective than the yeast consortium with 100% RDCFs, single strain applications with RDCFs (75 and 100%), and RDCFs alone (75 and 100%). Additionally, this treatment improved leaf metabolite levels compared to control rice plants.

CONCLUSIONS

Overall, a 25% reduction in soil chemical fertilizers combined with yeast consortium foliar application improved rice growth, biochemicals, and yield. This study also advances the field of phyllosphere yeast research in agriculture.

Adaptive trade-offs between vertebrate defence and insect predation drive Amazonian ant venom evolution

Stinging ants have diversified into various ecological niches, and selective pressures may have contributed to shape the composition of their venom. To explore the drivers underlying venom variation in ants, we sampled 15 South American rainforest species and recorded a range of traits, including ecology, morphology and venom bioactivities. Principal component analysis of both morphological and venom bioactivity traits reveals that stinging ants display two functional strategies where species have evolved towards either an exclusively offensive venom or a multi-functional venom. Additionally, phylogenetic comparative analysis indicates that venom function (predatory, defensive or both) and mandible morphology correlate with venom bioactivity and volume. Further analysis of the venom biochemistry of the 15 species revealed switches between cytotoxic and neurotoxic venom compositions among species. Our study supports an evolutionary trade-off between the ability of venom to deter vertebrate predators and to paralyse insect prey which are correlated with different venom compositions and life-history strategies among Formicidae.

Evaluating the spatiotemporal patterns of drought characteristics in a semi-arid region of Limpopo Province, South Africa

Drought is a complex phenomenon resulting from below-average rainfall and is characterized by frequency, duration, and severity, occurring at a regional scale with dire consequences, especially in semiarid environments. This study used the Reconnaissance Drought Index (RDI) to assess drought severity in two district municipalities in Limpopo Province. Rainfall and air temperature data from 12 stations covering 1970-2020 were obtained from the Agricultural Research Council. The calculation of RDI relies on the monthly accumulation ratio of total rainfall to potential evapotranspiration (PET). For this study, PET was estimated using the Hargreaves and Samani temperature-based approach. The RDI results showed a high spatial-temporal variation in drought characteristics over the study area. All stations experienced extreme drought conditions in different years, with the maximum drought severity (-3.40) occurring from 2002-2003 in the western parts of the study area, indicating extreme drought. Furthermore, the results revealed continuous drought conditions over various periods, including severe droughts between 1995 and 1998 and between 2014 and 2016, with the severity varying between mild and moderate drought conditions. The results reveal notable but nonuniform drought patterns as the climate evolves, with potential implications for water availability and livelihoods. The study's findings underscore the significance of adopting multidimensional approaches to drought assessment that encompass meteorological and hydrological factors to inform strategies for adaptive water management and policy formulation in the face of a changing climate.

Neurochemical organization of cortical proteinopathy and neurophysiology along the Alzheimer's disease continuum

INTRODUCTION

Despite parallel research indicating amyloid-β accumulation, alterations in cortical neurophysiological signaling, and multi-system neurotransmitter disruptions in Alzheimer's disease (AD), the relationships between these phenomena remains unclear.

METHODS

Using magnetoencephalography, positron emission tomography, and an atlas of 19 neurotransmitters, we studied the alignment between neurophysiological alterations, amyloid-β deposition, and the neurochemical gradients of the cortex.

RESULTS

In patients with mild cognitive impairment and AD, changes in cortical rhythms were topographically aligned with cholinergic, serotonergic, and dopaminergic systems. These alignments correlated with the severity of clinical impairments. Additionally, cortical amyloid-β plaques were preferentially deposited along neurochemical boundaries, influencing how neurophysiological alterations align with muscarinic acetylcholine receptors. Most of the amyloid-β-neurochemical and alpha-band neuro-physio-chemical alignments replicated in an independent dataset of individuals with asymptomatic amyloid-β accumulation.

DISCUSSION

Our findings demonstrate that AD pathology aligns topographically with the cortical distribution of chemical neuromodulator systems and scales with clinical severity, with implications for potential pharmacotherapeutic pathways.

HIGHLIGHTS

Changes in cortical rhythms in Alzheimer's are organized along neurochemical boundaries. The strength of these alignments is related to clinical symptom severity. Deposition of amyloid-β (Aβ) is aligned with similar neurotransmitter systems. Aβ deposition mediates the alignment of beta rhythms with cholinergic systems. Most alignments replicate in participants with pre-clinical Alzheimer's pathology.

Sources, bioaccessibility and health risk of heavy metal(loid)s in the particulate matter of urban areas

Exposure to heavy metal(loid)s in airborne particulate matter (PM) could lead to various adverse health effects. The study investigated the total contents and the bioaccessibility of PM-bound heavy metal(loid)s (Cr, Mn, Co, Ni, Cu, Zn, As, Cd, and Pb), identified their potential sources, and evaluated the associated health risk via inhalation in eight typical cities in China (Nanjing, Mianyang, Huangshi, Nanchang, Kunming, Xiamen, Guangzhou, and Wuzhishan). The results showed that PM-bound Cr (VI) and As of all eight cities exceeded the limits of World Health Organization. The bioaccessibility of PM-bound heavy metal(loid)s exhibited large variations, with their means following the order of Cd > Mn > Co > Ni > Cu > Cr > As > Zn > Pb. Traffic and industrial emissions were identified as primary sources in most urban areas. The emission sources have important effects on the bioaccessibility of PM-bound heavy metal(loid)s. In particular, atmospheric Cu has its bioaccessibility significantly correlated with the contributions from traffic emissions. The bioaccessibility-based health risk assessment obtained different results from those using total contents, showing that the non-carcinogenic risks posed by most metal(loid)s were acceptable except for As in Huangshi and Nanchang. These findings highlight the source dependence of bioaccessibility of heavy metal(loid)s in airborne PM, facilitate the identification of priority pollution sources and enhance effective risk-oriented source regulatory strategies in urban areas.

