Numerical investigation of crack propagation regimes in snow fracture experiments

A snow slab avalanche releases after failure initiation and crack propagation in a highly porous weak snow layer buried below a cohesive slab. While our knowledge of crack propagation during avalanche formation has greatly improved over the last decades, it still remains unclear how snow mechanical properties affect the dynamics of crack propagation. This is partly due to a lack of non-invasive measurement methods to investigate the micro-mechanical aspects of the process. Using a DEM model, we therefore analyzed the influence of snow cover properties on the dynamics of crack propagation in weak snowpack layers. By focusing on the steady-state crack speed, our results showed two distinct fracture process regimes that depend on slope angle, leading to very different crack propagation speeds. For long experiments on level terrain, weak layer fracture is mainly driven by compressive stresses. Steady-state crack speed mainly depends on slab and weak layer elastic moduli as well as weak layer strength. We suggest a semi-empirical model to predict crack speed, which can be up to 0.6 times the slab shear wave speed. For long experiments on steep slopes, a supershear regime appeared, where the crack propagation speed reached approximately 1.6 times the slab shear wave speed. A detailed micro-mechanical analysis of stresses revealed a fracture principally driven by shear. Overall, our findings provide new insight into the micro-mechanics of dynamic crack propagation in snow, and how these are linked to snow cover properties.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s10035-024-01423-5.

Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle

Expression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so, the genomic variation is often called from short-read alignments, which are unable to comprehensively resolve structural variation. Here we build a pangenome from 16 HiFi haplotype-resolved cattle assemblies to identify small and structural variation and genotype them with PanGenie in 307 short-read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-called small variation and confidently genotype close to 21 million small and 43,000 structural variants in the larger population. We validate 85% of these structural variants (with MAF > 0.1) directly with a subset of 25 short-read samples that also have medium coverage HiFi reads. We then conduct e/sQTL mapping with this comprehensive variant set in a subset of 117 cattle that have testis transcriptome data, and find 92 structural variants as causal candidates for eQTL and 73 for sQTL. We find that roughly half of the top associated structural variants affecting expression or splicing are transposable elements, such as SV-eQTL for STN1 and MYH7 and SV-sQTL for CEP89 and ASAH2 Extensive linkage disequilibrium between small and structural variation results in only 28 additional eQTL and 17 sQTL discovered when including SVs, although many top associated SVs are compelling candidates.

Complex dental wear analysis reveals dietary shift in Triassic placodonts (Sauropsida, Sauropterygia)

Placodonts were durophagous reptiles of the Triassic seas with robust skulls, jaws, and enlarged, flat, pebble-like teeth. During their evolution, they underwent gradual craniodental changes from the Early Anisian to the Rhaetian, such as a reduction in the number of teeth, an increase in the size of the posterior palatal teeth, an elongation of the premaxilla/rostrum, and a widening of the temporal region. These changes are presumably related to changes in dietary habits, which, we hypothesise, are due to changes in the type and quality of food they consumed. In the present study, the dental wear pattern of a total of nine European Middle to Late Triassic placodont species were investigated using 2D and 3D microwear analyses to demonstrate whether there could have been a dietary shift or grouping among the different species and, whether the possible changes could be correlated with environmental changes affecting their habitats. The 3D analysis shows overlap between species with high variance between values and there is no distinct separation. The 2D analysis has distinguished two main groups. The first is characterised by low number of wear features and high percentage of large pits. The other group have a high feature number, but low percentage of small pits. The 2D analysis showed a correlation between the wear data and the size of the enlarged posterior crushing teeth. Teeth with larger sizes showed less wear feature (with higher pit ratio) but larger individual features. In contrast, the dental wear facet of smaller crushing teeth shows more but smaller wear features (with higher scratch number). This observation may be related to the size of the food consumed, i.e., the wider the crown, the larger food it could crush, producing larger features. Comparison with marine mammals suggests that the dietary preference of Placochelys, Psephoderma and Paraplacodus was not exclusively hard, thick-shelled food. They may have had a more mixed diet, similar to that of modern sea otters. The diet of Henodus may have included plant food, similar to the modern herbivore marine mammals and lizards.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13358-024-00304-x.

Rare copy-number variants as modulators of common disease susceptibility

BACKGROUND

Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described.

METHODS

Assessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank.

RESULTS

We identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs-and especially deletions-strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS.

CONCLUSIONS

Our results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.

De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression

In mammals, the adult testis is the tissue with the highest diversity in gene expression. Much of that diversity is attributed to germ cells, primarily meiotic spermatocytes and postmeiotic haploid spermatids. Exploiting a newly developed cell purification method, we profiled the transcriptomes of such postmitotic germ cells of mice. We used a de novo transcriptome assembly approach and identified thousands of novel expressed transcripts characterized by features distinct from those of known genes. Novel loci tend to be short in length, monoexonic, and lowly expressed. Most novel genes have arisen recently in evolutionary time and possess low coding potential. Nonetheless, we identify several novel protein-coding genes harboring open reading frames that encode proteins containing matches to conserved protein domains. Analysis of mass-spectrometry data from adult mouse testes confirms protein production from several of these novel genes. We also examine overlap between transcripts and repetitive elements. We find that although distinct families of repeats are expressed with differing temporal dynamics during spermatogenesis, we do not observe a general mode of regulation wherein repeats drive expression of nonrepetitive sequences in a cell type-specific manner. Finally, we observe many fairly long antisense transcripts originating from canonical gene promoters, pointing to pervasive bidirectional promoter activity during spermatogenesis that is distinct and more frequent compared with somatic cells.

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3'-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for continuous extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies, while the containers and reproducible workflows could easily be deployed and extended to evaluate new methods or data sets.

Targeted memory reactivation during slow-wave sleep vs. sleep stage N2: no significant differences in a vocabulary task

Sleep supports memory consolidation, and slow-wave sleep (SWS) in particular is assumed to benefit the consolidation of verbal learning material. Re-exposure to previously learned words during SWS with a technique known as targeted memory reactivation (TMR) consistently benefits memory. However, TMR has also been successfully applied during sleep stage N2, though a direct comparison between words selectively reactivated during SWS versus N2 is still missing. Here, we directly compared the effects of N2 TMR and SWS TMR on memory performance in a vocabulary learning task in a within-subject design. Thirty-four healthy young participants (21 in the main sample and 13 in an additional sample) learned 120 Dutch-German word pairs before sleep. Participants in the main sample slept for ∼8 h during the night, while participants in the additional sample slept ∼3 h. We reactivated the Dutch words selectively during N2 and SWS in one single night. Forty words were not cued. Participants in the main sample recalled the German translations of the Dutch words after sleep in the morning, while those in the additional sample did so at 2:00 a.m. As expected, we observed no differences in recall performance between words reactivated during N2 and SWS. However, we failed to find an overall memory benefit of reactivated over nonreactivated words. Detailed time-frequency analyses showed that words played during N2 elicited stronger characteristic oscillatory responses in several frequency bands, including spindle and theta frequencies, compared with SWS. These oscillatory responses did not vary with the memory strengths of individual words. Our results question the robustness and replicability of the TMR benefit on memory using our Dutch vocabulary learning task. We discuss potential boundary conditions for vocabulary reactivation paradigms and, most importantly, see the need for further replication studies, ideally including multiple laboratories and larger sample sizes.

Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites

Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (nuclear RNAi-defective 2), and CCDC174 (coiled-coil domain-containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP-specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use noncanonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice, and accurate pre-mRNA splicing.

Ultra-long-range interactions between active regulatory elements

Contacts between enhancers and promoters are thought to relate to their ability to activate transcription. Investigating factors that contribute to such chromatin interactions is therefore important for understanding gene regulation. Here, we have determined contact frequencies between millions of pairs of cis-regulatory elements from chromosome conformation capture data sets and analyzed a collection of hundreds of DNA-binding factors for binding at regions of enriched contacts. This analysis revealed enriched contacts at sites bound by many factors associated with active transcription. We show that active regulatory elements, independent of cohesin and polycomb, interact with each other across distances of tens of megabases in vertebrate and invertebrate genomes and that interactions correlate and change with activity. However, these ultra-long-range interactions are not dependent on RNA polymerase II transcription or individual transcription cofactors. Using simulations, we show that a model of chromatin and multivalent binding factors can give rise to long-range interactions via bridging-induced clustering. We propose that long-range interactions between cis-regulatory elements are driven by at least three distinct processes: cohesin-mediated loop extrusion, polycomb contacts, and clustering of active regions.

Testing of the siderophore deferoxamine amended in hydrogels for the cleaning of iron corrosion

Bioderived alternatives to commonly used complexing agents for the cleaning of iron artworks are sought for their natural origin and better biodegradability. Indeed, complexing agents currently used for the removal of undesired corrosion products from iron artworks can be difficult to control and their environmental impact is often overlooked. This paper studies the use of siderophores, focusing on the ability of one of them, deferoxamine, to be employed as an active agent loaded in polysaccharides hydrogels, on corrosion phases. Preliminary tests were conducted on artificially aged steel samples and further studies were performed on naturally corroded steel to assess the most performing application parameters. Long-term behavior of cleaned surface was assessed. Cleaning outcomes were compared with those obtainable with disodium ethylenediaminetetraacetic acid using optical microscopy, colorimetry and atomic absorption spectroscopy as well as Infrared and Raman micro-spectroscopies. Among the different gelling agents evaluated, agar applied when hot and gellan gum prepared at room temperature were the most effective gel formulations and agar left few residues over the treated surfaces. The protocol was then tested on altered steel artifacts belonging to heritage institutions in France. Encouraging outcomes in the removal of iron corrosion phases with green approaches are here presented.

Graphical abstract

The Economic Performance of Reunited Families in Switzerland, 2013-2018

Family migration has gained prominence as one of the main reasons for international mobility in both Switzerland and the rest of western European countries. However, research aimed at evaluating the economic performance of reunited families has been constrained by the unavailability of individual income and/or household composition data. The joint use of population registers and information about individuals' social security contributions has allowed us to overcome this limitation. Using transition matrices and logistic models, we assess the economic performance of reunited families at the household level and evaluate differences based on the region of birth of the person initiating the process, as well as the financial situation of these families 5 years after the reunion. The results show a process of economic convergence between the three groups under analysis despite the initial differences in the income level of families, and that most reunited families achieve satisfactory living conditions. They also highlight the hybrid nature of Swiss-headed reunited families, which initially resemble those headed by a non-EU/EFTA person, in terms of the contributions their members make to the household income, but after 5 years they contribute similarly to EU/EFTA headed reunited families.

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

BACKGROUND

We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases.

METHODS

We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.

RESULTS

No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P = 1.1 × 10-4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3-8.2], P = 2.1 × 10-4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1-2635.4], P = 3.4 × 10-3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3-8.4], P = 7.7 × 10-8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10-5).

CONCLUSIONS

Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.

Use of the head-twitch response to investigate the structure-activity relationships of 4-thio-substituted 2,5-dimethoxyphenylalkylamines

RATIONALE

4-Thio-substituted phenylalkylamines such as 2,5-dimethoxy-4-ethylthiophenethylamine (2C-T-2) and 2,5-dimethoxy-4-n-propylthiophenethylamine (2C-T-7) produce psychedelic effects in humans and have been distributed as recreational drugs.

OBJECTIVES

The present studies were conducted to examine the structure-activity relationships (SAR) of a series of 4-thio-substituted phenylalkylamines using the head twitch response (HTR), a 5-HT_2A receptor-mediated behavior induced by psychedelic drugs in mice. The HTR is commonly used as a behavioral proxy in rodents for human psychedelic effects and can be used to discriminate hallucinogenic and non-hallucinogenic 5-HT_2A agonists.

METHODS

HTR dose-response studies with twelve different 4-thio-substituted phenylalkylamines were conducted in male C57BL/6 J mice. To detect the HTR, head movement was recorded electronically using a magnetometer coil and then head twitches were identified in the recordings using a validated method based on artificial intelligence.

RESULTS

2C-T, the parent compound of this series, had relatively low potency in the HTR paradigm, but adding an α-methyl group increased potency fivefold. Potency was also increased when the 4-methylthio group was extended by one to three methylene units. Fluorination of the 4-position alkylthio chain, however, was detrimental for activity, as was the presence of a 4-allylthio substituent versus a propylthio group. 2C-T analogs containing a 4-benzylthio group showed little or no effect in the HTR paradigm, which is consistent with evidence that bulky 4-substituents can dampen agonist efficacy at the 5-HT_2A receptor. Binding and functional studies confirmed that the compounds have nanomolar affinity for 5-HT₂ receptor subtypes and act as partial agonists at 5-HT_2A.

CONCLUSIONS

In general, there were close parallels between the HTR data and the known SAR governing activity of phenylalkylamines at the 5-HT_2A receptor. These findings further support the classification of 2C-T compounds as psychedelic drugs.

Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development

Transposable elements (TEs) contribute to the evolution of gene regulatory networks and are dynamically expressed throughout human brain development and disease. One gene regulatory mechanism influenced by TEs is the miRNA system of post-transcriptional control. miRNA sequences frequently overlap TE loci and this miRNA expression landscape is crucial for control of gene expression in adult brain and different cellular contexts. Despite this, a thorough investigation of the spatiotemporal expression of TE-embedded miRNAs in human brain development is lacking. Here, we identify a spatiotemporally dynamic TE-embedded miRNA expression landscape between childhood and adolescent stages of human brain development. These miRNAs sometimes arise from two apposed TEs of the same subfamily, such as for L2 or MIR elements, but in the majority of cases stem from solo TEs. They give rise to in silico predicted high-confidence pre-miRNA hairpin structures, likely represent functional miRNAs, and have predicted genic targets associated with neurogenesis. TE-embedded miRNA expression is distinct in the cerebellum when compared to other brain regions, as has previously been described for gene and TE expression. Furthermore, we detect expression of previously nonannotated TE-embedded miRNAs throughout human brain development, suggestive of a previously undetected miRNA control network. Together, as with non-TE-embedded miRNAs, TE-embedded sequences give rise to spatiotemporally dynamic miRNA expression networks, the implications of which for human brain development constitute extensive avenues of future experimental research. To facilitate interactive exploration of these spatiotemporal miRNA expression dynamics, we provide the "Brain miRTExplorer" web application freely accessible for the community.

