Homeostatic IL-13 in healthy skin directs dendritic cell differentiation to promote TH2 and inhibit TH17 cell polarization.

The signals driving the adaptation of type 2 dendritic cells (DC2s) to diverse peripheral environments remain mostly undefined. We show that differentiation of CD11blo migratory DC2s-a DC2 population unique to the dermis-required IL-13 signaling dependent on the transcription factors STAT6 and KLF4, whereas DC2s in lung and small intestine were STAT6-independent. Similarly, human DC2s in skin expressed an IL-4 and IL-13 gene signature that was not found in blood, spleen and lung DCs. In mice, IL-13 was secreted homeostatically by dermal innate lymphoid cells and was independent of microbiota, TSLP or IL-33. In the absence of IL-13 signaling, dermal DC2s were stable in number but remained CD11bhi and showed defective activation in response to allergens, with diminished ability to support the development of IL-4+GATA3+ helper T cells (TH), whereas antifungal IL-17+RORγt+ TH cells were increased. Therefore, homeostatic IL-13 fosters a noninflammatory skin environment that supports allergic sensitization.

Advances in remote sensing of emperor penguins: first multi-year time series documenting trends in the global population.

Like many polar animals, emperor penguin populations are challenging to monitor because of the species' life history and remoteness. Consequently, it has been difficult to establish its global status, a subject important to resolve as polar environments change. To advance our understanding of emperor penguins, we combined remote sensing, validation surveys and using Bayesian modelling, we estimated a comprehensive population trajectory over a recent 10-year period, encompassing the entirety of the species' range. Reported as indices of abundance, our study indicates with 81% probability that there were fewer adult emperor penguins in 2018 than in 2009, with a posterior median decrease of 9.6% (95% credible interval (CI) -26.4% to +9.4%). The global population trend was -1.3% per year over this period (95% CI = -3.3% to +1.0%) and declines probably occurred in four of eight fast ice regions, irrespective of habitat conditions. Thus far, explanations have yet to be identified regarding trends, especially as we observed an apparent population uptick toward the end of time series. Our work potentially establishes a framework for monitoring other Antarctic coastal species detectable by satellite, while promoting a need for research to better understand factors driving biotic changes in the Southern Ocean ecosystem.

Disentangling single-cell omics representation with a power spectral density-based feature extraction.

Emerging single-cell technologies provide high-resolution measurements of distinct cellular modalities opening new avenues for generating detailed cellular atlases of many and diverse tissues. The high dimensionality, sparsity, and inaccuracy of single cell sequencing measurements, however, can obscure discriminatory information, mask cellular subtype variations and complicate downstream analyses which can limit our understanding of cell function and tissue heterogeneity. Here, we present a novel pre-processing method (scPSD) inspired by power spectral density analysis that enhances the accuracy for cell subtype separation from large-scale single-cell omics data. We comprehensively benchmarked our method on a wide range of single-cell RNA-sequencing datasets and showed that scPSD pre-processing, while being fast and scalable, significantly reduces data complexity, enhances cell-type separation, and enables rare cell identification. Additionally, we applied scPSD to transcriptomics and chromatin accessibility cell atlases and demonstrated its capacity to discriminate over 100 cell types across the whole organism and across different modalities of single-cell omics data.

Increased SARS-CoV-2 Infection, Protease, and Inflammatory Responses in Chronic Obstructive Pulmonary Disease Primary Bronchial Epithelial Cells Defined with Single-Cell RNA Sequencing.

