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Abstract Background The human gut microbiome produces and consumes a variety of compounds that interact with the host and impact health. Succinate is of particular interest as it intersects with both host and microbiome metabolism. However, which gut bacteria are most responsible for the consumption of intestinal succinate is poorly understood. Results We build upon an enrichment-based whole fecal sample culturing approach and identify two main bacterial taxa that are responsible for succinate consumption in the human intestinal microbiome, Phascolarctobacterium and Dialister. These two taxa have the hallmark of a functional guild and are strongly mutual exclusive across 21,459 fecal samples in 94 cohorts and can thus be used to assign a robust “succinotype” to an individual. We show that they differ with respect to their rate of succinate consumption in vitro and that this is associated with higher concentrations of fecal succinate. Finally, individuals suffering from inflammatory bowel disease (IBD) are more likely to have the Dialister succinotype compared to healthy subjects. Conclusions We identified that only two bacterial genera are the key succinate consumers in human gut microbiome, despite the fact that many more intestinal bacteria encode for the succinate pathway. This highlights the importance of phenotypic assays in functionally profiling intestinal microbiota. A stratification based on “succinotype” is to our knowledge the first function-based classification of human intestinal microbiota. The association of succinotype with IBD thus builds a bridge between microbiome function and IBD pathophysiology related to succinate homeostasis. Video Abstract

Abstract The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.

Abstract How extravagant ornamental traits evolve is a key question in evolutionary biology. Bird plumages are among the most elaborate ornaments, displaying almost all colours of the rainbow. Why and how birds evolved to be so colourful remains an open question with multiple and sometimes competing hypotheses. Different colours in different patches (i.e. body parts) might have different functions and thus result from different forms of selection (e.g. natural vs. sexual selection). Here we test the influence of three factors on colour diversity in sunbirds: (1) geographical distance, (2) differences in light environment and (3) phylogenetic distances. We show that both natural and sexual selection affect the evolution of sunbird colouration, but that their extent and direction differs between sexes, and varies with the extent of species overlap and across different patches on the body. Even though overlap in light environment partially explains colour differences among species, no colour metric (brightness, hue or chroma) covaries with light environment. Our results suggest that multiple forms of selection influence the colouration of different colour patches in different ways across an organism's body, highlighting the need to investigate colouration as a network of individual but inter‐connected colour patches. These results are likely to be generalizable across the multitude of colourful animals.

ABSTRACTThe success of fecal microbiota transplants (FMT) has provided the necessary proof-of-concept for microbiome therapeutics. Yet, feces-based therapies have many associated risks and uncertainties, and hence defined microbial consortia that modify the microbiome in a targeted manner have emerged as a promising safer alternative to FMT. The development of such live biotherapeutic products has important challenges, including the selection of appropriate strains and the controlled production of the consortia at scale. Here, we report on an ecology- and biotechnology-based approach to microbial consortium construction that overcomes these issues. We selected nine strains that form a consortium to emulate the central metabolic pathways of carbohydrate fermentation in the healthy human gut microbiota. Continuous co-culturing of the bacteria produces a stable and reproducible consortium whose growth and metabolic activity are distinct from an equivalent mix of individually cultured strains. Further, we showed that our function-based consortium is as effective as FMT in counteracting dysbiosis in a dextran sodium sulfate mouse model of acute colitis, while an equivalent mix of strains failed to match FMT. Finally, we showed robustness and general applicability of our approach by designing and producing additional stable consortia of controlled composition. We propose that combining a bottom-up functional design with continuous co-cultivation is a powerful strategy to produce robust functionally designed synthetic consortia for therapeutic use.

