Showing papers by "University of California, San Diego published in 2022"
TL;DR: This study surveyed the current progress of XAI and in particular its advances in healthcare applications, and introduced the solutions for XAI leveraging multi-modal and multi-centre data fusion, and subsequently validated in two showcases following real clinical scenarios.
231 citations
TL;DR: The Post-hospitalisation COVID-19 study (PHOSP-COVID) as mentioned in this paper is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID19 across the UK.
118 citations
TL;DR: The development of new classes of antibiotics has slowed in recent years due to pressur... as mentioned in this paper, which presents a substantial threat to the control of infectious diseases, especially antibiotic resistance in bacterial pathogens.
Abstract: Antibiotic resistance in bacterial pathogens presents a substantial threat to the control of infectious diseases. Development of new classes of antibiotics has slowed in recent years due to pressur...
96 citations
École Polytechnique1, University of Erlangen-Nuremberg2, South China University of Technology3, University of Windsor4, University of California, Santa Barbara5, Hong Kong University of Science and Technology6, Sungkyunkwan University7, University of Washington8, York University9, Shanghai Jiao Tong University10, University of Minnesota11, Hewlett-Packard12, King Abdullah University of Science and Technology13, University of California, Berkeley14, Rovira i Virgili University15, Chinese Academy of Sciences16, University of California, San Diego17, Åbo Akademi University18, University of Chicago19, Fudan University20, Northwestern University21, Columbia University22, PARC23, École Polytechnique Fédérale de Lausanne24, University of Bari25
TL;DR: Bonnassieux et al. as mentioned in this paper presented a roadmap for the key areas of flexible and printable electronics. And they highlighted the current status and future challenges in the areas covered by the roadmap and highlighted the breadth and wide-ranging opportunities made available by flexible electronics technologies.
Abstract: Author(s): Bonnassieux, Y; Brabec, CJ; Cao, Y; Carmichael, TB; Chabinyc, ML; Cheng, KT; Cho, G; Chung, A; Cobb, CL; Distler, A; Egelhaaf, HJ; Grau, G; Guo, X; Haghiashtiani, G; Huang, TC; Hussain, MM; Iniguez, B; Lee, TM; Li, L; Ma, Y; Ma, D; McAlpine, MC; Ng, TN; Osterbacka, R; Patel, SN; Peng, J; Peng, H; Rivnay, J; Shao, L; Steingart, D; Street, RA; Subramanian, V; Torsi, L; Wu, Y | Abstract: This roadmap includes the perspectives and visions of leading researchers in the key areas of flexible and printable electronics. The covered topics are broadly organized by the device technologies (sections 1–9), fabrication techniques (sections 10–12), and design and modeling approaches (sections 13 and 14) essential to the future development of new applications leveraging flexible electronics (FE). The interdisciplinary nature of this field involves everything from fundamental scientific discoveries to engineering challenges; from design and synthesis of new materials via novel device design to modelling and digital manufacturing of integrated systems. As such, this roadmap aims to serve as a resource on the current status and future challenges in the areas covered by the roadmap and to highlight the breadth and wide-ranging opportunities made available by FE technologies.
68 citations
27 Jan 2022
TL;DR: In this article , the authors analyzed faecal samples from 40 patients with ulcerative colitis and found a link between Bacteroides vulgatus protease activity and severity of disease symptoms.
Abstract: Ulcerative colitis (UC) is driven by disruptions in host–microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host–microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn’s disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease. Multi-omics analyses of faecal samples from patients with ulcerative colitis reveal a link between Bacteroides vulgatus protease activity and severity of disease symptoms.
63 citations
TL;DR: The IM-UNITI study and long-term extension (LTE) as mentioned in this paper evaluated the longterm efficacy, safety, and immunogenicity of subcutaneous ustekinumab maintenance therapy in patients with Crohn's disease.
58 citations
TL;DR: In this paper , the authors examined associations among access to gender-affirming hormone therapy (GAHT) with depression, thoughts of suicide, and attempted suicide among a large sample of transgender and nonbinary youth.
57 citations
Konstantinos N. Fountoulakis1, Grigorios N Karakatsoulis1, Seri Abraham2, Kristina Adorjan +153 more•Institutions (62)
TL;DR: In this article, the effects of the COVID-19 pandemic on mental health were investigated and the final model revealed multiple vulnerabilities and an interplay leading from simple anxiety to probable depression and suicidality through distress.
53 citations
TL;DR: In this paper , the authors examined the relationship between renewable and non-renewable electricity consumption, carbon dioxide (CO2) emissions and economic policy uncertainty for the United States and concluded that policymakers and political leadership of US should be aware of climate change consequences in order to fulfill carbon neutrality target and should develop economic policies accordingly in-line with energy security, clean and greener energy for all and sustainable cleaner production objectives.
