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

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

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

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

Direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation

Accurate and reliable measures of cortical thickness from magnetic resonance imaging are an important biomarker to study neurodegenerative and neurological disorders. Diffeomorphic registration-based cortical thickness (DiReCT) is a known technique to derive such measures from non-surface-based volumetric tissue maps. ANTs provides an open-source method for estimating cortical thickness, derived by applying DiReCT to an atlas-based segmentation. In this paper, we propose DL+DiReCT, a method using high-quality deep learning-based neuroanatomy segmentations followed by DiReCT, yielding accurate and reliable cortical thickness measures in a short time. We evaluate the methods on two independent datasets and compare the results against surface-based measures from FreeSurfer. Good correlation of DL+DiReCT with FreeSurfer was observed (r = .887) for global mean cortical thickness compared to ANTs versus FreeSurfer (r = .608). Experiments suggest that both DiReCT-based methods had higher sensitivity to changes in cortical thickness than Freesurfer. However, while ANTs showed low scan-rescan robustness, DL+DiReCT showed similar robustness to Freesurfer. Effect-sizes for group-wise differences of healthy controls compared to individuals with dementia were highest with the deep learning-based segmentation. DL+DiReCT is a promising combination of a deep learning-based method with a traditional registration technique to detect subtle changes in cortical thickness.

A Single-Stranded DNA-Encoded Chemical Library Based on a Stereoisomeric Scaffold Enables Ligand Discovery by Modular Assembly of Building Blocks

A versatile and Lipinski-compliant DNA-encoded library (DEL), comprising 366 600 glutamic acid derivatives coupled to oligonucleotides serving as amplifiable identification barcodes is designed, constructed, and characterized. The GB-DEL library, constructed in single-stranded DNA format, allows de novo identification of specific binders against several pharmaceutically relevant proteins. Moreover, hybridization of the single-stranded DEL with a set of known protein ligands of low to medium affinity coupled to a complementary DNA strand results in self-assembled selectable chemical structures, leading to the identification of affinity-matured compounds.

Differences in directed functional brain connectivity related to age, sex and mental health

Functional interconnections between brain regions define the "connectome" which is of central interest for understanding human brain function. Resting-state functional magnetic resonance (rsfMRI) work has revealed changes in static connectivity related to age, sex, cognitive abilities and psychiatric symptoms, yet little is known how these factors may alter the information flow. The commonly used approach infers functional brain connectivity using stationary coefficients yielding static estimates of the undirected connection strength between brain regions. Dynamic graphical models (DGMs) are a multivariate model with dynamic coefficients reflecting directed temporal associations between nodes, and can yield novel insight into directed functional connectivity. Here, we leveraged this approach to test for associations between edge-wise estimates of direction flow across the functional connectome and age, sex, intellectual abilities and mental health. We applied DGM to investigate patterns of information flow in data from 984 individuals from the Human Connectome Project (HCP) and 10,249 individuals from the UK Biobank. Our analysis yielded patterns of directed connectivity in independent HCP and UK Biobank data similar to those previously reported, including that the cerebellum consistently receives information from other networks. We show robust associations between information flow and age and sex for several connections, with strongest effects of age observed in the sensorimotor network. Visual, auditory and sensorimotor nodes were also linked to mental health. Our findings support the use of DGM as a measure of directed connectivity in rsfMRI data and provide new insight into the shaping of the connectome during aging.

Superior Acetone Selectivity in Gas Mixtures by Catalyst-Filtered Chemoresistive Sensors

Acetone is a toxic air pollutant and a key breath marker for non-invasively monitoring fat metabolism. Its routine detection in realistic gas mixtures (i.e., human breath and indoor air), however, is challenging, as low-cost acetone sensors suffer from insufficient selectivity. Here, a compact detector for acetone sensing is introduced, having unprecedented selectivity (>250) over the most challenging interferants (e.g., alcohols, aldehydes, aromatics, isoprene, ammonia, H2, and CO). That way, acetone is quantified with fast response (<1 min) down to, at least, 50 parts per billion (ppb) in gas mixtures with such interferants having up to two orders of magnitude higher concentration than acetone at realistic relative humidities (RH = 30-90%). The detector consists of a catalytic packed bed (30 mg) of flame-made Al2O3 nanoparticles (120 m2 g-1) decorated with Pt nanoclusters (average size 9 nm) and a highly sensitive chemo-resistive sensor made by flame aerosol deposition and in situ annealing of nanostructured Si-doped ε-WO3 (Si/WO3). Most importantly, the catalytic packed bed converts interferants continuously enabling highly selective acetone sensing even in the exhaled breath of a volunteer. The detector exhibits stable performance over, at least, 145 days at 90% RH, as validated by mass spectrometry.

Organic Broadband THz Generators Optimized for Efficient Near-Infrared Optical Pumping

New organic THz generators are designed herein by molecular engineering of the refractive index, phonon mode, and spatial asymmetry. These benzothiazolium crystals simultaneously satisfy the crucial requirements for efficient THz wave generation, including having nonlinear optical chromophores with parallel alignment that provide large optical nonlinearity; good phase matching for enhancing the THz generation efficiency in the near-infrared region; strong intermolecular interactions that provide restraining THz self-absorption; high solubility that promotes good crystal growth ability; and a plate-like crystal morphology with excellent optical quality. Consequently, the as-grown benzothiazolium crystals exhibit excellent characteristics for THz wave generation, particularly at near-infrared pump wavelengths around 1100 nm, which is very promising given the availability of femtosecond laser sources at this wavelength, where current conventional THz generators deliver relatively low optical-to-THz conversion efficiencies. Compared to a 1.0-mm-thick ZnTe crystal as an inorganic benchmark, the 0.28-mm-thick benzothiazolium crystal yields a 19 times higher peak-to-peak THz electric field with a broader spectral bandwidth (>6.5 THz) when pumped at 1140 nm. The present work provides a valuable approach toward realizing organic crystals that can be pumped by near-infrared sources for efficient THz wave generation.

[18F]AZD2461, an Insight on Difference in PARP Binding Profiles for DNA Damage Response PET Imaging

BACKGROUND

Poly (ADP-ribose) polymerase (PARP) inhibitors are extensively studied and used as anti-cancer drugs, as single agents or in combination with other therapies. Most radiotracers developed to date have been chosen on the basis of strong PARP1-3 affinity. Herein, we propose to study AZD2461, a PARP inhibitor with lower affinity towards PARP3, and to investigate its potential for PARP targeting in vivo.

METHODS

Using the Cu-mediated 18F-fluorodeboronation of a carefully designed radiolabelling precursor, we accessed the 18F-labelled isotopologue of the PARP inhibitor AZD2461. Cell uptake of [18F]AZD2461 in vitro was assessed in a range of pancreatic cell lines (PSN-1, PANC-1, CFPAC-1 and AsPC-1) to assess PARP expression and in vivo in xenograft-bearing mice. Blocking experiments were performed with both olaparib and AZD2461.

RESULTS

[18F]AZD2461 was efficiently radiolabelled via both manual and automated procedures (9 % ± 3 % and 3 % ± 1 % activity yields non-decay corrected). [18F]AZD2461 was taken up in vivo in PARP1-expressing tumours, and the highest uptake was observed for PSN-1 cells (7.34 ± 1.16 %ID/g). In vitro blocking experiments showed a lesser ability of olaparib to reduce [18F]AZD2461 binding, indicating a difference in selectivity between olaparib and AZD2461.

CONCLUSION

Taken together, we show the importance of screening the PARP selectivity profile of radiolabelled PARP inhibitors for use as PET imaging agents.

