SIRV: spatial inference of RNA velocity at the single-cell resolution.

RNA Velocity allows the inference of cellular differentiation trajectories from single-cell RNA sequencing (scRNA-seq) data. It would be highly interesting to study these differentiation dynamics in the spatial context of tissues. Estimating spatial RNA velocities is, however, limited by the inability to spatially capture spliced and unspliced mRNA molecules in high-resolution spatial transcriptomics. We present SIRV, a method to spatially infer RNA velocities at the single-cell resolution by enriching spatial transcriptomics data with the expression of spliced and unspliced mRNA from reference scRNA-seq data. We used SIRV to infer spatial differentiation trajectories in the developing mouse brain, including the differentiation of midbrain-hindbrain boundary cells and marking the forebrain origin of the cortical hem and diencephalon cells. Our results show that SIRV reveals spatial differentiation patterns not identifiable with scRNA-seq data alone. Additionally, we applied SIRV to mouse organogenesis data and obtained robust spatial differentiation trajectories. Finally, we verified the spatial RNA velocities obtained by SIRV using 10x Visium data of the developing chicken heart and MERFISH data from human osteosarcoma cells. Altogether, SIRV allows the inference of spatial RNA velocities at the single-cell resolution to facilitate studying tissue development.

Systematic profiling of conditional pathway activation identifies context-dependent synthetic lethalities.

The paradigm of cancer-targeted therapies has focused largely on inhibition of critical pathways in cancer. Conversely, conditional activation of signaling pathways as a new source of selective cancer vulnerabilities has not been deeply characterized. In this study, we sought to systematically identify context-specific gene-activation-induced lethalities in cancer. To this end, we developed a method for gain-of-function genetic perturbations simultaneously across ~500 barcoded cancer cell lines. Using this approach, we queried the pan-cancer vulnerability landscape upon activating ten key pathway nodes, revealing selective activation dependencies of MAPK and PI3K pathways associated with specific biomarkers. Notably, we discovered new pathway hyperactivation dependencies in subsets of APC-mutant colorectal cancers where further activation of the WNT pathway by APC knockdown or direct ß-catenin overexpression led to robust antitumor effects in xenograft and patient-derived organoid models. Together, this study reveals a new class of conditional gene-activation dependencies in cancer.

Improved daily estimates of relative humidity at high resolution across Germany: A random forest approach.

The lack of readily available methods for estimating high-resolution near-surface relative humidity (RH) and the incapability of weather stations to fully capture the spatiotemporal variability can lead to exposure misclassification in studies of environmental epidemiology. We therefore aimed to predict German-wide 1 × 1 km daily mean RH during 2000-2021. RH observations, longitude and latitude, modelled air temperature, precipitation and wind speed as well as remote sensing information on topographic elevation, vegetation, and the true color band composite were incorporated in a Random Forest (RF) model, in addition to date for capturing the temporal variations of the response-explanatory variables relationship. The model achieved high accuracy (R2 = 0.83) and low errors (Root Mean Square Error (RMSE) of 5.07%, Mean Absolute Percentage Error (MAPE) of 5.19% and Mean Percentage Error (MPE) of - 0.53%), calculated via ten-fold cross-validation. A comparison of our RH predictions with measurements from a dense monitoring network in the city of Augsburg, South Germany confirmed the good performance (R2 ≥ 0.86, RMSE ≤ 5.45%, MAPE ≤ 5.59%, MPE ≤ 3.11%). The model displayed high German-wide RH (22y-average of 79.00%) and high spatial variability across the country, exceeding 12% on yearly averages. Our findings indicate that the proposed RF model is suitable for estimating RH for a whole country in high-resolution and provide a reliable RH dataset for epidemiological analyses and other environmental research purposes.

Decision-support tools to build climate resilience against emerging infectious diseases in Europe and beyond.

Climate change is one of several drivers of recurrent outbreaks and geographical range expansion of infectious diseases in Europe. We propose a framework for the co-production of policy-relevant indicators and decision-support tools that track past, present, and future climate-induced disease risks across hazard, exposure, and vulnerability domains at the animal, human, and environmental interface. This entails the co-development of early warning and response systems and tools to assess the costs and benefits of climate change adaptation and mitigation measures across sectors, to increase health system resilience at regional and local levels and reveal novel policy entry points and opportunities. Our approach involves multi-level engagement, innovative methodologies, and novel data streams. We take advantage of intelligence generated locally and empirically to quantify effects in areas experiencing rapid urban transformation and heterogeneous climate-induced disease threats. Our goal is to reduce the knowledge-to-action gap by developing an integrated One Health-Climate Risk framework.