Forensic genetic genealogy (FGG) benefits largely from popularity of genealogical research within (mostly) American society and the advent of new sequencing techniques that allow typing of challenging forensic samples. It is considered a true breakthrough for both active and especially cold cases where all other resources and methods have failed during investigation. Despite media coverage generally highlighting its powers, the method itself is considered very laborious and the investigation may easily got suspended at every stage due to many factors including no hits in the database or breaks in traceable lineages within the family tree. This review summarizes the scope of FGG use, mentions most concerns and misconceptions associated with the technique and points to the plausible solutions already suggested. It also brings together current guidelines and regulations intended to be followed by law enforcement authorities wishing to utilize genetic genealogy research

IntroductionThe chemoattractant receptor, G protein-coupled receptor 15 (GPR15), promotes colon homing of T cells in health and colitis. GPR15 function in colon cancer is largely unexplored, motivating our current studies.MethodsIn human study, immune cells were isolated from tumor tissues and healthy surgical tumor margins (STM), and their proportions as well as expression of GPR15 was analyzed by flow cytometry. In mouse studies, colon cancer was induced in GPR15-deficient (KO) and GPR15-suficient (Het) mice using azoxymethane (AOM) and dextran sulfate sodium (DSS) solution in drinking water. Serial endoscopy was performed in mice to monitor and visualize the distal region of colon. Mice were euthanized 10 weeks after the initial DSS administration, and the colon length and the number of polyps were recorded. Next, we identified the effects of GPR15L on established tumors in the MC38-colorectal cancer (CRC) mouse model. Immune cells were isolated from the mice colons or tumors and assessed by flow cytometry.ResultsOur analysis of human CRC tissue revealed a significant reduction in GPR15+ immune cell frequencies in tumors compared to ‘tumor-free’ surgical margins. Similarly, our data analysis using The Cancer Genome Atlas (TCGA) indicated that lower GPR15 expression is associated with poor survival in human colon cancer. In the AOM/DSS colitis-associated colon cancer model, we observed increased colonic polyps and lower survival in Gpr15+-KO compared to Gpr15-Het mice. Analysis of immune cell infiltrates in the colonic polyps showed significantly decreased CD8+ T cells and increased IL-17+ CD4+ and IL-17+ CD8+ T cells in Gpr15-KO than in Het mice. Consistent with a protective role of GPR15, administration of GPR15L to established tumors in the MC38-CRC model increased CD45+ cell infiltration, enhanced TNFa expression on CD4+ and CD8+ T cells at the tumor site and dramatically reduced tumor burden.DiscussionOur findings highlight an important, unidentified role of the GPR15-GPR15L axis in promoting a tumor-suppressive immune microenvironment and unveils a novel, colon-specific therapeutic target for CRC.

Abstract HfO2 thin films are appealing for microelectronic applications such as high‐κ dielectric layers, memristors, and ferroelectric memory devices. To fulfill the different requirements of each application, the properties of the deposited material need to be tuned accordingly. In this context, plasma‐enhanced atomic layer deposition (PEALD) is a powerful processing route to tailor the properties of HfO2 thin films, especially at low temperatures. Herein, a comprehensive bottom‐up approach is presented, ranging from the synthesis of molecularly engineered Hf precursors to the development of a HfO2 PEALD process and a detailed evaluation where plasma can be exploited to tune the dielectric properties. With the example of the newly synthesized bis‐(dialkylamido)‐bis‐(formamidinato) Hf(IV) precursor, [Hf{η2‐(iPrN)2CH}2(NMe2)2] which is reactive, thermally robust and volatile, successful implementation in a PEALD process for HfO2 at low temperatures is demonstrated. The typical atomic layer deposition (ALD) characteristics of precursor saturation, linearity, and ALD temperature window are demonstrated with constant growth of 0.7 Å per cycle from 125 to 200 °C, yielding high‐purity layers. The effect of plasma pulse duration on the chemical composition alongside structural, topographical, as well as dielectric properties of the films is investigated. For the latter, the films are incorporated in metal‐insulator semiconductor (MIS) structures.