Lossless indexing with counting de Bruijn graphs

Sequencing data are rapidly accumulating in public repositories. Making this resource accessible for interactive analysis at scale requires efficient approaches for its storage and indexing. There have recently been remarkable advances in building compressed representations of annotated (or colored) de Bruijn graphs for efficiently indexing k-mer sets. However, approaches for representing quantitative attributes such as gene expression or genome positions in a general manner have remained underexplored. In this work, we propose counting de Bruijn graphs, a notion generalizing annotated de Bruijn graphs by supplementing each node-label relation with one or many attributes (e.g., a k-mer count or its positions). Counting de Bruijn graphs index k-mer abundances from 2652 human RNA-seq samples in over eightfold smaller representations compared with state-of-the-art bioinformatics tools and is faster to construct and query. Furthermore, counting de Bruijn graphs with positional annotations losslessly represent entire reads in indexes on average 27% smaller than the input compressed with gzip for human Illumina RNA-seq and 57% smaller for Pacific Biosciences (PacBio) HiFi sequencing of viral samples. A complete searchable index of all viral PacBio SMRT reads from NCBI's Sequence Read Archive (SRA) (152,884 samples, 875 Gbp) comprises only 178 GB. Finally, on the full RefSeq collection, we generate a lossless and fully queryable index that is 4.6-fold smaller than the MegaBLAST index. The techniques proposed in this work naturally complement existing methods and tools using de Bruijn graphs, and significantly broaden their applicability: from indexing k-mer counts and genome positions to implementing novel sequence alignment algorithms on top of highly compressed graph-based sequence indexes.

Altered within- and between-host transmission under coinfection underpin parasite co-occurrence patterns in the wild

Interactions among parasite species coinfecting the same host individual can have far reaching consequences for parasite ecology and evolution. How these within-host interactions affect epidemics may depend on two non-exclusive mechanisms: parasite growth and reproduction within hosts, and parasite transmission between hosts. Yet, how these two mechanisms operate under coinfection, and how sensitive they are to the composition of the coinfecting parasite community, remains poorly understood. Here, we test the hypothesis that the relationship between within- and between-host transmission of the fungal pathogen, Phomopsis subordinaria, is affected by co-occurring parasites infecting the host plant, Plantago lanceolata. We conducted a field experiment manipulating the parasite community of transmission source plants, then tracked P. subordinaria within-host transmission, as well as between-host transmission to naïve recipient plants. We find that coinfection with the powdery mildew pathogen, Podosphaera plantaginis, causes increased between-host transmission of P. subordinaria by affecting the number of infected flower stalks in the source plants, resulting from altered auto-infection. In contrast, coinfection with viruses did not have an effect on either within- or between-host transmission. We then analyzed data on the occurrence of P. subordinaria in 2018 and the powdery mildew in a multi-year survey data set from natural host populations to test whether the positive association predicted by our experimental results is evident in field epidemiological data. Consistent with our experimental findings, we observed a positive association in the occurrence of P. subordinaria and historical powdery mildew persistence. Jointly, our experimental and epidemiological results suggest that within- and between-host transmission of P. subordinaria depends on the identity of coinfecting parasites, with potentially far-reaching effects on disease dynamics and parasite co-occurrence patterns in wild populations.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10682-022-10182-9.

An introduction to thermodynamic integration and application to dynamic causal models

In generative modeling of neuroimaging data, such as dynamic causal modeling (DCM), one typically considers several alternative models, either to determine the most plausible explanation for observed data (Bayesian model selection) or to account for model uncertainty (Bayesian model averaging). Both procedures rest on estimates of the model evidence, a principled trade-off between model accuracy and complexity. In the context of DCM, the log evidence is usually approximated using variational Bayes. Although this approach is highly efficient, it makes distributional assumptions and is vulnerable to local extrema. This paper introduces the use of thermodynamic integration (TI) for Bayesian model selection and averaging in the context of DCM. TI is based on Markov chain Monte Carlo sampling which is asymptotically exact but orders of magnitude slower than variational Bayes. In this paper, we explain the theoretical foundations of TI, covering key concepts such as the free energy and its origins in statistical physics. Our aim is to convey an in-depth understanding of the method starting from its historical origin in statistical physics. In addition, we demonstrate the practical application of TI via a series of examples which serve to guide the user in applying this method. Furthermore, these examples demonstrate that, given an efficient implementation and hardware capable of parallel processing, the challenge of high computational demand can be overcome successfully. The TI implementation presented in this paper is freely available as part of the open source software TAPAS.

The extreme rainfall gradient of the Cape Horn Biosphere Reserve and its impact on forest bird richness

A natural laboratory is a place supporting the conditions for hypothesis testing under non-anthropogenic settings. Located at the southern end of the Magellanic sub-Antarctic ecoregion in southwestern South America, the Cape Horn Biosphere Reserve (CHBR) has one of the most extreme rainfall gradients in the world. Subject to oceanic climate conditions, it is also characterized by moderate thermal fluctuations throughout the year. This makes it a unique natural laboratory for studying the effects of extreme rainfall variations on forest bird communities. Here, we monitor the bird species richness in the different forest types present in the CHBR. We found that species richness decreased with increasing precipitation, in which an increase of 100 mm in average annual precipitation showed about 1% decrease in species richness. Similar patterns were found among different forest types within the CHBR. These results provide a baseline to investigate the interactions between physical and biotic factors in a subpolar region that climatically contrasts with boreal forests, which is subject to continental climatic conditions. This research highlights the importance of ecological and ornithological long-term studies in the CHBR, which can contribute both to a higher resolution of the heterogeneity of climate changes in different regions of the world, and to orient conservation policies in the Magellanic sub-Antarctic ecoregion in the face of growing development pressures.

Determining the effects of training duration on the behavioral expression of habitual control in humans: a multilaboratory investigation

It has been suggested that there are two distinct and parallel mechanisms for controlling instrumental behavior in mammals: goal-directed actions and habits. To gain an understanding of how these two systems interact to control behavior, it is essential to characterize the mechanisms by which the balance between these systems is influenced by experience. Studies in rodents have shown that the amount of training governs the relative expression of these two systems: Behavior is goal-directed following moderate training, but the more extensively an instrumental action is trained, the more it becomes habitual. It is less clear whether humans exhibit similar training effects on the expression of goal-directed and habitual behavior, as human studies have reported contradictory findings. To tackle these contradictory findings, we formed a consortium, where four laboratories undertook a preregistered experimental induction of habits by manipulating the amount of training. There was no statistical evidence for a main effect of the amount of training on the formation and expression of habits. However, exploratory analyses suggest a moderating effect of the affective component of stress on the impact of training over habit expression. Participants who were lower in affective stress appeared to be initially goal-directed, but became habitual with increased training, whereas participants who were high in affective stress were already habitual even after moderate training, thereby manifesting insensitivity to overtraining effects. Our findings highlight the importance of the role of moderating variables such as individual differences in stress and anxiety when studying the experimental induction of habits in humans.