46 citations
TL;DR: In this article , the authors used Songbird to investigate mycobiome changes in patients with non-alcoholic fatty liver disease (NAFLD) and advanced fibrosis.
46 citations
TL;DR: In this paper , a circular ADAR-recruiting guide RNAs (cadRNAs) was proposed to enable more efficient programmable adenosine-to-inosine RNA editing without requiring co-delivery of any exogenous proteins.
Abstract: Recruiting endogenous adenosine deaminases using exogenous guide RNAs to edit cellular RNAs is a promising therapeutic strategy, but editing efficiency and durability remain low using current guide RNA designs. In this study, we engineered circular ADAR-recruiting guide RNAs (cadRNAs) to enable more efficient programmable adenosine-to-inosine RNA editing without requiring co-delivery of any exogenous proteins. Using these cadRNAs, we observed robust and durable RNA editing across multiple sites and cell lines, in both untranslated and coding regions of RNAs, and high transcriptome-wide specificity. Additionally, we increased transcript-level specificity for the target adenosine by incorporating interspersed loops in the antisense domains, reducing bystander editing. In vivo delivery of cadRNAs via adeno-associated viruses enabled 53% RNA editing of the mPCSK9 transcript in C57BL/6J mice livers and 12% UAG-to-UGG RNA correction of the amber nonsense mutation in the IDUA-W392X mouse model of mucopolysaccharidosis type I-Hurler syndrome. cadRNAs enable efficient programmable RNA editing in vivo with diverse protein modulation and gene therapeutic applications. Circular guide RNAs boost the efficiency of RNA editing with endogenous ADARs.
TL;DR: In this article , the authors describe a dataset of more than 100,000 chest X-ray scans that were retrospectively collected from two major hospitals in Vietnam and release 18,000 images that were manually annotated by a total of 17 experienced radiologists with 22 local labels of rectangles surrounding abnormalities and 6 global labels of suspected diseases.
Abstract: Abstract Most of the existing chest X-ray datasets include labels from a list of findings without specifying their locations on the radiographs. This limits the development of machine learning algorithms for the detection and localization of chest abnormalities. In this work, we describe a dataset of more than 100,000 chest X-ray scans that were retrospectively collected from two major hospitals in Vietnam. Out of this raw data, we release 18,000 images that were manually annotated by a total of 17 experienced radiologists with 22 local labels of rectangles surrounding abnormalities and 6 global labels of suspected diseases. The released dataset is divided into a training set of 15,000 and a test set of 3,000. Each scan in the training set was independently labeled by 3 radiologists, while each scan in the test set was labeled by the consensus of 5 radiologists. We designed and built a labeling platform for DICOM images to facilitate these annotation procedures. All images are made publicly available in DICOM format along with the labels of both the training set and the test set.
TL;DR: In this paper , the impacts of microplastics on bioaccumulation of heavy metals in vegetables in terrestrial environment are investigated, and the results showed that microplastic in soil would facilitate heavy metals entering rape plants.
TL;DR: In this article, the authors investigated the main microbiome alterations in Parkinson's disease, their correlations with disease severity, and the impact of study and geographical differences, finding that the differences in microbiome composition and correlations with clinical variables were analyzed using multivariate statistics.
TL;DR: The Lung CellCards as mentioned in this paper is a comprehensive and practical cellular census of the lung, which includes cell types in the normal lung with delineation of function, markers, developmental lineages, heterogeneity, regenerative potential, disease links, and key experimental tools.
14 Jan 2022
TL;DR: In this article , a combination of modular substrate and gold colloids was used to detect the main protease (Mpro) via visual readout in the COVID-19 pandemic.
Abstract: The transmission of SARS-CoV-2 coronavirus has led to the COVID-19 pandemic. Nucleic acid testing while specific has limitations for mass surveillance. One alternative is the main protease (Mpro) due to its functional importance in mediating the viral life cycle. Here, we describe a combination of modular substrate and gold colloids to detect Mpro via visual readout. The strategy involves zwitterionic peptide that carries opposite charges at the C-/N-terminus to exploit the specific recognition by Mpro. Autolytic cleavage releases a positively charged moiety that assembles the nanoparticles with rapid color changes (t<10 min). We determine a limit of detection for Mpro in breath condensate matrices <10 nM. We further assayed ten COVID-negative subjects and found no false-positive result. In the light of simplicity, our test for viral protease is not limited to an equipped laboratory, but also is amenable to integrating as portable point-of-care devices including those on face-coverings.
TL;DR: In this paper , the authors used native E. coli as chassis for transgene delivery to impact host physiology and found that the reintroduction of these strains induces perpetual engraftment in the intestine.