Background: The blood-nerve and myelin barrier shield peripheral neurons and their axons. These barriers are sealed by tight junction proteins, which control the passage of potentially noxious molecules including proinflammatory cytokines via paracellular pathways. Peripheral nerve barrier breakdown occurs in various neuropathies, such as chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) and traumatic neuropathy. Here, we studied the functional role of the tight junction protein claudin-12 in regulating peripheral nerve barrier integrity and CIDP pathogenesis. Methods: Sections from sural nerve biopsies from 23 patients with CIDP and non-inflammatory idiopathic polyneuropathy (PNP) were analyzed for claudin-12 and -19 immunoreactivity. Cldn12-KO mice were generated and subjected to the chronic constriction injury (CCI) model of neuropathy. These mice were then characterized using a battery of barrier and behavioral tests, histology, immunohistochemistry, and mRNA/protein expression. In phenotype rescue experiments, the proinflammatory cytokine TNFα was neutralized with the anti-TNFα antibody etanercept; the peripheral nerve barrier was stabilized with the sonic hedgehog agonist smoothened (SAG). Results: Compared to those without pain, patients with painful neuropathy exhibited reduced claudin-12 expression independently of fiber loss. Accordingly, global Cldn12-KO in male mice, but not fertile female mice, selectively caused mechanical allodynia associated with a leaky myelin barrier, increased TNFα, decreased sonic hedgehog (SHH), and loss of small axons accompanied by reduced peripheral myelin protein 22 (Pmp22). Other barriers and neurological functions remained intact. The Cldn12-KO phenotype could be rescued either by neutralizing TNFα with etanercept or stabilizing the barrier with SAG, which both also upregulated the Schwann cell barrier proteins Cldn19 and Pmp22. Conclusion: These results point to a critical role for claudin-12 in maintaining the myelin barrier presumably via Pmp22 and highlight restoration of the hedgehog pathway as a potential treatment strategy for painful inflammatory neuropathy.

The analysis of the function of acylamino acid-releasing enzymes (AARE) in Physcomitrella and Arabidopsis reveals a connection between AARE and plant ageing, suggesting a unified concept of ageing may exist across domains of life.

IntroductionIn patients with severe auditory impairment, partial hearing restoration can be achieved by sensory prostheses for the electrical stimulation of the central nervous system. However, these state-of-the-art approaches suffer from limited spectral resolution: electrical field spread depends on the impedance of the surrounding medium, impeding spatially focused electrical stimulation in neural tissue. To overcome these limitations, optogenetic activation could be applied in such prostheses to achieve enhanced resolution through precise and differential stimulation of nearby neuronal ensembles. Previous experiments have provided a first proof for behavioral detectability of optogenetic activation in the rodent auditory system, but little is known about the generation of complex and behaviorally relevant sensory patterns involving differential activation.MethodsIn this study, we developed and behaviorally tested an optogenetic implant to excite two spatially separated points along the tonotopy of the murine inferior colliculus (ICc).ResultsUsing a reward based operant Go/No-Go paradigm, we show that differential optogenetic activation of a sub-cortical sensory pathway is possible and efficient. We demonstrate how animals which were previously trained in a frequency discrimination paradigm (a) rapidly respond to either sound or optogenetic stimulation, (b) generally detect optogenetic stimulation of two different neuronal ensembles, and (c) discriminate between them.DiscussionOur results demonstrate that optogenetic excitatory stimulation at different points of the ICc tonotopy elicits a stable response behavior over time periods of several months. With this study, we provide the first proof of principle for sub-cortical differential stimulation of sensory systems using complex artificial cues in freely moving animals.

Abstract Quantum information processing (QIP) with solid state spin qubits strongly depends on the efficient initialisation of the qubit’s desired charge state. While the negatively charged tin-vacancy (SnV−) centre in diamond has emerged as an excellent platform for realising QIP protocols due to long spin coherence times at liquid helium temperature and lifetime limited optical transitions, its usefulness is severely limited by termination of the fluorescence under resonant excitation. Here, we unveil the underlying charge cycle, potentially applicable to all group IV-vacancy (G4V) centres, and exploit it to demonstrate highly efficient and rapid initialisation of the desired negative charge state of single SnV centres while preserving long term stable optical resonances. In addition to investigating the optical coherence, we all-optically probe the coherence of the ground state spins by means of coherent population trapping and find a spin dephasing time of 5(1) μs. Furthermore, we demonstrate proof-of-principle single shot spin state readout without the necessity of a magnetic field aligned to the symmetry axis of the defect.