Understanding motivation for implementing cooperative learning methods: a value-based approach

The implementation of cooperative learning methods remains disparate in primary schools despite their widely recognised benefits. To explain this paradox, we first examined whether teachers’ inclination towards cooperative methods is motivated by their values. Second, we tested whether motivational connections between personal values and cooperative methods are undermined when conflictual values are activated in context. Study 1 demonstrated that pre-service teachers strongly endorsed self-transcendence (ST) values (expressing compatible motivations with cooperation) relative to self-enhancement (SE) values (expressing conflictual motivations with cooperation). Adherence to ST values was also positively associated with their beliefs and attitudes regarding cooperative methods. In Studies 2, 3 and 4, educational sciences students were experimentally exposed to different contexts, wherein ST, SE or neutral values were promoted. Our findings indicate that when SE values were emphasised in the context, the positive association between ST values and beliefs/attitudes regarding cooperative methods disappeared. Although the results of Study 4 regarding the intention to use cooperative methods were not statistically significant, the pattern was similar. Finally, Study 5 showed that primary school teachers’ ST values positively predicted the self-reported use of cooperative methods when they perceived their school to weakly endorse SE values, but not when they perceived it to strongly endorse them.

Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism

During pre-mRNA maturation 3' end processing can occur at different polyadenylation sites in the 3' untranslated region (3' UTR) to give rise to transcript isoforms that differ in the length of their 3' UTRs. Longer 3' UTRs contain additional cis-regulatory elements that impact the fate of the transcript and/or of the resulting protein. Extensive alternative polyadenylation (APA) has been observed in cancers, but the mechanisms and roles remain elusive. In particular, it is unclear whether the APA occurs in the malignant cells or in other cell types that infiltrate the tumor. To resolve this, we developed a computational method, called SCUREL, that quantifies changes in 3' UTR length between groups of cells, including cells of the same type originating from tumor and control tissue. We used this method to study APA in human lung adenocarcinoma (LUAD). SCUREL relies solely on annotated 3' UTRs and on control systems such as T cell activation, and spermatogenesis gives qualitatively similar results at much greater sensitivity compared to the previously published scAPA method. In the LUAD samples, we find a general trend toward 3' UTR shortening not only in cancer cells compared to the cell type of origin, but also when comparing other cell types from the tumor vs. the control tissue environment. However, we also find high variability in the individual targets between patients. The findings help in understanding the extent and impact of APA in LUAD, which may support improvements in diagnosis and treatment.

Long-Term Imaging of Wound Angiogenesis with Large Scale Optoacoustic Microscopy

Wound healing is a well-coordinated process, necessitating efficient formation of new blood vessels. Vascularization defects are therefore a major risk factor for chronic, non-healing wounds. The dynamics of mammalian tissue revascularization, vessel maturation, and remodeling remain poorly understood due to lack of suitable in vivo imaging tools. A label-free large-scale optoacoustic microscopy (LSOM) approach is developed for rapid, non-invasive, volumetric imaging of tissue regeneration over large areas spanning up to 50 mm with a depth penetration of 1.5 mm. Vascular networks in dorsal mouse skin and full-thickness excisional wounds are imaged with capillary resolution during the course of healing, revealing previously undocumented views of the angiogenesis process in an unperturbed wound environment. Development of an automatic analysis framework enables the identification of key features of wound angiogenesis, including vessel length, diameter, tortuosity, and angular alignment. The approach offers a versatile tool for preclinical research in tissue engineering and regenerative medicine, empowering label-free, longitudinal, high-throughput, and quantitative studies of the microcirculation in processes associated with normal and impaired vascular remodeling, and analysis of vascular responses to pharmacological interventions in vivo.

Screening potential insect vectors in a museum biorepository reveals undiscovered diversity of plant pathogens in natural areas

Phytoplasmas (Mollicutes, Acholeplasmataceae), vector-borne obligate bacterial plant parasites, infect nearly 1,000 plant species and unknown numbers of insects, mainly leafhoppers (Hemiptera, Deltocephalinae), which play a key role in transmission and epidemiology. Although the plant-phytoplasma-insect association has been evolving for >300 million years, nearly all known phytoplasmas have been discovered as a result of the damage inflicted by phytoplasma diseases on crops. Few efforts have been made to study phytoplasmas occurring in noneconomically important plants in natural habitats. In this study, a subsample of leafhopper specimens preserved in a large museum biorepository was analyzed to unveil potential new associations. PCR screening for phytoplasmas performed on 227 phloem-feeding leafhoppers collected worldwide from natural habitats revealed the presence of 6 different previously unknown phytoplasma strains. This indicates that museum collections of herbivorous insects represent a rich and largely untapped resource for discovery of new plant pathogens, that natural areas worldwide harbor a diverse but largely undiscovered diversity of phytoplasmas and potential insect vectors, and that independent epidemiological cycles occur in such habitats, posing a potential threat of disease spillover into agricultural systems. Larger-scale future investigations will contribute to a better understanding of phytoplasma genetic diversity, insect host range, and insect-borne phytoplasma transmission and provide an early warning for the emergence of new phytoplasma diseases across global agroecosystems.

Large and interacting effects of temperature and nutrient addition on stratified microbial ecosystems in a small, replicated, and liquid-dominated Winogradsky column approach

Aquatic ecosystems are often stratified, with cyanobacteria in oxic layers and phototrophic sulfur bacteria in anoxic zones. Changes in stratification caused by the global environmental change are an ongoing concern. Increasing understanding of how such aerobic and anaerobic microbial communities, and associated abiotic conditions, respond to multifarious environmental changes is an important endeavor in microbial ecology. Insights can come from observational and experimental studies of naturally occurring stratified aquatic ecosystems, theoretical models of ecological processes, and experimental studies of replicated microbial communities in the laboratory. Here, we demonstrate a laboratory-based approach with small, replicated, and liquid-dominated Winogradsky columns, with distinct oxic/anoxic strata in a highly replicable manner. Our objective was to apply simultaneous global change scenarios (temperature, nutrient addition) on this micro-ecosystem to report how the microbial communities (full-length 16S rRNA gene seq.) and the abiotic conditions (O2 , H2 S, TOC) of the oxic/anoxic layer responded to these environmental changes. The composition of the strongly stratified microbial communities was greatly affected by temperature and by the interaction of temperature and nutrient addition, demonstrating the need of investigating global change treatments simultaneously. Especially phototrophic sulfur bacteria dominated the water column at higher temperatures and may indicate the presence of alternative stable states. We show that the establishment of such a micro-ecosystem has the potential to test global change scenarios in stratified eutrophic limnic systems.

Popular Attitudes Toward the Distribution of Vaccines Against COVID-19: The Swiss Case

With the arrival of vaccines against the novel coronavirus in late 2020, the issue of how vaccines should be distributed and which groups should be prioritized has become salient. We study popular attitudes toward the distribution of COVID-19 vaccines and how these have changed over the course of the pandemic in Switzerland, drawing on data from two rounds of an original public opinion survey conducted in the spring and winter of 2020. We find that the public supports prioritizing vulnerable groups such as health care workers or the elderly. We also find a notable degree of cross-generational solidarity: younger age cohorts prioritize the elderly, while older groups prioritize (typically younger) health care workers. We then examine whether this finding is not in fact driven by vaccine hesitancy. This is not the case for older age groups, whose solidarity thus seems to be genuine. Vaccine hesitancy is an issue among younger groups, however.