Decoding the inflammatory signature of the major depressive episode: insights from peripheral immunophenotyping in active and remitted condition, a case-control study

Depression is a prevalent and incapacitating condition with a significant impact on global morbidity and mortality. Although the immune system's role in its pathogenesis is increasingly recognized, there is a lack of comprehensive understanding regarding the involvement of innate and adaptive immune cells. To address this gap, we conducted a multicenter case-control study involving 121 participants matched for sex and age. These participants had either an active (or current) major depressive episode (MDE) (39 cases) or a remitted MDE (40 cases), including individuals with major depressive disorder or bipolar disorder. We compared these 79 patients to 42 healthy controls (HC), analyzing their immunological profiles. In blood samples, we determined the complete cell count and the monocyte subtypes and lymphocyte T-cell populations using flow cytometry. Additionally, we measured a panel of cytokines, chemokines, and neurotrophic factors in the plasma. Compared with HC, people endorsing a current MDE showed monocytosis (p = 0.001), increased high-sensitivity C-reactive protein (p = 0.002), and erythrocyte sedimentation rate (p = 0.003), and an altered proportion of specific monocyte subsets. CD4 lymphocytes presented increased median percentages of activation markers CD69+ (p = 0.007) and exhaustion markers PD1+ (p = 0.013) and LAG3+ (p = 0.014), as well as a higher frequency of CD4+CD25+FOXP3+ regulatory T cells (p = 0.003). Additionally, patients showed increased plasma levels of sTREM2 (p = 0.0089). These changes are more likely state markers, indicating the presence of an ongoing inflammatory response during an active MDE. The Random Forest model achieved remarkable classification accuracies of 83.8% for MDE vs. HC and 70% for differentiating active and remitted MDE. Interestingly, the cluster analysis identified three distinct immunological profiles among MDE patients. Cluster 1 has the highest number of leukocytes, mainly given by the increment in lymphocyte count and the lowest proinflammatory cytokine levels. Cluster 3 displayed the most robust inflammatory pattern, with high levels of TNFα, CX3CL1, IL-12p70, IL-17A, IL-23, and IL-33, associated with the highest level of IL-10, as well as β-NGF and the lowest level for BDNF. This profile is also associated with the highest absolute number and percentage of circulating monocytes and the lowest absolute number and percentage of circulating lymphocytes, denoting an active inflammatory process. Cluster 2 has some cardinal signs of more acute inflammation, such as elevated levels of CCL2 and increased levels of proinflammatory cytokines such as IL-1β, IFNγ, and CXCL8. Similarly, the absolute number of monocytes is closer to a HC value, as well as the percentage of lymphocytes, suggesting a possible initiation of the inflammatory process. The study provides new insights into the immune system's role in MDE, paving the ground for replication prospective studies targeting the development of diagnostic and prognostic tools and new therapeutic targets.

Less spatial exploration is associated with poorer spatial memory in midlife adults

Introduction

Despite its importance for navigation, very little is known about how the normal aging process affects spatial exploration behavior. We aimed to investigate: (1) how spatial exploration behavior may be altered early in the aging process, (2) the relationship between exploration behavior and subsequent spatial memory, and (3) whether exploration behavior can classify participants according to age.

Methods

Fifty healthy young (aged 18-28) and 87 healthy midlife adults (aged 43-61) freely explored a desktop virtual maze, learning the locations of nine target objects. Various exploration behaviors (object visits, distance traveled, turns made, etc.) were measured. In the test phase, participants navigated from one target object to another without feedback, and their wayfinding success (% correct trials) was measured.

Results

In the exploration phase, midlife adults exhibited less exploration overall compared to young adults, and prioritized learning target object locations over maze layout. In the test phase, midlife adults exhibited less wayfinding success when compared to the young adults. Furthermore, following principal components analysis (PCA), regression analyses indicated that both exploration quantity and quality components were associated with wayfinding success in the midlife group, but not the young adults. Finally, we could classify participants according to age with similar accuracy using either their exploration behavior or wayfinding success scores.

Discussion

Our results aid in the understanding of how aging impacts spatial exploration, and encourages future investigations into how pathological aging may affect spatial exploration behavior.