Data obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adjacent populations of common origin. Machine learning (ML) techniques seem to be especially well suited for analyzing large datasets obtained using MPS. The Slavic populations constitute about a third of the population of Europe and inhabit a large area of the continent, while being relatively closely related in population genetics terms. In this proof-of-concept study, various ML techniques were used to classify DNA samples from Slavic and non-Slavic individuals. The primary objective of this study was to empirically evaluate the feasibility of discerning the genetic provenance of individuals of Slavic descent who exhibit genetic similarity, with the overarching goal of categorizing DNA specimens derived from diverse Slavic population representatives. Raw sequencing data were pre-processed, to obtain a 1200 character-long binary vector. A total of three classifiers were used—Random Forest, Support Vector Machine (SVM), and XGBoost. The most-promising results were obtained using SVM with a linear kernel, with 99.9% accuracy and F1-scores of 0.9846–1.000 for all classes.

In addition to their main functionality of converting DC input power to AC output power, today’s photovoltaic inverters are generally required to be capable of providing reactive power. While there are well-established mathematical models that use the correlation between inverter losses and the transmitted active power to estimate inverter efficiency for any given active power operating point, the additional losses in the inverter due to the supply of reactive power are less well studied. In this work, the conversion efficiencies of three different photovoltaic inverters were measured for various active power and reactive power setpoints. Based on these measurements, two mathematical models are proposed to represent the conversion losses as a function of active and reactive output power. One model is of empirical nature and expands preexisting models to include terms that take the reactive power into consideration. The other model takes the dominant loss mechanisms in the conversion stage of inverters into account and considers the effect of reactive power provision on them. Both models were compared with a model variant proposed in literature. They are shown to perform with high accuracy over the entire operating range, while requiring only a small number of known efficiency values for parametrization. There are several fields of application for these new models: They allow photovoltaic park operators to precisely estimate the individual losses of a solar power plant that feeds reactive power into the grid. For grid operators, they enable a comparative loss analysis for different reactive power sources.

Accidental injury to the cardiac conduction system (CCS), a network of specialized cells embedded within the heart and indistinguishable from the surrounding heart muscle tissue, is a major complication in cardiac surgeries. Here, we addressed this unmet need by engineering targeted antibody-dye conjugates directed against the CCS, allowing for the visualization of the CCS in vivo following a single intravenous injection in mice. These optical imaging tools showed high sensitivity, specificity, and resolution, with no adverse effects on CCS function. Further, with the goal of creating a viable prototype for human use, we generated a fully human monoclonal Fab that similarly targets the CCS with high specificity. We demonstrate that, when conjugated to an alternative cargo, this Fab can also be used to modulate CCS biology in vivo, providing a proof of principle for targeted cardiac therapeutics. Finally, in performing differential gene expression analyses of the entire murine CCS at single-cell resolution, we uncovered and validated a suite of additional cell surface markers that can be used to molecularly target the distinct subcomponents of the CCS, each prone to distinct life-threatening arrhythmias. These findings lay the foundation for translational approaches targeting the CCS for visualization and therapy in cardiothoracic surgery, cardiac imaging, and arrhythmia management.

Introduction: Molecular profiling of tumor tissue is the gold standard for treatment decision-making in advanced non-small cell lung cancer (NSCLC). Results may be delayed or unavailable due to insufficient tissue, prolonged wait times for biopsy, pathology assessment and testing. We piloted the use of plasma testing in the initial diagnostic workup for patients with suspected advanced lung cancer. Methods: Patients with ⩽15 pack-year smoking history and suspected advanced lung cancer referred to the lung cancer rapid diagnostic program underwent plasma circulating-tumor DNA testing using a DNA-based mutation panel. Tissue testing was performed per standard of care, including comprehensive next-generation sequencing (NGS). The primary endpoint was time from diagnostic program referral to cancer treatment in stage IV NSCLC patients (Cohort A) compared to a contemporary cohort not enrolled in the study (Cohort B) and an historical pre-COVID cohort referred to the program between 2018 and 2019 (Cohort C). Results: From January to June 2021, 20 patients were enrolled in Cohort A; median age was 70.5 years (range 33–87), 70% were female, 55% Caucasian, 85% never smokers, and 75% were diagnosed with NSCLC. Seven had actionable alterations detected in plasma or tissue (4/7 concordant). Fusions, not tested in plasma, were identified by immunohistochemistry for three patients. Mean result turnaround time was 17.8 days for plasma NGS and 23.6 days for tissue ( p = 0.10). Mean time from referral to treatment initiation was significantly shorter in cohort A at 32.6 days (SD 13.1) versus 62.2 days (SD 31.2) in cohort B and 61.5 days (SD 29.1) in cohort C, both p

