Interactions between U and V sex chromosomes during the life cycle of Ectocarpus

In many animals and flowering plants, sex determination occurs in the diploid phase of the life cycle with XX/XY or ZW/ZZ sex chromosomes. However, in early diverging plants and most macroalgae, sex is determined by female (U) or male (V) sex chromosomes in a haploid phase called the gametophyte. Once the U and V chromosomes unite at fertilization to produce a diploid sporophyte, sex determination no longer occurs, raising key questions about the fate of the U and V sex chromosomes in the sporophyte phase. Here, we investigate genetic and molecular interactions of the UV sex chromosomes in both the haploid and diploid phases of the brown alga Ectocarpus. We reveal extensive developmental regulation of sex chromosome genes across its life cycle and implicate the TALE-HD transcription factor OUROBOROS in suppressing sex determination in the diploid phase. Small RNAs may also play a role in the repression of a female sex-linked gene, and transition to the diploid sporophyte coincides with major reconfiguration of histone H3K79me2, suggesting a more intricate role for this histone mark in Ectocarpus development than previously appreciated.

KATANIN-mediated microtubule severing is required for MTOC organisation and function in Marchantia polymorpha

Microtubule organising centres (MTOCs) are sites of localised microtubule nucleation in eukaryotic cells. Regulation of microtubule dynamics often involves KATANIN (KTN): a microtubule severing enzyme that cuts microtubules to generate new negative ends, leading to catastrophic depolymerisation. In Arabidopsis thaliana, KTN is required for the organisation of microtubules in the cell cortex, preprophase band, mitotic spindle and phragmoplast. However, as angiosperms lack MTOCs, the role of KTN in MTOC formation has yet to be studied in plants. Two unique MTOCs - the polar organisers - form on opposing sides of the preprophase nucleus in liverworts. Here, we show that KTN-mediated microtubule depolymerisation regulates the number and organisation of polar organisers formed in Marchantia polymorpha. Mpktn mutants that lacked KTN function had supernumerary disorganised polar organisers compared with wild type. This was in addition to defects in the microtubule organisation in the cell cortex, preprophase band, mitotic spindle and phragmoplast. These data are consistent with the hypothesis that KTN-mediated microtubule dynamics are required for the de novo formation of MTOCs, a previously unreported function in plants.

Spectral libraries from nucleobases and deoxyribonucleosides facilitate the identification of ribonucleosides by nano-flow liquid chromatography-tandem mass spectrometry

RATIONALE

The study addresses the challenge of identifying RNA post-transcriptional modifications when commercial standards are not available to generate reference spectral libraries. It proposes employing homologous nucleobases and deoxyribonucleosides as alternative reference spectral libraries to aid in identifying modified ribonucleosides and distinguishing them from their positional isomers when the standards are unavailable.

METHODS

Complete sets of ribonucleoside, deoxyribonucleoside and nucleobase standards were analyzed using high-performance nano-flow liquid chromatography coupled to an Orbitrap Eclipse Tribrid mass spectrometer. Spectral libraries were constructed from homologous nucleobases and deoxyribonucleosides using targeted MS2 and neutral-loss-triggered MS3 methods, and collision energies were optimized. The feasibility of using these libraries for identifying modified ribonucleosides and their positional isomers was assessed through comparison of spectral fragmentation patterns.

RESULTS

Our analysis reveals that both MS2 and neutral-loss-triggered MS3 methods yielded rich spectra with similar fragmentation patterns across ribonucleosides, deoxyribonucleosides and nucleobases. Moreover, we demonstrate that spectra from nucleobases and deoxyribonucleosides, generated at optimized collision energies, exhibited sufficient similarity to those of modified ribonucleosides to enable their use as reference spectra for accurate identification of positional isomers within ribonucleoside families.

CONCLUSIONS

The study demonstrates the efficacy of utilizing homologous nucleobases and deoxyribonucleosides as interchangeable reference spectral libraries for identifying modified ribonucleosides and their positional isomers. This approach offers a valuable solution for overcoming limitations posed by the unavailability of commercial standards, enhancing the analysis of RNA post-transcriptional modifications via mass spectrometry.