A Visible-Light Promoted Amine Oxidation Catalyzed by a Cp*Ir Complex

Through a rapid screening of Cp*Ir complexes based on a turn-on type fluorescence readout, a [Cp*Ir(dipyrido[3,2-a : 2',3'-c]phenazine)Cl]+ complex was found to catalyze the blue-light promoted dehydrogenation of N-heterocycles under physiological conditions. In the dehydrogenation of tetrahydroisoquinolines, the catalyst preferentially yielded the monodehydrogenated product, accompanying H2O2 generation. We surmise that this mechanism may be reminiscent of flavin-dependent oxidases.

Head-to-head comparison of DFO* and DFO chelators: selection of the best candidate for clinical 89Zr-immuno-PET

Purpose

Almost all radiolabellings of antibodies with ⁸⁹Zr currently employ the hexadentate chelator desferrioxamine (DFO). However, DFO can lead to unwanted uptake of ⁸⁹Zr in bones due to instability of the resulting metal complex. DFO*-NCS and the squaramide ester of DFO, DFOSq, are novel analogues that gave more stable ⁸⁹Zr complexes than DFO in pilot experiments. Here, we directly compare these linker-chelator systems to identify optimal immuno-PET reagents.

Methods

Cetuximab, trastuzumab and B12 (non-binding control antibody) were labelled with ⁸⁹Zr via DFO*-NCS, DFOSq, DFO-NCS or DFO*Sq. Stability in vitro was compared at 37 °C in serum (7 days), in formulation solution (24 h ± chelator challenges) and in vivo with N87 and A431 tumour-bearing mice. Finally, to demonstrate the practical benefit of more stable complexation for the accurate detection of bone metastases, [⁸⁹Zr]Zr-DFO*-NCS and [⁸⁹Zr]Zr-DFO-NCS-labelled trastuzumab and B12 were evaluated in a bone metastasis mouse model where BT-474 breast cancer cells were injected intratibially.

Results

[⁸⁹Zr]Zr-DFO*-NCS-trastuzumab and [⁸⁹Zr]Zr-DFO*Sq-trastuzumab showed excellent stability in vitro, superior to their [⁸⁹Zr]Zr-DFO counterparts under all conditions. While tumour uptake was similar for all conjugates, bone uptake was lower for DFO* conjugates. Lower bone uptake for DFO* conjugates was confirmed using a second xenograft model: A431 combined with cetuximab. Finally, in the intratibial BT-474 bone metastasis model, the DFO* conjugates provided superior detection of tumour-specific signal over the DFO conjugates.

Conclusion

DFO*-mAb conjugates provide lower bone uptake than their DFO analogues; thus, DFO* is a superior candidate for preclinical and clinical ⁸⁹Zr-immuno-PET.

Electronic supplementary material

The online version of this article (10.1007/s00259-020-05002-7) contains supplementary material, which is available to authorized users.

Protein NMR Spectroscopy at 150 kHz Magic-Angle Spinning Continues To Improve Resolution and Mass Sensitivity

Spectral resolution is the key to unleashing the structural and dynamic information contained in NMR spectra. Fast magic-angle spinning (MAS) has recently revolutionized the spectroscopy of biomolecular solids. Herein, we report a further remarkable improvement in the resolution of the spectra of four fully protonated proteins and a small drug molecule by pushing the MAS rotation frequency higher (150 kHz) than the more routinely used 100 kHz. We observed a reduction in the average homogeneous linewidth by a factor of 1.5 and a decrease in the observed linewidth by a factor 1.25. We conclude that even faster MAS is highly attractive and increases mass sensitivity at a moderate price in overall sensitivity.

3D Bioprinting of Macroporous Materials Based on Entangled Hydrogel Microstrands

Hydrogels are excellent mimetics of mammalian extracellular matrices and have found widespread use in tissue engineering. Nanoporosity of monolithic bulk hydrogels, however, limits mass transport of key biomolecules. Microgels used in 3D bioprinting achieve both custom shape and vastly improved permissivity to an array of cell functions, however spherical-microbead-based bioinks are challenging to upscale, are inherently isotropic, and require secondary crosslinking. Here, bioinks based on high-aspect-ratio hydrogel microstrands are introduced to overcome these limitations. Pre-crosslinked, bulk hydrogels are deconstructed into microstrands by sizing through a grid with apertures of 40-100 µm. The microstrands are moldable and form a porous, entangled structure, stable in aqueous medium without further crosslinking. Entangled microstrands have rheological properties characteristic of excellent bioinks for extrusion bioprinting. Furthermore, individual microstrands align during extrusion and facilitate the alignment of myotubes. Cells can be placed either inside or outside the hydrogel phase with >90% viability. Chondrocytes co-printed with the microstrands deposit abundant extracellular matrix, resulting in a modulus increase from 2.7 to 780.2 kPa after 6 weeks of culture. This powerful approach to deconstruct bulk hydrogels into advanced bioinks is both scalable and versatile, representing an important toolbox for 3D bioprinting of architected hydrogels.

Climate change considerations are fundamental to management of deep-sea resource extraction

Climate change manifestation in the ocean, through warming, oxygen loss, increasing acidification, and changing particulate organic carbon flux (one metric of altered food supply), is projected to affect most deep-ocean ecosystems concomitantly with increasing direct human disturbance. Climate drivers will alter deep-sea biodiversity and associated ecosystem services, and may interact with disturbance from resource extraction activities or even climate geoengineering. We suggest that to ensure the effective management of increasing use of the deep ocean (e.g., for bottom fishing, oil and gas extraction, and deep-seabed mining), environmental management and developing regulations must consider climate change. Strategic planning, impact assessment and monitoring, spatial management, application of the precautionary approach, and full-cost accounting of extraction activities should embrace climate consciousness. Coupled climate and biological modeling approaches applied in the water and on the seafloor can help accomplish this goal. For example, Earth-System Model projections of climate-change parameters at the seafloor reveal heterogeneity in projected climate hazard and time of emergence (beyond natural variability) in regions targeted for deep-seabed mining. Models that combine climate-induced changes in ocean circulation with particle tracking predict altered transport of early life stages (larvae) under climate change. Habitat suitability models can help assess the consequences of altered larval dispersal, predict climate refugia, and identify vulnerable regions for multiple species under climate change. Engaging the deep observing community can support the necessary data provisioning to mainstream climate into the development of environmental management plans. To illustrate this approach, we focus on deep-seabed mining and the International Seabed Authority, whose mandates include regulation of all mineral-related activities in international waters and protecting the marine environment from the harmful effects of mining. However, achieving deep-ocean sustainability under the UN Sustainable Development Goals will require integration of climate consideration across all policy sectors.

An extracellular vesicle epitope profile is associated with acute myocardial infarction

The current standard biomarker for myocardial infarction (MI) is high-sensitive troponin. Although powerful in clinical setting, search for new markers is warranted as early diagnosis of MI is associated with improved outcomes. Extracellular vesicles (EVs) attracted considerable interest as new blood biomarkers. A training cohort used for diagnostic modelling included 30 patients with STEMI, 38 with stable angina (SA) and 30 matched-controls. Extracellular vesicle concentration was assessed by nanoparticle tracking analysis. Extracellular vesicle surface-epitopes were measured by flow cytometry. Diagnostic models were developed using machine learning algorithms and validated on an independent cohort of 80 patients. Serum EV concentration from STEMI patients was increased as compared to controls and SA. EV levels of CD62P, CD42a, CD41b, CD31 and CD40 increased in STEMI, and to a lesser extent in SA patients. An aggregate marker including EV concentration and CD62P/CD42a levels achieved non-inferiority to troponin, discriminating STEMI from controls (AUC = 0.969). A random forest model based on EV biomarkers discriminated the two groups with 100% accuracy. EV markers and RF model confirmed high diagnostic performance at validation. In conclusion, patients with acute MI or SA exhibit characteristic EV biomarker profiles. EV biomarkers hold great potential as early markers for the management of patients with MI.