Development, wiring and function of dopamine neuron subtypes.

The midbrain dopamine (mDA) system is composed of molecularly and functionally distinct neuron subtypes that mediate specific behaviours and are linked to various brain diseases. Considerable progress has been made in identifying mDA neuron subtypes, and recent work has begun to unveil how these neuronal subtypes develop and organize into functional brain structures. This progress is important for further understanding the disparate physiological functions of mDA neurons and their selective vulnerability in disease, and will ultimately accelerate therapy development. This Review discusses recent advances in our understanding of molecularly defined mDA neuron subtypes and their circuits, ranging from early developmental events, such as neuron migration and axon guidance, to their wiring and function, and future implications for therapeutic strategies.

High-resolution spatiotemporal modeling of daily near-surface air temperature in Germany over the period 2000-2020.

The commonly used weather stations cannot fully capture the spatiotemporal variability of near-surface air temperature (Tair), leading to exposure misclassification and biased health effect estimates. We aimed to improve the spatiotemporal coverage of Tair data in Germany by using multi-stage modeling to estimate daily 1 × 1 km minimum (Tmin), mean (Tmean), maximum (Tmax) Tair and diurnal Tair range during 2000-2020. We used weather station Tair observations, satellite-based land surface temperature (LST), elevation, vegetation and various land use predictors. In the first stage, we built a linear mixed model with daily random intercepts and slopes for LST adjusted for several spatial predictors to estimate Tair from cells with both Tair and LST available. In the second stage, we used this model to predict Tair for cells with only LST available. In the third stage, we regressed the second stage predictions against interpolated Tair values to obtain Tair countrywide. All models achieved high accuracy (0.91 ≤ R2 ≤ 0.98) and low errors (1.03 °C ≤ Root Mean Square Error (RMSE) ≤ 2.02 °C). Validation with external data confirmed the good performance, locally, i.e., in Augsburg for all models (0.74 ≤ R2 ≤ 0.99, 0.87 °C ≤ RMSE ≤ 2.05 °C) and countrywide, for the Tmean model (0.71 ≤ R2 ≤ 0.99, 0.79 °C ≤ RMSE ≤ 1.19 °C). Annual Tmean averages ranged from 8.56 °C to 10.42 °C with the years beyond 2016 being constantly hotter than the 21-year average. The spatial variability within Germany exceeded 15 °C annually on average following patterns including mountains, rivers and urbanization. Using a case study, we showed that modeling leads to broader Tair variability representation for exposure assessment of participants in health cohorts. Our results indicate the proposed models as suitable for estimating nationwide Tair at high resolution. Our product is critical for temperature-based epidemiological studies and is also available for other research purposes.

The existential risk space of climate change.

Climate change is widely recognized as a major risk to societies and natural ecosystems but the high end of the risk, i.e., where risks become existential, is poorly framed, defined, and analyzed in the scientific literature. This gap is at odds with the fundamental relevance of existential risks for humanity, and it also limits the ability of scientific communities to engage with emerging debates and narratives about the existential dimension of climate change that have recently gained considerable traction. This paper intends to address this gap by scoping and defining existential risks related to climate change. We first review the context of existential risks and climate change, drawing on research in fields on global catastrophic risks, and on key risks and the so-called Reasons for Concern in the reports of the Intergovernmental Panel on Climate Change. We also consider how existential risks are framed in the civil society climate movement as well as what can be learned in this respect from the COVID-19 crisis. To better frame existential risks in the context of climate change, we propose to define them as those risks that threaten the existence of a subject, where this subject can be an individual person, a community, or nation state or humanity. The threat to their existence is defined by two levels of severity: conditions that threaten (1) survival and (2) basic human needs. A third level, well-being, is commonly not part of the space of existential risks. Our definition covers a range of different scales, which leads us into further defining six analytical dimensions: physical and social processes involved, systems affected, magnitude, spatial scale, timing, and probability of occurrence. In conclusion, we suggest that a clearer and more precise definition and framing of existential risks of climate change such as we offer here facilitates scientific analysis as well societal and political discourse and action.

The accuracy of MRI for the diagnosis of ramp lesions.

