From regional climate models to usable information

Today, a major challenge for climate science is to overcome what is called the "usability gap" between the projections derived fromclimate models and the needs of the end-users. Regional Climate Models (RCMs) are expected to provide usable information concerning a variety of impacts and for a wide range of end-users. It is often assumed that the development of more accurate, more complex RCMs with higher spatial resolution should bring process understanding and better local projections, thus overcoming the usability gap. In this paper, I rather assume that the credibility of climate information should be pursued together with two other criteria of usability, which are salience and legitimacy. Based on the Swiss climate change scenarios, I study the attempts at meeting the needs of end-users and outline the trade-off modellers and users have to face with respect to the cascade of uncertainty. A conclusion of this paper is that the trade-off between salience and credibility sets the conditions under which RCMs can be deemed adequate for the purposes of addressing the needs of end-users and gearing the communication of the projections toward direct use and action.

Job satisfaction across Europe: An analysis of the heterogeneous temporary workforce in 27 countries

The consequences of temporary jobs for job satisfaction are not clear. This article examines the effect of two crucial moderators in the association between temporary contracts and job satisfaction: the reason for being a temporary worker and the duration of temporary contracts. Using the ad-hoc module of the 2017 EU Labour Force Survey (EU-LFS), this study examines 27 European countries separately. Results show that involuntary temporary workers (those who wanted a permanent contract but could not find one) tend to be less satisfied than permanent employees. However, voluntary temporary workers (those who prefer temporary over permanent jobs) and temporary workers in apprenticeships or probation periods are generally as satisfied as permanent employees. Shorter contracts frequently exert negative effects on job satisfaction, but only among involuntary temporary workers. Results differ between countries: the differences between temporary and permanent workers are insignificant in Scandinavian countries but large in the post-Socialist states.

Renouncing the attempt versus perpetration distinction

Legal and moral luck goes against the basic principle of criminal law that responsibility ascriptions are based on the mental state of the perpetrator, rather than merely the outcome of her action. If outcome should not play a decisive role in responsibility ascriptions, the attempt versus perpetration distinction becomes more difficult to justify. One potential justification is that we never know whether the attempter would not have resigned from pursuing her criminal intent even at the last moment. However, this paper argues that resigning from criminal intent and trying to stop the criminal outcome, which is called the renunciation defense, can be just as subject to outcome luck as the attempt versus perpetration distinction. And yet the availability of the renunciation defense in court is outcome dependent. I show with a series of experiments (N = 479) that outcome dependence for the renunciation defense is perceived as unjust and discuss the implications for the renunciation defense as well as attempt versus perpetration distinction.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11229-022-04000-6.

Taming the torrent: changes in flood protection at the Gürbe River (Switzerland) from the nineteenth century until today

This paper analyses the flood protection history of the Gürbe River (Switzerland), a 29-km-long tributary of the Aare River. The upper reach of the river has the character of a mountain torrent and an exceptionally difficult flooding situation. For centuries, riparian communities were only able to take small protective measures. In the mid-nineteenth century, the flood protection strategy changed: between 1855 and 1881, the Gürbe River was channelised and stabilised by a torrent control system. Although the situation improved, flood damage could not be prevented as intended. Therefore, dozens of consecutive projects were implemented-without interruption until today. This paper examines why small watercourses are useful case studies, which protection measures were taken at the Gürbe River, how they corresponded to the prevailing flood protection philosophy, whether they were linked to floods and how flood protection influenced land use. The Gürbe regulation, its consecutive projects and the connected drainages had far-reaching effects: They allowed an intensive agricultural use of the valley floor, the construction of roads, a railway, and new settlements. Consequently, the social and economic pressure on the hazard area increased steadily over the decades. It created a vicious circle: the more that protective structures were built, the more important and profitable flood prevention became, and the more structures were raised. A reevaluation finally took place in the late twentieth century, based on increasing environmental awareness, and fostered by a catastrophic flood. However, the implementation of new projects proved to be difficult due to conflicting interests.

In vivo Imaging of Cannabinoid Type 2 Receptors: Functional and Structural Alterations in Mouse Model of Cerebral Ischemia by PET and MRI

PURPOSE

Stroke is one of the most prevalent vascular diseases. Non-invasive molecular imaging methods have the potential to provide critical insights into the temporal dynamics and follow alterations of receptor expression and metabolism in ischemic stroke. The aim of this study was to assess the cannabinoid type 2 receptor (CB2R) levels in transient middle cerebral artery occlusion (tMCAO) mouse models at subacute stage using positron emission tomography (PET) with our novel tracer [18F]RoSMA-18-d6 and structural imaging by magnetic resonance imaging (MRI).

PROCEDURES

Our recently developed CB2R PET tracer [18F]RoSMA-18-d6 was used for imaging neuroinflammation at 24 h after reperfusion in tMCAO mice. The RNA expression levels of CB2R and other inflammatory markers were analyzed by quantitative real-time polymerase chain reaction using brain tissues from tMCAO (1 h occlusion) and sham-operated mice. [18F]fluorodeoxyglucose (FDG) was included for evaluation of the cerebral metabolic rate of glucose (CMRglc). In addition, diffusion-weighted imaging and T2-weighted imaging were performed for anatomical reference and delineating the lesion in tMCAO mice.

RESULTS

mRNA expressions of inflammatory markers TNF-α, Iba1, MMP9 and GFAP, CNR2 were increased to 1.3-2.5 fold at 24 h after reperfusion in the ipsilateral compared to contralateral hemisphere of tMCAO mice, while mRNA expression of the neuronal marker MAP-2 was markedly reduced to ca. 50 %. Reduced [18F]FDG uptake was observed in the ischemic striatum of tMCAO mouse brain at 24 h after reperfusion. Although higher activity of [18F]RoSMA-18-d6 in ex vivo biodistribution studies and higher standard uptake value ratio (SUVR) were detected in the ischemic ipsilateral compared to contralateral striatum in tMCAO mice, the in vivo specificity of [18F]RoSMA-18-d6 was confirmed only in the CB2R-rich spleen.

CONCLUSIONS

This study revealed an increased [18F]RoSMA-18-d6 measure of CB2R and a reduced [18F]FDG measure of CMRglc in the ischemic striatum of tMCAO mice at subacute stage. [18F]RoSMA-18-d6 might be a promising PET tracer for detecting CB2R alterations in animal models of neuroinflammation without neuronal loss.

The Importance of Understanding Deep Learning

Some machine learning models, in particular deep neural networks (DNNs), are not very well understood; nevertheless, they are frequently used in science. Does this lack of understanding pose a problem for using DNNs to understand empirical phenomena? Emily Sullivan has recently argued that understanding with DNNs is not limited by our lack of understanding of DNNs themselves. In the present paper, we will argue, contra Sullivan, that our current lack of understanding of DNNs does limit our ability to understand with DNNs. Sullivan's claim hinges on which notion of understanding is at play. If we employ a weak notion of understanding, then her claim is tenable, but rather weak. If, however, we employ a strong notion of understanding, particularly explanatory understanding, then her claim is not tenable.

Technology Adoption and Early Network Infrastructure Provision in the Market for Electric Vehicles

We document non-linear stock effects in the relationship linking emerging technology adoption and network infrastructure increments. We exploit 2010-2017 data covering nascent to mature electric vehicle (EV) markets across 422 Norwegian municipalities together with two complementary identification strategies: control function regressions of EV sales on flexible polynomials in the stock of charging stations and charging points, and synthetic control methods to quantify the impact of initial infrastructure provision in municipalities that previously had none. Our results are consistent with indirect network effects and the behavioral bias called "range anxiety," and support policies targeting early infrastructure provision to incentivize EV adoption.