Drivers of future alien species impacts: An expert-based assessment

Understanding the likely future impacts of biological invasions is crucial yet highly challenging given the multiple relevant environmental, socio-economic and societal contexts and drivers. In the absence of quantitative models, methods based on expert knowledge are the best option for assessing future invasion trajectories. Here, we present an expert assessment of the drivers of potential alien species impacts under contrasting scenarios and socioecological contexts through the mid-21st century. Based on responses from 36 experts in biological invasions, moderate (20%-30%) increases in invasions, compared to the current conditions, are expected to cause major impacts on biodiversity in most socioecological contexts. Three main drivers of biological invasions-transport, climate change and socio-economic change-were predicted to significantly affect future impacts of alien species on biodiversity even under a best-case scenario. Other drivers (e.g. human demography and migration in tropical and subtropical regions) were also of high importance in specific global contexts (e.g. for individual taxonomic groups or biomes). We show that some best-case scenarios can substantially reduce potential future impacts of biological invasions. However, rapid and comprehensive actions are necessary to use this potential and achieve the goals of the Post-2020 Framework of the Convention on Biological Diversity.

Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary. Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272-Mb genome of the Mediterranean grass Brachypodium distachyon. We find that much of the recent transpositional activity in the B. distachyon genome is due to centromeric Gypsy families and Copia elements belonging to the Angela lineage. With a half-life as low as 66 kyr, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-rich Gypsy elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains > 20% of the genome-wide variation in GC content and is associated with higher methylation levels. Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.

Deep learning-guided joint attenuation and scatter correction in multitracer neuroimaging studies

PET attenuation correction (AC) on systems lacking CT/transmission scanning, such as dedicated brain PET scanners and hybrid PET/MRI, is challenging. Direct AC in image-space, wherein PET images corrected for attenuation and scatter are synthesized from nonattenuation corrected PET (PET-nonAC) images in an end-to-end fashion using deep learning approaches (DLAC) is evaluated for various radiotracers used in molecular neuroimaging studies. One hundred eighty brain PET scans acquired using 18 F-FDG, 18 F-DOPA, 18 F-Flortaucipir (targeting tau pathology), and 18 F-Flutemetamol (targeting amyloid pathology) radiotracers (40 + 5, training/validation + external test, subjects for each radiotracer) were included. The PET data were reconstructed using CT-based AC (CTAC) to generate reference PET-CTAC and without AC to produce PET-nonAC images. A deep convolutional neural network was trained to generate PET attenuation corrected images (PET-DLAC) from PET-nonAC. The quantitative accuracy of this approach was investigated separately for each radiotracer considering the values obtained from PET-CTAC images as reference. A segmented AC map (PET-SegAC) containing soft-tissue and background air was also included in the evaluation. Quantitative analysis of PET images demonstrated superior performance of the DLAC approach compared to SegAC technique for all tracers. Despite the relatively low quantitative bias observed when using the DLAC approach, this approach appears vulnerable to outliers, resulting in noticeable local pseudo uptake and false cold regions. Direct AC in image-space using deep learning demonstrated quantitatively acceptable performance with less than 9% absolute SUV bias for the four different investigated neuroimaging radiotracers. However, this approach is vulnerable to outliers which result in large local quantitative bias.

Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1

Mitochondria are eukaryotic organelles of bacterial origin where respiration takes place to produce cellular chemical energy. These reactions are catalyzed by the respiratory chain complexes located in the inner mitochondrial membrane. Notably, key components of the respiratory chain complexes are encoded on the mitochondrial chromosome and their expression relies on a dedicated mitochondrial translation machinery. Defects in the mitochondrial gene expression machinery lead to a variety of diseases in humans mostly affecting tissues with high energy demand such as the nervous system, the heart, or the muscles. The mitochondrial translation system has substantially diverged from its bacterial ancestor, including alterations in the mitoribosomal architecture, multiple changes to the set of translation factors and striking reductions in otherwise conserved tRNA elements. Although a number of structures of mitochondrial ribosomes from different species have been determined, our mechanistic understanding of the mitochondrial translation cycle remains largely unexplored. Here, we present two cryo-EM reconstructions of human mitochondrial elongation factor G1 bound to the mammalian mitochondrial ribosome at two different steps of the tRNA translocation reaction during translation elongation. Our structures explain the mechanism of tRNA and mRNA translocation on the mitoribosome, the regulation of mtEFG1 activity by the ribosomal GTPase-associated center, and the basis of decreased susceptibility of mtEFG1 to the commonly used antibiotic fusidic acid.

Time of Emergence and Large Ensemble Intercomparison for Ocean Biogeochemical Trends

Anthropogenically forced changes in ocean biogeochemistry are underway and critical for the ocean carbon sink and marine habitat. Detecting such changes in ocean biogeochemistry will require quantification of the magnitude of the change (anthropogenic signal) and the natural variability inherent to the climate system (noise). Here we use Large Ensemble (LE) experiments from four Earth system models (ESMs) with multiple emissions scenarios to estimate Time of Emergence (ToE) and partition projection uncertainty for anthropogenic signals in five biogeochemically important upper-ocean variables. We find ToEs are robust across ESMs for sea surface temperature and the invasion of anthropogenic carbon; emergence time scales are 20-30 yr. For the biological carbon pump, and sea surface chlorophyll and salinity, emergence time scales are longer (50+ yr), less robust across the ESMs, and more sensitive to the forcing scenario considered. We find internal variability uncertainty, and model differences in the internal variability uncertainty, can be consequential sources of uncertainty for projecting regional changes in ocean biogeochemistry over the coming decades. In combining structural, scenario, and internal variability uncertainty, this study represents the most comprehensive characterization of biogeochemical emergence time scales and uncertainty to date. Our findings delineate critical spatial and duration requirements for marine observing systems to robustly detect anthropogenic change.

Multiscale Analysis of Metal Oxide Nanoparticles in Tissue: Insights into Biodistribution and Biotransformation

Metal oxide nanoparticles have emerged as exceptionally potent biomedical sensors and actuators due to their unique physicochemical features. Despite fascinating achievements, the current limited understanding of the molecular interplay between nanoparticles and the surrounding tissue remains a major obstacle in the rationalized development of nanomedicines, which is reflected in their poor clinical approval rate. This work reports on the nanoscopic characterization of inorganic nanoparticles in tissue by the example of complex metal oxide nanoparticle hybrids consisting of crystalline cerium oxide and the biodegradable ceramic bioglass. A validated analytical method based on semiquantitative X-ray fluorescence and inductively coupled plasma spectrometry is used to assess nanoparticle biodistribution following intravenous and topical application. Then, a correlative multiscale analytical cascade based on a combination of microscopy and spectroscopy techniques shows that the topically applied hybrid nanoparticles remain at the initial site and are preferentially taken up into macrophages, form apatite on their surface, and lead to increased accumulation of lipids in their surroundings. Taken together, this work displays how modern analytical techniques can be harnessed to gain unprecedented insights into the biodistribution and biotransformation of complex inorganic nanoparticles. Such nanoscopic characterization is imperative for the rationalized engineering of safe and efficacious nanoparticle-based systems.