An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors

More than 500 kinases are implicated in the control of most cellular process in mammals, and deregulation of their activity is linked to cancer and inflammatory disorders. 80 clinical kinase inhibitors (CKIs) have been approved for clinical use and hundreds are in various stages of development. However, CKIs inhibit other kinases in addition to the intended target(s), causing both enhanced clinical effects and undesired side effects that are only partially predictable based on in vitro selectivity profiling. Here, we report an integrative approach grounded on the use of chromatin modifications as unbiased, information-rich readouts of the functional effects of CKIs on macrophage activation. This approach exceeded the performance of transcriptome-based approaches and allowed us to identify similarities and differences among CKIs with identical intended targets, to recognize novel CKI specificities and to pinpoint CKIs that may be repurposed to control inflammation, thus supporting the utility of this strategy to improve selection and use of CKIs in clinical settings.

Contrasting physiological strategies explain heterogeneous responses to severe drought conditions within local populations of a widespread conifer

Understanding how trees prioritize carbon gain at the cost of drought vulnerability under severe drought conditions is crucial for predicting which genetic groups and individuals will be resilient to future climate conditions. In this study, we investigated variations in growth, tree-ring anatomy as well as carbon and oxygen isotope ratios to assess the sensitivity and the xylem formation process in response to an episode of severe drought in 29 mature white spruce (Picea glauca [Moench] Voss) families grown in a common garden trial. During the drought episode, the majority of families displayed decreased growth and exhibited either sustained or increased intrinsic water-use efficiency (iWUE), which was largely influenced by reduced stomatal conductance as revealed by the dual carbon‑oxygen isotope approach. Different water-use strategies were detected within white spruce populations in response to drought conditions. Our results revealed intraspecific variation in the prevailing physiological mechanisms underlying drought response within and among populations of Picea glauca. The presence of different genetic groups reflecting diverse water-use strategies within this largely-distributed conifer is likely to lessen the negative effects of drought and decrease the overall forest ecosystems' sensitivity to it.

Towards establishing a fungal economics spectrum in soil saprobic fungi

Trait-based frameworks are promising tools to understand the functional consequences of community shifts in response to environmental change. The applicability of these tools to soil microbes is limited by a lack of functional trait data and a focus on categorical traits. To address this gap for an important group of soil microorganisms, we identify trade-offs underlying a fungal economics spectrum based on a large trait collection in 28 saprobic fungal isolates, derived from a common grassland soil and grown in culture plates. In this dataset, ecologically relevant trait variation is best captured by a three-dimensional fungal economics space. The primary explanatory axis represents a dense-fast continuum, resembling dominant life-history trade-offs in other taxa. A second significant axis reflects mycelial flexibility, and a third one carbon acquisition traits. All three axes correlate with traits involved in soil carbon cycling. Since stress tolerance and fundamental niche gradients are primarily related to the dense-fast continuum, traits of the 2nd (carbon-use efficiency) and especially the 3rd (decomposition) orthogonal axes are independent of tested environmental stressors. These findings suggest a fungal economics space which can now be tested at broader scales.

Creek systems in restored coastal wetlands: Morphological evolution and design implications

Saltmarsh restoration such as managed realignment (MR) projects often include excavation of simplified tidal creek networks to improve drainage and marsh functioning, but their design is based on limited evidence. This paper compares the morphological evolution of creek networks in current MR projects in the UK with creek networks in natural saltmarshes, in order to provide improved guidance. The evolution of creek networks was monitored for 2-20 years post-breach at 10 MR sites across the UK by semi-automatically extracting 12 morphological creek parameters from lidar. The rates of creek evolution in MR sites are linked to the initial tidal, morphological and sedimentological conditions using principal component analysis, then compared with power law relationships of morphological equilibrium defined from 13 mature natural saltmarshes. MR creeks evolved into larger, more complex, better distributed systems, with a total creek length and volume statistically similar to their natural counterparts. However, the creek volume remains poorly distributed, with a mean distance between creeks ranging from 33 to 101 m versus 5-15 m for natural mature saltmarshes. MR creeks are also clustered around the breach area, leaving the marsh interior poorly drained. MR creek network morphologies remain strongly influenced by the initial creek template, as evidenced by unnaturally straight creeks inherited from former drainage ditches. A combination of external conditions (i.e., tidal range, sediment concentration in the wider estuary) and local conditions (i.e., site elevation, topographical heterogeneity, soil compaction) controls how easily creeks can form within MR sites. This in turn determines the amount of engineering effort required to help achieve reference site conditions. The end goal of creek design is to create MR sites that closely resemble reference site conditions, however the final design is also likely to be affected by a range of practical factors (e.g. engineering/cost) unique to each site and project.

Alignments between cortical neurochemical systems, proteinopathy and neurophysiological alterations along the Alzheimer's disease continuum