Drought alters the carbon footprint of trees in soils-tracking the spatio-temporal fate of 13 C-labelled assimilates in the soil of an old-growth pine forest

Above and belowground compartments in ecosystems are closely coupled on daily to annual timescales. In mature forests, this interlinkage and how it is impacted by drought is still poorly understood. Here, we pulse-labelled 100-year-old trees with ¹³ CO₂ within a 15-year-long irrigation experiment in a naturally dry pine forest to quantify how drought regime affects the transfer and use of assimilates from trees to the rhizosphere and associated microbial communities. It took 4 days until new ¹³ C-labelled assimilates were allocated to the rhizosphere. One year later, the ¹³ C signal of the 3-h long pulse labelling was still detectable in stem and soil respiration, which provides evidence that parts of the assimilates are stored in trees before they are used for metabolic processes in the rhizosphere. Irrigation removing the natural water stress reduced the mean C residence time from canopy uptake until soil respiration from 89 to 40 days. Moreover, irrigation increased the amount of assimilates transferred to and respired in the soil within the first 10 days by 370%. A small precipitation event rewetting surface soils altered this pattern rapidly and reduced the effect size to +35%. Microbial biomass incorporated 46 ± 5% and 31 ± 7% of the C used in the rhizosphere in the dry control and irrigation treatment respectively. Mapping the spatial distribution of soil-respired ¹³ CO₂ around the 10 pulse-labelled trees showed that tree rhizospheres extended laterally 2.8 times beyond tree canopies, implying that there is a strong overlap of the rhizosphere among adjacent trees. Irrigation increased the rhizosphere area by 60%, which gives evidence of a long-term acclimation of trees and their rhizosphere to the drought regime. The moisture-sensitive transfer and use of C in the rhizosphere has consequences for C allocation within trees, soil microbial communities and soil carbon storage.

Integrating high-speed videos in capture-mark-recapture studies of insects

Capture-mark-recapture (CMR) studies have been used extensively in ecology and evolution. While it is feasible to apply CMR in some animals, it is considerably more challenging in small fast-moving species such as insects. In these groups, low recapture rates can bias estimates of demographic parameters, thereby handicapping effective analysis and management of wild populations. Here, we use high-speed videos (HSV) to capture two large dragonfly species, Anax junius and Rhionaeschna multicolor, that rarely land and, thus, are particularly challenging for CMR studies. We test whether HSV, compared to conventional "eye" observations, increases the "resighting" rates and, consequently, improves estimates of both survival rates and the effects of demographic covariates on survival. We show that the use of HSV increases the number of resights by 64% in A. junius and 48% in R. multicolor. HSV improved our estimates of resighting and survival probability which were either under- or overestimated with the conventional observations. Including HSV improved credible intervals for resighting rate and survival probability by 190% and 130% in A. junius and R. multicolor, respectively. Hence, it has the potential to open the door to a wide range of research possibilities on species that are traditionally difficult to monitor with distance sampling, including within insects and birds.

Contagious Policies? Studying National Responses to a Global Pandemic in Europe

Not only Covid-19 has spread all over the world-the policies responding to this pandemic have also diffused rapidly across countries. In this research note, we present findings from an original dataset that features mobility restrictions in all EU/EFTA states as well as the United Kingdom during the first wave of the pandemic. We find that most countries adopted restrictions within a few days only and that restrictions on internal mobility had been introduced prior to restrictions on cross-border mobility, but that the latter have been more persistent. Furthermore, we observe an evolution from great variation of policy choices at the outset of the pandemic towards convergence. Analyzing the mobility restrictions through a policy diffusion lens, we find tentative evidence for interdependent policy-making especially in the temporal patterns of adoption. Our research note can serve a basis for future research on policy-making and policy diffusion in times of crisis.

Porous Silica Microspheres with Immobilized Titania Nanoparticles for In-Flow Solar-Driven Purification of Wastewater

In this paper, inorganic silica microspheres with interconnected macroporosity are tested as a platform for designing robust and efficient photocatalytic systems for a continuous flow reactor, enabling a low cost and straightforward purification of wastewater through solar-driven photocatalysis. The photocatalytically active microspheres are prepared by wet impregnation of porous silica scaffolds with Trizma-functionalized anatase titania (TiO2) nanoparticles (NPs). NPs loading of 22 wt% is obtained in the form of a thin and well-attached layer, covering the external surface of the microspheres as well as the internal surface of the pores. The TiO2 loading leads to an increase of the specific surface area by 26%, without impacting the typically interconnected macroporosity (≈60%) of the microspheres, which is essential for an efficient flow of the pollutant solution during the photocatalytic tests. These are carried out in a liquid medium for the decomposition of methyl orange and paracetamol. In addition to photocatalytic activity under continuous flow, the microspheres offer the advantage that they can be easily removed from the reaction medium, which is an appealing aspect for industrial applications. In this work, the typical issues of TiO2 NPs photocatalysts are circumvented, without the need for elaborate chemistries, and for low availability and expensive raw materials.

Guidelines for the diagnosis and management of methylmalonic acidaemia and propionic acidaemia: First revision

Isolated methylmalonic acidaemia (MMA) and propionic acidaemia (PA) are rare inherited metabolic diseases. Six years ago, a detailed evaluation of the available evidence on diagnosis and management of these disorders has been published for the first time. The article received considerable attention, illustrating the importance of an expert panel to evaluate and compile recommendations to guide rare disease patient care. Since that time, a growing body of evidence on transplant outcomes in MMA and PA patients and use of precursor free amino acid mixtures allows for updates of the guidelines. In this article, we aim to incorporate this newly published knowledge and provide a revised version of the guidelines. The analysis was performed by a panel of multidisciplinary health care experts, who followed an updated guideline development methodology (GRADE). Hence, the full body of evidence up until autumn 2019 was re-evaluated, analysed and graded. As a result, 21 updated recommendations were compiled in a more concise paper with a focus on the existing evidence to enable well-informed decisions in the context of MMA and PA patient care.

Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction

Multiparameter tissue imaging enables analysis of cell-cell interactions in situ, the cellular basis for tissue structure, and novel cell types that are spatially restricted, giving clues to biological mechanisms behind tissue homeostasis and disease. Here, we streamlined and simplified the multiplexed imaging method CO-Detection by indEXing (CODEX) by validating 58 unique oligonucleotide barcodes that can be conjugated to antibodies. We showed that barcoded antibodies retained their specificity for staining cognate targets in human tissue. Antibodies were visualized one at a time by adding a fluorescently labeled oligonucleotide complementary to oligonucleotide barcode, imaging, stripping, and repeating this cycle. With this we developed a panel of 46 antibodies that was used to stain five human lymphoid tissues: three tonsils, a spleen, and a LN. To analyze the data produced, an image processing and analysis pipeline was developed that enabled single-cell analysis on the data, including unsupervised clustering, that revealed 31 cell types across all tissues. We compared cell-type compositions within and directly surrounding follicles from the different lymphoid organs and evaluated cell-cell density correlations. This sequential oligonucleotide exchange technique enables a facile imaging of tissues that leverages pre-existing imaging infrastructure to decrease the barriers to broad use of multiplexed imaging.

