eulerAPE: drawing area-proportional 3-Venn diagrams using ellipses

Optimizing in vitro spherulation cues in the fungal pathogen Coccidioides

Coccidioides spp . are part of a group of thermally dimorphic fungal pathogens, which grow as filamentous cells (hyphae) in the soil and transform to a different morphology upon inhalation into the host. The Coccidioides host form, the spherule, is unique and highly under characterized due to both technical and biocontainment challenges. Each spherule arises from an environmental spore (arthroconidium), matures, and develops hundreds of internal endospores, which are released from the spherule upon rupture. Each endospore can then go on to form another spherule in a cycle called spherulation. One of the foremost technical challenges has been reliably growing spherules in culture without the formation of contaminating hyphae, and consistently inducing endospore release from spherules. Here, we present optimization of in vitro spherule growth and endospore release, by closely controlling starting cell density in the culture, using freshly-harvested arthroconidia, and decreasing the concentration of multiple salts in spherulation media. We developed a minimal media to test spherule growth on various carbon and nitrogen sources. We defined a critical role for the dispersant Tamol in both early spherule formation and prevention of the accumulation of a visible film around spherules. Finally, we examined how the conditions under which arthroconidia are generated influence their transcriptome and subsequent development into spherules, demonstrating that this is an important variable to control when designing spherulation experiments. Together, our data reveal multiple strategies to optimize in vitro spherulation growth, enabling characterization of this virulence-relevant morphology.

Expansion of artemisinin partial resistance mutations and lack of histidine rich protein-2 and -3 deletions in Plasmodium falciparum infections from Rukara, Rwanda

BACKGROUND

Emerging artemisinin partial resistance and diagnostic resistance are a threat to malaria control in Africa. Plasmodium falciparum kelch13 (k13) propeller-domain mutations that confer artemisinin partial resistance have emerged in Africa. k13-561H was initially described at a frequency of 7.4% from Masaka in 2014-2015, but not present in nearby Rukara. By 2018, 19.6% of isolates in Masaka and 22% of isolates in Rukara contained the mutation. Longitudinal monitoring is essential to inform control efforts. In Rukara, an assessment was conducted to evaluate recent k13-561H prevalence changes, as well as other key mutations. Prevalence of hrp2/3 deletions was also assessed.

METHODS

Samples collected in Rukara in 2021 were genotyped for key artemisinin and partner drug resistance mutations using molecular inversion probe assays and for hrp2/3 deletions using qPCR.

RESULTS

Clinically validated k13 artemisinin partial resistance mutations continue to increase in prevalence with the overall level of mutant infections reaching 32% in Rwanda. The increase appears to be due to the rapid emergence of k13-675V (6.4%, 6/94 infections), previously not observed, rather than continued expansion of 561H (23.5% 20/85). Mutations to partner drugs and other anti-malarials were variable, with high levels of multidrug resistance 1 (mdr1) N86 (95.5%) associated with lumefantrine decreased susceptibility and dihydrofolate reductase (dhfr) 164L (24.7%) associated with a high level of antifolate resistance, but low levels of amodiaquine resistance polymorphisms with chloroquine resistance transporter (crt) 76T: at 6.1% prevalence. No hrp2 or hrp3 gene deletions associated with diagnostic resistance were found.

CONCLUSIONS

Increasing prevalence of artemisinin partial resistance due to k13-561H and the rapid expansion of k13-675V is concerning for the longevity of artemisinin effectiveness in the region. False negative RDT results do not appear to be an issue with no hrp2 or hpr3 deletions detected. Continued molecular surveillance in this region and surrounding areas is needed to follow artemisinin partial resistance and provide early detection of partner drug resistance, which would likely compromise control and increase malaria morbidity and mortality in East Africa.

Comprehensive species- and processing-specific peptide profiling of pasteurized, extended shelf-life and ultra-high temperature milk from cow, goat, sheep, buffalo, and mare

The present study aimed to identify endogenous milk peptides for species differentiation independent of heat exposure. Thus, comprehensive milk peptide profiles from five species and three types of heat treatments were analyzed by micro-flow liquid chromatography ion mobility quadrupole time-of-flight mass spectrometry (microLC-IM-QTOF) with subsequent database search leading to ≥ 3000 identified peptides. In the milks, 1154 peptides were unique for cow, 712 for sheep, 466 for goat, 197 for buffalo, and 69 for mare. Most peptides were detected in extended-shelf life (ESL) milk (2010), followed by ultra-high temperature (UHT) processed (1474) and pasteurized milk (1459 peptides), with 693 peptides present in all milk types. A blind test set of 64 samples confirmed eight species-specific, but heat-independent marker peptides in milk from cow, seven from goat, six from sheep, nine from buffalo, and three from mare. The generated peptide profiles can also be used to identify species- and heat-specific markers.

Geographical variation of bacterial and ciliophoran communities in tidal flats in a continental archipelago

In tidal flats, which are located at the transition zone between terrestrial and marine ecosystems, environmental factors such as temperature, sediment particle size, and tidal range exhibit geographic variation. Accordingly, the composition and structure of the microbial communities in the tidal flats are likely to vary in geographically different habitats. To clarify these differences with environmental factors causing them, we analyzed microbial communities consisting of bacteria and ciliates in sediments collected from nine tidal flats in geographical diverse region from Hokkaido to Kagoshima, Japan. The results confirmed that the community structures of bacteria and ciliophora in tidal flat sediments differed at the geographical scale of the Japanese archipelago. However, the variation could not be explained by the physical distance between the tidal flats nor by the differences in the trophic conditions among the tidal flats. Instead, the OTU richness of both the bacterial and ciliophoran communities was significantly related to the tidal range. The results also showed that bacteria and ciliophora tended to form similar communities among the tidal flats with similar median particle sizes. Furthermore, ciliophoran communities were similar among the tidal flats with similar bacterial communities. The results suggest that bacteria and ciliophora interact each other through trophic relationships or physical and chemical processes in the sediment habitats.

The binding of Mint/X11 PDZ domains to Ca V 2 calcium channels predates bilaterian animals

PDZ domain mediated interactions with voltage-gated calcium (Ca V ) channel C-termini play important roles in localizing and compartmentalizing membrane Ca 2+ signaling. The first such interaction discovered was between the neuronal multi-domain protein Mint-1, and the presynaptc calcium channel Ca V 2.2 in mammals. Although the physiological significance of this interaction is unclear, its occurrence in vertebrates and bilaterian invertebrates suggests important and conserved functions. In this study, we explore the evolutionary origins of Mint and its interaction with Ca V 2 channels. Phylogenetic and structural in silico analyses revealed that Mint is an animal-specific gene, like Ca V 2 channels, which bears a highly divergent N-terminus but strongly conserved C-terminus comprised of a phosphotyrosine binding domain, two tandem PDZ domains (PDZ-1 and PDZ-2), and a C-terminal auto-inhibitory element that binds and inhibits PDZ-1. Also deeply conserved are other Mint interacting proteins, namely amyloid precursor and related proteins, presenilins, neurexin, as well as CASK and Veli which form a tripartite complex with Mint in bilaterians. Through yeast 2-hybrid and bacterial 2-hybrid experiments, we show that Mint and Ca V 2 channels from cnidarians and placozoans interact in vitro , and in situ hybridization revealed co-expression of corresponding transcripts in dissociated neurons from the cnidarian Nematostella vectensis . Unexpectedly, the Mint orthologue from the ctenophore Hormiphora californiensis was able to strongly bind the divergent C-terminal ligands of cnidarian and placozoan Ca V 2 channels, despite neither the ctenophore Mint, nor the placozoan and cnidarian orthologues, binding the ctenophore Ca V 2 channel C-terminus. Altogether, our analyses provide a model for the emergence of this interaction in early animals first via adoption of a PDZ ligand by Ca V 2 channels, followed by sequence changes in the ligand that caused a modality switch for binding to Mint.

Graspable foods and tools elicit similar responses in visual cortex

Extrastriatal visual cortex is known to exhibit distinct response profiles to complex stimuli of varying ecological importance (e.g., faces, scenes, and tools). The dominant interpretation of these effects is that they reflect activation of distinct "category-selective" brain regions specialized to represent these and other stimulus categories. We sought to explore an alternative perspective: that the response to these stimuli is determined less by whether they form distinct categories, and more by their relevance to different forms of natural behavior. In this regard, food is an interesting test case, since it is primarily distinguished from other objects by its edibility, not its appearance, and there is evidence of food-selectivity in human visual cortex. Food is also associated with a common behavior, eating, and food consumption typically also involves the manipulation of food, often with the hands. In this context, food items share many properties in common with tools: they are graspable objects that we manipulate in self-directed and stereotyped forms of action. Thus, food items may be preferentially represented in extrastriatal visual cortex in part because of these shared affordance properties, rather than because they reflect a wholly distinct kind of category. We conducted fMRI and behavioral experiments to test this hypothesis. We found that behaviorally graspable food items and tools were judged to be similar in their action-related properties, and that the location, magnitude, and patterns of neural responses for images of graspable food items were similar in profile to the responses for tool stimuli. Our findings suggest that food-selectivity may reflect the behavioral affordances of food items rather than a distinct form of category-selectivity.