LCM-seq reveals unique transcriptional adaptation mechanisms of resistant neurons and identifies protective pathways in spinal muscular atrophy

Somatic motor neurons are selectively vulnerable in spinal muscular atrophy (SMA), which is caused by a deficiency of the ubiquitously expressed survival of motor neuron protein. However, some motor neuron groups, including oculomotor and trochlear (ocular), which innervate eye muscles, are for unknown reasons spared. To reveal mechanisms of vulnerability and resistance in SMA, we investigate the transcriptional dynamics in discrete neuronal populations using laser capture microdissection coupled with RNA sequencing (LCM-seq). Using gene correlation network analysis, we reveal a TRP53-mediated stress response that is intrinsic to all somatic motor neurons independent of their vulnerability, but absent in relatively resistant red nucleus and visceral motor neurons. However, the temporal and spatial expression analysis across neuron types shows that the majority of SMA-induced modulations are cell type-specific. Using Gene Ontology and protein network analyses, we show that ocular motor neurons present unique disease-adaptation mechanisms that could explain their resilience. Specifically, ocular motor neurons up-regulate (1) Syt1, Syt5, and Cplx2, which modulate neurotransmitter release; (2) the neuronal survival factors Gdf15, Chl1, and Lif; (3) Aldh4, that protects cells from oxidative stress; and (4) the caspase inhibitor Pak4. Finally, we show that GDF15 can rescue vulnerable human spinal motor neurons from degeneration. This confirms that adaptation mechanisms identified in resilient neurons can be used to reduce susceptibility of vulnerable neurons. In conclusion, this in-depth longitudinal transcriptomics analysis in SMA reveals novel cell type-specific changes that, alone and combined, present compelling targets, including Gdf15, for future gene therapy studies aimed toward preserving vulnerable motor neurons.

The role of the subgenual anterior cingulate cortex in dorsomedial prefrontal-amygdala neural circuitry during positive-social emotion regulation

Positive-social emotions mediate one's cognitive performance, mood, well-being, and social bonds, and represent a critical variable within therapeutic settings. It has been shown that the upregulation of positive emotions in social situations is associated with increased top-down signals that stem from the prefrontal cortices (PFC) which modulate bottom-up emotional responses in the amygdala. However, it remains unclear if positive-social emotion upregulation of the amygdala occurs directly through the dorsomedial PFC (dmPFC) or indirectly linking the bilateral amygdala with the dmPFC via the subgenual anterior cingulate cortex (sgACC), an area which typically serves as a gatekeeper between cognitive and emotion networks. We performed functional MRI (fMRI) experiments with and without effortful positive-social emotion upregulation to demonstrate the functional architecture of a network involving the amygdala, the dmPFC, and the sgACC. We found that effortful positive-social emotion upregulation was associated with an increase in top-down connectivity from the dmPFC on the amygdala via both direct and indirect connections with the sgACC. Conversely, we found that emotion processes without effortful regulation increased network modulation by the sgACC and amygdala. We also found that more anxious individuals with a greater tendency to suppress emotions and intrusive thoughts, were likely to display decreased amygdala, dmPFC, and sgACC activity and stronger connectivity strength from the sgACC onto the left amygdala during effortful emotion upregulation. Analyzed brain network suggests a more general role of the sgACC in cognitive control and sheds light on neurobiological informed treatment interventions.

Hallmarks of frailty and osteosarcopenia in prematurely aged PolgA(D257A/D257A) mice

BACKGROUND

Frailty is a geriatric syndrome characterized by increased susceptibility to adverse health outcomes. One major determinant thereof is the gradual weakening of the musculoskeletal system and the associated osteosarcopenia. To improve our understanding of the underlying pathophysiology and, more importantly, to test potential interventions aimed at counteracting frailty, suitable animal models are needed.

METHODS

To evaluate the relevance of prematurely aged PolgA(D257A/D257A) mice as a model for frailty and osteosarcopenia, we quantified the clinical mouse frailty index in PolgA(D257A/D257A) and wild-type littermates (PolgA(+/+) , WT) with age and concertedly assessed the quantity and quality of bone and muscle tissue. Lastly, the anabolic responsiveness of skeletal muscle, muscle progenitors, and bone was assessed.

RESULTS

PolgA(D257A/D257A) accumulated health deficits at a higher rate compared with WT, resulting in a higher frailty index at 40 and 46 weeks of age (+166%, +278%, P < 0.0001), respectively, with no differences between genotypes at 34 weeks. Concomitantly, PolgA(D257A/D257A) displayed progressive musculoskeletal deterioration such as reduced bone and muscle mass as well as impaired functionality thereof. In addition to lower muscle weights (-14%, P < 0.05, -23%, P < 0.0001) and fibre area (-20%, P < 0.05, -22%, P < 0.0001) at 40 and 46 weeks, respectively, PolgA(D257A/D257A) showed impairments in grip strength and concentric muscle forces (P < 0.05). PolgA(D257A/D257A) mutation altered the acute response to various anabolic stimuli in skeletal muscle and muscle progenitors. While PolgA(D257A/D257A) muscles were hypersensitive to eccentric contractions as well as leucine administration, shown by larger downstream signalling response of the mechanistic target of rapamycin complex 1, myogenic progenitors cultured in vitro showed severe anabolic resistance to leucine and robust impairments in cell proliferation. Longitudinal micro-computed tomography analysis of the sixth caudal vertebrae showed that PolgA(D257A/D257A) had lower bone morphometric parameters (e.g. bone volume fraction, trabecular, and cortical thickness, P < 0.05) as well as reduced remodelling activities (e.g. bone formation and resorption rate, P < 0.05) compared with WT. When subjected to 4 weeks of cyclic loading, young but not aged PolgA(D257A/D257A) caudal vertebrae showed load-induced bone adaptation, suggesting reduced mechanosensitivity with age.

CONCLUSIONS

PolgA(D257A/D257A) mutation leads to hallmarks of age-related frailty and osteosarcopenia and provides a powerful model to better understand the relationship between frailty and the aging musculoskeletal system.

Macrophage NCOR1 Deficiency Ameliorates Myocardial Infarction and Neointimal Hyperplasia in Mice

Background

NCOR1 (nuclear receptor corepressor 1) is an essential coregulator of gene transcription. It has been shown that NCOR1 in macrophages plays important roles in metabolic regulation. However, the function of macrophage NCOR1 in response to myocardial infarction (MI) or vascular wire injury has not been elucidated.

Methods and Results

Here, using macrophage Ncor1 knockout mouse in combination with a mouse model of MI, we demonstrated that macrophage NCOR1 deficiency significantly reduced infarct size and improved cardiac function after MI. In addition, macrophage NCOR1 deficiency markedly inhibited neointimal hyperplasia and vascular remodeling in a mouse model of arterial wire injury. Inflammation and macrophage proliferation were substantially attenuated in hearts and arteries of macrophage Ncor1 knockout mice after MI and arterial wire injury, respectively. Cultured primary macrophages from macrophage Ncor1 knockout mice manifested lower expression of inflammatory genes upon stimulation by interleukin‐1β, interleukin‐6, or lipopolysaccharide, together with much less activation of inflammatory signaling cascades including signal transducer and activator of transcription 1 and nuclear factor‐κB. Furthermore, macrophage Ncor1 knockout macrophages were much less proliferative in culture, with inhibited cell cycle progression compared with control cells.

Conclusions

Collectively, our data have demonstrated that NCOR1 is a critical regulator of macrophage inflammation and proliferation and that deficiency of NCOR1 in macrophages attenuates MI and neointimal hyperplasia. Therefore, macrophage NCOR1 may serve as a potential therapeutic target for MI and restenosis.

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

BACKGROUND

The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references.

RESULTS

We augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using the vg toolkit. We find that read mapping is more accurate to variation-aware than linear references if pre-selected variants are used to construct the genome graphs. Graphs that contain random variants do not improve read mapping over the linear reference sequence. Breed-specific augmented and pan-genome graphs enable almost similar mapping accuracy improvements over the linear reference. We construct a whole-genome graph that contains the Hereford-based reference sequence and 14 million alleles that have alternate allele frequency greater than 0.03 in the Brown Swiss cattle breed. Our novel variation-aware reference facilitates accurate read mapping and unbiased sequence variant genotyping for SNPs and Indels.

CONCLUSIONS

We develop the first variation-aware reference graph for an agricultural animal ( https://doi.org/10.5281/zenodo.3759712 ). Our novel reference structure improves sequence read mapping and variant genotyping over the linear reference. Our work is a first step towards the transition from linear to variation-aware reference structures in species with high genetic diversity and many sub-populations.