Two neuropathological hallmarks of Alzheimer's disease (AD) are the accumulation of amyloid-β (Aβ) proteins and alterations in cortical neurophysiological signaling. Despite parallel research indicating disruption of multiple neurotransmitter systems in AD, it has been unclear whether these two phenomena are related to the neurochemical organization of the cortex. We leveraged task-free magnetoencephalography and positron emission tomography, with a cortical atlas of 19 neurotransmitters to study the alignment and interactions between alterations of neurophysiological signaling, Aβ deposition, and the neurochemical gradients of the human cortex. In patients with amnestic mild cognitive impairment (N = 18) and probable AD (N = 20), we found that changes in rhythmic, but not arrhythmic, cortical neurophysiological signaling relative to healthy controls (N = 20) are topographically aligned with cholinergic, serotonergic, and dopaminergic neurochemical systems. These neuro-physio-chemical alignments are related to the severity of cognitive and behavioral impairments. We also found that cortical Aβ plaques are preferentially deposited along neurochemical boundaries, and mediate how beta-band rhythmic cortical activity maps align with muscarinic acetylcholine receptors. Finally, we show in an independent dataset that many of these alignments manifest in the asymptomatic stages of cortical Aβ accumulation (N = 33; N = 71 healthy controls), particularly the Aβ-neurochemical alignments (57.1%) and neuro-physio-chemical alignments in the alpha frequency band (62.5%). Overall, the present study demonstrates that the expression of pathology in pre-clinical and clinical AD aligns topographically with the cortical distribution of chemical neuromodulator systems, scaling with clinical severity and with implications for potential pharmacotherapeutic pathways.

Determination of the geographical origin of chicken (breast and drumstick) using ICP-OES and ICP-MS: Chemometric analysis

This study aimed to develop a geographical origin discrimination analytical method for chicken breasts and drumsticks based on inductively coupled plasma (ICP). The sixty elements were set as variables, and the geographical origin discrimination analysis was conducted through chemometrics. In orthogonal partial least square discriminant analysis (OPLS-DA), twenty-three variable importance in projection (VIP) elements were selected in chicken breasts, and twenty-eight VIP elements were selected in drumsticks. The importance of the selected elements was displayed by the area under the curve (AUC) value of the receiver operating characteristic (ROC). Verification of OPLS-DA was performed through permutation test and good results were obtained. A heatmap was also used as a method for determining the geographical origin, and each top element discriminant classification was 100 % accurate, as determined through canonical discriminant analysis (CDA). This method shows potential as a food analysis tool and can accurately determine the geographic origin of chicken.

Morphological differentiation of peritumoral brain zone microglia

The Peritumoral Brain Zone (PBZ) contributes to Glioblastoma (GBM) relapse months after the resection of the original tumor, which is influenced by a variety of pathological factors. Among those, microglia are recognized as one of the main regulators of GBM progression and probably relapse. Although microglial morphology has been analyzed inside GBM and its immediate surroundings, it has not been objectively characterized throughout the PBZ. Thus, we aimed to perform a thorough characterization of microglial morphology in the PBZ and its likely differentiation not just from the tumor-associated microglia but from control tissue microglia. For this purpose, Sprague Dawley rats were intrastriatally implanted with C6 cells to induce a GBM formation. Gadolinium-based magnetic resonance imaging (MRI) was performed to locate the tumor and to define the PBZ (2 mm beyond the tumor border), thus delimitating the different regions of interest (ROIs: core tumoral zone and immediate interface; contralateral striatum as control). Brain slices were obtained and immunolabeled with the microglia marker Iba-1. Sixteen morphological parameters were measured for each cell, significative differences were found in all parameters when comparing the four ROIs. To determine if PBZ microglia could be morphologically differentiated from microglia in other ROIs, hierarchical clustering analysis was performed, revealing that microglia can be separated into four morphologically differentiated clusters, each of them mostly integrated by cells sampled in each ROI. Furthermore, a classifier based on linear discriminant analysis, including only three morphological parameters, categorized microglial cells across the studied ROIs and showed a gradual transition between them. The robustness of this classification was assessed through principal component analysis with the remaining 13 morphological parameters, corroborating the obtained results. Thus, in this study we provided objective and quantitative evidence that PBZ microglia represent a differentiable microglial morphotype that could contribute to the recurrence of GBM in this area.

An evaluation of the antioxidant potential and in vitro enzyme inhibition profile of selected bryophytes from Northeast Anatolia (Türkiye)

Interest in the use of bryophytes in pharmaceutical, cosmetic, and food industrial applications is growing worldwide due to their secondary metabolites. In this study, n-hexane crude extracts and further fractions (aqueous, ethyl acetate and n-butanol) of aqueous ethanol (80:20, ethanol:H2O, v/v) were obtained from five different bryophytes (Pellia epiphylla, Conocephalum conicum, Porella platyphylla, Plagiomnium cuspidatum and Mnium spinulosum) collected from Trabzon, Türkiye. The total phenolic compound (TPC) content, antioxidant capacity (AC) and enzyme inhibition activity (acetylcholine esterase, butyrylcholine esterase, tyrosinase, α-amylase and α-glucosidase) of the extracts and fractions were species-specific and varied significantly between the crude extracts and fractions. Among the different bryophytes, Porella platyphylla and Pellia epiphylla in n-butanol and Plagiomnium cuspidatum and Mnium spinulosum in ethyl acetate fraction exhibited the highest TPC contents and AC values. The contents of phenolic acids liberated in free, ester and glycoside forms were also species-specific. p-Hydroxybenzoic acid (p-HBA) in free form in P. cuspidatum and P. platyphylla, p-coumaric acid (p-CoA) in ester form and m-hydroxybenzoic acid (m-HBA) in glycoside form in M. spinulosum were the major phenolic acids in the bryophytes. The n-hexane extracts of the bryophytes, in particular M. spinulosum, had IC50 values ​​almost 100 times lower than acarbose. This suggests that M. spinulosum in particular may represent a possible candidate for the production of new antidiabetic agents.