Rationale: Patients with chronic obstructive pulmonary disease (COPD) develop more severe coronavirus disease (COVID-19); however, it is unclear whether they are more susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and what mechanisms are responsible for severe disease. Objectives: To determine whether SARS-CoV-2 inoculated primary bronchial epithelial cells (pBECs) from patients with COPD support greater infection and elucidate the effects and mechanisms involved. Methods: We performed single-cell RNA sequencing analysis on differentiated pBECs from healthy subjects and patients with COPD 7 days after SARS-CoV-2 inoculation. We correlated changes with viral titers, proinflammatory responses, and IFN production. Measurements and Main Results: Single-cell RNA sequencing revealed that COPD pBECs had 24-fold greater infection than healthy cells, which was supported by plaque assays. Club/goblet and basal cells were the predominant populations infected and expressed mRNAs involved in viral replication. Proteases involved in SARS-CoV-2 entry/infection (TMPRSS2 and CTSB) were increased, and protease inhibitors (serpins) were downregulated more so in COPD. Inflammatory cytokines linked to COPD exacerbations and severe COVID-19 were increased, whereas IFN responses were blunted. Coexpression analysis revealed a prominent population of club/goblet cells with high type 1/2 IFN responses that were important drivers of immune responses to infection in both healthy and COPD pBECs. Therapeutic inhibition of proteases and inflammatory imbalances reduced viral titers and cytokine responses, particularly in COPD pBECs. Conclusions: COPD pBECs are more susceptible to SARS-CoV-2 infection because of increases in coreceptor expression and protease imbalances and have greater inflammatory responses. A prominent cluster of IFN-responsive club/goblet cells emerges during infection, which may be important drivers of immunity. Therapeutic interventions suppress SARS-CoV-2 replication and consequent inflammation.

Food values drive Chinese consumers' demand for meat and milk substitutes.

Increasing consumption of alternatives to animal-based food products can have significant implications for the sustainability of global food systems. We utilize consumers' food values to identify the drivers of demand for alternative meat and milk products in China, the world's largest consumer market. Using data from 3015 Chinese consumers, we find that public food values, such as environmental impacts and animal welfare, drive consumers' demand for alternative meat and milk. We estimate that approximately 35% of urban food shoppers constitute the potential market for these products. Plant-based meat alternatives to products with strong consumption dependence, such as pork, must compete on price, while alternatives to products with weak consumption dependence, like milk, are likely to earn market premiums. We estimate that modest consumption of alternative meat and milk products in these markets can improve food system sustainability by lowering China's animal production greenhouse gas emissions by 3.4% in addition to reducing animal slaughtering and potentially decreasing health risks associated with the consumption of animal-based food products.

ELF5 modulates the estrogen receptor cistrome in breast cancer.

Acquired resistance to endocrine therapy is responsible for half of the therapeutic failures in the treatment of breast cancer. Recent findings have implicated increased expression of the ETS transcription factor ELF5 as a potential modulator of estrogen action and driver of endocrine resistance, and here we provide the first insight into the mechanisms by which ELF5 modulates estrogen sensitivity. Using chromatin immunoprecipitation sequencing we found that ELF5 binding overlapped with FOXA1 and ER at super enhancers, enhancers and promoters, and when elevated, caused FOXA1 and ER to bind to new regions of the genome, in a pattern that replicated the alterations to the ER/FOXA1 cistrome caused by the acquisition of resistance to endocrine therapy. RNA sequencing demonstrated that these changes altered estrogen-driven patterns of gene expression, the expression of ER transcription-complex members, and 6 genes known to be involved in driving the acquisition of endocrine resistance. Using rapid immunoprecipitation mass spectrometry of endogenous proteins, and proximity ligation assays, we found that ELF5 interacted physically with members of the ER transcription complex, such as DNA-PKcs. We found 2 cases of endocrine-resistant brain metastases where ELF5 levels were greatly increased and ELF5 patterns of gene expression were enriched, compared to the matched primary tumour. Thus ELF5 alters ER-driven gene expression by modulating the ER/FOXA1 cistrome, by interacting with it, and by modulating the expression of members of the ER transcriptional complex, providing multiple mechanisms by which ELF5 can drive endocrine resistance.

Right on the money? U.S. dairy farmers' varied understanding of consumer preferences and attitudes towards animal health, welfare and biotechnology.