Designing libraries for pooled CRISPR functional screens of long noncoding RNAs

Human and other genomes encode tens of thousands of long noncoding RNAs (lncRNAs), the vast majority of which remain uncharacterised. High-throughput functional screening methods, notably those based on pooled CRISPR-Cas perturbations, promise to unlock the biological significance and biomedical potential of lncRNAs. Such screens are based on libraries of single guide RNAs (sgRNAs) whose design is critical for success. Few off-the-shelf libraries are presently available, and lncRNAs tend to have cell-type-specific expression profiles, meaning that library design remains in the hands of researchers. Here we introduce the topic of pooled CRISPR screens for lncRNAs and guide readers through the three key steps of library design: accurate annotation of transcript structures, curation of optimal candidate sets, and design of sgRNAs. This review is a starting point and reference for researchers seeking to design custom CRISPR screening libraries for lncRNAs.

DNA Methyltransferase 3 (MET3) is regulated by Polycomb group complex during Arabidopsis endosperm development

Complex epigenetic changes occur during plant reproduction. These regulations ensure the proper transmission of epigenetic information as well as allowing for zygotic totipotency. In Arabidopsis, the main DNA methyltransferase is called MET1 and is responsible for methylating cytosine in the CG context. The Arabidopsis genome encodes for three additional reproduction-specific homologs of MET1, namely MET2a, MET2b and MET3. In this paper, we show that the DNA methyltransferase MET3 is expressed in the seed endosperm and its expression is later restricted to the chalazal endosperm. MET3 is biallelically expressed in the endosperm but displays a paternal expression bias. We found that MET3 expression is regulated by the Polycomb complex proteins FIE and MSI1. Seed development is not impaired in met3 mutant, and we could not observe significant transcriptional changes in met3 mutant. MET3 might regulates gene expression in a Polycomb mutant background suggesting a further complexification of the interplay between H3K27me3 and DNA methylation in the seed endosperm. KEY MESSAGE: The DNA METHYLTRANSFERASE MET3 is controlled by Polycomb group complex during endosperm development.

Detailing the effects of polypharmacy in psychiatry: longitudinal study of 320 patients hospitalized for depression or schizophrenia

Current treatment standards in psychiatry are oriented towards polypharmacy, that is, patients receive combinations of several antidepressants, antipsychotics, mood stabilizers, anxiolytics, hypnotics, antihistamines, and anticholinergics, along with other somatic treatments. In tandem with the beneficial effects of psychopharmacological drug treatment, patients experience significant adverse reactions which appear to have become more frequent and more severe with the rise of ubiquitous polypharmacy. In this study, we aimed to assess today's acute inpatient treatment of depressive and schizophrenic disorders with focus on therapeutic strategies, medications, adverse side effects, time course of recovery, and efficacy of treatments. Of particular interest was the weighing of the benefits and drawbacks of polypharmacy regimens. We recruited a total of 320 patients hospitalized at three residential mental health treatment centers with a diagnosis of either schizophrenic (ICD-10: "F2x.x"; n = 94; "F2 patients") or depressive disorders (ICD-10: "F3x.x"; n = 226; "F3 patients"). The study protocol included (1) assessment of previous history by means of the SADS Syndrome Check List SSCL-16 (lifetime version); (2) repeated measurements over 5 weeks assessing the time course of improvement by the Hamilton Depression Scale HAM-D and the Positive and Negative Syndrome Scale PANSS, along with medications and adverse side effects through the Medication and Side Effects Inventory MEDIS; and (3) the collection of blood samples from which DNA and serum were extracted. Polypharmacy was by far the most common treatment regimen (85%) in this study. On average, patients received 4.50 ± 2.68 medications, consisting of 3.30 ± 1.84 psychotropic drugs, plus 0.79 ± 1.13 medications that alleviate adverse side effects, plus 0.41 ± 0.89 other somatic medications. The treating psychiatrists appeared to be the main determining factor in this context, while «previous history» and «severity at baseline» played a minor role, if at all. Adverse drug reactions were found to be an inherent component of polypharmacy and tended to have a 2-3 times higher incidence compared to monotherapy. Severe adverse reactions could not be attributed to a particular drug or drug combination. Rather, the empirical data suggested that severe side effects can be triggered by virtually all combinations of drugs, provided patients have a respective vulnerability. In terms of efficacy, there were no advantages of polypharmacy over monotherapy. The results of this study underlined the fact that polypharmacy regimens are not equally suited for every patient. Specifically, such regimens appeared to have a negative impact on treatment outcome and to obfuscate the "natural" time course of recovery through a multitude of interfering factors. Evidence clearly speaks against starting just every therapeutic intervention in psychiatry with a combination of psychopharmaceuticals. We think that it is time for psychiatry to reconsider its treatment strategies, which are far too one-sidedly fixated on psychopharmacology and pay far too little attention to alternative approaches, especially in mild cases where psychotherapy without concurrent medication should still be an option. Also, regular exercises and sports can definitely be an effective therapeutic means in a considerable number of cases. General practitioners (GPs) are particularly in demand here.

Leveraging human resources for outbreak analysis: lessons from an international collaboration to support the sub-Saharan African COVID-19 response

Emerging infectious diseases are a growing threat in sub-Saharan African countries, but the human and technical capacity to quickly respond to outbreaks remains limited. Here, we describe the experience and lessons learned from a joint project with the WHO Regional Office for Africa (WHO AFRO) to support the sub-Saharan African COVID-19 response.In June 2020, WHO AFRO contracted a number of consultants to reinforce the COVID-19 response in member states by providing actionable epidemiological analysis. Given the urgency of the situation and the magnitude of work required, we recruited a worldwide network of field experts, academics and students in the areas of public health, data science and social science to support the effort. Most analyses were performed on a merged line list of COVID-19 cases using a reverse engineering model (line listing built using data extracted from national situation reports shared by countries with the Regional Office for Africa as per the IHR (2005) obligations). The data analysis platform The Renku Project ( https://renkulab.io ) provided secure data storage and permitted collaborative coding.Over a period of 6 months, 63 contributors from 32 nations (including 17 African countries) participated in the project. A total of 45 in-depth country-specific epidemiological reports and data quality reports were prepared for 28 countries. Spatial transmission and mortality risk indices were developed for 23 countries. Text and video-based training modules were developed to integrate and mentor new members. The team also began to develop EpiGraph Hub, a web application that automates the generation of reports similar to those we created, and includes more advanced data analyses features (e.g. mathematical models, geospatial analyses) to deliver real-time, actionable results to decision-makers.Within a short period, we implemented a global collaborative approach to health data management and analyses to advance national responses to health emergencies and outbreaks. The interdisciplinary team, the hands-on training and mentoring, and the participation of local researchers were key to the success of this initiative.

CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation

Characterising gene function for the ever-increasing number and diversity of species with annotated genomes relies almost entirely on computational prediction methods. These software are also numerous and diverse, each with different strengths and weaknesses as revealed through community benchmarking efforts. Meta-predictors that assess consensus and conflict from individual algorithms should deliver enhanced functional annotations. To exploit the benefits of meta-approaches, we developed CrowdGO, an open-source consensus-based Gene Ontology (GO) term meta-predictor that employs machine learning models with GO term semantic similarities and information contents. By re-evaluating each gene-term annotation, a consensus dataset is produced with high-scoring confident annotations and low-scoring rejected annotations. Applying CrowdGO to results from a deep learning-based, a sequence similarity-based, and two protein domain-based methods, delivers consensus annotations with improved precision and recall. Furthermore, using standard evaluation measures CrowdGO performance matches that of the community’s best performing individual methods. CrowdGO therefore offers a model-informed approach to leverage strengths of individual predictors and produce comprehensive and accurate gene functional annotations.

New technologies mean that we are able to read the genetic blueprints in the form of complete genome sequences from many different species. We are also able to use computational methods combined with evidence from experiments to map out the locations in the genomes of many thousands of genes and other important regions. However, discovering and characterising the biological functions of all these genes and their protein products requires considerably more experimental work. In order to gain insights into the possible functions of the many genes currently lacking functional information from experiments we must therefore rely on methods that computationally predict protein functions. Many different software tools have been developed to tackle this challenge, each with their own strengths and weaknesses as shown by several community-based competitions that assess the performance of the predictors. Taking advantage of powerful modern machine learning techniques, we developed CrowdGO, a new software that aims to combine predictions from several tools and produce comprehensive and accurate gene functional annotations. CrowdGO is able to computationally assess agreements and conflicts amongst annotations from different predictors to then re-evaluate the results and deliver enhanced predictions of protein functions.