Shift in virus composition in honeybees (Apis mellifera) following worldwide invasion by the parasitic mite and virus vector Varroa destructor

Invasive vectors can induce dramatic changes in disease epidemiology. While viral emergence following geographical range expansion of a vector is well known, the influence a vector can have at the level of the host's pathobiome is less well understood. Taking advantage of the formerly heterogeneous spatial distribution of the ectoparasitic mite Varroa destructor that acts as potent virus vector among honeybees Apis mellifera, we investigated the impact of its recent global spread on the viral community of honeybees in a retrospective study of historical samples. We hypothesized that the vector has had an effect on the epidemiology of several bee viruses, potentially altering their transmissibility and/or virulence, and consequently their prevalence, abundance, or both. To test this, we quantified the prevalence and loads of 14 viruses from honeybee samples collected in mite-free and mite-infested populations in four independent geographical regions. The presence of the mite dramatically increased the prevalence and load of deformed wing virus, a cause of unsustainably high colony losses. In addition, several other viruses became more prevalent or were found at higher load in mite-infested areas, including viruses not known to be actively varroa-transmitted, but which may increase opportunistically in varroa-parasitized bees.

Estimating the number of principal components via Split-Half Eigenvector Matching (SHEM)

Estimating the number of principal components to retain for dimension reduction is a critical step in many applications of principal component analysis. Common methods may not be optimal, however. The current paper presents an alternative procedure that aims to recover the true number of principal components, in the sense of the number of independent vectors involved in the generation of the data.•Data are split into random halves repeatedly.•For each split, the eigenvectors in one half are compared to those in the other.•The split between high and low similarities is used to estimate the number of principal components. The method is a proof of principle that similarity over split-halves of the data may provide a useful approach to estimating the number of components in dimension reduction, or of similar dimensions in other models.

Quantitative relationships among high-throughput sequencing, cyanobacteria toxigenic genotype abundance and microcystin occurrence in bathing waters

Toxin-producing cyanobacteria pose significant threats to human and animal health if exposed during recreational activities in bathing waters. To better safeguard public health and reduce health risks during the bathing season, an effective monitoring and management strategy is required. Molecular tools used to monitor toxigenic cyanobacteria have been evaluated on the basis of the efficiency and applicability of the method used to (i) establish an early-warning monitoring strategy for EU bathing water sites using both targeted quantitative polymerase chain reaction (qPCR) and non-targeted high-throughput sequencing (HTS) genotype analysis and (ii) to compare the toxigenic potential of cyanobacteria with actual microcystin (MC) occurrence and concentrations. For this purpose, 16 bathing water sites were monitored according to the bathing water directive (BWD) of the European Union (EU) during the bathing season of the summer of 2020 in eastern Austria. The cyanobacterial community composition was analyzed through HTS and qPCR by targeting the microcystin synthetase B gene (mcyB), which indicates MC synthesis within the genera Microcystis and Planktothrix. Within the genus Microcystis, which was identified as the primary MC producer, the mcyB genotypes formed stable subpopulations that increased linearly in correlation with the total Microcystis population. Notably, the HTS cell equivalents assigned to Microcystis and Planktothrix correlated with the corresponding qPCR estimates of genotype abundance, which serves as a confirmation of the suitability of (semi)-quantitative sequencing through HTS. In addition to the elevated trophic state, reduced transparency, increasing water temperatures, as well as cyanobacterial HTS read numbers and Microcystis cell number equivalents per mL estimated through qPCR, were associated with positive MC samples. Therefore, in combination with the monitoring of standard environmental parameters, the use of HTS and qPCR techniques is considered highly useful to ensure the timely identification of health risks to recreational users, as mandated by the BWD.

A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from the Thai-Malay Peninsula and the independent evolution of cave ecomorphology on opposite sides of the Gulf of Thailand

An integrative taxonomic analysis recovers a distinctive new species of the gekkonid genus Cyrtodactylus Gray, 1827 from Satun Province in extreme southern Thailand as the sister species to the Cyrtodactylus intermedius group of southern Indochina, approximately 600 km to the northeast across the Gulf of Thailand. Based on 1449 base pairs of the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and its flanking tRNAs, the new species, C. disjunctus sp. nov., bears a pairwise sequence divergence from the mean divergences of the intermedius group species ranging from 17.923.6%. Three different principal component analyses (PCA) and a multiple factor analysis (MFA) recover C. disjunctus sp. nov. as a highly distinctive karst cave-adapted species based on morphology and color pattern. Its sister species relationship to the intermedius groupto which it is added herefurther underscores a growing body of analyses that have recovered a trans-Gulf of Thailand connection across the submerged Sunda Shelf between the southern Thai-Malay Peninsula and southern Indochina. Fragmented karstic archipelagos stretching across Indochina have served as foci for the independent evolution of nearly 25% of the species of Cyrtodactylus. The description of C. disjunctus sp. nov. continues to highlight the fact that karstic habitats support an ever-increasing number of threatened site-specific endemics that compose much of the reptile diversity of many Asian nations but, as of yet, most of these landscapes have no legal protection.