Wnt signal-dependent antero-posterior specification of early-stage CNS primordia modeled in EpiSC-derived neural stem cells

The specification of the embryonic central nervous system (CNS) into future brain (forebrain, midbrain, or hindbrain) and spinal cord (SC) regions is a critical step of CNS development. A previous chicken embryo study indicated that anterior epiblast cells marked by Sox2 N2 enhancer activity are specified to the respective brain regions during the transition phase of the epiblast to the neural plate-forming neural primordium. The present study showed that the SC precursors positioned posterior to the hindbrain precursors in the anterior epiblast migrated posteriorly in contrast to the anterior migration of brain precursors. The anteroposterior specification of the CNS precursors occurs at an analogous time (∼E7.5) in mouse embryos, in which an anterior-to-posterior incremental gradient of Wnt signal strength was observed. To examine the possible Wnt signal contribution to the anteroposterior CNS primordium specification, we utilized mouse epiblast stem cell (EpiSC)-derived neurogenesis in culture. EpiSCs maintained in an activin- and FGF2-containing medium start neural development after the removal of activin, following a day in a transitory state. We placed activin-free EpiSCs in EGF- and FGF2-containing medium to arrest neural development and expand the cells into neural stem cells (NSCs). Simultaneously, a Wnt antagonist or agonist was added to the culture, with the anticipation that different levels of Wnt signals would act on the transitory cells to specify CNS regionality; then, the Wnt-treated cells were expanded as NSCs. Gene expression profiles of six NSC lines were analyzed using microarrays and single-cell RNA-seq. The NSC lines demonstrated anteroposterior regional specification in response to increasing Wnt signal input levels: forebrain-midbrain-, hindbrain-, cervical SC-, and thoracic SC-like lines. The regional coverage of these NSC lines had a range; for instance, the XN1 line expressed Otx2 and En2, indicating midbrain characteristics, but additionally expressed the SC-characteristic Hoxa5. The ranges in the anteroposterior specification of neural primordia may be narrowed as neural development proceeds. The thoracic SC is presumably the posterior limit of the contribution by anterior epiblast-derived neural progenitors, as the characteristics of more posterior SC regions were not displayed.

Methylglyoxal-Derived Nucleoside Adducts Drive Vascular Dysfunction in a RAGE-Dependent Manner

Diabetic kidney disease (DKD) is a leading cause of death in patients with diabetes. An early precursor to DKD is endothelial cell dysfunction (ECD), which often precedes and exacerbates vascular disease progression. We previously discovered that covalent adducts formed on DNA, RNA, and proteins by the reactive metabolic by-product methylglyoxal (MG) predict DKD risk in patients with type 1 diabetes up to 16 years pre-diagnosis. However, the mechanisms by which MG adducts contribute to vascular disease onset and progression remain unclear. Here, we report that the most predominant MG-induced nucleoside adducts, N2-(1-carboxyethyl)-deoxyguanosine (CEdG) and N2-(1-carboxyethyl)-guanosine (CEG), drive endothelial dysfunction. Following CEdG or CEG exposure, primary human umbilical vein endothelial cells (HUVECs) undergo endothelial dysfunction, resulting in enhanced monocyte adhesion, increased reactive oxygen species production, endothelial permeability, impaired endothelial homeostasis, and exhibit a dysfunctional transcriptomic signature. These effects were discovered to be mediated through the receptor for advanced glycation end products (RAGE), as an inhibitor for intracellular RAGE signaling diminished these dysfunctional phenotypes. Therefore, we found that not only are MG adducts biomarkers for DKD, but that they may also have a role as potential drivers of vascular disease onset and progression and a new therapeutic modality.

Expansion of Artemisinin Partial Resistance Mutations and Lack of Histidine Rich Protein-2 and -3 Deletions in Plasmodium falciparum infections from Rukara, Rwanda

Background

Emerging artemisinin resistance and diagnostic resistance are a threat to malaria control in Africa. Plasmodium falciparum kelch13 (K13) propeller-domain mutations that confer artemisinin partial resistance have emerged in Africa. K13-561H was initially described at a frequency of 7.4% from Masaka in 2014-2015 but not present in nearby Rukara. By 2018, 19.6% of isolates in Masaka and 22% of isolates in Rukara contained the mutation. Longitudinal monitoring is essential to inform control efforts. In Rukara, we sought to assess recent K13-561H prevalence changes, as well as for other key mutations. Prevalence of hrp2/3 deletions was also assessed.

Methods

We genotyped samples collected in Rukara in 2021 for key artemisinin and partner drug resistance mutations using molecular inversion probe assays and for hrp2/3 deletions using qPCR.

Results

Clinically validated K13 artemisinin partial resistance mutations continue to increase in prevalence with the overall level of artemisinin resistance mutant infections reaching 32% in Rwanda. The increase appears to be due to the rapid emergence of K13-675V (6.4%, 6/94 infections), previously not observed, rather than continued expansion of 561H (23.5% 20/85). Mutations to partner drugs and other antimalarials were variable, with high levels of multidrug resistance 1 (MDR1) N86 (95.5%) associated with lumefantrine resistance and dihydrofolate reductase (DHFR) 164L (24.7%) associated with antifolate resistance, but low levels of amodiaquine resistance polymorphisms with chloroquine resistance transporter (CRT ) 76T: at 6.1% prevalence. No hrp2 or hrp3 gene deletions associated with diagnostic resistance were found.

Conclusions

Increasing prevalence of artemisinin partial resistance due to K13-561H and the rapid expansion of K13-675V is concerning for the longevity of artemisinin effectiveness in the region. False negative mRDT results do not appear to be an issue with no hrp2 or hpr3 deletions detected. Continued molecular surveillance in this region and surrounding areas is needed to follow artemisinin resistance and provide early detection of partner drug resistance, which would likely compromise control and increase malaria morbidity and mortality in East Africa.

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

Background

Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.

Results

Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes were more abundant and species rich than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.

Conclusions

Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits.

A reference genome for the long-term kleptoplast-retaining sea slug Elysia crispata morphotype clarki

Several species of sacoglossan sea slugs possess the incredible ability to sequester chloroplasts from the algae they consume. These "photosynthetic animals" incorporate stolen chloroplasts, called kleptoplasts, into the epithelial cells of tubules that extend from their digestive tracts throughout their bodies. The mechanism by which these slugs maintain functioning kleptoplasts in the absence of an algal nuclear genome is unknown. Here, we report a draft genome of the sacoglossan slug Elysia crispata morphotype clarki, a morphotype native to the Florida Keys that can retain photosynthetically active kleptoplasts for several months without feeding. We used a combination of Oxford Nanopore Technologies long reads and Illumina short reads to produce a 786-Mb assembly (N50 = 0.459 Mb) containing 68,514 predicted protein-coding genes. A phylogenetic analysis found no evidence of horizontal acquisition of genes from algae. We performed gene family and gene expression analyses to identify E. crispata genes unique to kleptoplast-containing slugs that were more highly expressed in fed versus unfed developmental life stages. Consistent with analyses in other kleptoplastic slugs, our investigation suggests that genes encoding lectin carbohydrate-binding proteins and those involved in regulation of reactive oxygen species and immunity may play a role in kleptoplast retention. Lastly, we identified four polyketide synthase genes that could potentially encode proteins producing UV- and oxidation-blocking compounds in slug cell membranes. The genome of E. crispata is a quality resource that provides potential targets for functional analyses and enables further investigation into the evolution and mechanisms of kleptoplasty in animals.

Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses

Antibody (Ab)-based imaging techniques rely on reagents whose performance may be application specific. Because commercial antibodies are validated for only a few purposes, users interested in other applications may have to perform extensive in-house antibody testing. Here, we present a novel application-specific proxy screening step to efficiently identify candidate antibodies for array tomography (AT), a serial section volume microscopy technique for high-dimensional quantitative analysis of the cellular proteome. To identify antibodies suitable for AT-based analysis of synapses in mammalian brain, we introduce a heterologous cell-based assay that simulates characteristic features of AT, such as chemical fixation and resin embedding that are likely to influence antibody binding. The assay was included into an initial screening strategy to generate monoclonal antibodies that can be used for AT. This approach simplifies the screening of candidate antibodies and has high predictive value for identifying antibodies suitable for AT analyses. In addition, we have created a comprehensive database of AT-validated antibodies with a neuroscience focus and show that these antibodies have a high likelihood of success for postembedding applications in general, including immunogold electron microscopy. The generation of a large and growing toolbox of AT-compatible antibodies will further enhance the value of this imaging technique.

Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses

Antibody-based imaging techniques rely on reagents whose performance may be application-specific. Because commercial antibodies are validated for only a few purposes, users interested in other applications may have to perform extensive in-house antibody testing. Here we present a novel application-specific proxy screening step to efficiently identify candidate antibodies for array tomography (AT), a serial section volume microscopy technique for high-dimensional quantitative analysis of the cellular proteome. To identify antibodies suitable for AT-based analysis of synapses in mammalian brain, we introduce a heterologous cell-based assay that simulates characteristic features of AT, such as chemical fixation and resin embedding that are likely to influence antibody binding. The assay was included into an initial screening strategy to generate monoclonal antibodies that can be used for AT. This approach simplifies the screening of candidate antibodies and has high predictive value for identifying antibodies suitable for AT analyses. In addition, we have created a comprehensive database of AT-validated antibodies with a neuroscience focus and show that these antibodies have a high likelihood of success for postembedding applications in general, including immunogold electron microscopy. The generation of a large and growing toolbox of AT-compatible antibodies will further enhance the value of this imaging technique.

Left ventricular structural abnormalities in the assessment of diastolic function in the elderly: source of discrepancies between the 2009 and 2016 criteria

Diastolic dysfunction (DD) is routinely evaluated in echocardiography to support diagnosis, prognostication, and management of heart failure, a condition highly prevalent in elderly patients. Clinical guidelines were published in 2009, and updated in 2016, pursuing to standardize and improve DD categorization. We aimed to assess the concordance of DD between these two documents in an elderly population and to investigate how left ventricular structural abnormalities (LVSA) impact the reclassification. To evaluate this we analyzed the 308 consecutive transthoracic echocardiograms in patients older than 60 years (70.4 ± 7.7 years-old, 59% women) that fulfilled the inclusion criteria out of the 1438 echocardiograms performed in a tertiary hospital. We found that the prevalence of DD was lower according to the 2016 criteria (64% vs. 91%; p < 0.001), with 207 (67.2%) patients changing category, indicating poor agreement between the guidelines (kappa = 0.21). There were 188 (61%) patients with LVSA, which drove most of the reclassifications in 2016 Grade I DD cases. The prevalence of elevated filling pressures by Doppler halved in this elderly population using the updated recommendations (20.9% vs. 39.2%; p < 0.001). In conclusion the prevalence of DD was lower applying the 2016 guidelines, with a poor agreement with 2009 guidelines in all DD grades. The role of LVSA in reclassifications was particularly evident in Grade I DD, while Doppler parameters drove reclassifications among the more severe grades. If not properly addressed, these discrepancies may undermine the reliance on DD as a diagnostic and prognostic tool, particularly in an elderly population at a higher risk of heart failure.

Characterizing online social support for alcohol use disorder: A mixed-methods approach

BACKGROUND

Online social media communities are increasingly popular venues for discussing alcohol use disorder (AUD) and recovery. Little is known about distinct contexts of social support that are exchanged in this milieu, which are critical to understanding the social dynamics of online recovery support.

METHODS

We randomly selected one post per day over the span of a year from the StopDrinking recovery forum. Direct responses to posts were double coded within an established theoretical framework of social support. Within a mixed-methods research framework, we quantified the linguistic characteristics of 1386 responses (i.e., text length, complexity, and sentiment) and qualitatively explored themes within and among different types of social support.

RESULTS

Emotional support was most prevalent (74% of responses) and appeared as the sole form of support in 38% of responses. Emotionally supportive responses were significantly shorter, less complex, and more positively valenced than other support types. Appraisal support was also common in 55% of responses, while informational support was identified in only 17%. There was substantial overlap among support types, with 40% of responses including two or more types. Salient themes included the common use of community-specific acronyms in emotional support. Appraisal support conveyed feedback about attitudes and behaviors that are perceived as (un-) favorable for AUD recovery. Informational support responses were composed primarily of recommendations for self-help literature, clinical treatment approaches, and peer recovery programs.

CONCLUSIONS

Social support in this sample was primarily emotional in nature, with other types of support included to provide feedback and guidance (i.e., appraisal support) and supplemental recovery resources (i.e., informational support). The provided social support framework can be helpful in characterizing community dynamics among heterogeneous online AUD recovery support forums. This framework could also be helpful in considering changes in support approaches that correspond to progress in recovery.

Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms

Cohesin connects CTCF-binding sites and other genomic loci in cis to form chromatin loops and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here, we describe a cohesin hinge mutant that can extrude DNA into loops but is unable to mediate cohesion in human cells. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin's cohesion and loop extrusion activities can be partially separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wild-type cohesin. This suggests that cohesion establishment and cohesin's interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring.

Is radiographic osteoarthritis associated with pain and disability of the ankle?

Objective

Ankle osteoarthritis (OA) is relatively understudied. It often affects younger people compared to OA in other joints. Evidence on the association between radiographic OA and ankle symptoms remains contradicting. We therefore examined the association of degree of radiographic talocrural, subtalar and talonavicular OA with severity of ankle pain, disability and predominant symptoms.

Method

A cross-sectional study was conducted in a radiology department serving primary and secondary care. From the total study population (adults referred for ankle radiography), patients with chronic ankle complaints were selected (N ​= ​231). Before radiography, participants completed a questionnaire on severity of ankle pain and disability using the Ankle Osteoarthritis Scale (AOS), and on their predominant symptoms, i.e. pain, functional loss, stiffness and/or instability. To assess the associations of the Kellgren-Lawrence scores (0, 1 or ≥2) with the primary outcomes (AOS), linear regression, and with the secondary outcomes predominant symptoms, logistic regression analyses were applied.

Results

Radiographic OA was not associated with AOS-pain and -disability. Radiographic talocrural OA was associated with functional loss (OR 3.26, 95% CI: 1.31; 8.11). A positive trend was seen between radiographic talonavicular OA and stiffness (OR 2.63, 95% CI: 0.97; 7.15).

Conclusion

The presence of radiographic OA is not associated with severity of ankle pain and disability in patients with chronic ankle complaints referred for ankle radiography. However, radiographic talocrural OA is associated with functional loss and radiographic talonavicular OA with stiffness as predominant symptom. These findings may contribute to better recognition of ankle OA in clinical practice.

Sex shapes cell-type-specific transcriptional signatures of stress exposure in the mouse hypothalamus

Stress-related psychiatric disorders and the stress system show prominent differences between males and females, as well as strongly divergent transcriptional changes. Despite several proposed mechanisms, we still lack the understanding of the molecular processes at play. Here, we explore the contribution of cell types to transcriptional sex dimorphism using single-cell RNA sequencing. We identify cell-type-specific signatures of acute restraint stress in the paraventricular nucleus of the hypothalamus, a central hub of the stress response, in male and female mice. Further, we show that a history of chronic mild stress alters these signatures in a sex-specific way, and we identify oligodendrocytes as a major target for these sex-specific effects. This dataset, which we provide as an online interactive app, offers the transcriptomes of thousands of individual cells as a molecular resource for an in-depth dissection of the interplay between cell types and sex on the mechanisms of the stress response.

Two opposing gene expression patterns within ATRX aberrant neuroblastoma

Neuroblastoma is the most common extracranial solid tumor in children. A subgroup of high-risk patients is characterized by aberrations in the chromatin remodeller ATRX that is encoded by 35 exons. In contrast to other pediatric cancer where ATRX point mutations are most frequent, multi-exon deletions (MEDs) are the most frequent type of ATRX aberrations in neuroblastoma. 75% of these MEDs are predicted to produce in-frame fusion proteins, suggesting a potential gain-of-function effect compared to nonsense mutations. For neuroblastoma there are only a few patient-derived ATRX aberrant models. Therefore, we created isogenic ATRX aberrant models using CRISPR-Cas9 in several neuroblastoma cell lines and one tumoroid and performed total RNA-sequencing on these and the patient-derived models. Gene set enrichment analysis (GSEA) showed decreased expression of genes related to both ribosome biogenesis and several metabolic processes in our isogenic ATRX exon 2-10 MED model systems, the patient-derived MED models and in tumor data containing two patients with an ATRX exon 2-10 MED. In sharp contrast, these same processes showed an increased expression in our isogenic ATRX knock-out and exon 2-13 MED models. Our validations confirmed a role of ATRX in the regulation of ribosome homeostasis. The two distinct molecular expression patterns within ATRX aberrant neuroblastomas that we identified imply that there might be a need for distinct treatment regimens.

Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life

Milk production is an ancient adaptation that unites all mammals. Milk contains a microbiome that can contribute to offspring health and microbial-immunological development. We generated a comprehensive milk microbiome dataset (16S rRNA gene) for the class Mammalia, representing 47 species from all placental superorders, to determine processes structuring milk microbiomes. We show that across Mammalia, milk exposes offspring to maternal bacterial and archaeal symbionts throughout lactation. Deterministic processes of environmental selection accounted for 20% of milk microbiome assembly processes; milk microbiomes were similar from mammals with the same host superorder (Afrotheria, Laurasiathera, Euarchontoglires, and Xenarthra: 6%), environment (marine captive, marine wild, terrestrial captive, and terrestrial wild: 6%), diet (carnivore, omnivore, herbivore, and insectivore: 5%), and milk nutrient content (sugar, fat, and protein: 3%). We found that diet directly and indirectly impacted milk microbiomes, with indirect effects being mediated by milk sugar content. Stochastic processes, such as ecological drift, accounted for 80% of milk microbiome assembly processes, which was high compared to mammalian gut and mammalian skin microbiomes (69% and 45%, respectively). Even amid high stochasticity and indirect effects, our results of direct dietary effects on milk microbiomes provide support for enteromammary trafficking, representing a mechanism by which bacteria are transferred from the mother's gut to mammary gland and then to offspring postnatally. The microbial species present in milk reflect both selective pressures and stochastic processes at the host level, exemplifying various ecological and evolutionary factors acting on milk microbiomes, which, in turn, set the stage for offspring health and development.

Patients with clinically diagnosed hand OA not fulfilling the ACR classification criteria are in an earlier disease phase and more often have thumb base OA

Objective

To investigate the performance of the American College of Rheumatology (ACR) classification criteria for hand osteoarthritis.

Design

Longitudinal data up to four years from a cohort of consecutive patients with primary hand osteoarthritis diagnosed by their rheumatologist (Hostas study) were used to classify presence or absence of hand osteoarthritis according to the 1990 ACR criteria (traditional format: one major and 4 minor ACR criteria) (ACR⁺/ACR^-). Demographics, Australian/Canadian osteoarthritis hand index (AUSCAN) pain and function were obtained. Hand radiographs were scored according to Kellgren-Lawrence; radiographic osteoarthritis was defined as Kellgren-Lawrence ≥2 in ≥1 CMC1 joint or ≥2 DIP/PIP/MCP joints.

Results

Of 538 patients (mean age 61 years, 86.1% women) 485 (90.1%) fulfilled ACR criteria at baseline. Except for the minor criterion swelling of <3 MCP joints, all criteria differed between the groups. ACR^- patients were younger, with higher BMI, a shorter time since diagnosis, and less bony enlargements, joint deformities and radiographic osteoarthritis, except for radiographic CMC1 osteoarthritis which was seen more often in ACR^- patients. No difference in AUSCAN pain or function was seen between ACR^- versus ACR⁺ patients. After follow-up 37/53 (69.8%) converted to ACR⁺, 2/53 (3.8%) did not, and 14/53 (26.4%) were lost to follow-up.

Conclusions

In clinical practice the majority of patients fulfill the ACR classification criteria, but those in an earlier disease phase, with less signs of hand osteoarthritis or with primarily thumb base osteoarthritis are less likely to fulfill them. New classification criteria also including earlier disease stages and with attention for hand osteoarthritis subtypes are required.

The Symbiodinium Proteome Response to Thermal and Nutrient Stresses

Coral bleaching is primarily caused by high sea surface temperatures, and nutrient enrichment of reefs is associated with lower resilience to thermal stress and ecological degradation. Excess inorganic nitrogen relative to phosphate has been proposed to sensitize corals to thermal bleaching. We assessed the physiological and proteomic responses of cultures of the dinoflagellate coral symbiont Symbiodinium microadriaticum to elevated temperature under low-nutrient, high-nutrient and phosphate-limited conditions. Elevated temperature induced reductions of many chloroplast proteins, particularly the light-harvesting complexes, and simultaneously increased the abundance of many chaperone proteins. Proteomes were similar when the N:P ratio was near the Redfield ratio, regardless of absolute N and P concentrations, but were strongly affected by phosphate limitation. Very high N:P inhibited Symbiodinium cell division while increasing the abundance of chloroplast proteins. The proteome response to phosphate limitation was greater than that to elevated temperature, as measured by the number of differentially abundant proteins. Increased physiological sensitivity to high temperatures under high nutrients or imbalanced N:P ratios was not apparent; however, oxidative stress response proteins were enriched among proteins responding to thermal stress under imbalanced N:P ratios. These data provide a detailed catalog of the effects of high temperatures and nutrients on a coral symbiont proteome.

The Relationship between Executive Functions, Working Memory, and Intelligence in Kindergarten Children

Executive functions (EF), working memory (WM), and intelligence are closely associated, but distinct constructs. What underlies the associations between these constructs, especially in childhood, is not well understood. In this pre-registered study, along with the traditional aggregate accuracy and RT-based measures of EF, we investigated post-error slowing (PES) in EF as a manifestation of metacognitive processes (i.e., monitoring and cognitive control) in relation to WM and intelligence. Thereby, we aimed to elucidate whether these metacognitive processes may be one underlying component to explain the associations between these constructs. We tested kindergarten children (M_age = 6.4 years, SD_age = 0.3) in an EF, WM (verbal and visuospatial), and fluid (non-verbal) intelligence task. We found significant associations of mainly the inhibition component of EF with fluid intelligence and verbal WM, and between verbal WM and intelligence. No significant associations emerged between the PES in EF and intelligence or WM. These results suggest that in the kindergarten age, inhibition rather than monitoring and cognitive control might be the underlying component that explains the associations between EF, WM, and intelligence.

Hidden sources of bias in diagnostic studies: the example of visceral leishmaniasis in east Africa

A clear understanding of the accuracy of diagnostic tests is essential for the management of infections such as visceral leishmaniasis in endemic areas. Using both published and unpublished datasets from field diagnostic trials of visceral leishmaniasis in the past ten years, we show the potential effects of unrecognised sources of bias including work-up bias, referral bias, and reference test bias on the results. We outline why these biases, which can occur in diagnostic studies of any disease, can go unrecognised despite adherence to current STARD and QUADAS-2 guidelines. Using these examples and referring to others seen in studies of bacterial and viral infections, we make specific recommendations on how these biases might be avoided through specific steps in study design, study reporting, and the locations where studies are conducted.

Prevalence of radiographic ankle osteoarthritis in different subgroups of patients referred for ankle radiography

BACKGROUND

Ankle osteoarthritis(OA) has detrimental effects on physical health and has a relatively early disease onset compared to OA in other joints. However, the prevalence of radiographic ankle OA in different subgroups of patients referred for ankle radiography remains unknown. Therefore, we aimed to determine the prevalence of radiographic talocrural, subtalar and talonavicular OA(Kellgren-Lawrence scale ≥2) in a population referred for ankle radiography. Moreover, we aimed to identify differences in prevalence between specific subgroups of patients i.e. Body Mass Index (BMI), sex, age and reason for referral.

METHODS

A cross-sectional study was conducted at a radiology department serving primary and secondary care. Patients completed a questionnaire before radiography. Features of radiographic ankle OA were assessed for subgroups of patients, including; BMI, sex, age and reason for referral (chronic vs (sub)acute complaints). To examine the difference in (features of) radiographic OA for subgroups, multinomial and logistic regression were used to calculate Odds Ratios (ORs), with adjustment for age, sex and BMI.

RESULTS

Data from 893 patients that visited the radiology department across 16 months in 2017 or 2018 were included for analysis. Prevalence of radiographic ankle OA was 9.2%, 0.4% and 7.0%, for the talocrural, subtalar and talonavicular joint, respectively. Obesity was associated with radiographic talonavicular OA (adjusted OR 2.16, 95%CI:1.09; 5.26). Radiographic talocrural and talonavicular OA were both positively associated with male sex [(adjusted OR 4.64, 95%CI:276; 7.81) and (adjusted OR 1.95, 95%CI:1.13; 3.35), respectively].

CONCLUSION

Radiographic ankle OA was more common in men and obese patients that were referred to radiology.

Reconstructing dropout: Building from multiple definitions, therapist effects, and center effects

Objective: The literature regarding dropout from psychotherapy has suffered from issues of diverse operationalization of the construct. Some have called for a more uniform definition to aid in generalization across research; this study aimed to assess the viability of such a definition by examining the rate of occurrence for three distinct definitions simultaneously. In addition, therapist and center level variances are explored to further understand the differences between definitions.

Method: We compared the prevalence rates and overlap of three distinct operationalizations of dropout (based on last session attendance, therapist judgment, and symptom change) using data gathered from a national practice research network (N = 2977). Higher-order therapist and center-level effects were assessed for each definition.