Conservation of Forces and Total Work at the Interface Using the Internodes Method

The Internodes method is a general purpose method to deal with non-conforming discretizations of partial differential equations on 2D and 3D regions partitioned into disjoint subdomains. In this paper we are interested in measuring how much the Internodes method is conservative across the interface. If hp-fem discretizations are employed, we prove that both the total force and total work generated by the numerical solution at the interface of the decomposition vanish in an optimal way when the mesh size tends to zero, i.e., like O ( h p ) , where p is the local polynomial degree and h the mesh-size. This is the same as the error decay in the H ¹-broken norm. We observe that the conservation properties of a method are intrinsic to the method itself because they depend on the way the interface conditions are enforced rather then on the problem we are called to approximate. For this reason, in this paper, we focus on second-order elliptic PDEs, although we use the terminology (of forces and works) proper of linear elasticity. Two and three dimensional numerical experiments corroborate the theoretical findings, also by comparing Internodes with Mortar and WACA methods.

Quadrature-free immersed isogeometric analysis

This paper presents a novel method for solving partial differential equations on three-dimensional CAD geometries by means of immersed isogeometric discretizations that do not require quadrature schemes. It relies on a newly developed technique for the evaluation of polynomial integrals over spline boundary representations that is exclusively based on analytical computations. First, through a consistent polynomial approximation step, the finite element operators of the Galerkin method are transformed into integrals involving only polynomial integrands. Then, by successive applications of the divergence theorem, those integrals over B-Reps are transformed into the first surface and then line integrals with polynomials integrands. Eventually, these line integrals are evaluated analytically with machine precision accuracy. The performance of the proposed method is demonstrated by means of numerical experiments in the context of 2D and 3D elliptic problems, retrieving optimal error convergence order in all cases. Finally, the methodology is illustrated for 3D CAD models with an industrial level of complexity.

Traces of a prehistoric and potentially tsunamigenic mass movement in the sediments of Lake Thun (Switzerland)

Mass movements constitute major natural hazards in the Alpine realm. When triggered on slopes adjacent to lakes, these mass movements can generate tsunami-like waves that may cause additional damage along the shore. For hazard assessment, knowledge about the occurrence, the trigger and the geomechanical and hydrogeological mechanisms of these mass movements is necessary. For reconstructing mass movements that occurred in or adjacent to lakes, the lakes's sedimentary record can be used as an archive. Here, we present a prehistorical mass-movement event, of which the traces were found in an alpine lake, Lake Thun, in central Switzerland. The mass movement is identified by large blocks on the bathymetric map, a chaotic to transparent facies on the reflection seismic profiles, and by a mixture of deformed lake sediments and sandy organic-rich layers in the sediment-core record. The event is dated at 2642-2407 cal year BP. With an estimated volume of ~ 20 × 10⁶ m³ it might have generated a wave with an initial amplitude of > 30 m. In addition to this prehistorical event, two younger deposits were identified in the sedimentary record. One could be dated at 1523-1361 cal year BP and thus can be potentially related to an event in 598/599 AD documented in historical reports. The youngest deposit is dated at 304-151 cal year BP (1646-1799 AD) and is interpreted to be related to the artificial Kander river deviation into Lake Thun (1714 AD).

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s00015-022-00405-0.

TMED2 binding restricts SMO to the ER and Golgi compartments

Hedgehog (HH) signaling is important for embryonic pattering and stem cell differentiation. The G protein–coupled receptor (GPCR) Smoothened (SMO) is the key HH signal transducer modulating both transcription-dependent and transcription-independent responses. We show that SMO protects naive mouse embryonic stem cells (ESCs) from dissociation-induced cell death. We exploited this SMO dependency to perform a genetic screen in haploid ESCs where we identify the Golgi proteins TMED2 and TMED10 as factors for SMO regulation. Super-resolution microscopy shows that SMO is normally retained in the endoplasmic reticulum (ER) and Golgi compartments, and we demonstrate that TMED2 binds to SMO, preventing localization to the plasma membrane. Mutation of TMED2 allows SMO accumulation at the plasma membrane, recapitulating early events after HH stimulation. We demonstrate the physiologic relevance of this interaction in neural differentiation, where TMED2 functions to repress HH signal strength. Identification of TMED2 as a binder and upstream regulator of SMO opens the way for unraveling the events in the ER–Golgi leading to HH signaling activation.

Hedgehog signals orchestrate tissue patterning by binding the receptor Patched and restricting the signal transducer Smoothened. A genetic screen reveals Tmed2 as a new interactor of Smoothened that is required for regulating Smoothened transport from the endoplasmic reticulum and Golgi to the plasma membrane and hence modulating the strength of Hedgehog signal transduction.

Reaching articular limits can negatively impact embodiment in virtual reality

Providing Virtual Reality(VR) users with a 3D representation of their body complements the experience of immersion and presence in the virtual world with the experience of being physically located and more personally involved. A full-body avatar representation is known to induce a Sense of Embodiment (SoE) for this virtual body, which is associated with improvements in task performance, motivation and motor learning. Recent experimental research on embodiment provides useful guidelines, indicating the extent of discrepancy tolerated by users and, conversely, the limits and disruptive events that lead to a break in embodiment (BiE). Based on previous works on the limit of agency under movement distortion, this paper describes, studies and analyses the impact of a very common yet overlooked embodiment limitation linked to articular limits when performing a reaching movement. We demonstrate that perceiving the articular limit when fully extending the arm provides users with an additional internal proprioceptive feedback which, if not matched in the avatar’s movement, leads to the disruptive realization of an incorrect posture mapping. This study complements previous works on self-contact and visuo-haptic conflicts and emphasizes the risk of disrupting the SoE when distorting users’ movements or using a poorly-calibrated avatar.

Window of the World: Sino-African Encounters through Copies and Simulations

Located in the manufacturing hub of Shenzhen is Window of the World: a Chinese theme park that features miniature copies of heritage sites from around the world. The individuals living within this constructed simulation are imported from diverse countries. They come to work as performers, animating the different cultural pavilions. As such, the transnationalism made possible by this park provides a window through which we can observe cultural interactivity, as well as the ways in which culture is constructed and re-presented. This article examines some of the processes of cultural encounters through copies of commodified cultural heritage. It also sheds light on the ways in which Kung Fu movies circulating in Africa have inspired the imaginations of young people, revealing cultural feedback loops that provide openings for new contact. Grounded in ethnographic research, the findings here are based on interviews with Kenyan and South African contract workers at this theme park. This article explores young people's pursuits of new opportunities of identity-formation and self-representation, as well as economic stability and forward mobility.

Joint Income-Wealth Inequality: Evidence from Lucerne Tax Data

Using tax data from the Swiss canton of Lucerne, we study how measures of economic inequality change if they account for income and wealth rather than income alone. Joint income-wealth, the sum of labor income and annuitized wealth, serves as a measure of combined inequality of income and wealth. Inequality measured using joint income-wealth is higher than measured using income alone. We refine existing annuitization techniques by introducing heterogeneous returns. The joint distribution of labor income and annuitized wealth displays strong tail dependence at the top and a negative association for negative annuitized wealth. A decomposition shows that the underlying marginal distributions of labor income and annuitized wealth account for most of joint income-wealth inequality, whereas their association matters only in the tails.

Learning as filtering: Implications for spike-based plasticity

Most normative models in computational neuroscience describe the task of learning as the optimisation of a cost function with respect to a set of parameters. However, learning as optimisation fails to account for a time-varying environment during the learning process and the resulting point estimate in parameter space does not account for uncertainty. Here, we frame learning as filtering, i.e., a principled method for including time and parameter uncertainty. We derive the filtering-based learning rule for a spiking neuronal network—the Synaptic Filter—and show its computational and biological relevance. For the computational relevance, we show that filtering improves the weight estimation performance compared to a gradient learning rule with optimal learning rate. The dynamics of the mean of the Synaptic Filter is consistent with spike-timing dependent plasticity (STDP) while the dynamics of the variance makes novel predictions regarding spike-timing dependent changes of EPSP variability. Moreover, the Synaptic Filter explains experimentally observed negative correlations between homo- and heterosynaptic plasticity.