The direct liquid injection chemical vapor deposition (DLI-CVD) of uniform and dense zirconium oxide (ZrO2) thin films applicable as corrosion protection coatings (CPCs) is reported. We present the entire development chain from the rational choice and thermal evaluation of the suitable heteroleptic precursor [Zr(OiPr)2(tbaoac)2] over the detailed DLI-CVD process design and finally benchmarking the CPC behavior using electrochemical impedance spectroscopy (EIS). For a thorough development of the growth process, the deposition temperature (Tdep) is varied in the range of 400 – 700 °C on Si(100) and stainless steel (AISI 304) substrates. Resulting thin films are thoroughly analyzed in terms of structure, composition, and morphology. Grazing incidence X-ray diffractometry (GIXRD) reveals an onset of crystallization at Tdep ≥ 500 °C yielding monoclinic and even cubic phase at low temperatures. At Tdep = 400 °C, isotropic growth of XRD amorphous material is shown to feature cubic crystalline domains at the interfacial region as revealed by electron diffraction. Corrosion results obtained through EIS measurements and further immersion tests revealed improved CPC characteristic for the 400 °C processed ZrO2 coatings compared to the ones deposited at Tdep ≥ 500 °C, yielding valuable insights into the correlation between growth parameter and CPC performance which are of high relevance for future exploration of CPCs.

Abstract COVID-19 spread across the globe at an immense rate and has left healthcare systems incapacitated to diagnose and test patients at the needed rate. Studies have shown promising results for detection of COVID-19 from viral bacterial pneumonia in chest X-rays. Automation of COVID-19 testing using medical images can speed up the testing process of patients where health care systems lack sufficient numbers of the reverse-transcription polymerase chain reaction tests. Supervised deep learning models such as convolutional neural networks need enough labeled data for all classes to correctly learn the task of detection. Gathering labeled data is a cumbersome task and requires time and resources which could further strain health care systems and radiologists at the early stages of a pandemic such as COVID-19. In this study, we propose a randomized generative adversarial network (RANDGAN) that detects images of an unknown class (COVID-19) from known and labelled classes (Normal and Viral Pneumonia) without the need for labels and training data from the unknown class of images (COVID-19). We used the largest publicly available COVID-19 chest X-ray dataset, COVIDx, which is comprised of Normal, Pneumonia, and COVID-19 images from multiple public databases. In this work, we use transfer learning to segment the lungs in the COVIDx dataset. Next, we show why segmentation of the region of interest (lungs) is vital to correctly learn the task of classification, specifically in datasets that contain images from different resources as it is the case for the COVIDx dataset. Finally, we show improved results in detection of COVID-19 cases using our generative model (RANDGAN) compared to conventional generative adversarial networks for anomaly detection in medical images, improving the area under the ROC curve from 0.71 to 0.77.

The reaction Be(p7,γ)8B plays an important role in the Sun, where it determines the high energy component of the solar neutrino spectrum. The importance of this reaction triggered several experiments over the last decades. A combined analysis of their results produces an overall consistent picture for the energy dependence of the cross section, while an inflation of the quoted uncertainties is needed to accommodate the observed discrepancy in the absolute scale of the different data sets. The origin of this discrepancy needs to be understood for a reliable estimate of the astrophysical rate of Be(p7,γ)8B and its uncertainty. In addition, there is a question about possible common systematic effects, considering that all measurements performed so far share the same experimental approach, i.e. an intense proton beam impinging on a Be7 radioactive target. A direct measurement using a radioactive Be7 ion beam on a pure hydrogen gas target has been since long envisioned as a way to improve the situation. First attempts showed the feasibility of an experiment based on the use of a recoil mass separator to collect reaction products with high efficiency, but failed to reach a useful statistical significance because of the low beam intensity. Here we present the results obtained using the intense Be7 beam available at the Tandem Accelerator Laboratory at CIRCE, University of Campania, Italy coupled to the recoil mass separator ERNA in the energy range Ecm=367 to 812 keV. Our results are compatible only with a part of previous measurements, in particular those indicating a low value of the astrophysical S-factor at zero energy S17, thus exacerbating the discrepancy between existing measurements. The analysis of our data together with the results of previous data provides an estimate S17(0)=20.0±0.8 eV⋅b, where systematic uncertainties are inflated to obtain a statistically compatible data set.