This Research Communication investigates how well U.S. dairy farmers understand the voting behaviour and willingness to pay of consumers for products with production traits relevant to animal health, welfare and biotechnology. Accurately understanding consumer behaviour is key to making sound production decisions and reducing risks. Comparing survey data with the literature shows that U.S. dairy farmers correctly assess consumer attitudes and behaviour over animal welfare practices like pain-controlled dehorning but could improve knowledge of attitudes towards antibiotic use and novel biotechnologies like gene editing.

Design of a Tension Infiltrometer with Automated Data Collection Using a Supervisory Control and Data Acquisition System.

This study highlights the importance of water infiltration in hydrological basin management, emphasizing its role in water services, water quality regulation, and temporal patterns. To measure this crucial function, this study introduces a portable and user-friendly tension infiltrometer designed for easy assembly and data collection. The tension infiltrometer, based on the 2009 design by Spongrová and Kechavarzi, offers a comprehensive characterization of the soil properties related to water flow. It eliminates the influence of preferential flow, providing accurate data. Additionally, it accommodates changes in pore size distribution within the soil, which is crucial for understanding water movement. This study discusses the challenges associated with traditional infiltration measurement tools, like double-ring infiltrometers and single rings, which are not easily transported and can lead to inaccuracies. In response, the proposed infiltrometer simplifies data collection, making it accessible to a broader range of users. This study also explores the use of the VL53L0X distance sensor in the infiltrometer, providing an innovative solution for measuring the water column height. The system's user interface allows real-time data collection and analysis, significantly reducing the processing time compared to that of the manual methods. Overall, this work demonstrates the potential for advancement in hydrological basin management using user-friendly instrumentation and automated data collection, paving the way for improved research and decision making in environmental services, conservation, and restoration efforts within these ecosystems.

Activation of the viral sensor oligoadenylate synthetase 2 (Oas2) prevents pregnancy-driven mammary cancer metastases.

BACKGROUND: The interferon response can influence the primary and metastatic activity of breast cancers and can interact with checkpoint immunotherapy to modulate its effects. Using N-ethyl-N-nitrosourea mutagenesis, we found a mouse with an activating mutation in oligoadenylate synthetase 2 (Oas2), a sensor of viral double stranded RNA, that resulted in an interferon response and prevented lactation in otherwise healthy mice. METHODS: To determine if sole activation of Oas2 could alter the course of mammary cancer, we combined the Oas2 mutation with the MMTV-PyMT oncogene model of breast cancer and examined disease progression and the effects of checkpoint immunotherapy using Kaplan-Meier survival analysis with immunohistochemistry and flow cytometry. RESULTS: Oas2 mutation prevented pregnancy from increasing metastases to lung. Checkpoint immunotherapy with antibodies against programmed death-ligand 1 was more effective when the Oas2 mutation was present. CONCLUSIONS: These data establish OAS2 as a therapeutic target for agents designed to reduce metastases and increase the effectiveness of checkpoint immunotherapy.

Upconversion nanoparticle-assisted single-molecule assay for detecting circulating antigens of aggressive prostate cancer.

Sensitive and quantitative detection of molecular biomarkers is crucial for the early diagnosis of diseases like metabolic syndrome and cancer. Here we present a single-molecule sandwich immunoassay by imaging the number of single nanoparticles to diagnose aggressive prostate cancer. Our assay employed the photo-stable upconversion nanoparticles (UCNPs) as labels to detect the four types of circulating antigens in blood circulation, including glypican-1 (GPC-1), leptin, osteopontin (OPN), and vascular endothelial growth factor (VEGF), as their serum concentrations indicate aggressive prostate cancer. Under a wide-field microscope, a single UCNP doped with thousands of lanthanide ions can emit sufficiently bright anti-Stokes' luminescence to become quantitatively detectable. By counting every single streptavidin-functionalized UCNP which specifically labeled on each sandwich immune complex across multiple fields of views, we achieved the Limit of Detection (LOD) of 0.0123 ng/ml, 0.2711 ng/ml, 0.1238 ng/ml, and 0.0158 ng/ml for GPC-1, leptin, OPN and VEGF, respectively. The serum circulating level of GPC-1, leptin, OPN, and VEGF in a mixture of 10 healthy normal human serum was 25.17 ng/ml, 18.04 ng/ml, 11.34 ng/ml, and 1.55 ng/ml, which was within the assay dynamic detection range for each analyte. Moreover, a 20% increase of GPC-1 and OPN was observed by spiking the normal human serum with recombinant antigens to confirm the accuracy of the assay. We observed no cross-reactivity among the four biomarker analytes, which eliminates the false positives and enhances the detection accuracy. The developed single upconversion nanoparticle-assisted single-molecule assay suggests its potential in clinical usage for prostate cancer detection by monitoring tiny concentration differences in a panel of serum biomarkers.