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

BACKGROUND

The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references.

RESULTS

We augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using the vg toolkit. We find that read mapping is more accurate to variation-aware than linear references if pre-selected variants are used to construct the genome graphs. Graphs that contain random variants do not improve read mapping over the linear reference sequence. Breed-specific augmented and pan-genome graphs enable almost similar mapping accuracy improvements over the linear reference. We construct a whole-genome graph that contains the Hereford-based reference sequence and 14 million alleles that have alternate allele frequency greater than 0.03 in the Brown Swiss cattle breed. Our novel variation-aware reference facilitates accurate read mapping and unbiased sequence variant genotyping for SNPs and Indels.

CONCLUSIONS

We develop the first variation-aware reference graph for an agricultural animal ( https://doi.org/10.5281/zenodo.3759712 ). Our novel reference structure improves sequence read mapping and variant genotyping over the linear reference. Our work is a first step towards the transition from linear to variation-aware reference structures in species with high genetic diversity and many sub-populations.

Divergent Synthesis of Novel Cylindrocyclophanes that Inhibit Methicillin-Resistant Staphylococcus aureus (MRSA)

The cylindrocyclophanes are a family of macrocyclic natural products reported to exhibit antibacterial activity. Little is known about the structural basis of this activity due to the challenges associated with their synthesis or isolation. We hypothesised that structural modification of the cylindrocyclophane scaffold could streamline their synthesis without significant loss of activity. Herein, we report a divergent synthesis of the cylindrocyclophane core enabling access to symmetrical macrocycles by means of a catalytic, domino cross-metathesis-ring-closing metathesis cascade, followed by late-stage diversification. Phenotypic screening identified several novel inhibitors of methicillin-resistant Staphylococcus aureus. The most potent inhibitor has a unique tetrabrominated [7,7]paracyclophane core with no known counterpart in nature. Together these illustrate the potential of divergent synthesis using catalysis and unbiased screening methods in modern antibacterial discovery.

Spatial Charge Separation as the Origin of Anomalous Stark Effect in Fluorous 2D Hybrid Perovskites

2D hybrid perovskites (2DP) are versatile materials, whose electronic and optical properties can be tuned through the nature of the organic cations (even when those are seemingly electronically inert). Here, it is demonstrated that fluorination of the organic ligands yields glassy 2DP materials featuring long-lived correlated electron-hole pairs. Such states have a marked charge-transfer character, as revealed by the persistent Stark effect in the form of a second derivative in electroabsorption. Modeling shows that electrostatic effects associated with fluorination, combined with the steric hindrance due to the bulky side groups, drive the formation of spatially dislocated charge pairs with reduced recombination rates. This work enriches and broadens the current knowledge of the photophysics of 2DP, which will hopefully guide synthesis efforts toward novel materials with improved functionalities.

Quantification of Protein Secretion from Circulating Tumor Cells in Microfluidic Chambers

Cancer cells can be released from a cancerous lesion and migrate into the circulatory system, from whereon they may form metastases at distant sites. Today, it is possible to infer cancer progression and treatment efficacy by determining the number of circulating tumor cells (CTCs) in the patient's blood at multiple time points; further valuable information about CTC phenotypes remains inaccessible. In this article, a microfluidic method for integrated capture, isolation, and analysis of membrane markers as well as quantification of proteins secreted by single CTCs and CTC clusters is introduced. CTCs are isolated from whole blood with extraordinary efficiencies above 95% using dedicated trapping structures that allow co-capture of functionalized magnetic beads to assess protein secretion. The patform is tested with multiple breast cancer cell lines spiked into human blood and mouse-model-derived CTCs. In addition to immunostaining, the secretion level of granulocyte growth stimulating factor (G-CSF), which is shown to be involved in neutrophil recruitment, is quantified The bead-based assay provides a limit of detection of 1.5 ng mL^-1 or less than 3700 molecules per cell. Employing barcoded magnetic beads, this platform can be adapted for multiplexed analysis and can enable comprehensive functional CTC profiling in the future.

Development and validation of a multiplex UHPLC-MS/MS assay with stable isotopic internal standards for the monitoring of the plasma concentrations of the antiretroviral drugs bictegravir, cabotegravir, doravirine, and rilpivirine in people living with HIV

The widespread use of highly active antiretroviral treatments has dramatically changed the prognosis of people living with HIV (PLWH). However, such treatments have to be taken lifelong raising issues regarding the maintenance of both therapeutic effectiveness and long-term tolerability. Recently approved or investigational antiretroviral drugs present considerable advantages, allowing once daily oral dosage along with activity against resistant variants (eg, bictegravir and doravirine) and also parenteral intramuscular administration that facilitates treatment adherence (eg, long-acting injectable formulations such as cabotegravir and rilpivirine). Still, there remains a risk of insufficient or exaggerated circulating exposure due to absorption issues, abnormal elimination, drug-drug interactions, and others. In this context, a multiplex ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) bioassay has been developed for the monitoring of plasma levels of bictegravir, cabotegravir, doravirine, and rilpivirine in PLWH. A simple and convenient protein precipitation was performed followed by direct injection of the supernatant into the UHPLC-MS/MS system. The four analytes were eluted in less than 3 minutes using a reversed-phase chromatography method coupled with triple quadrupole mass spectrometry detection. This bioassay was fully validated following international guidelines and achieved good performances in terms of trueness (94.7%-107.5%), repeatability (2.6%-11%), and intermediate precision (3.0%-11.2%) over the clinically relevant concentration ranges (from 30 to 9000 ng/mL for bictegravir, cabotegravir, and doravirine and from 10 to 1800 ng/mL for rilpivirine). This sensitive, accurate, and rapid UHPLC-MS/MS assay is currently applied in our laboratory for routine therapeutic drug monitoring of the oral drugs bictegravir and doravirine and is also intended to be applied for the monitoring of cabotegravir/rilpivirine levels in plasma from PLWH receiving once monthly or every 2-month intramuscular injection of these long-acting antiretroviral drugs.

Matter-wave interference and deflection of tripeptides decorated with fluorinated alkyl chains

Studies of neutral biomolecules in the gas phase allow for the study of molecular properties in the absence of solvent and charge effects, thus complementing spectroscopic and analytical methods in solution or in ion traps. Some properties, such as the static electronic susceptibility, are best accessed in experiments that act on the motion of the neutral molecules in an electric field. Here, we screen seven peptides for their thermal stability and electron impact ionizability. We identify two tripeptides as sufficiently volatile and thermostable to be evaporated and interfered in the long-baseline universal matter-wave interferometer. Monitoring the deflection of the interferometric molecular nanopattern in a tailored external electric field allows us to measure the static molecular susceptibility of Ala-Trp-Ala and Ala-Ala-Trp bearing fluorinated alkyl chains at C- and N-termini. The respective values are 4 π ε 0 × 330 ± 150 Å 3 and 4 π ε 0 × 270 ± 80 Å 3 .

Simultaneous Nanothermometry and Deep-Tissue Imaging

Bright, stable, and biocompatible fluorescent contrast agents operating in the second biological window (1000-1350 nm) are attractive for imaging of deep-lying structures (e.g., tumors) within tissues. Ideally, these contrast agents also provide functional insights, such as information on local temperature. Here, water-dispersible barium phosphate nanoparticles doped with Mn5+ are made by scalable, continuous, and sterile flame aerosol technology and explored as fluorescent contrast agents with temperature-sensitive peak emission in the NIR-II (1190 nm). Detailed assessment of their stability, toxicity with three representative cell lines (HeLa, THP-1, NHDF), and deep-tissue imaging down to about 3 cm are presented. In addition, their high quantum yield (up to 34%) combined with excellent temperature sensitivity paves the way for concurrent deep-tissue imaging and nanothermometry, with biologically well-tolerated nanoparticles.