The nucleotide-binding domain of NRC-dependent disease resistance proteins is sufficient to activate downstream helper NLR oligomerization and immune signaling

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins with pathogen sensor activities have evolved to initiate immune signaling by activating helper NLRs. However, the mechanisms underpinning helper NLR activation by sensor NLRs remain poorly understood. Although coiled coil (CC) type sensor NLRs such as the Potato virus X disease resistance protein Rx have been shown to activate the oligomerization of their downstream helpers NRC2, NRC3 and NRC4, the domains involved in sensor-helper signaling are not known. Here, we used Agrobacterium tumefaciens-mediated transient expression in Nicotiana benthamiana to show that the nucleotide-binding (NB) domain within the NB-ARC of Rx is necessary and sufficient for oligomerization and immune signaling of downstream helper NLRs. In addition, the NB domains of the disease resistance proteins Gpa2 (cyst nematode resistance), Rpi-amr1, Rpi-amr3 (oomycete resistance) and Sw-5b (virus resistance) are also sufficient to activate their respective downstream NRC helpers. Using transient expression in the lettuce (Lactuca sativa), we show that Rx (both as full length or as NB domain truncation) and its helper NRC2 form a minimal functional unit that can be transferred from solanaceous plants (lamiids) to Campanulid species. Our results challenge the prevailing paradigm that NLR proteins exclusively signal via their N-terminal domains and reveal a signaling activity for the NB domain of NRC-dependent sensor NLRs. We propose a model in which helper NLRs can perceive the status of the NB domain of their upstream sensors.

Microglial TNFα controls daily changes in synaptic GABAARs and sleep slow waves

Microglia sense the changes in their environment. How microglia actively translate these changes into suitable cues to adapt brain physiology is unknown. We reveal an activity-dependent regulation of cortical inhibitory synapses by microglia, driven by purinergic signaling acting on P2RX7 and mediated by microglia-derived TNFα. We demonstrate that sleep induces microglia-dependent synaptic enrichment of GABAARs in a manner dependent on microglial TNFα and P2RX7. We further show that microglia-specific depletion of TNFα alters slow waves during NREM sleep and blunt memory consolidation in sleep-dependent learning tasks. Together, our results reveal that microglia orchestrate sleep-intrinsic plasticity of synaptic GABAARs, sculpt sleep slow waves, and support memory consolidation.

Trends in Life Expectancy in Residential Long-Term Care by Sociodemographic Position in 1999-2018: A Multistate Life Table Study of Finnish Older Adults

OBJECTIVES

Residential long-term care (LTC) use has declined in many countries over the past years. This study quantifies how changing rates of entry, exit, and mortality have contributed to trends in life expectancy in LTC (i.e., average time spent in LTC after age 65) across sociodemographic groups.

METHODS

We analyzed population-register data of all Finns aged ≥65 during 1999-2018 (n = 2,016,987) with dates of LTC and death and sociodemographic characteristics. We estimated transition rates between home, LTC, and death using Poisson generalized additive models, and calculated multistate life tables across 1999-2003, 2004-2008, 2009-2013, and 2014-2018.

RESULTS

Between 1999-2003 and 2004-2008, life expectancy in LTC increased from 0.75 (95% CI: 0.74-0.76) to 0.89 (95% CI: 0.88-0.90) years among men and from 1.61 (95% CI: 1.59-1.62) to 1.83 (95% CI: 1.81-1.85) years among women, mainly due to declining exit rates from LTC. Thereafter, life expectancy in LTC decreased, reaching 0.80 (95% CI: 0.79-0.81) and 1.51 (95% CI: 1.50-1.53) years among men and women, respectively, in 2014-2018. Especially among women and nonmarried men, the decline was largely due to increasing death rates in LTC. Admission rates declined throughout the study period, which offset the increase in life expectancy in LTC attributable to declining mortality in the community. Marital status differences in life expectancy in LTC narrowed over time.

DISCUSSION

Recent declines in LTC use were driven by postponed LTC admission closer to death. The results suggest that across sociodemographic strata older adults enter LTC in even worse health and spend a shorter time in care than before.