Two new karst-adapted species in the Cyrtodactyluspulchellus group (Reptilia, Gekkonidae) from southern Thailand

The exploration of unsurveyed areas in southern Thailand discovered two new karst-adapted species, Cyrtodactylussungaiupesp. nov. and Cyrtodactyluswangkhramensissp. nov., from Thung Wa and La-ngu Districts, Satun Province, respectively. These new species are members of the C.pulchellus group that occur along the Thai-Malay Peninsula. The new species can be distinguished from all other congeners by their key morphological characters and genetic divergence. Morphologically, Cyrtodactylussungaiupesp. nov. and Cyrtodactyluswangkhramensissp. nov. can be diagnosed from other members by having a combination of differences in body size; degree of dorsal tuberculation; absence of tubercles on ventral surfaces; number of ventral scales, paravertebral tubercles and femoroprecloacal pores in males only; deep precloacal groove only in males; absence of a scattered pattern of white dorsal tubercles; number of dark body bands; and the extent of caudal tubercles on an original tail. Although the two species are sister taxa and have nearly identical morphologies, they are considered to be different species, based on a relatively high uncorrected pairwise genetic divergence of the mitochondrial ND2 gene (6.59-6.89%), statistically significant univariate and multivariate morphological differences (PERMANOVA and ANOVA) and diagnostic characteristics of caudal tuberculation on the original tail. Moreover, Cyrtodactylussungaiupesp. nov. and Cyrtodactyluswangkhramensissp. nov. are currently restricted to their karstic type localities which may serve as a geographic barrier to dispersal and gene flow.

Spatial configuration of patches with different ecological maturity: Implications for service supply at the landscape level

Traditional agrarian landscapes have been managed over centuries to provide complementary ecosystem services (provision and regulation) in a sustainable manner. The spatial arrangement of patches in these landscapes seems to connect ecosystems of different maturity that complement each other functionally, through exchanges of matter and energy, optimizing provisioning services supply while minimizing management effort (e.g., water and fertilizers supply). In this study we explored the implications that the spatial pattern of patches with different degrees of maturity (grasslands, scrublands, and oak groves) may have on service provision within an agrarian multifunctional landscape. To assess the ecological maturity of the evaluated patches, we sampled biotic and abiotic variables related to compositional and structural complexity of the plant community, as well as soil characteristics. Our results show that less mature ecosystems (grasslands) adjacent to the most mature ones (oak groves) had a higher structural complexity of the plant community than those adjacent to ecosystems with intermediate maturity (scrublands), which could be associated to a higher resource flow from oak groves. Furthermore, the relative topographic position of oak groves and scrublands influenced the ecological maturity of grasslands. Grasslands topographically located below oak groves and scrublands had more herbaceous biomass and fertile soils than grasslands located above them, which suggests that resource flow is accelerated by gravitational forces. This indicates that grassland patches can have higher human exploitation rates when located below the more mature patches, which can increase agricultural provisioning services (e.g., biomass extraction). Overall, our findings suggest that agrarian provisioning services can be improved by spatially arranging the patches that provide such services (e.g., grasslands) in the landscape, as well as those patches responsible for ecosystem regulating services, such as water flow regulation and material accumulation (e.g., forests).

Comprehensive Analysis to Reveal Amino Acid Metabolism-Associated Genes as a Prognostic Index in Gastric Cancer

Background

Amino acid metabolism (AAM) is related to tumor growth, prognosis, and therapeutic response. Tumor cells use more amino acids with less synthetic energy than normal cells for rapid proliferation. However, the possible significance of AAM-related genes in the tumor microenvironment (TME) is poorly understood.

Methods

Gastric cancer (GC) patients were classified into molecular subtypes by consensus clustering analysis using AAMs genes. AAM pattern, transcriptional patterns, prognosis, and TME in distinct molecular subtypes were systematically investigated. AAM gene score was built by least absolute shrinkage and selection operator (Lasso) regression.

Results

The study revealed that copy number variation (CNV) changes were prevalent in selected AAM-related genes, and most of these genes exhibited a high frequency of CNV deletion. Three molecular subtypes (clusters A, B, and C) were developed based on 99 AAM genes, which cluster B had better prognosis outcome. We developed a scoring system (AAM score) based on 4 AAM gene expressions to measure the AAM patterns of each patient. Importantly, we constructed a survival probability prediction nomogram. The AAM score was substantially associated with the index of cancer stem cells and sensitivity to chemotherapy intervention.

Conclusion

Overall, we detected prognostic AAM features in GC patients, which may help define TME characteristics and explore more effective treatment approaches.