SERS Barcode Libraries: A Microfluidic Approach

Microfluidic technologies have emerged as advanced tools for surface-enhanced Raman spectroscopy (SERS). They have proved to be particularly appealing for in situ and real-time detection of analytes at extremely low concentrations and down to the 10 × 10-15 m level. However, the ability to prepare reconfigurable and reusable devices endowing multiple detection capabilities is an unresolved challenge. Herein, a microfluidic-based method that allows an extraordinary spatial control over the localization of multiple active SERS substrates in a single microfluidic channel is presented. It is shown that this technology provides for exquisite control over analyte transport to specific detection points, while avoiding cross-contamination; a feature that enables the simultaneous detection of multiple analytes within the same microfluidic channel. Additionally, it is demonstrated that the SERS substrates can be rationally designed in a straightforward manner and that they allow for the detection of single molecules (at concentrations as low as 10-14 m). Finally, it is shown that rapid etching and reconstruction of SERS substrates provides for reconfigurable and reusable operation.

Assessing the response of forest productivity to climate extremes in Switzerland using model-data fusion

The response of forest productivity to climate extremes strongly depends on ambient environmental and site conditions. To better understand these relationships at a regional scale, we used nearly 800 observation years from 271 permanent long-term forest monitoring plots across Switzerland, obtained between 1980 and 2017. We assimilated these data into the 3-PG forest ecosystem model using Bayesian inference, reducing the bias of model predictions from 14% to 5% for forest stem carbon stocks and from 45% to 9% for stem carbon stock changes. We then estimated the productivity of forests dominated by Picea abies and Fagus sylvatica for the period of 1960-2018, and tested for productivity shifts in response to climate along elevational gradient and in extreme years. Simulated net primary productivity (NPP) decreased with elevation (2.86 ± 0.006 Mg C ha-1  year-1  km-1 for P. abies and 0.93 ± 0.010 Mg C ha-1  year-1  km-1 for F. sylvatica). During warm-dry extremes, simulated NPP for both species increased at higher and decreased at lower elevations, with reductions in NPP of more than 25% for up to 21% of the potential species distribution range in Switzerland. Reduced plant water availability had a stronger effect on NPP than temperature during warm-dry extremes. Importantly, cold-dry extremes had negative impacts on regional forest NPP comparable to warm-dry extremes. Overall, our calibrated model suggests that the response of forest productivity to climate extremes is more complex than simple shift toward higher elevation. Such robust estimates of NPP are key for increasing our understanding of forests ecosystems carbon dynamics under climate extremes.

Engineered Polymersomes for the Treatment of Fish Odor Syndrome: A First Randomized Double Blind Olfactory Study

Trimethylamine (TMA) is a metabolite overtly present in patients suffering from trimethylaminuria (TMAU), a rare genetic disorder characterized by a strong "fishy" body odor. To date, no approved pharmacological treatment to sequester excess TMA on the skin of patients exists. Here, transmembrane pH gradient poly(isoprene)-block-poly(ethylene glycol) (PI-b-PEG) polymersomes are investigated for the topical removal of TMA. PI-b-PEG amphiphiles of varying chain length are synthesized and evaluated for their ability to form vesicular structures in aqueous media. The optimization of the PI/PEG ratio of transmembrane pH gradient polymersomes allows for the rapid and efficient capture of TMA both in solution and after incorporation into a topical hydrogel matrix at the pH of the skin. A subsequent double blind olfactory study reveals a significant decrease in perceived odor intensity after application of the polymersome-based formulation on artificial skin substrates that has been incubated in TMA-containing medium. This simple and novel approach has the potential to ease the burden of people suffering from TMAU.

PHYTOCHROME INTERACTING FACTOR 7 is important for early responses to elevated temperature in Arabidopsis seedlings

In response to elevated ambient temperature Arabidopsis thaliana seedlings display a thermomorphogenic response that includes elongation of hypocotyls and petioles. Phytochrome B and cryptochrome 1 are two photoreceptors also playing a role in thermomorphogenesis. Downstream of both environmental sensors PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is essential to trigger this response at least in part through the production of the growth promoting hormone auxin. Using a genetic approach, we identified PHYTOCHROME INTERACTING FACTOR 7 (PIF7) as a novel player for thermomorphogenesis and compared the phenotypes of pif7 and pif4 mutants. We investigated the role of PIF7 during temperature-regulated gene expression and the regulation of PIF7 transcript and protein by temperature. Furthermore, pif7 and pif4 loss-of-function mutants were similarly unresponsive to increased temperature. This included hypocotyl elongation and induction of genes encoding auxin biosynthetic or signalling proteins. PIF7 bound to the promoters of auxin biosynthesis and signalling genes. In response to temperature elevation PIF7 transcripts decreased while PIF7 protein levels increased rapidly. Our results reveal the importance of PIF7 for thermomorphogenesis and indicate that PIF7 and PIF4 likely depend on each other possibly by forming heterodimers. Elevated temperature rapidly enhances PIF7 protein accumulation, which may contribute to the thermomorphogenic response.

Outcomes of second-line antiretroviral therapy among children living with HIV: a global cohort analysis

INTRODUCTION

Limited data describe outcomes on second-line antiretroviral therapy (ART) among children globally. Our objective was to contribute data on outcomes among children living with HIV after initiation of second-line ART in the context of routine care within a large global cohort collaboration.

METHODS

Patient-level data from 1993 through 2015 from 11 paediatric HIV cohorts were pooled. Characteristics at switch and through two years of follow-up were summarized for children who switched to second-line ART after starting a standard first-line regimen in North America, Latin America, Europe, Asia, Southern Africa (South Africa & Botswana) and the rest of sub-Saharan Africa (SSA). Cumulative incidences of mortality and loss to follow-up (LTFU) were estimated using a competing risks framework.

RESULTS

Of the 85,389 children on first-line ART, 3,555 (4%) switched to second-line after a median of 2.8 years on ART (IQR: 1.6, 4.7); 69% were from Southern Africa or SSA and 86% of second-line regimens were protease inhibitor-based. At switch, median age was 8.4 years and 50% had a prior AIDS diagnosis. Median follow-up after switch to second-line ranged from 1.8 years in SSA to 5.3 years in North America. Median CD4 counts at switch to second-line ranged from 235 cells/mm3 in SSA to 828 cells/mm3 in North America. Improvements in CD4 counts were observed over two years of follow-up, particularly in regions with lower CD4 counts at second-line switch. Improvements in weight-for-age z-scores were not observed during follow-up. Cumulative incidence of LTFU at two years was <5% in all regions except SSA (7.1%) and Southern Africa (7.4%). Risk of mortality was <3% at two years of follow-up in all regions, except Latin America (4.9%) and SSA (5.5%).

CONCLUSIONS

Children switched to second-line ART experience CD4 count increases as well as low to moderate rates of LTFU and mortality within two years after switch. Severe immune deficiency at time of switch in some settings suggests need for improved recognition and management of treatment failure in children.

SciFi detector and associated method for real-time determination of profile and output factor for small fields in stereotactic radiotherapy

PURPOSE

For determining small-field profile and output factor during stereotactic radiotherapy quality assurance (QA) procedures, we propose a novel system based on the scintillating fiber (SciFi) detector with output image acquisition and processing to allow real-time monitoring of profile and output factor.

MATERIALS AND METHODS

The employed detector is a SciFi detector made of tissue-equivalent scintillating plastic fibers arranged in 6-layer fiber ribbons with a fiber pitch of 275 μm in each layer. The scintillating signal at the detector output is acquired by a sCMOS (scientific complementary metal-oxide-semiconductor) camera and represents the projected field profile along the fibers axis. An iterative reconstruction method of the field from its projected profile based on a priori knowledge of some features of the radiation field defined by the stereotactic cones is suggested. The detector with implemented data processing has been tested in clinical conditions, for determining beam profiles and output factors, using cone collimators of different sizes from 4 to 15 mm diameter. The detector under test was placed at 1.4 cm depth and 98.6 cm source to surface distance (SSD) in a water-equivalent phantom and irradiated by a 6 MV photon beam.