Beyond peaks and troughs: Multiplexed performance monitoring signals in the EEG

With the discovery of event-related potentials elicited by errors more than 30 years ago, a new avenue of research on performance monitoring, cognitive control, and decision making emerged. Since then, the field has developed and expanded fulminantly. After a brief overview on the EEG correlates of performance monitoring, this article reviews recent advancements based on single-trial analyses using independent component analysis, multiple regression, and multivariate pattern classification. Given the close interconnection between performance monitoring and reinforcement learning, computational modeling and model-based EEG analyses have made a particularly strong impact. The reviewed findings demonstrate that error- and feedback-related EEG dynamics represent variables reflecting how performance-monitoring signals are weighted and transformed into an adaptation signal that guides future decisions and actions. The model-based single-trial analysis approach goes far beyond conventional peak-and-trough analyses of event-related potentials and enables testing mechanistic theories of performance monitoring, cognitive control, and decision making.

The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

Computational evidences of a misfolding event in an aggregation-prone light chain preceding the formation of the non-native pathogenic dimer

Antibody light chain amyloidosis is a disorder in which protein aggregates, mainly composed of immunoglobulin light chains, deposit in diverse tissues impairing the correct functioning of organs. Interestingly, due to the high susceptibility of antibodies to mutations, AL amyloidosis appears to be strongly patient-specific. Indeed, every patient will display their own mutations that will make the proteins involved prone to aggregation thus hindering the study of this disease on a wide scale. In this framework, determining the molecular mechanisms that drive the aggregation could pave the way to the development of patient-specific therapeutics. Here, we focus on a particular patient-derived light chain, which has been experimentally characterized. We investigated the early phases of the aggregation pathway through extensive full-atom molecular dynamics simulations, highlighting a structural rearrangement and the exposure of two hydrophobic regions in the aggregation-prone species. Next, we moved to consider the pathological dimerization process through docking and molecular dynamics simulations, proposing a dimeric structure as a candidate pathological first assembly. Overall, our results shed light on the first phases of the aggregation pathway for a light chain at an atomic level detail, offering new structural insights into the corresponding aggregation process.

Exposure to prenatal infection and the development of internalizing and externalizing problems in children: a longitudinal population-based study

BACKGROUND

A large body of work has reported a link between prenatal exposure to infection and increased psychiatric risk in offspring. However, studies to date have focused primarily on exposure to severe prenatal infections and/or individual psychiatric diagnoses in clinical samples, typically measured at single time points, and without accounting for important genetic and environmental confounders. In this study, we investigated whether exposure to common infections during pregnancy is prospectively associated with repeatedly assessed child psychiatric symptoms in a large population-based study.

METHODS

Our study was embedded in a prospective pregnancy cohort (Generation R; n = 3,598 mother-child dyads). We constructed a comprehensive prenatal infection score comprising common infections for each trimester of pregnancy. Child total, internalizing, and externalizing problems were assessed repeatedly using the parent-rated Child Behavioral Checklist (average age: 1.5, 3, 6, 10, and 14 years). Linear mixed-effects models were run adjusting for a range of confounders, including child polygenic scores for psychopathology, maternal chronic illness, birth complications, and infections during childhood. We also investigated trimester-specific effects and child sex as a potential moderator.

RESULTS

Prenatal exposure to infections was associated with higher child total, internalizing, and externalizing problems, showing temporally persistent effects, even after adjusting for important genetic and environmental confounders. We found no evidence that prenatal infections were associated with changes in child psychiatric symptoms over time. Moreover, in our trimester-specific analysis, we did not find evidence of significant timing effects of prenatal infection on child psychiatric symptoms. No interactions with child sex were identified.

CONCLUSIONS

Our research adds to evidence that common prenatal infections may be a risk factor for psychiatric symptoms in children. We also extend previous findings by showing that these associations are present early on, and that rather than changing over time, they persist into adolescence. However, unmeasured confounding may still explain in part these associations. In the future, employing more advanced causal inference designs will be crucial to establishing the degree to which these effects are causal.

Towards global insect biomonitoring with frugal methods

None of the global targets for protecting nature are currently met, although humanity is critically dependent on biodiversity. A significant issue is the lack of data for most biodiverse regions of the planet where the use of frugal methods for biomonitoring would be particularly important because the available funding for monitoring is insufficient, especially in low-income countries. We here discuss how three approaches to insect biomonitoring (computer vision, lidar, DNA sequences) could be made more frugal and urge that all biomonitoring techniques should be evaluated for global suitability before becoming the default in high-income countries. This requires that techniques popular in high-income countries should undergo a phase of 'innovation through simplification' before they are implemented more broadly. We predict that techniques that acquire raw data at low cost and are suitable for analysis with AI (e.g. images, lidar-signals) will be particularly suitable for global biomonitoring, while techniques that rely heavily on patented technologies may be less promising (e.g. DNA sequences). We conclude the opinion piece by pointing out that the widespread use of AI for data analysis will require a global strategy for providing the necessary computational resources and training. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Living jewels: iterative evolution of iridescent blue leaves from helicoidal cell walls