Water reuse is a safe and often the least energy-intensive method of providing water from non-conventional sources in water stressed regions. Although public perception can be a challenge, water reuse is gaining acceptance. Recent advances in membrane technology allow for reclamation of wastewater through the production of high-quality treated water, including potable reuse. This study takes an in-depth evaluation of a combination of membrane-based tertiary processes for its application in reuse of brewery wastewater, and is one of the few studies that evaluates long-term membrane performance at the pilot-scale. Two different advanced tertiary treatment trains were tested with secondary wastewater from a brewery wastewater treatment plant (A) ultrafiltration (UF) and reverse osmosis (RO), and (B) ozonation, coagulation, microfiltration with ceramic membranes (MF) and RO. Three specific criteria were used for membrane comparison: 1) pilot plant optimisation to identify ideal operating conditions, 2) Clean-In-Place (CIP) procedures to restore permeability, and 3) final water quality obtained. Both UF and Micro-Filtration membranes were operated at increasing fluxes, filtration intervals and alternating phases of backwash (BW) and chemically enhanced backwash (CEB) to control fouling. Operation of polymeric UF membranes was optimized at a flux of 25–30 LMH with 15–20 min of filtration time to obtain longer production periods and avoid frequent CIP membrane cleaning procedures. Combination of ozone and coagulation with ceramic MF membranes resulted in high flux values up to 120 LMH with CEB:BW ratios of 1:4 to 1:10. Coagulation doses of 3–6 ppm were required to deal with the high concentrations of polyphenols (coagulation inhibitors) in the feed, but higher concentrations led to increasing fouling resistance of the MF membrane. Varying the ozone concentration stepwise from 0 to 25 mg/L had no noticeable effect on coagulation. The most effective cleaning strategy was found to be a combination of 2000 mg/L NaOCl followed by 5% HCl which enabled to recover permeability up to 400 LMH·bar−1. Both polymeric UF and ceramic MF membranes produced effluents that fulfil the limits of the national regulatory framework for reuse in industrial services (RD 1620/2007). Coupling to the RO units in both tertiary trains led to further water polishing and an improved treated water quality.

Microalgae cultures were used for a WW treatment to remediate nutrients while producing biomass and recycling water. In these trials, raceway ponds (RWPs; 1 and 0.5 ha) were located next to a municipal (WW) treatment plant in Mérida, Spain. The ponds were used for continuous, all-year-round microalgae production using WW as a source of nutrients. Neither CO2 nor air was supplied to cultures. The objective was to validate photosynthesis monitoring techniques in large-scale bioreactors. Various in-situ/ex-situ methods based on chlorophyll fluorescence and oxygen evolution measurements were used to follow culture performance. Photosynthesis variables gathered with these techniques were compared to the physiological behavior and growth of cultures. Good photosynthetic activity was indicated by the build-up of dissolved oxygen concentration up to 380% saturation, high photochemical yield (Fv/Fm = 0.62–0.71), and relative electron transport rate rETR between 200 and 450 μmol e− m−2 s−1 at midday, which resulted in biomass productivity of about 15–25 g DW m−2 day−1. The variables represent reliable markers reflecting the physiological status of microalgae cultures. Using waste nutrients, the biomass production cost can be significantly decreased for abundant biomass production in large-scale bioreactors, which can be exploited for agricultural purposes.

Abstract Nodular pulmonary amyloidosis is a rare and localized manifestation of amyloid deposition in the lungs. This rare entity, though asymptomatic, is often misdiagnosed on imaging alone, due to its resemblance to metastatic pulmonary nodules. This report highlights the significance of histologic confirmation before treatment, as a preventive measure against overtreatment.