OBJECTIVES: To assess the diagnostic accuracy of MRI in diagnosing ramp lesions in patients with an acute lesion of the anterior cruciate ligament (ACL). MATERIALS AND METHODS: All consecutive patients over 15 years of age who underwent surgical repair of the ACL at a single hospital between January and May 2019, with MRI data available, were included in this retrospective study, except patients who had previous knee surgery. The gold standard was arthroscopic evaluation. Two trained radiologists with 5 and 14 years of experience did a blinded review of the MRIs. The following pathological signs were studied: complete fluid filling between the capsule and the posterior horn of the medial meniscus, irregular appearance of the posterior wall of the medial meniscus, oedema of the capsule, fluid hyperintensity in contact with the medial meniscus and anterior subluxation of the medial meniscus. Logistic regressions in univariate then multivariate analysis were carried out and measures of diagnostic accuracy and interobserver agreement were calculated with R software (version 3.6). RESULTS: Fifty-seven patients were included. Twelve had a ramp lesion diagnosed by arthroscopy (21%). Only complete fluid hyperintensity between the posterior horn of the medial meniscus and the capsule was significantly associated with ramp lesions (P value < 0.01). The diagnostic accuracy of this specific sign was moderate, with a specificity of 84%, sensitivity of 75%, PPV of 56%, NPV of 93% and a good level of inter-observer agreement (k = 0.79). CONCLUSION: The complete fluid filling is the only significant pathological MRI sign for ramp lesions, with moderate accuracy.

Improved Transferability of Data-Driven Damage Models Through Sample Selection Bias Correction.

Damage models for natural hazards are used for decision making on reducing and transferring risk. The damage estimates from these models depend on many variables and their complex sometimes nonlinear relationships with the damage. In recent years, data-driven modeling techniques have been used to capture those relationships. The available data to build such models are often limited. Therefore, in practice it is usually necessary to transfer models to a different context. In this article, we show that this implies the samples used to build the model are often not fully representative for the situation where they need to be applied on, which leads to a "sample selection bias." In this article, we enhance data-driven damage models by applying methods, not previously applied to damage modeling, to correct for this bias before the machine learning (ML) models are trained. We demonstrate this with case studies on flooding in Europe, and typhoon wind damage in the Philippines. Two sample selection bias correction methods from the ML literature are applied and one of these methods is also adjusted to our problem. These three methods are combined with stochastic generation of synthetic damage data. We demonstrate that for both case studies, the sample selection bias correction techniques reduce model errors, especially for the mean bias error this reduction can be larger than 30%. The novel combination with stochastic data generation seems to enhance these techniques. This shows that sample selection bias correction methods are beneficial for damage model transfer.

Remotely Produced and Axon-Derived Netrin-1 Instructs GABAergic Neuron Migration and Dopaminergic Substantia Nigra Development.

The midbrain dopamine (mDA) system is composed of molecularly and functionally distinct neuron subtypes that mediate specific behaviors and show select disease vulnerability, including in Parkinson's disease. Despite progress in identifying mDA neuron subtypes, how these neuronal subsets develop and organize into functional brain structures remains poorly understood. Here we generate and use an intersectional genetic platform, Pitx3-ITC, to dissect the mechanisms of substantia nigra (SN) development and implicate the guidance molecule Netrin-1 in the migration and positioning of mDA neuron subtypes in the SN. Unexpectedly, we show that Netrin-1, produced in the forebrain and provided to the midbrain through axon projections, instructs the migration of GABAergic neurons into the ventral SN. This migration is required to confine mDA neurons to the dorsal SN. These data demonstrate that neuron migration can be controlled by remotely produced and axon-derived secreted guidance cues, a principle that is likely to apply more generally.

Short-course antibiotic treatment of bone and joint infections in children: a retrospective study at Montpellier University Hospital from 2009 to 2013.