BACKGROUND AND AIMS

Structural colour is responsible for the remarkable metallic blue colour seen in the leaves of several plants. Species belonging to only ten genera have been investigated to date, revealing four photonic structures responsible for structurally coloured leaves. One of these is the helicoidal cell wall, known to create structural colour in the leaf cells of five taxa. Here we investigate a broad selection of land plants to understand the phylogenetic distribution of this photonic structure in leaves.

METHODS

We identified helicoidal structures in the leaf epidermal cells of 19 species using transmission electron microscopy. Pitch measurements of the helicoids were compared with the reflectance spectra of circularly polarized light from the cells to confirm the structure-colour relationship.

RESULTS

By incorporating species examined with a polarizing filter, our results increase the number of taxa with photonic helicoidal cell walls to species belonging to at least 35 genera. These include 19 monocot genera, from the orders Asparagales (Orchidaceae) and Poales (Cyperaceae, Eriocaulaceae, Rapateaceae) and 16 fern genera, from the orders Marattiales (Marattiaceae), Schizaeales (Anemiaceae) and Polypodiales (Blechnaceae, Dryopteridaceae, Lomariopsidaceae, Polypodiaceae, Pteridaceae, Tectariaceae).

CONCLUSIONS

Our investigation adds considerably to the recorded diversity of plants with structurally coloured leaves. The iterative evolution of photonic helicoidal walls has resulted in a broad phylogenetic distribution, centred on ferns and monocots. We speculate that the primary function of the helicoidal wall is to provide strength and support, so structural colour could have evolved as a potentially beneficial chance function of this structure.

Communicative efficiency in multimodal language directed at children and adults

The ecology of human communication is face to face. In these contexts, speakers dynamically modify their communication across vocal (e.g., speaking rate) and gestural (e.g., cospeech gestures related in meaning to the content of speech) channels while speaking. What is the function of these adjustments? Here we ask whether speakers dynamically make these adjustments to increase communicative success, and decrease cognitive effort while speaking. We assess whether speakers modulate word durations and produce iconic (i.e., imagistically evoking properties of referents) gestures depending on the predictability of each word they utter. Predictability is operationalized as surprisal and computed from computational language models trained on corpora of child-directed, or adult-directed language. Using data from a novel corpus (Ecological Language Corpus) of naturalistic interactions between adult-child (aged 3-4), and adult-adult, we show that surprisal predicts speakers' multimodal adjustments and that some of these effects are modulated by whether the comprehender is a child or an adult. Thus, communicative efficiency applies generally across vocal and gestural communicative channels not being limited to structural properties of language or vocal modality. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Novel Insights Into the Architecture of Macro and Microstructures in Cattle Ossa Cordis

Ossa cordis, bones located within the heart trigones, are often classified as heterotopic or ectopic bones. Despite their high prevalence in cattle and some other bovids, little is known about their structure or development. Scanning electron microscopy, X-ray microtomography, gross dissections, and measurements showed the anatomical locations, prevalence, shapes, and measurements of the cardiac bones in both Egyptian Baladi cattle and Holstein-Friesians. All cattle (n = 12) had an Ossa cordis dextrum (average = 50.70 × 20.91 × 5.40 mm). Additionally, 80% Egyptian Baladi and 57% Holstein-Friesian had a smaller Ossa cordis sinistrum (average = 24.94 × 12.75 × 4.12 mm). Egyptian Baladi Ossa cordis were smaller than observed in Holstein-Friesians. Energy-dispersive X-ray analysis showed the elemental constitution (carbon, oxygen, calcium, nitrogen, phosphorus, sodium, and magnesium) of Ossa cordis and Cartilago cordis. These imaging techniques, plus four histological stains (hematoxylin and eosin, Crossman's trichrome, Alcian blue with Van Gieson, and Sirius Red) and microscopy, demonstrated osteoblasts, osteocytes, osteoclasts, astrocytes, blood vessels, bone marrow, lamellar and woven bone, cortical bone, trabeculations with pores and canaliculi, and fibrous components including collagen in the Ossa cordis dextrum and sinistrum. Hyaline cartilage and fibrocartilage (chondrocytes and cartilage matrix) were found within and surrounding the Ossa cordis. These findings were additionally compared against other cattle breeds and species.

Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198

Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.

The role of microglial TREM2 in development: A path toward neurodegeneration?

The nervous and the immune systems undergo a continuous cross talk, starting from early development and continuing throughout adulthood and aging. Defects in this cross talk contribute to neurodevelopmental and neurodegenerative diseases. Microglia are the resident immune cells in the brain that are primarily involved in this bidirectional communication. Among the microglial genes, trem2 is a key player, controlling the functional state of microglia and being at the forefront of many processes that require interaction between microglia and other brain components, such as neurons and oligodendrocytes. The present review focuses on the early developmental window, describing the early brain processes in which TREM2 is primarily involved, including the modulation of synapse formation and elimination, the control of neuronal bioenergetic states as well as the contribution to myelination processes and neuronal circuit formation. By causing imbalances during these early maturation phases, dysfunctional TREM2 may have a striking impact on the adult brain, making it a more sensitive target for insults occurring during adulthood and aging.

A loss of function mutation in CLDN25 causing Pelizaeus-Merzbacher-like leukodystrophy

Claudin-25 (CLDN-25), also known as Claudin containing domain 1, is an uncharacterized claudin family member. It has less conserved amino acid sequences when compared to other claudins. It also has a very broad tissue expression profile and there is currently a lack of functional information from murine knockout models. Here, we report a de novo missense heterozygous variant in CLDN25 (c. 745G>C, p. A249P) found in a patient diagnosed with Pelizaeus-Merzbacher-like leukodystrophy and presenting with symptoms such as delayed motor development, several episodes of tonic absent seizures and generalized dystonia. The variant protein does not localize to the cell-cell borders where it would normally be expected to be expressed. Amino acid position 249 is located 4 amino acids from the C-terminal end of the protein where most claudin family members have a conserved binding motif for the key scaffolding protein ZO-1. However, CLDN-25 does not contain this motif. Here, we show that the C-terminal end of CLDN-25 is required for its junctional localization in a ZO-1 independent manner. The A249P mutant protein as well as a deletion mutant lacking its last 5 C-terminal amino acids also failed to localize to the cell-cell border in vitro. Intriguingly, cellular knockout of CLDN25, in vitro, appeared to increase the integrity of the tight junction between 2 contacting cells, while driving highly unusual increased movement of solutes between cells. We propose that the barrier function of CLDN-25 is akin to a decoy claudin, whereby decreasing its expression in "leaky" epithelial cells and endothelial cells will drive dynamic changes in the adhesion and interaction capacity of cell-cell contact points. While it remains unclear how this de novo CLDN-25 mutant induces leukodystrophy, our findings strongly suggest that this mutation induces haploinsufficiency of CLDN-25. Elucidating the function of this uncharacterized claudin protein will lead to a better understanding of the role of claudin proteins in health and disease.

A Multi-Dimensional Approach to Map Disease Relationships Challenges Classical Disease Views

The categorization of human diseases is mainly based on the affected organ system and phenotypic characteristics. This is limiting the view to the pathological manifestations, while it neglects mechanistic relationships that are crucial to develop therapeutic strategies. This work aims to advance the understanding of diseases and their relatedness beyond traditional phenotypic views. Hence, the similarity among 502 diseases is mapped using six different data dimensions encompassing molecular, clinical, and pharmacological information retrieved from public sources. Multiple distance measures and multi-view clustering are used to assess the patterns of disease relatedness. The integration of all six dimensions into a consensus map of disease relationships reveals a divergent disease view from the International Classification of Diseases (ICD), emphasizing novel insights offered by a multi-view disease map. Disease features such as genes, pathways, and chemicals that are enriched in distinct disease groups are identified. Finally, an evaluation of the top similar diseases of three candidate diseases common in the Western population shows concordance with known epidemiological associations and reveals rare features shared between Type 2 diabetes (T2D) and Alzheimer's disease. A revision of disease relationships holds promise for facilitating the reconstruction of comorbidity patterns, repurposing drugs, and advancing drug discovery in the future.