Results: There was very little overlap among definitions, with less than one percent of clients simultaneously meeting criteria for all three definitions. Additionally, therapist and center effects were found for each definition, especially notable for therapist-rated and last-session attendance definitions of dropout.

Conclusion: Rather than a singular definition of dropout, these results instead suggest that multiple, specific, and unique definitions more accurately depict clinical reality, and future research might benefit from uncovering predictors of different "classes" of dropouts and examining the different practices of therapists and centers.

Success Rate of Transcranial Doppler Scanning of Cerebral Arteries at Different Transtemporal Windows in Healthy Elderly Individuals

This study measured the rates of success in applying transcranial Doppler (TCD) scanning at the middle, posterior and anterior temporal windows (MTW, PTW and ATW) in the elderly. A hand-held 1.6-MHz pulsed-wave TCD transducer was used to search for cerebral arteries at MTW, PTW and ATW locations. Physical attributes of the head, including head circumference and the distance between tragi on both sides ("tragus-to-tragus arc length"), were also measured to explore the associations with successful rates. Among 396 healthy elderly participants (aged 62.6 ± 6.0 y, 140 men), 81.1% (n = 321; 127 men) had one or more temporal windows penetrable by TCD ultrasound (n = 286 [72.2%] at MTW, n = 195 [49.2%] at PTW and n = 106 [26.8%] at ATW). Regression analysis revealed that successful scanning increased significantly in male participants at three window locations. Younger age significantly increased successful scanning at the MTW and ATW. Smaller tragus-to-tragus arc length increased successful scanning at the MTW, but unsuccessful scanning at the ATW. Our findings support using MTW as the first location when positioning the TCD transducer for the scanning of cerebral arteries in the elderly population. When performing TCD scanning on two temporal windows, we propose choosing the MTW and PTW.

Ready for handwriting? A reference data study on handwriting readiness assessments

INTRODUCTION

Early evaluation of writing readiness is essential to predict and prevent handwriting difficulties and its negative influences on school occupations. An occupation-based measurement for kindergarten children has been previously developed: Writing Readiness Inventory Tool In Context (WRITIC). In addition, to assess fine motor coordination two tests are frequently used in children with handwriting difficulties: the modified Timed Test of In-Hand Manipulation (Timed TIHM) and the Nine-Hole Peg Test (9-HPT). However, no Dutch reference data are available.

AIM

To provide reference data for (1) WRITIC, (2) Timed-TIHM and (3) 9-HPT for handwriting readiness assessment in kindergarten children.

METHODS

Three hundred and seventy-four children from Dutch kindergartens in the age of 5 to 6.5 years (5.6±0.4 years, 190 boys/184 girls) participated in the study. Children were recruited at Dutch kindergartens. Full classes of the last year were tested, children were excluded if there was a medical diagnosis such as a visual, auditory, motor or intellectual impairment that hinder handwriting performance. Descriptive statistics and percentiles scores were calculated. The score of the WRITIC (possible score 0-48 points) and the performance time on the Timed-TIHM and 9-HPT are classified as percentile scores lower than the 15th percentile to distinguish low performance from adequate performance. The percentile scores can be used to identify children that are possibly at risk developing handwriting difficulties in first grade.

RESULTS

WRITIC scores ranged from 23 to 48 (41±4.4), Timed-TIHM ranged from 17.9 to 64.5 seconds (31.4± 7.4 seconds) and 9-HPT ranged from 18.2 to 48.3 seconds (28.4± 5.4). A WRITIC score between 0-36, a performance time of more than 39.6 seconds on the Timed-TIHM and more than 33.8 seconds on the 9-HPT were classified as low performance.

CONCLUSION

The reference data of the WRITIC allow to assess which children are possibly at risk developing handwriting difficulties.

PGC-1β modulates catabolism and fiber atrophy in the fasting-response of specific skeletal muscle beds

OBJECTIVE

Skeletal muscle is a pivotal organ for the coordination of systemic metabolism, constituting one of the largest storage site for glucose, lipids and amino acids. Tight temporal orchestration of protein breakdown in times of fasting has to be balanced with preservation of muscle mass and function. However, the molecular mechanisms that control the fasting response in muscle are poorly understood.

METHODS

We now have identified a role for the peroxisome proliferator-activated receptor γ coactivator 1β (PGC-1β) in the regulation of catabolic pathways in this context in muscle-specific loss-of-function mouse models.

RESULTS

Muscle-specific knockouts for PGC-1β experience mitigated muscle atrophy in fasting, linked to reduced expression of myostatin, atrogenes, activation of AMP-dependent protein kinase (AMPK) and other energy deprivation signaling pathways. At least in part, the muscle fasting response is modulated by a negative effect of PGC-1β on the nuclear factor of activated T-cells 1 (NFATC1).

CONCLUSIONS

Collectively, these data highlight the complex regulation of muscle metabolism and reveal a new role for muscle PGC-1β in the control of proteostasis in fasting.

Criteria for prediabetes and posttransplant diabetes mellitus after kidney transplantation: A 2-year diagnostic accuracy study of participants from a randomized controlled trial

Posttransplant diabetes mellitus (PTDM) and prediabetes (impaired glucose tolerance [IGT] and impaired fasting glucose [IFG]) are associated with cardiovascular events. We assessed the diagnostic performance of fasting plasma glucose (FPG) and HbA_1c as alternatives to oral glucose tolerance test (OGTT)-derived 2-hour plasma glucose (2hPG) using sensitivity and specificity in 263 kidney transplant recipients (KTRs) from a clinical trial. Between visits at 6, 12, and 24 months after transplantation, 28%-31% of patients switched glycemic category (normal glucose tolerance [NGT], IGT/IFG, PTDM). Correlations of FPG and HbA_1c against 2hPG were lower at 6 months (r = 0.59 [FPG against 2hPG]; r = 0.45 [HbA_1c against 2hPG]) vs. 24 months (r = 0.73 [FPG against 2hPG]; r = 0.74 [HbA_1c against 2hPG]). Up to 69% of 2hPG-defined PTDM cases were missed by conventional HbA_1c and FPG thresholds. For prediabetes, concordance of FPG and HbA_1c with 2hPG ranged from 6%-9%. In conclusion, in our well-defined randomized trial cohort, one-third of KTRs switched glycemic category over 2 years and although the correlations of FPG and HbA_1c with 2hPG improved with time, their diagnostic concordance was poor for PTDM and, especially, prediabetes. Considering posttransplant metabolic instability, FPG's and HbA_1c 's diagnostic performance, the OGTT remains indispensable to diagnose PTDM and prediabetes after kidney transplantation.

Benthic invertebrates in Svalbard fjords-when metabarcoding does not outperform traditional biodiversity assessment

To protect and restore ecosystems and biodiversity is one of the 10 challenges identified by the United Nations's Decade of the Ocean Science. In this study we used eDNA from sediments collected in two fjords of the Svalbard archipelago and compared the taxonomic composition with traditional methods through metabarcoding, targeting mitochondrial CO1, to survey benthos. Clustering of 21.6 mill sequence reads with a d value of 13 in swarm, returned about 25 K OTU reads. An identification search with the BOLD database returned 12,000 taxonomy annotated sequences spanning a similarity range of 50% to 100%. Using an acceptance filter of minimum 90% similarity to the CO1 reference sequence, we found that 74% of the ca 100 taxon identified sequence reads were Polychaeta and 22% Nematoda. Relatively few other benthic invertebrate species were detected. Many of the identified sequence reads were extra-organismal DNA from terrestrial, planktonic, and photic zone sources. For the species rich Polychaeta, we found that, on average, only 20.6% of the species identified from morphology were also detected with DNA. This discrepancy was not due to missing reference sequences in the search database, because 90-100% (mean 96.7%) of the visually identified species at each station were represented with barcodes in Boldsystems. The volume of DNA samples is small compared with the volume searched in visual sorting, and the replicate DNA-samples in sum covered only about 2% of the surface area of a grab. This may considerably reduce the detection rate of species that are not uniformly distributed in the sediments. Along with PCR amplification bias and primer mismatch, this may be an important reason for the limited congruence of species identified with the two approaches. However, metabarcoding also identified 69 additional species that are usually overlooked in visual sample sorting, demonstrating how metabarcoding can complement traditional methodology by detecting additional, less conspicuous groups of organisms.

The microbial community associated with Parascaris spp. infecting juvenile horses

Background

Parasitic nematodes, including large roundworms colloquially known as ascarids, affect the health and well-being of livestock animals worldwide. The equine ascarids, Parascaris spp., are important parasites of juvenile horses and the first ascarids to develop widespread anthelmintic resistance. The microbiota has been shown to be an important factor in the fitness of many organisms, including parasitic nematodes, where endosymbiotic Wolbachia have been exploited for treatment of filariasis in humans.