RESULTS

The reconstructed field profiles obtained from the detector are coherent with data from EBT3 radiochromic films, with differences within ±0.32 mm for both the FWHM and the penumbra region. For real-time determination of the field output factor, the measured data are also in good agreement with data independently determined by the French Institute for Radiological Protection and Nuclear Safety (IRSN) based on radiochromic films and thermoluminescent 1 × 1 mm2 micro-cubes dosimeters (TLD). The differences are within ±1.6% for all the tested cone sizes.

CONCLUSIONS

We propose and have tested a SciFi plastic scintillating detector with an optimized signal processing method to characterize small fields defined by cone collimators. It allows the determination of key field parameters such as full width at half maximum (FWHM) and field output factors. The results are consistent with those independently measured using TLD and radiochromic films. As the SciFi detector does not require a correction factor, it is in line with the International Atomic Energy Agency (IAEA) and the American Association of Physicists in Medicine (AAPM) TRS-483 recommendations, and can be suitable for online QA of small radiation fields used in photon beam radiotherapy, and is compatible with MRI-LINAC.

Rapid and Selective NH3 Sensing by Porous CuBr

Fast and selective detection of NH3 at parts-per-billion (ppb) concentrations with inexpensive and low-power sensors represents a long-standing challenge. Here, a room temperature, solid-state sensor is presented consisting of nanostructured porous (78%) CuBr films. These are prepared by flame-aerosol deposition of CuO onto sensor substrates followed by dry reduction and bromination. Each step is monitored in situ through the film resistance affording excellent process control. Such porous CuBr films feature an order of magnitude higher NH3 sensitivity and five times faster response times than conventional denser CuBr films. That way, rapid (within 2.2 min) sensing of even the lowest (e.g., 5 ppb) NH3 concentrations at 90% relative humidity is attained with outstanding selectivity (30-260) over typical confounders including ethanol, acetone, H2, CH4, isoprene, acetic acid, formaldehyde, methanol, and CO, superior to state-of-the-art sensors. This sensor is ideal for hand-held and battery-driven devices or integration into wearable electronics as it does not require heating. From a broader perspective, the process opens exciting new avenues to also explore other bromides and classes of semiconductors (e.g., sulfides, nitrides, carbides) currently not accessible by flame-aerosol technology.

Enriching and Quantifying Porous Single Layer 2D Polymers by Exfoliation of Chemically Modified van der Waals Crystals

2D polymer sheets with six positively charged pyrylium groups at each pore edge in a stacked single crystal can be transformed into a 2D polymer with six pyridines per pore by exposure to gaseous ammonia. This reaction furnishes still a crystalline material with tunable protonation degree at regular nano-sized pores promising as separation membrane. The exfoliation is compared for both 2D polymers with the latter being superior. Its liquid phase exfoliation yields nanosheet dispersions, which can be size-selected using centrifugation cascades. Monolayer contents of ≈30 % are achieved with ≈130 nm sized sheets in mg quantities, corresponding to tens of trillions of monolayers. Quantification of nanosheet sizes, layer number and mass shows that this exfoliation is comparable to graphite. Thus, we expect that recent advances in exfoliation of graphite or inorganic crystals (e.g. scale-up, printing etc.) can be directly applied to this 2D polymer as well as to covalent organic frameworks.

Extensions of the probabilistic ranking metrics of competing treatments in network meta-analysis to reflect clinically important relative differences on many outcomes

One of the key features of network meta-analysis is ranking of interventions according to outcomes of interest. Ranking metrics are prone to misinterpretation because of two limitations associated with the current ranking methods. First, differences in relative treatment effects might not be clinically important and this is not reflected in the ranking metrics. Second, there are no established methods to include several health outcomes in the ranking assessments. To address these two issues, we extended the P-score method to allow for multiple outcomes and modified it to measure the mean extent of certainty that a treatment is better than the competing treatments by a certain amount, for example, the minimum clinical important difference. We suggest to present the tradeoff between beneficial and harmful outcomes allowing stakeholders to consider how much adverse effect they are willing to tolerate for specific gains in efficacy. We used a published network of 212 trials comparing 15 antipsychotics and placebo using a random effects network meta-analysis model, focusing on three outcomes; reduction in symptoms of schizophrenia in a standardized scale, all-cause discontinuation, and weight gain.

Bounding Global Aerosol Radiative Forcing of Climate Change

Aerosols interact with radiation and clouds. Substantial progress made over the past 40 years in observing, understanding, and modeling these processes helped quantify the imbalance in the Earth's radiation budget caused by anthropogenic aerosols, called aerosol radiative forcing, but uncertainties remain large. This review provides a new range of aerosol radiative forcing over the industrial era based on multiple, traceable, and arguable lines of evidence, including modeling approaches, theoretical considerations, and observations. Improved understanding of aerosol absorption and the causes of trends in surface radiative fluxes constrain the forcing from aerosol-radiation interactions. A robust theoretical foundation and convincing evidence constrain the forcing caused by aerosol-driven increases in liquid cloud droplet number concentration. However, the influence of anthropogenic aerosols on cloud liquid water content and cloud fraction is less clear, and the influence on mixed-phase and ice clouds remains poorly constrained. Observed changes in surface temperature and radiative fluxes provide additional constraints. These multiple lines of evidence lead to a 68% confidence interval for the total aerosol effective radiative forcing of -1.6 to -0.6 W m-2, or -2.0 to -0.4 W m-2 with a 90% likelihood. Those intervals are of similar width to the last Intergovernmental Panel on Climate Change assessment but shifted toward more negative values. The uncertainty will narrow in the future by continuing to critically combine multiple lines of evidence, especially those addressing industrial-era changes in aerosol sources and aerosol effects on liquid cloud amount and on ice clouds.

New genome assembly of the barn owl (Tyto alba alba)

New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the genome, we assembled de novo Illumina and Pacific Biosciences (PacBio) long reads sequences of its European counterpart (Tyto alba alba). This genome assembly of 1.219 Gbp comprises 21,509 scaffolds and results in a N50 of 4,615,526 bp. BUSCO (Universal Single-Copy Orthologs) analysis revealed an assembly completeness of 94.8% with only 1.8% of the genes missing out of 4,915 avian orthologs searched, a proportion similar to that found in the genomes of the zebra finch (Taeniopygia guttata) or the collared flycatcher (Ficedula albicollis). By mapping the reads of the female American barn owl to the male European barn owl reads, we detected several structural variants and identified 70 Mbp of the Z chromosome. The barn owl scaffolds were further mapped to the chromosomes of the zebra finch. In addition, the completeness of the European barn owl genome is demonstrated with 94 of 128 proteins missing in the chicken genome retrieved in the European barn owl transcripts. This improved genome will help future barn owl population genomic investigations.

Ischemic Stroke despite Oral Anticoagulant Therapy in Patients with Atrial Fibrillation

OBJECTIVE

It is not known whether patients with atrial fibrillation (AF) with ischemic stroke despite oral anticoagulant therapy are at increased risk for further recurrent strokes or how ongoing secondary prevention should be managed.

METHODS

We conducted an individual patient data pooled analysis of 7 prospective cohort studies that recruited patients with AF and recent cerebral ischemia. We compared patients taking oral anticoagulants (vitamin K antagonists [VKA] or direct oral anticoagulants [DOAC]) prior to index event (OACprior ) with those without prior oral anticoagulation (OACnaive ). We further compared those who changed the type (ie, from VKA or DOAC, vice versa, or DOAC to DOAC) of anticoagulation (OACchanged ) with those who continued the same anticoagulation as secondary prevention (OACunchanged ). Time to recurrent acute ischemic stroke (AIS) was analyzed using multivariate competing risk Fine-Gray models to calculate hazard ratios (HRs) and 95% confidence intervals (CIs).