Promoting the Furan Ring-Opening Reaction to Access New Donor-Acceptor Stenhouse Adducts with Hexafluoroisopropanol

Donor-acceptor Stenhouse adducts (DASAs) are visible-light-responsive photoswitches with a variety of emerging applications in photoresponsive materials. Their two-step modular synthesis, centered on the nucleophilic ring opening of an activated furan, makes DASAs readily accessible. However, the use of less reactive donors or acceptors renders the process slow and low yielding, which has limited their development. We demonstrate here that 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) promotes the ring-opening reaction and stabilizes the open isomer, allowing greatly reduced reaction times and increased yields for known derivatives. In addition, it provides access to previously unattainable DASA-based photoswitches and DASA-polymer conjugates. The role of HFIP and the photochromic properties of a set of new DASAs is probed using a combination of 1 H NMR and UV/Vis spectroscopy. The use of sterically hindered, electron-poor amines enabled the dark equilibrium to be decoupled from closed-isomer half-lives for the first time.

The NFIB-ERO1A axis promotes breast cancer metastatic colonization of disseminated tumour cells

Metastasis is the main cause of deaths related to solid cancers. Active transcriptional programmes are known to regulate the metastatic cascade but the molecular determinants of metastatic colonization remain elusive. Using an inducible piggyBac (PB) transposon mutagenesis screen, we have shown that overexpression of the transcription factor nuclear factor IB (NFIB) alone is sufficient to enhance primary mammary tumour growth and lung metastatic colonization. Mechanistically and functionally, NFIB directly increases expression of the oxidoreductase ERO1A, which enhances HIF1α-VEGFA-mediated angiogenesis and colonization, the last and fatal step of the metastatic cascade. NFIB is thus clinically relevant: it is preferentially expressed in the poor-prognostic group of basal-like breast cancers, and high expression of the NFIB/ERO1A/VEGFA pathway correlates with reduced breast cancer patient survival.

Helical Klinotactic Locomotion of Two-Link Nanoswimmers with Dual-Function Drug-Loaded Soft Polysaccharide Hinges

Inspired by the movement of bacteria and other microorganisms, researchers have developed artificial helical micro- and nanorobots that can perform corkscrew locomotion or helical path swimming under external energy actuation. In this paper, for the first time the locomotion of nonhelical multifunctional nanorobots that can swim in helical klinotactic trajectories, similarly to rod-shaped bacteria, under rotating magnetic fields is investigated. These nanorobots consist of a rigid ferromagnetic nickel head connected to a rhodium tail by a flexible hydrogel-based hollow hinge composed of chemically responsive chitosan and alginate multilayers. This design allows nanoswimmers switching between different dynamic behaviors-from in-plane tumbling to helical klinotactic swimming-by varying the rotating magnetic field frequency and strength. It also adds a rich spectrum of swimming capabilities that can be adjusted by varying the type of applied magnetic fields and/or frequencies. A theoretical model is developed to analyze the propulsion mechanisms and predict the swimming behavior at distinct rotating magnetic frequencies. The model shows good agreement with the experimental results. Additionally, the biomedical capabilities of the nanoswimmers as drug delivery platforms are demonstrated. Unlike previous designs constitute metallic segments, the proposed nanoswimmers can encapsulate drugs into their hollow hinge and successfully release them to cells.

Categorizing human vocal signals depends on an integrated auditory-frontal cortical network

Voice signals are relevant for auditory communication and suggested to be processed in dedicated auditory cortex (AC) regions. While recent reports highlighted an additional role of the inferior frontal cortex (IFC), a detailed description of the integrated functioning of the AC-IFC network and its task relevance for voice processing is missing. Using neuroimaging, we tested sound categorization while human participants either focused on the higher-order vocal-sound dimension (voice task) or feature-based intensity dimension (loudness task) while listening to the same sound material. We found differential involvements of the AC and IFC depending on the task performed and whether the voice dimension was of task relevance or not. First, when comparing neural vocal-sound processing of our task-based with previously reported passive listening designs we observed highly similar cortical activations in the AC and IFC. Second, during task-based vocal-sound processing we observed voice-sensitive responses in the AC and IFC whereas intensity processing was restricted to distinct AC regions. Third, the IFC flexibly adapted to the vocal-sounds' task relevance, being only active when the voice dimension was task relevant. Forth and finally, connectivity modeling revealed that vocal signals independent of their task relevance provided significant input to bilateral AC. However, only when attention was on the voice dimension, we found significant modulations of auditory-frontal connections. Our findings suggest an integrated auditory-frontal network to be essential for behaviorally relevant vocal-sounds processing. The IFC seems to be an important hub of the extended voice network when representing higher-order vocal objects and guiding goal-directed behavior.

Outbreaks of publications about emerging infectious diseases: the case of SARS-CoV-2 and Zika virus

BACKGROUND

Outbreaks of infectious diseases generate outbreaks of scientific evidence. In 2016 epidemics of Zika virus emerged, and in 2020, a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic of coronavirus disease 2019 (COVID-19). We compared patterns of scientific publications for the two infections to analyse the evolution of the evidence.

METHODS

We annotated publications on Zika virus and SARS-CoV-2 that we collected using living evidence databases according to study design. We used descriptive statistics to categorise and compare study designs over time.

RESULTS

We found 2286 publications about Zika virus in 2016 and 21,990 about SARS-CoV-2 up to 24 May 2020, of which we analysed a random sample of 5294 (24%). For both infections, there were more epidemiological than laboratory science studies. Amongst epidemiological studies for both infections, case reports, case series and cross-sectional studies emerged first, cohort and case-control studies were published later. Trials were the last to emerge. The number of preprints was much higher for SARS-CoV-2 than for Zika virus.

CONCLUSIONS

Similarities in the overall pattern of publications might be generalizable, whereas differences are compatible with differences in the characteristics of a disease. Understanding how evidence accumulates during disease outbreaks helps us understand which types of public health questions we can answer and when.

Tooling nurses to assess complexity in routine home care practice: Derivation of a complexity index from the interRAI-HC

AIM

Home care nurses often use the Resident Assessment Instrument-Home Care (interRAI-HC) to assess health needs. However, this tool does not assess complexity. This study proposes to derive a complexity index (CI) from the interRAI-HC using the operational definition of the dedicated COMID checklist (COmplexité Multidimensionnelle des prises en soins Infirmières à Domicile).

DESIGN

Data were collected at the baseline assessment of the fraXity study (N = 231, aged ≥ 65), which relied on an observational longitudinal design.

METHODS

Measures were the interRAI-HC, from which the CI binary variables were computed and the COMID, used as a reference.

RESULTS

Twenty-six CI variables were computed from the interRAI-HC, and all but three correlations were significant. The correlation between the CI score and the COMID score was ρ = 0.730 (p < .001).

CONCLUSIONS

The study demonstrates that complexity can be assessed directly from the interRAI-HC by deriving a CI.