Methods

This study used short-read 16S rRNA sequences and Illumina sequencing to characterize and compare microbiota of whole worm small intestinal stages and microbiota of male and female intestines and gonads. Diversity metrics including alpha and beta diversity, and the differential abundance analyses DESeq2, ANCOM-BC, corncob, and metagenomeSeq were used for comparisons.

Results

Alpha and beta diversity of whole worm microbiota did not differ significantly between groups, but Simpson alpha diversity was significantly different between female intestine (FI) and male gonad (MG) (P= 0.0018), and Shannon alpha diversity was significantly different between female and male gonads (P = 0.0130), FI and horse jejunum (HJ) (P = 0.0383), and FI and MG (P= 0.0001). Beta diversity (Fig. 2B) was significantly different between female and male gonads (P = 0.0006), male intestine (MI) and FG (P = 0.0093), and MG and FI (P = 0.0041). When comparing organs, Veillonella was differentially abundant for DESeq2 and ANCOM-BC (p < 0.0001), corncob (P = 0.0008), and metagenomeSeq (P = 0.0118), and Sarcina was differentially abundant across four methods (P < 0.0001). Finally, the microbiota of all individual Parascaris spp. specimens were compared to establish shared microbiota between groups.

Conclusions

Overall, this study provided important information regarding the Parascaris spp. microbiota and provides a first step towards determining whether the microbiota may be a viable target for future parasite control options.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05533-y.

How good are medical and death records for identifying dementia?

INTRODUCTION

Retrospective studies using administrative data may be an efficient way to assess risk factors for dementia if diagnostic accuracy is known.

METHODS

Within-individual clinical diagnoses of Alzheimer's disease (AD) and all-cause dementia in ambulatory (outpatient) surgery, inpatient, Medicare administrative records and death certificates were compared with research diagnoses among participants of Cache County Study on Memory, Health, and Aging (CCSMHA) (1995-2008, N = 5092).

RESULTS

Combining all sources of clinical health data increased sensitivity for identifying all-cause dementia (71%) and AD (48%), while maintaining relatively high specificity (81% and 93%, respectively). Medicare claims had the highest sensitivity for case identification (57% and 40%, respectively).

DISCUSSION

Administrative health data may provide a less accurate method than a research evaluation for identifying individuals with dementing disease, but accuracy is improved by combining health data sources. Assessing all-cause dementia versus a specific cause of dementia such as AD will result in increased sensitivity, but at a cost to specificity.

Cell type-specific calcium imaging of central sensitization in mouse dorsal horn

Allodynia is a state in which pain is elicited by innocuous stimuli. Capsaicin applied to the skin results in an allodynia that extends to a broad region beyond the application site. This sensitization is thought to be mediated by spinal networks; however, we do not have a clear picture of which spinal neurons mediate this phenomenon. To address this gap, we used two-photon calcium imaging of excitatory interneurons and spinal projection neurons in the mouse spinal dorsal horn. To distinguish among neuronal subtypes, we developed CICADA, a cell profiling approach to identify cell types during calcium imaging. We then identified capsaicin-responsive and capsaicin-sensitized neuronal populations. Capsaicin-sensitized neurons showed emergent responses to innocuous input and increased receptive field sizes consistent with psychophysical reports. Finally, we identified spinal output neurons that showed enhanced responses from innocuous input. These experiments provide a population-level view of central sensitization and a framework with which to model somatosensory integration in the dorsal horn.

RB1 loss triggers dependence on ESRRG in retinoblastoma

Retinoblastoma (Rb) is a deadly childhood eye cancer that is classically initiated by inactivation of the RB1 tumor suppressor. Clinical management continues to rely on nonspecific chemotherapeutic agents that are associated with treatment resistance and toxicity. Here, we analyzed 103 whole exomes, 20 whole transcriptomes, 5 single-cell transcriptomes, and 4 whole genomes from primary Rb tumors to identify previously unknown Rb dependencies. Several recurrent genomic aberrations implicate estrogen-related receptor gamma (ESRRG) in Rb pathogenesis. RB1 directly interacts with and inhibits ESRRG, and RB1 loss uncouples ESRRG from negative regulation. ESRRG regulates genes involved in retinogenesis and oxygen metabolism in Rb cells. ESRRG is preferentially expressed in hypoxic Rb cells in vivo. Depletion or inhibition of ESRRG causes marked Rb cell death, which is exacerbated in hypoxia. These findings reveal a previously unidentified dependency of Rb cells on ESRRG, and they implicate ESRRG as a potential therapeutic vulnerability in Rb.

Prognosis of Patients with Chronic Obstructive Pulmonary Disease Not Eligible for Major Clinical Trials

Rationale: Randomized controlled trials only include a subset of patients with chronic obstructive pulmonary disease (COPD) fulfilling strict inclusion criteria. Thus, most patients with COPD in a real-world setting do not have the necessary evidence to support treatment effectiveness. Objectives: To test the hypotheses that most individuals with COPD in the general population are not represented in major clinical trials despite clinically significant disease with exacerbations and early death. Methods: In 105,630 adults from a Danish contemporary population-based cohort, we defined COPD as age 40 or more years, chronic respiratory symptoms, history of smoking exposure, and airflow limitation with FEV₁/FVC < 0.70. Outcomes included acute exacerbations and all-cause mortality. Symptomatic smokers without COPD were used as a reference group. Measurements and Main Results: Of all, 7,516 (7%) and 16,079 (15%) were symptomatic smokers with and without COPD. Only 44% of those with COPD were eligible for major clinical trials when applying FEV₁ < 80% predicted, smoking history of 10 or more pack-years, and no comorbid asthma as common inclusion criteria. During the median 8.9 years of follow-up, we observed 2,130 acute exacerbations and 3,973 deaths in symptomatic smokers. Compared with symptomatic smokers without COPD, multivariable-adjusted hazard ratios for exacerbations were 7.45 (95% confidence interval, 5.41-10.3) and 29.0 (21.1-39.8) in those with COPD, respectively, excluded and eligible for clinical trials. Corresponding hazard ratios for all-cause mortality were 1.21 (1.11-1.31) and 1.67 (1.54-1.81), respectively. Conclusions: More than half of individuals with COPD in the general population are excluded from major clinical trials; however, these individuals have a clinically significant disease with exacerbations and early death compared with symptomatic smokers without COPD.

Spatial organization of heterogeneous immunotherapy target antigen expression in high-grade glioma

High-grade (WHO grades III-IV) glioma remains one of the most lethal human cancers. Adoptive transfer of tumor-targeting chimeric antigen receptor (CAR)-redirected T cells for high-grade glioma has revealed promising indications of anti-tumor activity, but objective clinical responses remain elusive for most patients. A significant challenge to effective immunotherapy is the highly heterogeneous structure of these tumors, including large variations in the magnitudes and distributions of target antigen expression, observed both within individual tumors and between patients. To obtain a more detailed understanding of immunotherapy target antigens within patient tumors, we immunochemically mapped at single cell resolution three clinically-relevant targets, IL13Rα2, HER2 and EGFR, on tumor samples drawn from a 43-patient cohort. We observed that within individual tumor samples, expression of these antigens was neither random nor uniform, but rather that they mapped into local neighborhoods - phenotypically similar cells within regions of cellular tumor - reflecting not well understood properties of tumor cells and their milieu. Notably, tumor cell neighborhoods of high antigen expression were not arranged independently within regions. For example, in cellular tumor regions, neighborhoods of high IL13Rα2 and HER2 expression appeared to be reciprocal to those of EGFR, while in areas of pseudopalisading necrosis, expression of IL13Rα2 and HER2, but not EGFR, appeared to reflect the radial organization of tumor cells around hypoxic cores. Other structural features affecting expression of immunotherapy target antigens remain to be elucidated. This structured but heterogeneous organization of antigen expression in high grade glioma is highly permissive for antigen escape, and combinatorial antigen targeting is a commonly suggested potential mitigating strategy. Deeper understanding of antigen expression within and between patient tumors will enhance optimization of combination immunotherapies, the most immediate clinical application of the observations presented here being the importance of including (wild-type) EGFR as a target antigen.