RESULTS

We included 5,413 patients (median age = 78 years [interquartile range (IQR) = 71-84 years]; 5,136 [96.7%] had ischemic stroke as the index event, median National Institutes of Health Stroke Scale on admission = 6 [IQR = 2-12]). The median CHA2 DS2 -Vasc score (congestive heart failure, hypertension, age≥ 75 years, diabetes mellitus, stroke/transient ischemic attack, vascular disease, age 65-74 years, sex category) was 5 (IQR = 4-6) and was similar for OACprior (n = 1,195) and OACnaive (n = 4,119, p = 0.103). During 6,128 patient-years of follow-up, 289 patients had AIS (4.7% per year, 95% CI = 4.2-5.3%). OACprior was associated with an increased risk of AIS (HR = 1.6, 95% CI = 1.2-2.3, p = 0.005). OACchanged (n = 307) was not associated with decreased risk of AIS (HR = 1.2, 95% CI = 0.7-2.1, p = 0.415) compared with OACunchanged (n = 585).

INTERPRETATION

Patients with AF who have an ischemic stroke despite previous oral anticoagulation are at a higher risk for recurrent ischemic stroke despite a CHA2 DS2 -Vasc score similar to those without prior oral anticoagulation. Better prevention strategies are needed for this high-risk patient group. ANN NEUROL 2020.

APOE4 moderates effects of cortical iron on synchronized default mode network activity in cognitively healthy old-aged adults

INTRODUCTION

Apolipoprotein E ε4 (APOE4)-related genetic risk for sporadic Alzheimer's disease is associated with an early impairment of cognitive brain networks. The current study determines relationships between APOE4 carrier status, cortical iron, and cortical network-functionality.

METHODS

Sixty-nine cognitively healthy old-aged individuals (mean age [SD] 66.1 [± 7.2] years; Mini-Mental State Exam [MMSE] 29.3 ± 1.1) were genotyped for APOE4 carrier-status and received 3 Tesla magnetic resonance imaging (MRI) for blood oxygen level-dependent functional magnetic resonance imaging (MRI) at rest, three-dimensional (3D)-gradient echo (six echoes) for cortical gray-matter, non-heme iron by quantitative susceptibility mapping, and 18F-flutemetamol positron emission tomography for amyloid-β.

RESULTS

A spatial pattern consistent with the default mode network (DMN) could be identified by independent component analysis. DMN activity was enhanced in APOE4 carriers and related to cortical iron burden. APOE4 and cortical iron synergistically interacted with DMN activity. Secondary analysis revealed a positive, APOE4 associated, relationship between cortical iron and DMN connectivity.

DISCUSSION

Our findings suggest that APOE4 moderates effects of iron on brain functionality prior to manifestation of cognitive impairment.

Nucleotide Binding Modes in a Motor Protein Revealed by 31 P- and 1 H-Detected MAS Solid-State NMR Spectroscopy

Protein-nucleic acid interactions play important roles not only in energy-providing reactions, such as ATP hydrolysis, but also in reading, extending, packaging, or repairing genomes. Although they can often be analyzed in detail with X-ray crystallography, complementary methods are needed to visualize them in complexes, which are not crystalline. Here, we show how solid-state NMR spectroscopy can detect and classify protein-nucleic interactions through site-specific 1 H- and 31 P-detected spectroscopic methods. The sensitivity of 1 H chemical-shift values on noncovalent interactions involved in these molecular recognition processes is exploited allowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecameric DnaB helicase in complex with ADP:AlF4- :DNA, and this despite the very challenging size of the complex.

Degradation of the transcription factors PIF4 and PIF5 under UV-B promotes UVR8-mediated inhibition of hypocotyl growth in Arabidopsis

Inhibition of hypocotyl growth is a well-established UV-B-induced photomorphogenic response that is mediated by the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8). However, the molecular mechanism by which UVR8 signaling triggers inhibition of hypocotyl growth is poorly understood. The bZIP protein ELONGATED HYPOCOTYL 5 (HY5) functions as the main positive regulatory transcription factor in the UVR8 signaling pathway, with HY5-HOMOLOG (HYH) playing a minor role. However, here we demonstrate that hy5 hyh double mutants maintain significant UVR8-dependent hypocotyl growth inhibition. We identify UVR8-dependent inhibition of the activities of bHLH transcription factors PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 as part of the UVR8 signaling pathway, which results in inhibition of hypocotyl growth. The UVR8-mediated repression of several hypocotyl elongation-related genes is independent of HY5 and HYH but largely associated with UVR8-dependent degradation of PIF4 and PIF5, a process that consequently diminishes PIF4/5 target promoter occupancy. Taken together, our data indicate that UVR8-mediated inhibition of hypocotyl growth involves degradation of PIF4 and PIF5. These findings contribute to our mechanistic understanding of UVR8-induced photomorphogenesis and further support the function of PIFs as integrators of different photoreceptor signaling pathways.

Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies

Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear-encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as 'basal' or 'early-diverging' with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.

Bioinspired Molecular Factories with Architecture and In Vivo Functionalities as Cell Mimics

Despite huge need in the medical domain and significant development efforts, artificial cells to date have limited composition and functionality. Although some artificial cells have proven successful for producing therapeutics or performing in vitro specific reactions, they have not been investigated in vivo to determine whether they preserve their architecture and functionality while avoiding toxicity. Here, these limitations are overcome and customizable cell mimic is achieved-molecular factories (MFs)-by supplementing giant plasma membrane vesicles derived from donor cells with nanometer-sized artificial organelles (AOs). MFs inherit the donor cell's natural cytoplasm and membrane, while the AOs house reactive components and provide cell-like architecture and functionality. It is demonstrated that reactions inside AOs take place in a close-to-nature environment due to the unprecedented level of complexity in the composition of the MFs. It is further demonstrated that in a zebrafish vertebrate animal model, these cell mimics show no apparent toxicity and retain their integrity and function. The unique advantages of highly varied composition, multicompartmentalized architecture, and preserved functionality in vivo open new biological avenues ranging from the study of biorelevant processes in robust cell-like environments to the production of specific bioactive compounds.

What's in a band? The function of the color and banding pattern of the Banded Swallowtail

Butterflies have evolved a diversity of color patterns, but the ecological functions for most of these patterns are still poorly understood. The Banded Swallowtail butterfly, Papilio demolion demolion, is a mostly black butterfly with a greenish-blue band that traverses the wings. The function of this wing pattern remains unknown. Here, we examined the morphology of black and green-blue colored scales, and how the color and banding pattern affects predation risk in the wild. The protective benefits of the transversal band and of its green-blue color were tested via the use of paper model replicas of the Banded Swallowtail with variations in band shape and band color in a full factorial design. A variant model where the continuous transversal green-blue band was shifted and made discontinuous tested the protective benefit of the transversal band, while grayscale variants of the wildtype and distorted band models assessed the protective benefit of the green-blue color. Paper models of the variants and the wildtype were placed simultaneously in the field with live baits. Wildtype models were the least preyed upon compared with all other variants, while gray models with distorted bands suffered the greatest predation. The color and the continuous band of the Banded Swallowtail hence confer antipredator qualities. We propose that the shape of the band hinders detection of the butterfly's true shape through coincident disruptive coloration; while the green color of the band prevents detection of the butterfly from its background via differential blending. Differential blending is aided by the green-blue color being due to pigments rather than via structural coloration. Both green and black scales have identical structures, and the scales follow the Bauplan of pigmented scales documented in other Papilio butterflies.