The task of learning is commonly framed as parameter optimisation. Here, we adopt the framework of learning as filtering where the task is to continuously estimate the uncertainty about the parameters to be learned. We apply this framework to synaptic plasticity in a spiking neuronal network. Filtering includes a time-varying environment and parameter uncertainty on the level of the learning task. We show that learning as filtering can qualitatively explain two biological experiments on synaptic plasticity that cannot be explained by learning as optimisation. Moreover, we make a new prediction and improve performance with respect to a gradient learning rule. Thus, learning as filtering is a promising candidate for learning models.

Heavy-tailed phase-type distributions: a unified approach

A phase-type distribution is the distribution of the time until absorption in a finite state-space time-homogeneous Markov jump process, with one absorbing state and the rest being transient. These distributions are mathematically tractable and conceptually attractive to model physical phenomena due to their interpretation in terms of a hidden Markov structure. Three recent extensions of regular phase-type distributions give rise to models which allow for heavy tails: discrete- or continuous-scaling; fractional-time semi-Markov extensions; and inhomogeneous time-change of the underlying Markov process. In this paper, we present a unifying theory for heavy-tailed phase-type distributions for which all three approaches are particular cases. Our main objective is to provide useful models for heavy-tailed phase-type distributions, but any other tail behavior is also captured by our specification. We provide relevant new examples and also show how existing approaches are naturally embedded. Subsequently, two multivariate extensions are presented, inspired by the univariate construction which can be considered as a matrix version of a frailty model. We provide fully explicit EM-algorithms for all models and illustrate them using synthetic and real-life data.

Model-based inference of neutralizing antibody avidities against influenza virus

To assess the response to vaccination, quantity (concentration) and quality (avidity) of neutralizing antibodies are the most important parameters. Specifically, an increase in avidity indicates germinal center formation, which is required for establishing long-term protection. For influenza, the classical hemagglutination inhibition (HI) assay, however, quantifies a combination of both, and to separately determine avidity requires high experimental effort. We developed from first principles a biophysical model of hemagglutination inhibition to infer IgG antibody avidities from measured HI titers and IgG concentrations. The model accurately describes the relationship between neutralizing antibody concentration/avidity and HI titer, and explains quantitative aspects of the HI assay, such as robustness to pipetting errors and detection limit. We applied our model to infer avidities against the pandemic 2009 H1N1 influenza virus in vaccinated patients (n = 45) after hematopoietic stem cell transplantation (HSCT) and validated our results with independent avidity measurements using an enzyme-linked immunosorbent assay with urea elution. Avidities inferred by the model correlated with experimentally determined avidities (ρ = 0.54, 95% CI = [0.31, 0.70], P < 10⁻⁴). The model predicted that increases in IgG concentration mainly contribute to the observed HI titer increases in HSCT patients and that immunosuppressive treatment is associated with lower baseline avidities. Since our approach requires only easy-to-establish measurements as input, we anticipate that it will help to disentangle causes for poor vaccination outcomes also in larger patient populations. This study demonstrates that biophysical modelling can provide quantitative insights into agglutination assays and complement experimental measurements to refine antibody response analyses.

Influenza vaccines are assessed based on the induced antibody response, where antibody quantity (concentration) and antibody binding strength (avidity) determine the potency to neutralize the virus. In addition, an increase in avidity indicates a successful germinal center reaction, which is required for establishing long-term protection. However, the hemagglutination inhibition (HI) assay—traditionally used to assess influenza vaccines—measures a combination of both antibody concentration and avidity, and to separately determine avidity requires high experimental effort. We developed a biophysical model of the HI assay, which enables the inference of antibody avidities from measured HI titers and antibody concentrations. We applied our approach to a vaccinated population of immunocompromised patients after blood stem cell transplantation and validated our results experimentally. The model predicted that vaccination induced an increase in avidity in only a few patients and that patients under immunosuppressive treatment show lower baseline avidities. Since our approach requires only easily measurable data as input, it can facilitate the investigation of vaccine responses in larger populations. This study demonstrates that biophysical modelling can complement experimental data and provide additional details on agglutination experiments and antibody responses.

Randomized Online Computation with High Probability Guarantees

We study the relationship between the competitive ratio and the tail distribution of randomized online problems. To this end, we identify a broad class of online problems for which the existence of a randomized online algorithm with constant expected competitive ratio r implies the existence of a randomized online algorithm that has a competitive ratio of ( 1 + ε ) r with high probability, measured with respect to the optimal profit or cost, respectively. The class of problems includes some of the well-studied online problems such as paging, k-server, and metrical task systems on finite metric spaces.

Tailor-made biochar systems: Interdisciplinary evaluations of ecosystem services and farmer livelihoods in tropical agro-ecosystems

Organic matter management is key to sustain ecosystem services provided by soils. However, it is rarely considered in a holistic view, considering local resources, agro-environmental effects and harmonization with farmers' needs. Organic inputs, like compost and biochar, could represent a sustainable solution to massive current challenges associated to the intensification of agriculture, in particular for tropical regions. Here we assess the potential of agricultural residues as a resource for farmer communities in southwestern India to reduce their dependency on external inputs and sustain ecosystem services. We propose a novel joint evaluation of farmers' aspirations together with agro-environmental effects of organic inputs on soils. Our soil quality evaluation showed that biochar alone or with compost did not improve unilaterally soils in the tropics (Anthroposol, Ferralsol and Vertisol). Many organic inputs led to an initial decrease in water-holding capacities of control soils (-27.3%: coconut shell biochar with compost on Anthroposol). Responses to organic matter inputs for carbon were strongest for Ferralsols (+33.4% with rice husk biochar), and mostly positive for Anthroposols and Vertisols (+12.5% to +13.8% respectively). Soil pH responses were surprisingly negative for Ferralsols and only positive if biochar was applied alone (between -5.6% to +1.9%). For Anthroposols and Vertisols, highest increases were achieved with rice husk biochar + vermicomposts (+7.2% and +5.2% respectively). Our socio-economic evaluation showed that farmers with a stronger economical position showed greater interest towards technology like biochar (factor 1.3 to 1.6 higher for farmers cultivating Anthroposols and/or Vertisols compared to Ferralsols), while poorer farmers more skepticism, which may lead to an increased economical gap within rural communities if technologies are not implemented with long-term guidance. These results advocate for an interdisciplinary evaluation of agricultural technology prior to its implementation as a development tool in the field.

KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences

BACKGROUND

Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells.

RESULTS

Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we identify the ape-restricted ZNF676 as the sequence-specific repressor of a subset of contemporary LTR12 integrants responsible for a large fraction of transpochimeric gene transcripts (TcGTs) generated during human early embryogenesis. We go on to reveal that the binding of this KZFP correlates with the epigenetic marking of these TEeRS in the germline, and is crucial to the control of genes involved in ciliogenesis/flagellogenesis, a biological process that dates back to the last common ancestor of eukaryotes.

CONCLUSION

These results illustrate how KZFPs and their TE targets contribute to the evolutionary turnover of transcription networks and participate in the transgenerational inheritance of epigenetic traits.

Restriction of extracellular lipids renders pancreatic cancer dependent on autophagy

BACKGROUND

KRAS is the predominant oncogene mutated in pancreatic ductal adenocarcinoma (PDAC), the fourth cause of cancer-related deaths worldwide. Mutant KRAS-driven tumors are metabolically programmed to support their growth and survival, which can be used to identify metabolic vulnerabilities. In the present study, we aimed to understand the role of extracellularly derived fatty acids in KRAS-driven pancreatic cancer.