Representations of imaginary scenes and their properties in cortical alpha activity

Imagining natural scenes enables us to engage with a myriad of simulated environments. How do our brains generate such complex mental images? Recent research suggests that cortical alpha activity carries information about individual objects during visual imagery. However, it remains unclear if more complex imagined contents such as natural scenes are similarly represented in alpha activity. Here, we answer this question by decoding the contents of imagined scenes from rhythmic cortical activity patterns. In an EEG experiment, participants imagined natural scenes based on detailed written descriptions, which conveyed four complementary scene properties: openness, naturalness, clutter level and brightness. By conducting classification analyses on EEG power patterns across neural frequencies, we were able to decode both individual imagined scenes as well as their properties from the alpha band, showing that also the contents of complex visual images are represented in alpha rhythms. A cross-classification analysis between alpha power patterns during the imagery task and during a perception task, in which participants were presented images of the described scenes, showed that scene representations in the alpha band are partly shared between imagery and late stages of perception. This suggests that alpha activity mediates the top-down re-activation of scene-related visual contents during imagery.

Comprehensive O-Glycan Analysis by Porous Graphitized Carbon Nanoliquid Chromatography-Mass Spectrometry

The diverse and unpredictable structures of O-GalNAc-type protein glycosylation present a challenge for its structural and functional characterization in a biological system. Porous graphitized carbon (PGC) liquid chromatography (LC) coupled to mass spectrometry (MS) has become one of the most powerful methods for the global analysis of glycans in complex biological samples, mainly due to the extensive chromatographic separation of (isomeric) glycan structures and the information delivered by collision induced fragmentation in negative mode MS for structural elucidation. However, current PGC-based methodologies fail to detect the smaller glycan species consisting of one or two monosaccharides, such as the Tn (single GalNAc) antigen, which is broadly implicated in cancer biology. This limitation is caused by the loss of small saccharides during sample preparation and LC. Here, we improved the conventional PGC nano-LC-MS/MS-based strategy for O-glycan analysis, enabling the detection of truncated O-glycan species and improving isomer separation. This was achieved by the implementation of 2.7 μm PGC particles in both the trap and analytical LC columns, which provided an enhanced binding capacity and isomer separation for O-glycans. Furthermore, a novel mixed-mode PGC-boronic acid-solid phase extraction during sample preparation was established to purify a broad range of glycans in an unbiased manner, including the previously missed mono- and disaccharides. Taken together, the optimized PGC nano-LC-MS/MS platform presents a powerful component of the toolbox for comprehensive O-glycan characterization.

Patient-specific placental vessel segmentation with limited data

A major obstacle in applying machine learning for medical fields is the disparity between the data distribution of the training images and the data encountered in clinics. This phenomenon can be explained by inconsistent acquisition techniques and large variations across the patient spectrum. The result is poor translation of the trained models to the clinic, which limits their implementation in medical practice. Patient-specific trained networks could provide a potential solution. Although patient-specific approaches are usually infeasible because of the expenses associated with on-the-fly labeling, the use of generative adversarial networks enables this approach. This study proposes a patient-specific approach based on generative adversarial networks. In the presented training pipeline, the user trains a patient-specific segmentation network with extremely limited data which is supplemented with artificial samples generated by generative adversarial models. This approach is demonstrated in endoscopic video data captured during fetoscopic laser coagulation, a procedure used for treating twin-to-twin transfusion syndrome by ablating the placental blood vessels. Compared to a standard deep learning segmentation approach, the pipeline was able to achieve an intersection over union score of 0.60 using only 20 annotated images compared to 100 images using a standard approach. Furthermore, training with 20 annotated images without the use of the pipeline achieves an intersection over union score of 0.30, which, therefore, corresponds to a 100% increase in performance when incorporating the pipeline. A pipeline using GANs was used to generate artificial data which supplements the real data, this allows patient-specific training of a segmentation network. We show that artificial images generated using GANs significantly improve performance in vessel segmentation and that training patient-specific models can be a viable solution to bring automated vessel segmentation to the clinic.