Unsupervised Machine Learning Driven Analysis of Verbatims of Treatment-Resistant Schizophrenia Patients Having Followed Avatar Therapy

(1) Background: The therapeutic mechanisms underlying psychotherapeutic interventions for individuals with treatment-resistant schizophrenia are mostly unknown. One of these treatment techniques is avatar therapy (AT), in which the patient engages in immersive sessions while interacting with an avatar representing their primary persistent auditory verbal hallucination. The aim of this study was to conduct an unsupervised machine-learning analysis of verbatims of treatment-resistant schizophrenia patients that have followed AT. The second aim of the study was to compare the data clusters obtained from the unsupervised machine-learning analysis with previously conducted qualitative analysis. (2) Methods: A k-means algorithm was performed over the immersive-session verbatims of 18 patients suffering from treatment-resistant schizophrenia who followed AT to cluster interactions of the avatar and the patient. Data were pre-processed using vectorization and data reduction. (3): Results: Three clusters of interactions were identified for the avatar's interactions whereas four clusters were identified for the patient's interactions. (4) Conclusion: This study was the first attempt to conduct unsupervised machine learning on AT and provided a quantitative insight into the inner interactions that take place during immersive sessions. The use of unsupervised machine learning could yield a better understanding of the type of interactions that take place in AT and their clinical implications.

Evidence for two morphologically cryptic species of Hysterolecitha Linton, 1910 (Trematoda: Lecithasteridae) infecting overlapping host ranges in Moreton Bay, Australia

Integration of morphological and molecular approaches to species delineation has become an essential part of digenean trematode taxonomy, particularly when delimiting cryptic species. Here, we use an integrated approach to distinguish and describe two morphologically cryptic species of Hysterolecitha Linton, 1910 (Trematoda: Lecithasteridae) from fishes of Moreton Bay, Queensland, Australia. Morphological analyses of Hysterolecitha specimens from six fish species demonstrated a complete overlap in morphometric data with no reliable differences in their gross morphological characters that suggested the presence of more than one species. Distinctions in ITS2 rDNA and cox1 mtDNA sequence data for corresponding specimens suggested the presence of two forms. A principal component analysis on an imputed dataset showed clear separation between the two forms. These two forms are partially separated on the basis of their host's identity. Therefore, we describe two morphologically cryptic species: Hysterolecitha melae n. sp. from three species of Abudefduf Forsskål and one species of Parma Günther (Pomacentridae), with the Bengal sergeant, Abudefduf bengalensis (Bloch), as the type-host; and Hysterolecitha phisoni n. sp. from species of Pomacentridae (including A. bengalensis), Pomatomidae and Siganidae, with the black rabbitfish, Siganus fuscescens (Houttuyn), as the type-host.

Structural and neurophysiological alterations in Parkinson's disease are aligned with cortical neurochemical systems

Parkinson's disease (PD) affects cortical structures and neurophysiology. How these deviations from normative variants relate to the neurochemical systems of the cortex in a manner corresponding to motor and cognitive symptoms is unknown. We measured cortical thickness and spectral neurophysiological alterations from structural magnetic resonance imaging and task-free magnetoencephalography in patients with idiopathic PD (NMEG = 79; NMRI = 65), contrasted with similar data from matched healthy controls (NMEG = 65; NMRI = 37). Using linear mixed-effects models and cortical atlases of 19 neurochemical systems, we found that the structural and neurophysiological alterations of PD align with several receptor and transporter systems (acetylcholine, serotonin, glutamate, and noradrenaline) albeit with different implications for motor and non-motor symptoms. Some neurophysiological alignments are protective of cognitive functions: the alignment of broadband power increases with acetylcholinergic systems is related to better attention function. However, neurochemical alignment with structural and other neurophysiological alterations is associated with motor and psychiatric impairments, respectively. Collectively, the present data advance understanding of the association between the nature of neurophysiological and structural cortical alterations in PD and the symptoms that are characteristic of the disease. They also demonstrate the value of a new nested atlas modeling approach to advance research on neurological and neuropsychiatric diseases.

An inclusive study of deleterious missense PAX9 variants using user-friendly tools reveals structural, functional alterations, as well as potential therapeutic targets

Mutations in the PAX9 are responsible for non-syndromic tooth agenesis in humans, although their structural and functional consequences on protein phenotype, stability, and posttranslational modifications (PTMs) have not yet been adequately investigated. This in silico study focuses on retrieving the six most deleterious mutations (L21P, R26W, R28P, G51S, I87F, and K91E) of PAX9 that has been linked to severe oligodontia. Several computational algorithm methods were used to determine the deleterious effects of PAX9 mutations. Analysis of gene ontology, protein interactions, and PTMs indicated significant functional changes caused by PAX9 mutations. The structural superimposition of the wild-type and mutant PAX9 variants revealed structural changes in locations that were present in the structures of all six variations. The conserved domain analysis revealed that the areas shared by all six variations contained unique sections that lacked DNA binding or protein-protein interaction sites, suggesting prospective drug target sites for functional restoration. The protein-protein interaction network showed KDM5B as PAX9's strongest interacting partner similar to MSX1. The PAX9 protein's structural conformations, compactness, stiffness, and function may all be impacted by changes, according to MD simulations. In addition, research on cell lines and animal models may be valuable in establishing their specific roles in functional annotations.