Computational prediction method to decipher receptor-glycoligand interactions in plant immunity

Microbial and plant cell walls have been selected by the plant immune system as a source of microbe- and plant damage-associated molecular patterns (MAMPs/DAMPs) that are perceived by extracellular ectodomains (ECDs) of plant pattern recognition receptors (PRRs) triggering immune responses. From the vast number of ligands that PRRs can bind, those composed of carbohydrate moieties are poorly studied, and only a handful of PRR/glycan pairs have been determined. Here we present a computational screening method, based on the first step of molecular dynamics simulation, that is able to predict putative ECD-PRR/glycan interactions. This method has been developed and optimized with Arabidopsis LysM-PRR members CERK1 and LYK4, which are involved in the perception of fungal MAMPs, chitohexaose (1,4-β-d-(GlcNAc)6 ) and laminarihexaose (1,3-β-d-(Glc)6 ). Our in silico results predicted CERK1 interactions with 1,4-β-d-(GlcNAc)6 whilst discarding its direct binding by LYK4. In contrast, no direct interaction between CERK1/laminarihexaose was predicted by the model despite CERK1 being required for laminarihexaose immune activation, suggesting that CERK1 may act as a co-receptor for its recognition. These in silico results were validated by isothermal titration calorimetry binding assays between these MAMPs and recombinant ECDs-LysM-PRRs. The robustness of the developed computational screening method was further validated by predicting that CERK1 does not bind the DAMP 1,4-β-d-(Glc)6 (cellohexaose), and then probing that immune responses triggered by this DAMP were not impaired in the Arabidopsis cerk1 mutant. The computational predictive glycan/PRR binding method developed here might accelerate the discovery of protein-glycan interactions and provide information on immune responses activated by glycoligands.

The circadian oscillator analysed at the single-transcript level

The circadian clock is an endogenous and self-sustained oscillator that anticipates daily environmental cycles. While rhythmic gene expression of circadian genes is well-described in populations of cells, the single-cell mRNA dynamics of multiple core clock genes remain largely unknown. Here we use single-molecule fluorescence in situ hybridisation (smFISH) at multiple time points to measure pairs of core clock transcripts, Rev-erbα (Nr1d1), Cry1 and Bmal1, in mouse fibroblasts. The mean mRNA level oscillates over 24 h for all three genes, but mRNA numbers show considerable spread between cells. We develop a probabilistic model for multivariate mRNA counts using mixtures of negative binomials, which accounts for transcriptional bursting, circadian time and cell-to-cell heterogeneity, notably in cell size. Decomposing the mRNA variability into distinct noise sources shows that clock time contributes a small fraction of the total variability in mRNA number between cells. Thus, our results highlight the intrinsic biological challenges in estimating circadian phase from single-cell mRNA counts and suggest that circadian phase in single cells is encoded post-transcriptionally.

Cost-effectiveness of statins for primary prevention of atherosclerotic cardiovascular disease among people living with HIV in the United States

BACKGROUND

Expanding statin use may help to alleviate the excess burden of atherosclerotic cardiovascular disease in people living with HIV (PLHIV). Pravastatin and pitavastatin are preferred agents due to their lack of substantial interaction with antiretroviral therapy. We aimed to evaluate the cost-effectiveness of pravastatin and pitavastatin for the primary prevention of atherosclerotic cardiovascular disease among PLHIV in the United States.

METHODS

We developed a microsimulation model that randomly selected (with replacement) individuals from the Data-collection on Adverse Effects of Anti-HIV Drugs study with follow-up between 2013 and 2016. Our study population was PLHIV aged 40 to 75 years, stable on antiretroviral therapy, and not currently using lipid-lowering therapy. Direct medical costs and quality-adjusted life-years (QALYs) were assigned in annual cycles and discounted at 3% per year. We assumed a willingness-to-pay threshold of $100,000/QALY gained. The interventions assessed were as follows: (1) treating no one with statins; (2) treating everyone with generic pravastatin 40 mg/day (drug cost $236/year) and (3) treating everyone with branded pitavastatin 4 mg/day (drug cost $2,828/year). The model simulated each individual's probability of experiencing atherosclerotic cardiovascular disease over 20 years.

RESULTS

Persons receiving pravastatin accrued 0.024 additional QALYs compared with those not receiving a statin, at an incremental cost of $1338, giving an incremental cost-effectiveness ratio of $56,000/QALY gained. Individuals receiving pitavastatin accumulated 0.013 additional QALYs compared with those using pravastatin, at an additional cost of $18,251, giving an incremental cost-effectiveness ratio of $1,444,000/QALY gained. These findings were most sensitive to the pill burden associated with daily statin administration, statin costs, statin efficacy and baseline atherosclerotic cardiovascular disease risk. In probabilistic sensitivity analysis, no statin was optimal in 5.2% of simulations, pravastatin was optimal in 94.8% of simulations and pitavastatin was never optimal.

CONCLUSIONS

Pravastatin was projected to be cost-effective compared with no statin. With substantial price reduction, pitavastatin may be cost-effective compared with pravastatin. These findings bode well for the expanded use of statins among PLHIV in the United States. To gain greater confidence in our conclusions it is important to generate strong, HIV-specific estimates on the efficacy of statins and the quality-of-life burden associated with taking an additional daily pill.

Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species

Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors. We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing. We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally. These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.

Band Structure Extraction at Hybrid Narrow-Gap Semiconductor-Metal Interfaces

The design of epitaxial semiconductor-superconductor and semiconductor-metal quantum devices requires a detailed understanding of the interfacial electronic band structure. However, the band alignment of buried interfaces is difficult to predict theoretically and to measure experimentally. This work presents a procedure that allows to reliably determine critical parameters for engineering quantum devices; band offset, band bending profile, and number of occupied quantum well subbands of interfacial accumulation layers at semiconductor-metal interfaces. Soft X-ray angle-resolved photoemission is used to directly measure the quantum well states as well as valence bands and core levels for the InAs(100)/Al interface, an important platform for Majorana-zero-mode based topological qubits, and demonstrate that the fabrication process strongly influences the band offset, which in turn controls the topological phase diagrams. Since the method is transferable to other narrow gap semiconductors, it can be used more generally for engineering semiconductor-metal and semiconductor-superconductor interfaces in gate-tunable superconducting devices.

Thermodynamics and Dynamics of Supercritical Water Pseudo-Boiling

Supercritical fluid pseudo-boiling (PB), recently brought to the attention of the scientific community, is the phenomenon occurring when fluid changes its structure from liquid-like (LL) to gas-like (GL) states across the Widom line. This work provides the first quantitative analysis on the thermodynamics and the dynamics of water's PB, since the understanding of this phase transition is mandatory for the successful implementation of technologies using supercritical water (scH2O) for environmental, energy, and nanomaterial applications. The study combines computational techniques with in situ neutron imaging measurements. The results demonstrate that, during isobaric heating close to the critical point, while water density drops by a factor of three in the PB transitional region, the system needs >16 times less energy to increase its temperature by 1 K than to change its structure from LL to GL phase. Above the PB-Widom line, the structure of LL water consists mainly of tetramers and trimers, while below the line mostly dimers and monomers form in the GL phase. At atomic level, the PB dynamics are similar to those of the subcritical water vaporization. This fundamental knowledge has great impact on water science, as it helps to establish the structure-properties relationship of scH2O.