Custom IMU-Based Wearable System for Robust 2.4 GHz Wireless Human Body Parts Orientation Tracking and 3D Movement Visualization on an Avatar.

Recent studies confirm the applicability of Inertial Measurement Unit (IMU)-based systems for human motion analysis. Notwithstanding, high-end IMU-based commercial solutions are yet too expensive and complex to democratize their use among a wide range of potential users. Less featured entry-level commercial solutions are being introduced in the market, trying to fill this gap, but still present some limitations that need to be overcome. At the same time, there is a growing number of scientific papers using not commercial, but custom do-it-yourself IMU-based systems in medical and sports applications. Even though these solutions can help to popularize the use of this technology, they have more limited features and the description on how to design and build them from scratch is yet too scarce in the literature. The aim of this work is two-fold: (1) Proving the feasibility of building an affordable custom solution aimed at simultaneous multiple body parts orientation tracking; while providing a detailed bottom-up description of the required hardware, tools, and mathematical operations to estimate and represent 3D movement in real-time. (2) Showing how the introduction of a custom 2.4 GHz communication protocol including a channel hopping strategy can address some of the current communication limitations of entry-level commercial solutions. The proposed system can be used for wireless real-time human body parts orientation tracking with up to 10 custom sensors, at least at 50 Hz. In addition, it provides a more reliable motion data acquisition in Bluetooth and Wi-Fi crowded environments, where the use of entry-level commercial solutions might be unfeasible. This system can be used as a groundwork for developing affordable human motion analysis solutions that do not require an accurate kinematic analysis.

The role of endoscopy in caustic ingestion in the pediatric population: experience in a tertiary center.

INTRODUCTION: caustic ingestion in children is rare but has potentially serious consequences. AIM: to analyze the clinical and endoscopic features and the type of caustic ingested in our population. METHODS: the upper endoscopies performed in this setting, as well as the characteristics of patients and caustics, were analyzed from 2010 to 2018. RESULTS: fifty-one endoscopies were performed (48 cases of witnessed intake or high suspicion and three with a low suspicion) in patients with a mean age of 2.55 years. Alkali ingestion was more frequent (88.2 %) and 56.9 % of the endoscopies were normal, which was more frequent among those who ingested bleach (72 %). Alkali tended to produce more esophageal injuries (31.1 %) and acids tended to produce esophageal (20 %) and esophageal-gastric injuries (20 %). Four patients developed esophageal stenosis during follow-up. DISCUSSION: even though more than half of the studies were normal, endoscopy is important in the diagnosis and prognosis of these patients.

Efficacy and safety of D,L-3-hydroxybutyrate (D,L-3-HB) treatment in multiple acyl-CoA dehydrogenase deficiency.