METHODS

To assess the dependence of PDAC cells on extracellular fatty acids we employed delipidated serum or RNAi-mediated suppression of ACSL3 (to inhibit the activation and cellular retention of extracellular fatty acids) followed by cell proliferation assays, qPCR, apoptosis assays, immunoblots and fluorescence microscopy experiments. To assess autophagy in vivo, we employed the KrasG12D/+;p53flox/flox;Pdx1-CreERT2 (KPC) mice crossed with Acsl3 knockout mice, and to assess the efficacy of the combination therapy of ACSL3 and autophagy inhibition we used xenografted human cancer cell-derived tumors in immunocompromised mice.

RESULTS

Here we show that depletion of extracellularly derived lipids either by serum lipid restriction or suppression of ACSL3, triggers autophagy, a process that protects PDAC cells from the reduction of bioenergetic intermediates. Combined extracellular lipid deprivation and autophagy inhibition exhibits anti-proliferative and pro-apoptotic effects against PDAC cell lines in vitro and promotes suppression of xenografted human pancreatic cancer cell-derived tumors in mice. Therefore, we propose lipid deprivation and autophagy blockade as a potential co-targeting strategy for PDAC treatment.

CONCLUSIONS

Our work unravels a central role of extracellular lipid supply in ensuring fatty acid provision in cancer cells, unmasking a previously unappreciated metabolic vulnerability of PDAC cells.

Modelling how cleaner fish approach an ephemeral reward task demonstrates a role for ecologically tuned chunking in the evolution of advanced cognition

What makes cognition “advanced” is an open and not precisely defined question. One perspective involves increasing the complexity of associative learning, from conditioning to learning sequences of events (“chaining”) to representing various cue combinations as “chunks.” Here we develop a weighted graph model to study the mechanism enabling chunking ability and the conditions for its evolution and success, based on the ecology of the cleaner fish Labroides dimidiatus. In some environments, cleaners must learn to serve visitor clients before resident clients, because a visitor leaves if not attended while a resident waits for service. This challenge has been captured in various versions of the ephemeral reward task, which has been proven difficult for a range of cognitively capable species. We show that chaining is the minimal requirement for solving this task in its common simplified laboratory format that involves repeated simultaneous exposure to an ephemeral and permanent food source. Adding ephemeral–ephemeral and permanent–permanent combinations, as cleaners face in the wild, requires individuals to have chunking abilities to solve the task. Importantly, chunking parameters need to be calibrated to ecological conditions in order to produce adaptive decisions. Thus, it is the fine-tuning of this ability, which may be the major target of selection during the evolution of advanced associative learning.

What makes cognition ‘advanced’ is an open and not precisely defined question. In this study, a cognitive model of cleaner fish learning the ephemeral-reward task demonstrates how a critical step in cognitive evolution may be understood as the evolution of chunking and its tuning to fit ecological conditions.

Geospatial model of COVID-19 spreading and vaccination with event Gillespie algorithm

We have developed a mathematical model and stochastic numerical simulation for the transmission of COVID-19 and other similar infectious diseases that accounts for the geographic distribution of population density, detailed down to the level of location of individuals, and age-structured contact rates. Our analytical framework includes a surrogate model optimization process to rapidly fit the parameters of the model to the observed epidemic curves for cases, hospitalizations, and deaths. This toolkit (the model, the simulation code, and the optimizer) is a useful tool for policy makers and epidemic response teams, who can use it to forecast epidemic development scenarios in local settings (at the scale of cities to large countries) and design optimal response strategies. The simulation code also enables spatial visualization, where detailed views of epidemic scenarios are displayed directly on maps of population density. The model and simulation also include the vaccination process, which can be tailored to different levels of efficiency and efficacy of different vaccines. We used the developed framework to generate predictions for the spread of COVID-19 in the canton of Geneva, Switzerland, and validated them by comparing the calculated number of cases and recoveries with data from local seroprevalence studies.

Middle Stone Age Bifacial Technology and Pressure Flaking at the MIS 3 Site of Toumboura III, Eastern Senegal

Over the past decade, the increasing wealth of new archaeological data on the Middle Stone Age (MSA) in Senegal and Mali has broadened our understanding of West Africa's contributions to cultural developments. Within the West African sequence, the phase of Marine Isotope Stage 3 (MIS 3, ca. 59-24 ka) yielded so far the best known and extensive archaeological information. The site of Toumboura III encompasses an occupation dated by optically stimulated luminescence (OSL) to between 40 ± 3 ka and 30 ± 3 ka. It provides the largest, well-dated, and stratified lithic assemblage in West Africa for the MSA and sheds light on an unprecedented cultural expression for this period, adding to the notable diversity of the late MSA in this region. We conducted a technological analysis of the lithic components following the chaîne opératoire approach. The lithic assemblage features a prevalence of bifacial technology and the exploitation of flakes as blanks for tool production. The craftspeople manufactured distinct types of bifacial tools, including small bifacial points shaped by pressure technique. The new data from Toumboura III demonstrate behavioral patterns that are entirely new in the region. By revealing behavioral innovations and technological particularities, these results on the techno-cultural dynamics during the MIS 3 phase of the MSA enhance our understanding of the complex Pleistocene population history in this part of Africa.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10437-021-09463-5.

Evolutionary development of the cephalopod arm armature: a review

The cephalopod arm armature is certainly one of the most important morphological innovations responsible for the evolutionary success of the Cephalopoda. New palaeontological discoveries in the recent past afford to review and reassess origin and homology of suckers, sucker rings, hooks, and cirri. Since a priori character state reconstructions are still ambiguous, we suggest and discuss three different evolutionary scenarios. Each of them is based on the following assumptions: (1) Neocoleoidea uniting extant Decabrachia and Octobrachia is monophyletic (= proostracum-bearing coleoids); (2) extinct Belemnitida and Diplobelida are stem decabrachians; (3) proostracum-less coleoids (Hematitida, Donovaniconida, Aulacoceratida) represent stem-neocoleoids; (4) Ammonoidea and Bactritoidea are stem coleoids. We consider a scenario where belemnoid hooks derived from primitive suckers as well-supported. Regarding belemnoid hooks and suckers as homologues implies that belemnoid, oegopsid, and probably ammonoid arm hooks arose through parallel evolution. Our conclusions challenge the widespread opinion, whereupon belemnoid hooks evolved de novo, and instead support earlier ideas formulated by Sigurd von Boletzky.

Black Hole Quasinormal Modes and Seiberg-Witten Theory

We present new analytic results on black hole perturbation theory. Our results are based on a novel relation to four-dimensional N = 2 supersymmetric gauge theories. We propose an exact version of Bohr-Sommerfeld quantization conditions on quasinormal mode frequencies in terms of the Nekrasov partition function in a particular phase of the Ω -background. Our quantization conditions also enable us to find exact expressions of eigenvalues of spin-weighted spheroidal harmonics. We test the validity of our conjecture by comparing against known numerical results for Kerr black holes as well as for Schwarzschild black holes. Some extensions are also discussed.

Correlates of interpersonal emotion regulation problems in Loss of Control eating (LOC) in youth: study protocol of the combined online and App based questionnaire, laboratory and randomized controlled online intervention i-BEAT trial

BACKGROUND

Binge Eating Disorder (BED) represents a common eating disorder associated with marked health impairments. A subclinical variant, loss of control eating (LOC) is prevalent in youth. LOC is associated with similar mental distress as full-blown BED, increases the risk to develop a BED and promotes continuous weight gain. The etiology of LOC is not yet fully understood and specialized treatment for youth is scarce.

METHODS

The i-BEAT study includes a cross-sectional and longitudinal online questionnaire study (N = 600), an App based daily-life approach and a laboratory virtual reality study in N = 60 youths (14-24 years) with and without LOC as well as a controlled randomized online treatment trial to investigate the feasibility, acceptance and efficacy of a CBT and an interpersonal emotion regulation module for youth (N = 120). The primary outcomes include self-reported as well as measured (heart rate variability, gaze behavior, reaction times in stop signal task) associations between emotion regulation problems (such as dealing with RS), psychological impairment and binge eating in a healthy control group and youth with LOC. Secondary outcomes encompass general eating disorder pathology, social anxiety, body mass index, hyperscanning behavior and therapists' rating of patients' condition pre and post treatment. Epigenetic correlates of RS are assessed in healthy controls and youth with LOC and explored before and after treatment.