Perceived Injustice in Patients With Chronic Pain: Prevalence, Relevance, and Associations With Long-Term Recovery and Deterioration

The Injustice Experience Questionnaire (IEQ) assesses the degree to which chronic pain sufferers perceive injustice in relation to their pain. The aim of the current study was to assess the prevalence and relevance of the IEQ and its association to perceived recovery and deterioration in a naturalistic pain clinic population. Data was obtained from the Oslo University Hospital's Pain Registry. Among 2,950 patients, the prevalence of low (<19), medium (19-29) and high (30+) IEQ was 39%, 32% and 29% respectively. High levels of injustice were positively associated with a wide range of adverse health outcomes. Differences between those with high vs low levels of IEQ were clinically significant for most health outcomes. A Venn diagram analysis showed considerable, but not complete, overlap between IEQ, pain catastrophizing, psychological distress and severe pain intensity. High IEQ was associated with reduced clinical recovery (OR 0.6, 95% CI 0.4-0.9) and deterioration (OR 3.6, 95% CI 2.1-6.2) at 12-months follow-up, however, not when controlling for pain-related disability and pain intensity. We conclude that perceived injustice is a prevalent and clinically relevant phenomenon in a chronic pain clinic population, and that more knowledge is needed regarding its role as indicator of poor prognosis and target for tailored treatment. PERSPECTIVE: This article shows that pain-related injustice is both prevalent and relevant in a large naturalistic pain clinic population. Higher levels of injustice were consistently associated with adverse pain outcomes. Injustice could as such be a viable target for treatment of chronic pain, with potential indirect effects on pain and disability.

Depolarizing NaV and Hyperpolarizing KV Channels Are Co-Trafficked in Sensory Neurons

Neuronal excitability relies on coordinated action of functionally distinction channels. Voltage-gated sodium (NaV) and potassium (KV) channels have distinct but complementary roles in firing action potentials: NaV channels provide depolarizing current while KV channels provide hyperpolarizing current. Mutations and dysfunction of multiple NaV and KV channels underlie disorders of excitability, including pain and epilepsy. Modulating ion channel trafficking may offer a potential therapeutic strategy for these diseases. A fundamental question, however, is whether these channels with distinct functional roles are transported independently or packaged together in the same vesicles in sensory axons. We have used Optical Pulse-Chase Axonal Long-distance imaging to investigate trafficking of NaV and KV channels and other axonal proteins from distinct functional classes in live rodent sensory neurons (from male and female rats). We show that, similar to NaV1.7 channels, NaV1.8 and KV7.2 channels are transported in Rab6a-positive vesicles, and that each of the NaV channel isoforms expressed in healthy, mature sensory neurons (NaV1.6, NaV1.7, NaV1.8, and NaV1.9) is cotransported in the same vesicles. Further, we show that multiple axonal membrane proteins with different physiological functions (NaV1.7, KV7.2, and TNFR1) are cotransported in the same vesicles. However, vesicular packaging of axonal membrane proteins is not indiscriminate, since another axonal membrane protein (NCX2) is transported in separate vesicles. These results shed new light on the development and organization of sensory neuron membranes, revealing complex sorting of axonal proteins with diverse physiological functions into specific transport vesicles.SIGNIFICANCE STATEMENT Normal neuronal excitability is dependent on precise regulation of membrane proteins, including NaV and KV channels, and imbalance in the level of these channels at the plasma membrane could lead to excitability disorders. Ion channel trafficking could potentially be targeted therapeutically, which would require better understanding of the mechanisms underlying trafficking of functionally diverse channels. Optical Pulse-chase Axonal Long-distance imaging in live neurons permitted examination of the specificity of ion channel trafficking, revealing co-packaging of axonal proteins with opposing physiological functions into the same transport vesicles. This suggests that additional trafficking mechanisms are necessary to regulate levels of surface channels, and reveals an important consideration for therapeutic strategies that target ion channel trafficking for the treatment of excitability disorders.

Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity

Intestinal microbiota dysbiosis can initiate overgrowth of commensal Candida species - a major predisposing factor for disseminated candidiasis. Commensal bacteria such as Lactobacillus rhamnosus can antagonize Candida albicans pathogenicity. Here, we investigate the interplay between C. albicans, L. rhamnosus, and intestinal epithelial cells by integrating transcriptional and metabolic profiling, and reverse genetics. Untargeted metabolomics and in silico modelling indicate that intestinal epithelial cells foster bacterial growth metabolically, leading to bacterial production of antivirulence compounds. In addition, bacterial growth modifies the metabolic environment, including removal of C. albicans' favoured nutrient sources. This is accompanied by transcriptional and metabolic changes in C. albicans, including altered expression of virulence-related genes. Our results indicate that intestinal colonization with bacteria can antagonize C. albicans by reshaping the metabolic environment, forcing metabolic adaptations that reduce fungal pathogenicity.

Comparative proteomic analysis on chloroplast proteins provides new insights into the effects of low temperature in sugar beet

BACKGROUND

Low temperature, which is one of the main environmental factors that limits geographical distribution and sucrose yield, is a common abiotic stress during the growth and development of sugar beet. As a regulatory hub of plant response to abiotic stress, activity in the chloroplasts is related to many molecular and physiological processes, particularly in response to low temperature stress.

RESULTS

The contents of chlorophyll (Chl) and malondialdehyde (MDA), relative electrical conductivity (REL), and superoxide dismutase (SOD) activity were measured. The results showed that sugar beet could manage low temperature stress by regulating the levels of Chl, REL and MDA, and the activity of SOD. The physiological responses indicated that sugar beets respond positively to low temperature treatments and are not significantly damaged. Moreover, to determine the precise time to response low temperature in sugar beet, well-known abiotic stresses-responsive transcript factor family, namely DEHYDRATION RESPONSIVE ELEMENT BINDING PROTEIN (DREB), was selected as the marker gene. The results of phylogenetic analyses showed that BvDREBA1 and BvDREBA4 were in the same branch as the cold- and drought-responsive AtDREB gene. In addition, the expression of BvDREBs reached its maximum level at 24 h after low temperature by RNA-Seq and qRT-PCR analysis. Furthermore, the changes in chloroplast proteome after low temperature at 24 h were detected using a label-free technique. A total of 416 differentially expressed proteins were identified. GO enrichment analysis showed that 16 GO terms were significantly enriched, particularly chloroplast stroma, chloroplast envelope, and chloroplast thylakoid membrane. It is notable that the transport of photosynthetic proteins (BvLTD and BvTOC100), the formation of starch granules (BvPU1, BvISA3, and BvGWD3) and the scavenging of reactive oxygen species (BvCu/Zn-SOD, BvCAT, BvPrx, and BvTrx) were the pathways used by sugar beets to respond to low temperatures at an early stage.

CONCLUSIONS

These results provide a preliminarily analysis of how chloroplasts of sugar beet respond to low temperature stress at the translational level and provide a theoretical basis for breeding low temperature resistant varieties of sugar beet.

Nickel penetration into stratum corneum in FLG null carriers - a human experimental study

Background

The filaggrin gene (FLG) plays a role in skin diseases, with the skin barrier function being impaired in FLG null carriers. The role of FLG status in relation to nickel penetration into the skin remains unclear.

Objectives

To elucidate the association between FLG status and nickel penetration into stratum corneum (SC) in individuals without self‐reported history of nickel allergy.

Methods

Forty participants (23 FLG wt and 17 FLG null) were exposed to a nickel solution (80 μg/cm²) which was applied onto 2 × 2 cm on their left forearm. After 4 h, the area was tape‐stripped with 10 consecutive tapes. Nickel in each tape was quantified using inductively coupled plasma mass spectrometry.

Results

The average recovered nickel dose was 35%–48%. A tendency towards lower recovery was seen in FLG null carriers compared to FLG wt carriers, and lower recovery in those with history of skin and/or respiratory symptoms compared to those without such history. This was however not statistically significant.

Conclusion

FLG null carriers had less nickel recovered by tape strips compared with FLG wt carriers and, compared with individuals without a history of skin and/or respiratory symptoms, indicating higher nickel penetration into SC for FLG null carriers, but further studies are needed.

Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant

The community structure in the plant-associated microbiome depends collectively on host–microbe, microbe–microbe and host–microbe–microbe interactions. The ensemble of interactions between the host and microbial consortia may lead to outcomes that are not easily predicted from pairwise interactions. Plant–microbe–microbe interactions are important to plant health but could depend on both host and microbe strain variation. Here we study interactions between groups of naturally co-existing commensal and pathogenic Pseudomonas strains in the Arabidopsis thaliana phyllosphere. We find that commensal Pseudomonas prompt a host response that leads to selective inhibition of a specific pathogenic lineage, resulting in plant protection. The extent of protection depends on plant genotype, supporting that these effects are host-mediated. Strain-specific effects are also demonstrated by one individual Pseudomonas isolate eluding the plant protection provided by commensals. Our work highlights how within-species genetic differences in both hosts and microbes can affect host–microbe–microbe dynamics.

The authors conduct competition experiments with multiple strains of Pseudomonas (some pathogenic and some commensal) in the phylosphere microbiome of Arabidopsis plants, showing that both the host and the commensal strains interact to inhibit the pathogenic strains.