Chemical Modification of Reducing End-Groups in Cellulose Nanocrystals

Native plant cellulose has an intrinsic supramolecular structure. Consequently, it can be isolated as nanocellulose species, which can be utilized as building blocks for renewable nanomaterials. The structure of cellulose also permits its end-wise modification, i.e., chemical reactions exclusively on one end of a cellulose chain or a nanocellulose particle. The premises for end-wise modification have been known for decades. Nevertheless, different approaches for the reactions have emerged only recently, because of formidable synthetic and analytical challenges associated with the issue, including the adverse reactivity of the cellulose reducing end and the low abundance of newly introduced functionalities. This Review gives a full account of the scientific underpinnings and challenges related to end-wise modification of cellulose nanocrystals. Furthermore, we present how the chemical modification of cellulose nanocrystal ends may be applied to directed assembly, resulting in numerous possibilities for the construction of new materials, such as responsive liquid crystal templates and composites with tailored interactions.

Underuse of medical thromboprophylaxis in mobile elderly inpatients: The SWITCO65+ cohort

BACKGROUND

Hospital-associated venous thromboembolism (HA-VTE) can be prevented by pharmacologic thromboprophylaxis. Thrombotic risk assessment models (RAMs) are essential tools to improve inadequately prescribed thromboprophylaxis. Among cases of HA-VTE, our study objectives are to explore the classifications of available thrombosis RAMs, the adequacy of thromboprophylaxis and risk factors for inadequate thromboprophylaxis.

METHODS

We identified cases of HA-VTE occurring during medical hospitalizations within a multicenter Swiss venous thromboembolism (VTE) cohort (2009-2013). We calculated the proportion of VTE cases deemed at high risk with 4 VTE RAMs (Geneva, Simplified Geneva, Padua, and Improve) and the adequacy of administered pharmacologic thromboprophylaxis, and explored risk factors for underprescription of thromboprophylaxis in high-risk inpatients.

RESULTS

Among 66 medical inpatients with HA-VTE, 60.6% had pulmonary embolism. The sensitivities of the Geneva, Simplified Geneva, Padua, and Improve RAMs were 86.4%, 80.3%, 72.7%, and 57.6%, respectively. The proportion of inadequate thromboprophylaxis was high, as 62.5%-71.1% of high-risk inpatients had not received it. Among the high-risk group according to the Simplified Geneva RAM, absence of immobilization was the only variable significantly associated with an inadequate use of thromboprophylaxis (odds ratio, 3.59; 95% confidence interval, 1.08-11.88).

CONCLUSIONS

We found a dramatically high proportion of inadequate medical thromboprophylaxis among inpatients who suffered from HA-VTE. This reinforces the need for global and local quality-improvement efforts to promote adequate use of thromboprophylaxis in elderly inpatients. Mobility may favor the underuse of thromboprophylaxis, and clinicians should stay alert to other thrombotic risk factors in mobile inpatients.

Kilogram-Scale Crystallogenesis of Halide Perovskites for Gamma-Rays Dose Rate Measurements

Gamma-rays (γ-rays), wherever present, e.g., in medicine, nuclear environment, or homeland security, due to their strong impact on biological matter, should be closely monitored. There is a need for simple, sensitive γ-ray detectors at affordable prices. Here, it is shown that γ-ray detectors based on crystals of methylammonium lead tribromide (MAPbBr3) ideally meet these requirements. Specifically, the γ-rays incident on a MAPbBr3 crystal generates photocarriers with a high mobility-lifetime product, allowing radiation detection by photocurrent measurements at room temperatures. Moreover, the MAPbBr3 crystal-based detectors, equipped with improved carbon electrodes, can operate at low bias (≈1.0 V), hence being suitable for applications in energy-sparse environments, including space. The γ-ray detectors reported herein are exposed to radiation from a 60Co source at dose rates up to 2.3 Gy h-1 under ambient conditions for over 100 h, without any sign of degradation. The excellent radiation tolerance stems from the intrinsic structural plasticity of the organic-inorganic halide perovskites, which can be attributed to a defect-healing process by fast ion migration at the nanoscale level. The sensitivity of the γ-ray detection upon volume is tested for MAPbBr3 crystals reaching up to 1000 cm3 (3.3 kg in weight) grown by a unique crystal growth technique.

Mechanistic Understanding of CaO-Based Sorbents for High-Temperature CO2 Capture: Advanced Characterization and Prospects

Carbon dioxide capture and storage technologies are short to mid-term solutions to reduce anthropogenic CO₂ emissions. CaO-based sorbents have emerged as a viable class of cost-efficient CO₂ sorbents for high temperature applications. Yet, CaO-based sorbents are prone to deactivation over repeated CO₂ capture and regeneration cycles. Various strategies have been proposed to improve their cyclic stability and rate of CO₂ uptake including the addition of promoters and stabilizers (e. g., alkali metal salts and metal oxides), as well as nano-structuring approaches. However, our fundamental understanding of the underlying mechanisms through which promoters or stabilizers affect the performance of the sorbents is limited. With the recent application of advanced characterization techniques, new insight into the structural and morphological changes that occur during CO₂ uptake and regeneration has been obtained. This review summarizes recent advances that have improved our mechanistic understanding of CaO-based CO₂ sorbents with and without the addition of stabilizers and/or promoters, with a specific emphasis on the application of advanced characterization techniques.

Mechanical and biological characterization of a composite annulus fibrosus repair strategy in an endplate delamination model

This study compares the mechanical response of the commonly used annulus fibrosus (AF) puncture injury model of the intervertebral disc (IVD) and a newly proposed AF failure at the endplate junction (delamination) on ex vivo bovine IVDs. Biocompatibility and mechanics of a newly developed repair strategy comprising of electrospun polycaprolactone (PCL) scaffold and fibrin-genipin (FibGen) adhesive was tested on the delamination model. The study found no significant difference in the mechanical response to compressive loading between the two models. Primary goals of the repair strategy to create a tight seal on the damage area and restore mechanical properties, while showing minimal cytotoxicity, were broadly achieved. Postrepair, the IVDs showed a significant restoration of mechanical properties compared to the injured samples for the delamination model. The FibGen glue showed a limited toxicity in the AF and produced a resilient and mechanically stable seal on the damaged area.

The core clock transcription factor BMAL1 drives circadian β-cell proliferation during compensatory regeneration of the endocrine pancreas

Circadian clocks in pancreatic islets participate in the regulation of glucose homeostasis. Here we examined the role of these timekeepers in β-cell regeneration after the massive ablation of β cells by doxycycline-induced expression of diphtheria toxin A (DTA) in Insulin-rtTA/TET-DTA mice. Since we crossed reporter genes expressing α- and β-cell-specific fluorescent proteins into these mice, we could follow the fate of α- and β cells separately. As expected, DTA induction resulted in an acute hyperglycemia, which was accompanied by dramatic changes in gene expression in residual β cells. In contrast, only temporal alterations of gene expression were observed in α cells. Interestingly, β cells entered S phase preferentially during the nocturnal activity phase, indicating that the diurnal rhythm also plays a role in the orchestration of β-cell regeneration. Indeed, in arrhythmic Bmal1-deficient mice, which lack circadian clocks, no compensatory β-cell proliferation was observed, and the β-cell ablation led to aggravated hyperglycemia, hyperglucagonemia, and fatal diabetes.