DISCUSSION

The expected findings will specify the role of interpersonal emotion regulation problems such as coping with the experience of social exclusion and rejection sensitivity (RS) in LOC and clarify, whether including a training to cope with RS adds to the efficacy of a cognitive behavioral treatment (CBT).

TRIAL REGISTRATION

German Clinical Trial Register: DRKS00023706. Registered 27 November 2020, https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00023706.

Do methane emissions converge? Evidence from global panel data on production- and consumption-based emissions

Methane emissions are the second most important contributor to global warming. Knowledge about the dynamics of methane emissions facilitates the formulation of climate policies and the understanding of their consequences. We investigate whether methane emissions released from production and embodied in consumption converge within and across regions. Our estimates rely on global panel data on methane per capita and methane intensities over 1997-2014. We find that emissions converge within countries. The short half-lives show that the emissions of countries are close to their steady states. There is no evidence for international convergence of aggregate emissions. Yet, convergence of emissions across regions occurs in a number of economic sectors. Our results highlight the difficulties to achieve methane abatement in the medium run. The formulation of climate policies should take into account the sectoral specificity of the dynamics of methane emissions.

SUPPLEMENTARY INFORMATION

The online version supplementary material available at 10.1007/s00181-021-02162-9.

Probing Upflowing Regions in the Quiet Sun and Coronal Holes

Recent observations from Parker Solar Probe have revealed that the solar wind has a highly variable structure. How this complex behaviour is formed in the solar corona is not yet known, since it requires omnipresent fluctuations, which constantly emit material to feed the wind. In this article we analyse 14 upflow regions in the solar corona to find potential sources for plasma flow. The upflow regions are derived from spectroscopic data from the EUV Imaging Spectrometer (EIS) on board Hinode determining their Doppler velocity and defining regions which have blueshifts stronger than - 6 km s - 1 . To identify the sources of these blueshift data from the Atmospheric Imaging Assembly (AIA) and the Helioseismic and Magnetic Imager (HMI), on board the Solar Dynamics Observatory (SDO), and the X-ray Telescope (XRT), on board Hinode, are used. The analysis reveals that only 5 out of 14 upflows are associated with frequent transients, like obvious jets or bright points. In contrast to that, seven events are associated with small-scale features, which show a large variety of dynamics. Some resemble small bright points, while others show an eruptive nature, all of which are faint and only live for a few minutes; we cannot rule out that several of these sources may be fainter and, hence, less obvious jets. Since the complex structure of the solar wind is known, this suggests that new sources have to be considered or better methods used to analyse the known sources. This work shows that small and frequent features, which were previously neglected, can cause strong upflows in the solar corona. These results emphasise the importance of the first observations from the Extreme-Ultraviolet Imager (EUI) on board Solar Orbiter, which revealed complex small-scale coronal structures.

Local force titration of wood surfaces by chemical force microscopy

Chemical force microcopy, a variation of atomic force microscopy, opened the door to visualize chemical nano-properties of various materials in their natural state. The key function of this method is given by translating adhesion forces between a functionalized tip and the sample to chemical surface behavior. In force titration, these adhesion forces are studied in different pH buffers, which allows estimating the pK _a value of the analyzed surface. Herein, we report the use of this method to study natural and chemically treated wood surfaces, which are of interest in sustainable material design. First, we show varying adhesion phenomena of OH- and COOH-functionalized tips on native spruce wood cells. Then, we demonstrate how peak force tapping with chemically functionalized tips can be used to estimate the pK _a value of gold substrates (pK _a ≈ 5.2) and different wood cell wall layers with high spatial resolution. Additionally, the swelling behavior of wood samples is analyzed in varying pH buffers. With the applied method, chemical surface properties of complex natural substrates can be analyzed.

ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

Genome-scale metabolic models (GEMs) provide a powerful framework for simulating the entire set of biochemical reactions in a cell using a constraint-based modeling strategy called flux balance analysis (FBA). FBA relies on an assumed metabolic objective for generating metabolic fluxes using GEMs. But, the most appropriate metabolic objective is not always obvious for a given condition and is likely context-specific, which often complicate the estimation of metabolic flux alterations between conditions. Here, we propose a new method, called ΔFBA (deltaFBA), that integrates differential gene expression data to evaluate directly metabolic flux differences between two conditions. Notably, ΔFBA does not require specifying the cellular objective. Rather, ΔFBA seeks to maximize the consistency and minimize inconsistency between the predicted flux differences and differential gene expression. We showcased the performance of ΔFBA through several case studies involving the prediction of metabolic alterations caused by genetic and environmental perturbations in Escherichia coli and caused by Type-2 diabetes in human muscle. Importantly, in comparison to existing methods, ΔFBA gives a more accurate prediction of flux differences.

Metabolic alterations are often used as hallmarks of observable phenotypes. In this regard, reconstructed genome-scale metabolic models (GEMs) provide a rich and computable representation of the entire set of biochemical reactions in a cell. However, the performance of analytical tools for predicting metabolic reaction rates or fluxes using GEMs is sensitive to the assumed metabolic objective that is often unknown and likely context-specific. Here, we propose a novel method called ΔFBA that combines differential gene expression data and GEMs to evaluate differences in the metabolic fluxes between two conditions (perturbation vs. control) without the need for specifying a metabolic objective. In our demonstration, ΔFBA outperformed other existing methods in predicting metabolic flux alterations.

Regular testing of asymptomatic healthcare workers identifies cost-efficient SARS-CoV-2 preventive measures

Protecting healthcare professionals is crucial in maintaining a functioning healthcare system. The risk of infection and optimal preventive strategies for healthcare workers during the COVID-19 pandemic remain poorly understood. Here we report the results of a cohort study that included pre- and asymptomatic healthcare workers. A weekly testing regime has been performed in this cohort since the beginning of the COVID-19 pandemic to identify infected healthcare workers. Based on these observations we have developed a mathematical model of SARS-CoV-2 transmission that integrates the sources of infection from inside and outside the hospital. The data were used to study how regular testing and a desynchronisation protocol are effective in preventing transmission of COVID-19 infection at work, and compared both strategies in terms of workforce availability and cost-effectiveness. We showed that case incidence among healthcare workers is higher than would be explained solely by community infection. Furthermore, while testing and desynchronisation protocols are both effective in preventing nosocomial transmission, regular testing maintains work productivity with implementation costs.

Direct Photoexcitation of Ethynylbenziodoxolones: An Alternative to Photocatalysis for Alkynylation Reactions*

Ethynylbenziodoxolones (EBXs) are commonly used as radical traps in photocatalytic alkynylations. Herein, we report that aryl-substituted EBX reagents can be directly activated by visible light irradiation. They act as both oxidants and radical traps, alleviating the need for a photocatalyst in several reported EBX-mediated processes, including decarboxylative and deboronative alkynylations, the oxyalkynylation of enamides and the C-H alkynylation of THF. Furthermore, the method could be applied to the synthesis of alkynylated quaternary centers from tertiary alcohols via stable oxalate salts and from tertiary amines via aryl imines. A photocatalytic process using 4CzIPN as an organic dye was also developed for the deoxyalkynylation of oxalates.