BACKGROUND: Acute haematogenous bone and joint infections (AHBJI) represent a diagnostic and therapeutic emergency in children, with significant potential sequelae in the case of delayed treatment. Although historically the recommendations for treatment have been based on surgery and prolonged antibiotic therapy, recent studies have demonstrated that short-course antibiotic therapy is also effective. OBJECTIVES: We evaluated a short-term antibiotic protocol for both osteomyelitis and septic arthritis in a 6 year retrospective study at the University Hospital of Montpellier. METHODS: This protocol was based on an initial intravenous treatment with a re-evaluation after 48 h and an early switch to oral therapy in the case of a favourable clinical course for a minimum total duration of 15 days. Antibiotics were selected based on local microbiological epidemiology and systematically adapted to bacteriological results. RESULTS: One hundred and seventy-six cases of AHBJI were included, comprising 56 patients with osteomyelitis, 95 with septic arthritis and 25 who had both of these. The aetiological agent was identified in 42% of the cases, with the main pathogens being Staphylococcus aureus (39%) and Kingella kingae (27%). The mean intravenous treatment duration was 4 days, while the total treatment duration was 15 days. There were no treatment failures, mild sequelae occurred in 1% of the cases and the secondary surgical revision rate was 7%. CONCLUSIONS: The results of this study are comparable to those reported for evaluations of prolonged antibiotic therapy protocols, thus indicating that a common short-term antimicrobial therapy for the management of both osteomyelitis and septic arthritis (minimum of 15 days) is a viable option for treating AHBJI in children. Further prospective studies to confirm these findings are hence warranted.

Quantifying work function differences using low-energy electron microscopy: The case of mixed-terminated strontium titanate.

For many applications, it is important to measure the local work function of a surface with high lateral resolution. Low-energy electron microscopy is regularly employed to this end since it is, in principle, very well suited as it combines high-resolution imaging with high sensitivity to local electrostatic potentials. For surfaces with areas of different work function, however, lateral electrostatic fields inevitably associated with work function discontinuities deflect the low-energy electrons and thereby cause artifacts near these discontinuities. We use ray-tracing simulations to show that these artifacts extend over hundreds of nanometers and cause an overestimation of the true work function difference near the discontinuity by a factor of 1.6 if the standard image analysis methods are used. We demonstrate on a mixed-terminated strontium titanate surface that comparing LEEM data with detailed ray-tracing simulations leads to much a more robust estimate of the work function difference.

Complement C4 Prevents Viral Infection through Capsid Inactivation.

The complement system is vital for anti-microbial defense. In the classical pathway, pathogen-bound antibody recruits the C1 complex (C1qC1r2C1s2) that initiates a cleavage cascade involving C2, C3, C4, and C5 and triggering microbial clearance. We demonstrate a C4-dependent antiviral mechanism that is independent of downstream complement components. C4 inhibits human adenovirus infection by directly inactivating the virus capsid. Rapid C4 activation and capsid deposition of cleaved C4b are catalyzed by antibodies via the classical pathway. Capsid-deposited C4b neutralizes infection independent of C2 and C3 but requires C1q antibody engagement. C4b inhibits capsid disassembly, preventing endosomal escape and cytosolic access. C4-deficient mice exhibit heightened viral burdens. Additionally, complement synergizes with the Fc receptor TRIM21 to block transduction by an adenovirus gene therapy vector but is partially restored by Fab virus shielding. These results suggest that the complement system could be altered to prevent virus infection and enhance virus gene therapy efficacy.

Bcl9 and Pygo synergise downstream of Apc to effect intestinal neoplasia in FAP mouse models.

Bcl9 and Pygo are Wnt enhanceosome components that effect ß-catenin-dependent transcription. Whether they mediate ß-catenin-dependent neoplasia is unclear. Here we assess their roles in intestinal tumourigenesis initiated by Apc loss-of-function (ApcMin), or by Apc1322T encoding a partially-functional Apc truncation commonly found in colorectal carcinomas. Intestinal deletion of Bcl9 extends disease-free survival in both models, and essentially cures Apc1322T mice of their neoplasia. Loss-of-Bcl9 synergises with loss-of-Pygo to shift gene expression within Apc-mutant adenomas from stem cell-like to differentiation along Notch-regulated secretory lineages. Bcl9 loss also promotes tumour retention in ApcMin mice, apparently via relocating nuclear ß-catenin to the cell surface, but this undesirable effect is not seen in Apc1322T mice whose Apc truncation retains partial function in regulating ß-catenin. Our results demonstrate a key role of the Wnt enhanceosome in ß-catenin-dependent intestinal tumourigenesis and reveal the potential of BCL9 as a therapeutic target during early stages of colorectal cancer.

TRIM21 mediates antibody inhibition of adenovirus-based gene delivery and vaccination.