PURPOSE: Multiple acyl-CoA dehydrogenase deficiency (MADD) is a life-threatening, ultrarare inborn error of metabolism. Case reports described successful D,L-3-hydroxybutyrate (D,L-3-HB) treatment in severely affected MADD patients, but systematic data on efficacy and safety is lacking. METHODS: A systematic literature review and an international, retrospective cohort study on clinical presentation, D,L-3-HB treatment method, and outcome in MADD(-like) patients. RESULTS: Our study summarizes 23 MADD(-like) patients, including 14 new cases. Median age at clinical onset was two months (interquartile range [IQR]: 8 months). Median age at starting D,L-3-HB was seven months (IQR: 4.5 years). D,L-3-HB doses ranged between 100 and 2600 mg/kg/day. Clinical improvement was reported in 16 patients (70%) for cardiomyopathy, leukodystrophy, liver symptoms, muscle symptoms, and/or respiratory failure. D,L-3-HB appeared not effective for neuropathy. Survival appeared longer upon D,L-3-HB compared with historical controls. Median time until first clinical improvement was one month, and ranged up to six months. Reported side effects included abdominal pain, constipation, dehydration, diarrhea, and vomiting/nausea. Median D,L-3-HB treatment duration was two years (IQR: 6 years). D,L-3-HB treatment was discontinued in 12 patients (52%). CONCLUSION: The strength of the current study is the international pooling of data demonstrating that D,L-3-HB treatment can be effective and safe in MADD(-like) patients.

Genomic Cytometry and New Modalities for Deep Single-Cell Interrogation.

In the past few years, the rapid development of single-cell analysis techniques has allowed for increasingly in-depth analysis of DNA, RNA, protein, and epigenetic states, at the level of the individual cell. This unprecedented characterization ability has been enabled through the combination of cytometry, microfluidics, genomics, and informatics. Although traditionally discrete, when properly integrated, these fields create the synergistic field of Genomic Cytometry. In this review, we look at the individual methods that together gave rise to the broad field of Genomic Cytometry. We further outline the basic concepts that drive the field and provide a framework to understand this increasingly complex, technology-intensive space. Thus, we introduce Genomic Cytometry as an emerging field and propose that synergistic rationalization of disparate modalities of cytometry, microfluidics, genomics, and informatics under one banner will enable massive leaps forward in the understanding of complex biology. © 2020 International Society for Advancement of Cytometry.

Variability in Arsenic Methylation Efficiency across Aerobic and Anaerobic Microorganisms.

Microbially-mediated methylation of arsenic (As) plays an important role in the As biogeochemical cycle, particularly in rice paddy soils where methylated As, generated microbially, is translocated into rice grains. The presence of the arsenite (As(III)) methyltransferase gene (arsM) in soil microbes has been used as an indication of their capacity for As methylation. Here, we evaluate the ability of seven microorganisms encoding active ArsM enzymes to methylate As. Amongst those, only the aerobic species were efficient methylators. The anaerobic microorganisms presented high resistance to As exposure, presumably through their efficient As(III) efflux, but methylated As poorly. The only exception were methanogens, for which efficient As methylation was seemingly an artifact of membrane disruption. Deletion of an efflux pump gene (acr3) in one of the anaerobes, Clostridium pasteurianum, rendered the strain sensitive to As and capable of more efficiently methylating As. Our results led to the following conclusions: (i) encoding a functional ArsM enzyme does not guarantee that a microorganism will actively drive As methylation in the presence of the metalloid and (ii) there is an inverse relationship between efficient microbial As efflux and its methylation, because the former prevents the intracellular accumulation of As.

A mutation in the viral sensor 2'-5'-oligoadenylate synthetase 2 causes failure of lactation.

We identified a non-synonymous mutation in Oas2 (I405N), a sensor of viral double-stranded RNA, from an ENU-mutagenesis screen designed to discover new genes involved in mammary development. The mutation caused post-partum failure of lactation in healthy mice with otherwise normally developed mammary glands, characterized by greatly reduced milk protein synthesis coupled with epithelial cell death, inhibition of proliferation and a robust interferon response. Expression of mutant but not wild type Oas2 in cultured HC-11 or T47D mammary cells recapitulated the phenotypic and transcriptional effects observed in the mouse. The mutation activates the OAS2 pathway, demonstrated by a 34-fold increase in RNase L activity, and its effects were dependent on expression of RNase L and IRF7, proximal and distal pathway members. This is the first report of a viral recognition pathway regulating lactation.