Closer Look at Inverse Electron Demand Diels–Alder and Nucleophilic Addition Reactions on s-Tetrazines Using Enhanced Sampling Methods

Inverse electron demand [4+2] Diels–Alder (iEDDA) reactions as well as unprecedented nucleophilic (azaphilic) additions of R-substituted silyl-enol ethers (where R is Phenyl, Methyl, and Hydrogen) to 1,2,4,5-tetrazine (s-tetrazine) catalyzed by \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {BF}_{3}$$\end{document}BF3 have recently been discovered (Simon et al. in Org Lett 23(7):2426–2430, 2021), where static calculations were employed for calculation of activation energies. In order to have a more realistic dynamic description of these reactions in explicit solution at ambient conditions, in this work we use a semiempirical tight-binding method combined with enhanced sampling techniques to calculate free energy surfaces (FESs) of the iEDDA and azaphilic addition reactions. Relevant products of not only s-tetrazine but also its derivatives such as \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {BF}_{3}$$\end{document}BF3-mediated s-tetrazine adducts are investigated. We reconstruct the FESs of the iEDDA and azaphilic addition reactions using metadynamics and blue moon ensemble, and compare the ability of different collective variables (CVs) including bond distances, Social PeRmutation INvarianT (SPRINT) coordinates, and path-CV to describe the reaction pathway. We find that when a bulky Phenyl is used as a substituent at the dienophile the azaphilic addition is preferred over the iEDDA reaction. In addition, we also investigate the effect of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {BF}_{3}$$\end{document}BF3 in the diene and steric hindrance in the dienophile on the competition between the iEDDA and azaphilic addition reactions, providing chemical insight for reaction design.

Impact of PET/CT among patients with suspected mycotic aortic aneurysms

Purpose

To determine the impact of ¹⁸F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) on clinical management in patients with suspected mycotic aortic aneurysms (MAA).

Materials and methods

For this observational cohort study 101 PET/CT were acquired in 50 patients, thereof 50 for the initial diagnosis/baseline scan, 51 for follow-up. Impact on patient management was defined in three categories: PET/CT results were “confirmed” (by clinical follow-up), “suspected” (conclusive, not confirmed), or “misleading” (proven wrong by follow-up). For clinical follow-up patient data were recorded at the time of imaging, and at the latest recorded clinical visit. It included patient demographics, clinical information, laboratory data, results of microbiology and other diagnostic procedures, information about treatment, and patient’s general health condition.

Results

In four patients (8%) no clinical follow-up was feasible, the other 46 patients were clinically followed for a median of 898 days (IQR 320–4105). The combined evaluation of all 101 PET/CT demonstrated an impact on patient management in 78,5% of cases (48,5% confirmed, 30% suspected). Results of 21,5% of the PET/CT examinations were misleading. Respective values at baseline and at follow-up were: impact on patient management in 82% and 74,5% (70% and 27.5% confirmed, and 12% and 47% suspected), misleading cases in 18% and 25.5%.

Conclusion

In MAA, PET/CT has a high impact on patient management, which is more pronounced with baseline than with follow-up examinations. However, PET/CT results may be misleading in a smaller proportion of cases.

Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning

Natural products (NPs) represent one of the most important resources for discovering new drugs. Here we asked whether NP origin can be assigned from their molecular structure in a subset of 60,171 NPs in the recently reported Collection of Open Natural Products (COCONUT) database assigned to plants, fungi, or bacteria. Visualizing this subset in an interactive tree-map (TMAP) calculated using MAP4 (MinHashed atom pair fingerprint) clustered NPs according to their assigned origin ( https://tm.gdb.tools/map4/coconut_tmap/ ), and a support vector machine (SVM) trained with MAP4 correctly assigned the origin for 94% of plant, 89% of fungal, and 89% of bacterial NPs in this subset. An online tool based on an SVM trained with the entire subset correctly assigned the origin of further NPs with similar performance ( https://np-svm-map4.gdb.tools/ ). Origin information might be useful when searching for biosynthetic genes of NPs isolated from plants but produced by endophytic microorganisms.

Offering ART refill through community health workers versus clinic-based follow-up after home-based same-day ART initiation in rural Lesotho: The VIBRA cluster-randomized clinical trial

BACKGROUND

Community-based antiretroviral therapy (ART) dispensing by lay workers is an important differentiated service delivery model in sub-Sahara Africa. However, patients new in care are generally excluded from such models. Home-based same-day ART initiation is becoming widespread practice, but linkage to the clinic is challenging. The pragmatic VIBRA (Village-Based Refill of ART) trial compared ART refill by existing lay village health workers (VHWs) versus clinic-based refill after home-based same-day ART initiation.

METHODS AND FINDINGS

The VIBRA trial is a cluster-randomized open-label clinical superiority trial conducted in 249 rural villages in the catchment areas of 20 health facilities in 2 districts (Butha-Buthe and Mokhotlong) in Lesotho. In villages (clusters) randomized to the intervention arm, individuals found to be HIV-positive during a door-to-door HIV testing campaign were offered same-day ART initiation with the option of refill by VHWs. The trained VHWs dispensed drugs and scheduled clinic visits for viral load measurement at 6 and 12 months. In villages randomized to the control arm, participants were offered same-day ART initiation with clinic-based ART refill. The primary outcome was 12-month viral suppression. Secondary endpoints included linkage and 12-month engagement in care. Analyses were intention-to-treat. The trial was registered on ClinicalTrials.gov (NCT03630549). From 16 August 2018 until 28 May 2019, 118 individuals from 108 households in 57 clusters in the intervention arm, and 139 individuals from 130 households in 60 clusters in the control arm, were enrolled (150 [58%] female; median age 36 years [interquartile range 30-48]; 200 [78%] newly diagnosed). In the intervention arm, 48/118 (41%) opted for VHW refill. At 12 months, 46/118 (39%) participants in the intervention arm and 64/139 (46%) in the control arm achieved viral suppression (adjusted risk difference -0.07 [95% CI -0.20 to 0.06]; p = 0.256). Arms were similar in linkage (adjusted risk difference 0.03 [-0.10 to 0.16]; p = 0.630), but engagement in care was non-significantly lower in the intervention arm (adjusted risk difference -0.12 [-0.23 to 0.003]; p = 0.058). Seven and 0 deaths occurred in the intervention and control arm, respectively. Of the intervention participants who did not opt for drug refill from the VHW at enrollment, 41/70 (59%) mentioned trust or conflict issues as the primary reason. Study limitations include a rather small sample size, 9% missing viral load measurements in the primary endpoint window, the low uptake of the VHW refill option in the intervention arm, and substantial migration among the study population.

CONCLUSIONS

The offer of village-based ART refill after same-day initiation led to similar outcomes as clinic-based refill. The intervention did not amplify the effect of home-based same-day ART initiation alone. The findings raise concerns about acceptance and safety of ART delivered by lay health workers after initiation in the community.

TRIAL REGISTRATION

Registered with Clinicaltrials.gov (NCT03630549).

Bivalent individualization during chromosome territory formation in Drosophila spermatocytes by controlled condensin II protein activity and additional force generators

Reduction of genome ploidy from diploid to haploid necessitates stable pairing of homologous chromosomes into bivalents before the start of the first meiotic division. Importantly, this chromosome pairing must avoid interlocking of non-homologous chromosomes. In spermatocytes of Drosophila melanogaster, where homolog pairing does not involve synaptonemal complex formation and crossovers, associations between non-homologous chromosomes are broken up by chromosome territory formation in early spermatocytes. Extensive non-homologous associations arise from the coalescence of the large blocks of pericentromeric heterochromatin into a chromocenter and from centromere clustering. Nevertheless, during territory formation, bivalents are moved apart into spatially separate subnuclear regions. The condensin II subunits, Cap-D3 and Cap-H2, have been implicated, but the remarkable separation of bivalents during interphase might require more than just condensin II. For further characterization of this process, we have applied time-lapse imaging using fluorescent markers of centromeres, telomeres and DNA satellites in pericentromeric heterochromatin. We describe the dynamics of the disruption of centromere clusters and the chromocenter in normal spermatocytes. Mutations in Cap-D3 and Cap-H2 abolish chromocenter disruption, resulting in excessive chromosome missegregation during M I. Chromocenter persistence in the mutants is not mediated by the special system, which conjoins homologs in compensation for the absence of crossovers in Drosophila spermatocytes. However, overexpression of Cap-H2 precluded conjunction between autosomal homologs, resulting in random segregation of univalents. Interestingly, Cap-D3 and Cap-H2 mutant spermatocytes displayed conspicuous stretching of the chromocenter, as well as occasional chromocenter disruption, suggesting that territory formation might involve forces unrelated to condensin II. While the molecular basis of these forces remains to be clarified, they are not destroyed by inhibitors of F actin and microtubules. Our results indicate that condensin II activity promotes chromosome territory formation in co-operation with additional force generators and that careful co-ordination with alternative homolog conjunction is crucial.