Attitudes toward deprescribing among older adults with dementia in the United States

BACKGROUND

People with dementia (PWD) take medications that may be unnecessary or harmful. This problem can be addressed through deprescribing, but it is unclear if PWD would be willing to engage in deprescribing with their providers. Our goal was to investigate attitudes toward deprescribing among PWD.

METHODS

This was a cross-sectional study of 422 PWD aged ≥65 years who completed the medications attitudes module of the National Health and Aging Trends Study (NHATS) in 2016. Proxies provided responses when a participant was unable to respond due to health or cognitive problems. Attitudinal outcomes comprised responses to two statements from the patients' attitudes toward deprescribing questionnaire and its revised version (representing belief about the necessity of one's medications and willingness to deprescribe); another elicited the maximum number of pills that a respondent would be comfortable taking.

RESULTS

The weighted sample represented over 1.8 million PWD; 39% were 75 to 84 years old and 38% were 85 years or older, 60% were female, and 55% reported six or more regular medications. Proxies provided responses for 26% of PWD. Overall, 22% believed that they may be taking one or more medicines that they no longer needed, 87% were willing to stop one or more of their medications, and 50% were uncomfortable taking five or more medications. Attitudinal outcomes were similar across sociodemographic and clinical factors. PWD taking ≥6 medications were more likely to endorse a belief that at least one medication was no longer necessary compared to those taking <6 (adjusted probability 29% [95% confidence interval (CI), 22%-38%] vs. 13% [95% CI, 8%-20%]; p = 0.004); the same applied for willingness to deprescribe (92% [95% CI, 87%-95%] vs. 83% [95% CI, 76%-89%]; p = 0.04).

CONCLUSIONS

A majority of PWD are willing to deprescribe, representing an opportunity to improve quality of life for this vulnerable population.

Broad Transcriptomic Impact of Sorafenib and Its Relation to the Antitumoral Properties in Liver Cancer Cells

Simple Summary

Hepatocellular carcinoma (HCC) is the fourth most frequent cause of cancer-related mortality worldwide. While ablation, resection and orthotopic liver transplantation are indicated at an early stage of the disease, Sorafenib (Sfb) is the current most administrated first-line treatment for advanced HCC, even though its therapeutic benefit is limited due to the appearance of resistance. Deep knowledge on the molecular consequences of Sfb-treatment is essentially required for optimizing novel therapeutic strategies to improve the outcomes for patients with advanced HCC. In this study, we analyzed differential gene expression changes in two well characterized liver cancer cell lines upon a Sfb-treatment, demonstrating that both lines responded similarly to the treatment. Our results provide valuable information on the molecular action of Sfb on diverse cellular fundamental processes such as DNA repair, translation and proteostasis and identify rationalization issues that could provide a different therapeutic perspective to Sfb.

Abstract

Hepatocellular carcinoma (HCC) is one of the most frequent and essentially incurable cancers in its advanced stages. The tyrosine kinase inhibitor Sorafenib (Sfb) remains the globally accepted treatment for advanced HCC. However, the extent of its therapeutic benefit is limited. Sfb exerts antitumor activity through its cytotoxic, anti-proliferative and pro-apoptotic roles in HCC cells. To better understand the molecular mechanisms underlying these effects, we used RNA sequencing to generate comprehensive transcriptome profiles of HepG2 and SNU423, hepatoblastoma- (HB) and HCC-derived cell lines, respectively, following a Sfb treatment at a pharmacological dose. This resulted in similar alterations of gene expression in both cell lines. Genes functionally related to membrane trafficking, stress-responsible and unfolded protein responses, circadian clock and activation of apoptosis were predominantly upregulated, while genes involved in cell growth and cycle, DNA replication and repair, ribosome biogenesis, translation initiation and proteostasis were downregulated. Our results suggest that Sfb causes primary effects on cellular stress that lead to upregulation of selective responses to compensate for its negative effect and restore homeostasis. No significant differences were found specifically affecting each cell line, indicating the robustness of the Sfb mechanism of action despite the heterogeneity of liver cancer. We discuss our results on terms of providing rationalization for possible strategies to improve Sfb clinical outcomes.

Prevalence and Prognostic Significance of Malnutrition in Hypertensive Patients in a Community Setting

BACKGROUND

Malnutrition is a significantly poor prognostic factor for a variety of cardiovascular diseases. However, its prevalence and prognostic value in hypertensive patients is still unclear. The present study sought to determine the prevalence and prognostic value of malnutrition in hypertensive patients in a community setting.

METHODS

We included 9,949 hypertensive patients from the National Health and Nutrition Examination Survey (NHANES) (2005-2014). The Controlling Nutritional Status (CONUT) score, the Nutritional Risk Index (NRI), and the Naples Prognostic Score (NPS) were applied to assess the nutritional status of participants. A Cox regression model was established to examine the association between malnutrition and cardiovascular and all-cause mortality.

RESULTS

In all, 19.9, 3.9, and 82.9% hypertensive patients were considered to have malnutrition as evaluated by the CONUT, NRI, and NPS, respectively. Malnutrition assessed by CONUT and NRI was independently associated with cardiovascular mortality (HR [95% CI]) for mild and moderate-to-severe degree of malnutrition, respectively: 1.41 (1.04-1.91) and 5.79 (2.34-14.29) for CONUT; 2.60 (1.34-5.07) and 3.30 (1.66-6.56) for NRI (all P < 0.05), and for all-cause mortality (HR [95% CI]) for mild and moderate-to-severe degree of malnutrition, respectively: 1.48 (1.30-1.70) and 4.87 (3.40-6.98) for CONUT; 1.72 (1.24-2.39) and 2.60 (1.96-3.44) for NRI (all P < 0.01). Naples Prognostic Score could only independently predict all-cause mortality.

CONCLUSIONS

Malnutrition was common among hypertensive patients and was closely associated with both long-term cardiovascular and all-cause mortality.

NuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis

Nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, but remains poorly characterized in plants. Here, we describe Arabidopsis homologs of the NuA4 scaffold proteins Enhancer of Polycomb-Like 1 (AtEPL1) and Esa1-Associated Factor 1 (AtEAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors, suggesting that NuA4 activates nuclear plastid genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished genome-wide in Atepl1, while another active chromatin mark, H3K9 acetylation (H3K9ac), is locally enhanced. Expression of many chloroplast-related genes depends on NuA4, as they are downregulated with loss of H4ac and H2A.Zac. Finally, we demonstrate that NuA4 promotes H2A.Z deposition and by doing so prevents spurious activation of stress response genes.

Function of nucleosomal acetyltransferase of H4 (NuA4), one major complex of HAT, remains unclear in plants. Here, the authors generate mutants targeting two components of the putative NuA4 complex in Arabidopsis (EAF1 and EPL1) and show their roles in photosynthesis genes regulation through H4K5ac and H2A.Z acetylation.

F2-Bubbles: Faithful Bubble Set Construction and Flexible Editing

In this paper, we propose F2-Bubbles, a set overlay visualization technique that addresses overlapping artifacts and supports interactive editing with intelligent suggestions. The core of our method is a new, efficient set overlay construction algorithm that approximates the optimal set overlay by considering set elements and their non-set neighbors. Thanks to the efficiency of the algorithm, interactive editing is achieved, and with intelligent suggestions, users can easily and flexibly edit visualizations through direct manipulations with local adaptations. A quantitative comparison with state-of-the-art set visualization techniques and case studies demonstrate the effectiveness of our method and suggests that F2-Bubbles is a helpful technique for set visualization.

Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light-harvesting system, i.e. fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)-FCPII and photosystem I (PSI)-FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identify 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggest that these FCPs can be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and the novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, have orthologous proteins in other diatoms, particularly those found in the PSI-FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII-FCPII complex, seems to be diversified in each diatom species, and the number of Lhcqs differs among species, indicating that their diversification may contribute to species-specific adaptations to light. Further phylogenetic analyses of FCPs/light-harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs is common among various red-lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provide insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage.

Automatic Polygon Layout for Primal-Dual Visualization of Hypergraphs

N-ary relationships, which relate $N$ entities where $N$ is not necessarily two, can be visually represented as polygons whose vertices are the entities of the relationships. Manually generating a high-quality layout using this representation is labor-intensive. In this paper, we provide an automatic polygon layout generation algorithm for the visualization of N-ary relationships. At the core of our algorithm is a set of objective functions motivated by a number of design principles that we have identified. These objective functions are then used in an optimization framework that we develop to achieve high-quality layouts. Recognizing the duality between entities and relationships in the data, we provide a second visualization in which the roles of entities and relationships in the original data are reversed. This can lead to additional insight about the data. Furthermore, we enhance our framework for a joint optimization on the primal layout (original data) and the dual layout (where the roles of entities and relationships are reversed). This allows users to inspect their data using two complementary views. We apply our visualization approach to a number of datasets that include co-authorship data and social contact pattern data.