Decision Tree Ensembles Utilizing Multivariate Splits Are Effective at Investigating Beta Diversity in Medically Relevant 16S Amplicon Sequencing Data

Developing an understanding of how microbial communities vary across conditions is an important analytical step. We used 16S rRNA data isolated from human stool samples to investigate whether learned dissimilarities, such as those produced using unsupervised decision tree ensembles, can be used to improve the analysis of the composition of bacterial communities in patients suffering from Crohn's disease and adenomas/colorectal cancers. We also introduce a workflow capable of learning dissimilarities, projecting them into a lower dimensional space, and identifying features that impact the location of samples in the projections. For example, when used with the centered log ratio transformation, our new workflow (TreeOrdination) could identify differences in the microbial communities of Crohn's disease patients and healthy controls. Further investigation of our models elucidated the global impact amplicon sequence variants (ASVs) had on the locations of samples in the projected space and how each ASV impacted individual samples in this space. Furthermore, this approach can be used to integrate patient data easily into the model and results in models that generalize well to unseen data. Models employing multivariate splits can improve the analysis of complex high-throughput sequencing data sets because they are better able to learn about the underlying structure of the data set. IMPORTANCE There is an ever-increasing level of interest in accurately modeling and understanding the roles that commensal organisms play in human health and disease. We show that learned representations can be used to create informative ordinations. We also demonstrate that the application of modern model introspection algorithms can be used to investigate and quantify the impacts of taxa in these ordinations, and that the taxa identified by these approaches have been associated with immune-mediated inflammatory diseases and colorectal cancer.

Deciphering nitrous oxide emissions from tropical soils of different land uses

Tropical regions are hotspots of increasing greenhouse gas emissions associated with land-use change. Although many field studies have quantified soil fluxes of nitrous oxide (N₂O; a potent greenhouse gas) from various land uses, the driving mechanisms remain uncertain. Here, we used tropical soils of diverse land uses and actively manipulated the soil moisture (35%, 60%, and 95% water-filled pore space [WFPS]) and substrate supply (control, nitrate, and nitrate plus glucose) to investigate the responses of N₂O emissions with short-term incubations. We then identified key factors regulating N₂O emissions out of a series of soil physicochemical and biological factors and explored how these factors interacted to drive N₂O emissions. Land-use changes from primary forest to oil palm or Acacia plantation risks emitting more N₂O, whereas low emissions could be maintained by conversion to Macaranga forest or Imperata grassland; these laboratory observations were corroborated by a literature synthesis of field N₂O measurements across tropical regions. Soil redox potential (Eh) and labile organic nitrogen (LON; amino acid mixture, arginine, and urea) mineralization were among the factors with greatest influence on N₂O emissions. In contrast to common understandings, the control of WFPS over N₂O emissions was largely indirect, and acted through Eh. The mineralization of LON, particularly arginine, potentially played multiple roles in N₂O production (e.g., bottlenecks of nitrifier-denitrification or simultaneous nitrification-denitrification versus substrate competition for co-denitrification). Structural equation models suggest that soil-environmental factors of different levels (from distal including land use, soil moisture, and pH to proximal such as LON mineralization) drive N₂O emissions through cascading interactions. Overall, we show that, despite identical initial soil conditions, land conversion can substantially alter the N₂O emission potential. Also, collectively considering soil-environmental regulators and their interactions associated with land conversion is crucial to predict and design mitigation strategies for N₂O emissions from land-use change.

Application of data integration for rice bacterial strain selection by combining their osmotic stress response and plant growth-promoting traits

Agricultural application of plant-beneficial bacteria to improve crop yield and alleviate the stress caused by environmental conditions, pests, and pathogens is gaining popularity. However, before using these bacterial strains in plant experiments, their environmental stress responses and plant health improvement potential should be examined. In this study, we explored the applicability of three unsupervised machine learning-based data integration methods, including principal component analysis (PCA) of concatenated data, multiple co-inertia analysis (MCIA), and multiple kernel learning (MKL), to select osmotic stress-tolerant plant growth-promoting (PGP) bacterial strains isolated from the rice phyllosphere. The studied datasets consisted of direct and indirect PGP activity measurements and osmotic stress responses of eight bacterial strains previously isolated from the phyllosphere of drought-tolerant rice cultivar. The production of phytohormones, such as indole-acetic acid (IAA), gibberellic acid (GA), abscisic acid (ABA), and cytokinin, were used as direct PGP traits, whereas the production of hydrogen cyanide and siderophore and antagonistic activity against the foliar pathogens Pyricularia oryzae and Helminthosporium oryzae were evaluated as measures of indirect PGP activity. The strains were subjected to a range of osmotic stress levels by adding PEG 6000 (0, 11, 21, and 32.6%) to their growth medium. The results of the osmotic stress response experiments showed that all bacterial strains accumulated endogenous proline and glycine betaine (GB) and exhibited an increase in growth, when osmotic stress levels were increased to a specific degree, while the production of IAA and GA considerably decreased. The three applied data integration methods did not provide a similar grouping of the strains. Especially deviant was the ordination of microbial strains based on the PCA of concatenated data. However, all three data integration methods indicated that the strains Bacillus altitudinis PB46 and B. megaterium PB50 shared high similarity in PGP traits and osmotic stress response. Overall, our results indicate that data integration methods complement the single-table data analysis approach and improve the selection process for PGP microbial strains.

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes

We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait-trait variations of 11 genomic traits from ~18,000 sequenced genomes. The studied trait-trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an oligotrophic-copiotrophic axis. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from traits associated with resource availability. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. Genome size distributions differ across habitats and our findings therefore point to habitat dependent tradeoffs between resistance and resilience. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.