Adenovirus has enormous potential as a gene-therapy vector, but preexisting immunity limits its widespread application. What is responsible for this immune block is unclear because antibodies potently inhibit transgene expression without impeding gene transfer into target cells. Here we show that antibody prevention of adenoviral gene delivery in vivo is mediated by the cytosolic antibody receptor TRIM21. Genetic KO of TRIM21 or a single-antibody point mutation is sufficient to restore transgene expression to near-naïve immune levels. TRIM21 is also responsible for blocking cytotoxic T cell induction by vaccine vectors, preventing a protective response against subsequent influenza infection and an engrafted tumor. Furthermore, adenoviral preexisting immunity can lead to an augmented immune response upon i.v. administration of the vector. Transcriptomic analysis of vector-transduced tissue reveals that TRIM21 is responsible for the specific up-regulation of hundreds of immune genes, the majority of which are components of the intrinsic or innate response. Together, these data define a major mechanism underlying the preimmune block to adenovirus gene therapy and demonstrate that TRIM21 efficiently blocks gene delivery in vivo while simultaneously inducing a rapid program of immune transcription.

Synthesis, antimicrobial activity and acid dissociation constants of methyl 5,5-diphenyl-1-(thiazol-2-yl)pyrrolidine-2-carboxylate derivatives.

In this study, a series of polysubstituted methyl 5,5-diphenyl-1-(thiazol-2-yl)pyrrolidine-2-carboxylate derivatives were designed and synthesized by the cyclization reaction of methyl 1-(benzoylcarbamothioyl)-5,5-diphenylpyrrolidine-2-carboxylates and 2-bromo-1-(4-substituted phenyl)ethanones in 70-96% yield. The starting pyrrolidine derivatives were synthesized via a 1,3-dipolar cycloaddition reaction in 83-88% yield. The stereochemistry of one of these methyl 5,5-diphenyl-1-(thiazol-2-yl)pyrrolidine-2-carboxylate derivatives was characterized by a single crystal X-ray diffraction study and the acid dissociation constants of these compounds were determined. An antimicrobial screening was performed against different bacterial and fungal strains and against the M. tuberculosis H37Rv strain. Interesting antibacterial activity was observed for two compounds against the A. baumannii strain with MIC values of 31.25 µg/mL (Ampicillin: 125 µg/mL) and against the M. tuberculosis H37Rv strain with MIC values of 0.98-1.96 µg/mL (Isoniazid: 0.98 µg/mL, Ethambutol: 1.96 µg/mL). Therefore, these structures can be considered as good starting points for the development of new powerful antimycobacterial agents.

Constitutive scaffolding of multiple Wnt enhanceosome components by Legless/BCL9.

Wnt/ß-catenin signaling elicits context-dependent transcription switches that determine normal development and oncogenesis. These are mediated by the Wnt enhanceosome, a multiprotein complex binding to the Pygo chromatin reader and acting through TCF/LEF-responsive enhancers. Pygo renders this complex Wnt-responsive, by capturing ß-catenin via the Legless/BCL9 adaptor. We used CRISPR/Cas9 genome engineering of Drosophila legless (lgs) and human BCL9 and B9L to show that the C-terminus downstream of their adaptor elements is crucial for Wnt responses. BioID proximity labeling revealed that BCL9 and B9L, like PYGO2, are constitutive components of the Wnt enhanceosome. Wnt-dependent docking of ß-catenin to the enhanceosome apparently causes a rearrangement that apposes the BCL9/B9L C-terminus to TCF. This C-terminus binds to the Groucho/TLE co-repressor, and also to the Chip/LDB1-SSDP enhanceosome core complex via an evolutionary conserved element. An unexpected link between BCL9/B9L, PYGO2 and nuclear co-receptor complexes suggests that these ß-catenin co-factors may coordinate Wnt and nuclear hormone responses.

Synthetic Entries to and Biological Activity of Pyrrolopyrimidines.

This review summarizes recent literature (2000-2015) on the synthesis and pharmaceutical properties of pyrrolopyrimidines. These modified pyrimidine bases, fused to a pyrrole ring, and their corresponding nucleosides display a broad applicability in medicinal chemistry. This overview is divided into three main sections, according to the respective isomers: pyrrolo[2,3-d]pyrimidines, pyrrolo[3,2-d]pyrimidines, and pyrrolo[3,4-d]pyrimidines. Each section contains a description of common retro-synthetic strategies, with particular attention for newly reported synthetic entries to the scaffold. Next, the synthetic strategies and the ways in which the scaffolds can be further modified are exemplified according to the biological properties of the obtained products.