Drawing the line between sustainable and unsustainable fish: product differentiation that supports sustainable development through trade measures

BACKGROUND

Unsustainable production practices and increased demand for fish have aggravated negative social, ecological, and environmental impacts in fisheries and aquaculture. Measures to correct bad practices have mainly been introduced by private actors. However, there is increased demand for state intervention, particularly regarding trade regulations for fish and other agricultural products. Building on discussions about product differentiation through trade measures that favour sustainable products, this study looked at how sustainable and unsustainable fish has been distinguished in Switzerland. In interviewing experts in the fish trade and sales business in Switzerland, the research aimed at understanding the actors and forces that shape the concept of sustainable fish in the country.

RESULTS

Three ways of product differentiation for sustainable fish by private actors were identified in Switzerland: ecolabels, "Swiss produce", and recommendations in the form of a "consumer guide for fish". Currently, price is the main constraint on consumption of sustainable products in the country. Defining "sustainable fish" is challenging and subject to interpretation. All existing measures to differentiate sustainable from unsustainable fish products in Switzerland have shortcomings, particularly in terms of discrimination and inclusiveness. Fish ecolabels play a key role in product differentiation, but experts believe that they fail to accommodate all aspects of sustainability.

CONCLUSION

Our findings imply that the Swiss state should play a more important role if it aims to fulfil the promise of article 104a of the Swiss Constitution, which seeks to foster sustainable production and cross-border trade relations that contribute towards this goal. Preferred trade treatment for sustainable fish products is a potential option to increase the production and consumption of sustainable fish. When designing measures for product differentiation, a careful choice is paramount to address sustainability in a holistic, inclusive, and transparent way and in order not to violate existing trade obligations. Due to similarities between the Swiss and other fish markets, we assume that governments in general and members of the European Union in particular must play an active role in shaping the definition and trade of sustainable fish products if they seek to comply with their sustainability commitments.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s12302-021-00551-6.

Chiral Distorted Hexa-peri-hexabenzocoronenes Bearing a Nonagon-Embedded Carbohelicene

A new family of chiral saddle-helix hybrid nanographenes is reported. The first hexa-peri-hexabenzocoronene (HBC) analogues bearing a nine-membered carbocycle are presented. Furthermore, for the first time, π-extended carbo[n]helicenes containing a nine-membered ring as part of the helical moiety have been synthesized. The combination of a [5]helicene moiety and a nonagon ring in a single chiral motif induces a tremendous distortion from planarity into the nanographenic structures compared to other saddle-helix hybrids such as heptagon- and octagon-containing π-extended carbo[5]helicenes. In fact, the interplanar angle of the two terminal rings reaches the largest angle (134.8°) of a carbohelicene reported to date, thus being by far the most twisted helicene yet prepared. Photophysical properties evaluation showed improved absorption dissymmetry factors (|gabs |=4.2×10-3 ) in the new family of nonagon-containing π-extended carbo[5]helicenes.

The swimming trace Undichna from the latest Devonian Hangenberg Sandstone equivalent of Morocco

Trace fossils occur in several strata of the Devonian and Carboniferous of the eastern Anti-Atlas, but they are still poorly documented. Here, we describe a fossil swimming trace from strata overlying the Hangenberg Black Shale (correlation largely based on lithostratigraphy; Postclymenia ammonoid genozone, ca. 370 Ma old). We discuss the systematic position of the tracemaker and its body size. This ichnofossil is important for three main reasons: (1) it is considered here to be the first record of Undichna from the Devonian of Gondwana, as far as we know; (2) it is the oldest record of vertebrate trace fossils from Africa; (3) it provides a unique window into the behaviour of Late Devonian fishes for which body-fossils cannot provide direct evidence. Further, we put this discovery into the macroecological context of the palaeoenvironment following the Late Devonian Hangenberg biodiversity crisis.

Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities

Reproduction is one of the requirements for evolution and a defining feature of life. Yet, across the tree of life, organisms reproduce in many different ways. Groups of cells (e.g., multicellular organisms, colonial microbes, or multispecies biofilms) divide by releasing propagules that can be single-celled or multicellular. What conditions determine the number and size of reproductive propagules? In multicellular organisms, existing theory suggests that single-cell propagules prevent the accumulation of deleterious mutations (e.g., cheaters). However, groups of cells, such as biofilms, sometimes contain multiple metabolically interdependent species. This creates a reproductive dilemma: small daughter groups, which prevent the accumulation of cheaters, are also unlikely to contain the species diversity that is required for ecological success. Here, we developed an individual-based, multilevel selection model to investigate how such multi-species groups can resolve this dilemma. By tracking the dynamics of groups of cells that reproduce by fragmenting into smaller groups, we identified fragmentation modes that can maintain cooperative interactions. We systematically varied the fragmentation mode and calculated the maximum mutation rate that communities can withstand before being driven to extinction by the accumulation of cheaters. We find that for groups consisting of a single species, the optimal fragmentation mode consists of releasing single-cell propagules. For multi-species groups we find various optimal strategies. With migration between groups, single-cell propagules are favored. Without migration, larger propagules sizes are optimal; in this case, group-size dependent fissioning rates can prevent the accumulation of cheaters. Our work shows that multi-species groups can evolve reproductive strategies that allow them to maintain cooperative interactions.

Does choice change preferences? An incentivized test of the mere choice effect

Widespread evidence from psychology and neuroscience documents that previous choices unconditionally increase the later desirability of chosen objects, even if those choices were uninformative. This is problematic for economists who use choice data to estimate latent preferences, demand functions, and social welfare. The evidence on this mere choice effect, however, exhibits serious shortcomings which prevent evaluating its possible relevance for economics. In this paper, we present a novel, parsimonious experimental design to test for the economic validity of the mere choice effect addressing these shortcomings. Our design uses well-defined, monetary lotteries, all decisions are incentivized, and we effectively randomize participants' initial choices without relying on deception. Results from a large, pre-registered online experiment find no support for the mere choice effect. Our results challenge conventional wisdom outside economics. The mere choice effect does not seem to be a concern for economics, at least in the domain of decision making under risk.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10683-021-09728-5.

Changes and prognostic value of cardiopulmonary exercise testing parameters in elderly patients undergoing cardiac rehabilitation: The EU-CaRE observational study

Objective

We aimed 1) to test the applicability of the previously suggested prognostic value of CPET to elderly cardiac rehabilitation patients and 2) to explore the underlying mechanism of the greater improvement in exercise capacity (peak oxygen consumption, VO₂) after CR in surgical compared to non-surgical cardiac patients.

Methods

Elderly patients (≥65 years) commencing CR after coronary artery bypass grafting, surgical valve replacement (surgery-group), percutaneous coronary intervention, percutaneous valve replacement or without revascularisation (non-surgery group) were included in the prospective multi-center EU-CaRE study. CPETs were performed at start of CR, end of CR and 1-year-follow-up. Logistic models and receiver operating characteristics were used to determine prognostic values of CPET parameters for major adverse cardiac events (MACE). Linear models were performed for change in peak VO₂ (start to follow-up) and parameters accounting for the difference between surgery and non-surgery patients were sought.

Results

1421 out of 1633 EU-CaRE patients performed a valid CPET at start of CR (age 73±5.4, 81% male). No CPET parameter further improved the receiver operation characteristics significantly beyond the model with only clinical parameters. The higher improvement in peak VO₂ (25% vs. 7%) in the surgical group disappeared when adjusted for changes in peak tidal volume and haemoglobin.

Conclusion

CPET did not improve the prediction of MACE in elderly CR patients. The higher improvement of exercise capacity in surgery patients was mainly driven by restoration of haemoglobin levels and improvement in respiratory function after sternotomy.

Trial registration

Netherlands Trial Register, Trial NL5166.