PPARG is dispensable for bovine embryo development up to tubular stages

Following blastocyst hatching, ungulate embryos undergo a prolonged preimplantation period termed conceptus elongation. Conceptus elongation constitutes a highly susceptible period for embryonic loss and the embryonic requirements during this process are largely unknown, but multiple lipid compounds have been identified in the fluid nourishing the elongating conceptuses. Peroxisome proliferator-activated receptors (PPARs) mediate the signaling actions of prostaglandins and other lipids and, between them, PPARG has been pointed out to play a relevant role on conceptus elongation by a functional study that depleted PPARG in both uterus and conceptus. The objective of this study has been to determine if embryonic PPARG is required for bovine embryo development. To that aim, we have generated bovine PPARG KO embryos in vitro by two independent gene ablation strategies and assess their developmental ability. In vitro development to Day (D) 8 blastocyst was unaffected by PPARG ablation, as total, inner cell mass and trophectoderm cell numbers were similar between WT and KO D8 embryos. In vitro post-hatching development to D12 was also comparable between different genotypes, as embryo diameter, epiblast cell number, and embryonic disc formation and hypoblast migration rates were unaffected by the ablation. The development to tubular stages equivalent to E14 was assessed in vivo, following a heterologous embryo transfer experiment, observing that the development of extra-embryonic membranes and of the embryonic disc was not altered by PPARG ablation. In conclusion, PPARG ablation did not impaired bovine embryo development up to tubular stages.

How Does Personal Hygiene Influence Indoor Air Quality?

Humans are known to be a continuous and potent indoor source of volatile organic compounds (VOCs). However, little is known about how personal hygiene, in terms of showering frequency, can influence these emissions and their impact on indoor air chemistry involving ozone. In this study, we characterized the VOC composition of the air in a controlled climate chamber (22.5 m3 with an air change rate at 3.2 h-1) occupied by four male volunteers on successive days under ozone-free (∼0 ppb) and ozone-present (37-40 ppb) conditions. The volunteers either showered the evening prior to the experiments or skipped showering for 24 and 48 h. Reduced shower frequency increased human emissions of gas-phase carboxylic acids, possibly originating from skin bacteria. With ozone present, increasing the number of no-shower days enhanced ozone-skin surface reactions, yielding higher levels of oxidation products. Wearing the same clothing over several days reduced the level of compounds generated from clothing-ozone reactions. When skin lotion was applied, the yield of the skin ozonolysis products decreased, while other compounds increased due to ozone reactions with lotion ingredients. These findings help determine the degree to which personal hygiene choices affect the indoor air composition and indoor air exposures.

Preliminary evidence that eye appearance in parrots (Psittaciformes) co-varies with latitude and altitude

External eye appearance in avian taxa has been proposed to be driven by social and ecological functions. Recent research in primates suggests, instead, that, photoprotective functions are important drivers of external eye appearance. Using similar methods, we examined the variation in external eye appearance of 132 parrot species (Psittaciformes) in relation to their ecology and sociality. Breeding systems, flock size and sexual dimorphism, as well as species' latitude and maximum living altitude, and estimated UV-B incidence in species' ranges were used to explore the contribution of social and ecological factors in driving external eye appearance. We measured the hue and brightness of visible parts of the eye and the difference in measurements of brightness between adjacent parts of the eye. We found no link between social variables and our measurements. We did, however, find a negative association between the brightness of the inner part of the iris and latitude and altitude. Darker inner irises were more prevalent farther away from the equator and for those species living at higher altitudes. We found no link between UV-B and brightness measurements of the iris, or tissue surrounding the eye. We speculate that these results are consistent with an adaptation for visual functions. While preliminary, these results suggest that external eye appearance in parrots is influenced by ecological, but not social factors.

Revealing short-term dynamics of tropical cyclone wind speeds from satellite synthetic aperture radar

Both unresolved physics in numerical models and limited theoretical understanding of the small-scale diffusion processes occurring near the ocean surface hamper predictability of tropical cyclone (TC) wind changes. An analytical model is here developed to diagnose the short-term evolution of the TC wind profile. An effective frictional parameter is introduced to control the unknown diffusion effects. When this frictional parameter is adjusted to match the TC intensity change, solutions are consistent with observed high-resolution ocean surface wind speeds from satellite synthetic aperture radar (SAR). The initial high-resolution estimate of the near-core wind structure is then found to strongly modulate the wind profile evolution. The frictional parameter can, unfortunately, not efficiently be calibrated using outer-core wind speed changes. Low-resolution observations or standard numerical weather predictions may thus not be directly used to reinterpret and anticipate short-term TC wind changes. The expected accumulation of orbiting SAR sensors as well as improved measurements of the ocean-atmosphere boundary layer characteristics shall then become essential to more precisely monitor TC dynamics.