Comparative Analysis of Kinect-Based and Oculus-Based Gaze Region Estimation Methods in a Driving Simulator.

Driver's gaze information can be crucial in driving research because of its relation to driver attention. Particularly, the inclusion of gaze data in driving simulators broadens the scope of research studies as they can relate drivers' gaze patterns to their features and performance. In this paper, we present two gaze region estimation modules integrated in a driving simulator. One uses the 3D Kinect device and another uses the virtual reality Oculus Rift device. The modules are able to detect the region, out of seven in which the driving scene was divided, where a driver is gazing at in every route processed frame. Four methods were implemented and compared for gaze estimation, which learn the relation between gaze displacement and head movement. Two are simpler and based on points that try to capture this relation and two are based on classifiers such as MLP and SVM. Experiments were carried out with 12 users that drove on the same scenario twice, each one with a different visualization display, first with a big screen and later with Oculus Rift. On the whole, Oculus Rift outperformed Kinect as the best hardware for gaze estimation. The Oculus-based gaze region estimation method with the highest performance achieved an accuracy of 97.94%. The information provided by the Oculus Rift module enriches the driving simulator data and makes it possible a multimodal driving performance analysis apart from the immersion and realism obtained with the virtual reality experience provided by Oculus.

A Physiological Sensor-Based Android Application Synchronized with a Driving Simulator for Driver Monitoring.

In this paper, we present an Android application to control and monitor the physiological sensors from the Shimmer platform and its synchronized working with a driving simulator. The Android app can monitor drivers and their parameters can be used to analyze the relation between their physiological states and driving performance. The app can configure, select, receive, process, represent graphically, and store the signals from electrocardiogram (ECG), electromyogram (EMG) and galvanic skin response (GSR) modules and accelerometers, a magnetometer and a gyroscope. The Android app is synchronized in two steps with a driving simulator that we previously developed using the Unity game engine to analyze driving security and efficiency. The Android app was tested with different sensors working simultaneously at various sampling rates and in different Android devices. We also tested the synchronized working of the driving simulator and the Android app with 25 people and analyzed the relation between data from the ECG, EMG, GSR, and gyroscope sensors and from the simulator. Among others, some significant correlations between a gyroscope-based feature calculated by the Android app and vehicle data and particular traffic offences were found. The Android app can be applied with minor adaptations to other different users such as patients with chronic diseases or athletes.

PREPL deficiency: delineation of the phenotype and development of a functional blood assay.

PurposePREPL deficiency causes neonatal hypotonia, ptosis, neonatal feeding difficulties, childhood obesity, xerostomia, and growth hormone deficiency. Different recessive contiguous gene deletion syndromes involving PREPL and a variable combination of SLC3A1 (hypotonia-cystinuria syndrome), CAMKMT (atypical hypotonia-cystinuria syndrome), and PPM1B (2p21 deletion syndrome) have been described. In isolated PREPL deficiency, previously described only once, the absence of cystinuria complicates the diagnosis. Therefore, we developed a PREPL blood assay and further delineated the phenotype.MethodsClinical features of new subjects with PREPL deficiency were recorded. The presence of PREPL in lymphocytes and its reactivity with an activity-based probe were evaluated by western blot.ResultsFive subjects with isolated PREPL deficiency, three with hypotonia-cystinuria syndrome, and two with atypical hypotonia-cystinuria syndrome had nine novel alleles. Their IQs ranged from 64 to 112. Adult neuromuscular signs included ptosis, nasal dysarthria, facial weakness, and variable proximal and neck flexor weakness. Autonomic features are prevalent. PREPL protein and reactivity were absent in lymphocytes from subjects with PREPL deficiency, but normal in the clinically similar Prader-Willi syndrome.ConclusionPREPL deficiency causes neuromuscular, autonomic, cognitive, endocrine, and dysmorphic clinical features. PREPL is not deficient in Prader-Willi syndrome. The novel blood test should facilitate the confirmation of PREPL deficiency.