TL;DR: In this article , the authors use the COVID-19-induced increase in remote work to provide empirical evidence for this mechanism and its role in shaping the pandemic's economic impact.
TL;DR: A methodology that exploits the large bridge responses induced by train passage while rejecting the confounding influences of the environment in such a way that false positive detections are mitigated is proposed, and an adaptable confidence decision threshold is introduced that further improves damage detection over time.
Imperial College London1, Pacific Northwest National Laboratory2, Met Office3, NOAA Chemical Sciences Laboratory4, University of Maryland, Baltimore County5, University of Arizona6, Delft University of Technology7, University of Oxford8, University of Colorado Boulder9, University of Rochester10, University of Tartu11, Icahn School of Medicine at Mount Sinai12, University of Oklahoma13, Hebrew University of Jerusalem14, Brno University of Technology15, University of California, San Diego16, National Centre for Atmospheric Science17, University of Maryland, College Park18, University of Cambridge19, Texas Tech University20, National Centre for Earth Observation21, University of Washington22, Leibniz Institute for Tropospheric Research23, Goethe University Frankfurt24
TL;DR: Aerosol-cloud interactions (ACI) are considered to be the most uncertain driver of present-day radiative forcing due to human activities as discussed by the authors , and using correlations to infer causality can be challenging when meteorological variability also drives both aerosol and cloud changes independently.
Abstract: Aerosol-cloud interactions (ACIs) are considered to be the most uncertain driver of present-day radiative forcing due to human activities. The nonlinearity of cloud-state changes to aerosol perturbations make it challenging to attribute causality in observed relationships of aerosol radiative forcing. Using correlations to infer causality can be challenging when meteorological variability also drives both aerosol and cloud changes independently. Natural and anthropogenic aerosol perturbations from well-defined sources provide "opportunistic experiments" (also known as natural experiments) to investigate ACI in cases where causality may be more confidently inferred. These perturbations cover a wide range of locations and spatiotemporal scales, including point sources such as volcanic eruptions or industrial sources, plumes from biomass burning or forest fires, and tracks from individual ships or shipping corridors. We review the different experimental conditions and conduct a synthesis of the available satellite datasets and field campaigns to place these opportunistic experiments on a common footing, facilitating new insights and a clearer understanding of key uncertainties in aerosol radiative forcing. Cloud albedo perturbations are strongly sensitive to background meteorological conditions. Strong liquid water path increases due to aerosol perturbations are largely ruled out by averaging across experiments. Opportunistic experiments have significantly improved process-level understanding of ACI, but it remains unclear how reliably the relationships found can be scaled to the global level, thus demonstrating a need for deeper investigation in order to improve assessments of aerosol radiative forcing and climate change.
TL;DR: In this paper, the co-selection of heavy metal/biocide and antibiotic resistance genes (ARGs) has been suggested as one potential mechanism promoting the proliferation of antimicrobial resistance (AMR).
TL;DR: In this article, a short, 7-d treatment of preweaned male mice with high-dose ABX is associated with reductions of Aβ amyloidosis, plaque-localized microglia morphologies, and Aβ-associated degenerative changes at 9 wk of age in male mice only.
Abstract: We previously demonstrated that lifelong antibiotic (ABX) perturbations of the gut microbiome in male APPPS1-21 mice lead to reductions in amyloid β (Aβ) plaque pathology and altered phenotypes of plaque-associated microglia. Here, we show that a short, 7-d treatment of preweaned male mice with high-dose ABX is associated with reductions of Aβ amyloidosis, plaque-localized microglia morphologies, and Aβ-associated degenerative changes at 9 wk of age in male mice only. More importantly, fecal microbiota transplantation (FMT) from transgenic (Tg) or WT male donors into ABX-treated male mice completely restored Aβ amyloidosis, plaque-localized microglia morphologies, and Aβ-associated degenerative changes. Transcriptomic studies revealed significant differences between vehicle versus ABX-treated male mice and FMT from Tg mice into ABX-treated mice largely restored the transcriptome profiles to that of the Tg donor animals. Finally, colony-stimulating factor 1 receptor (CSF1R) inhibitor-mediated depletion of microglia in ABX-treated male mice failed to reduce cerebral Aβ amyloidosis. Thus, microglia play a critical role in driving gut microbiome-mediated alterations of cerebral Aβ deposition.
TL;DR: IGV.js as mentioned in this paper is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV), which can be easily dropped into any web page with a single line of code and has no external dependencies.
Abstract: igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has no external dependencies. The viewer runs completely in the web browser, with no backend server and no data pre-processing required.The igv.js JavaScript component can be installed from NPM at https://www.npmjs.com/package/igv. The source code is available at https://github.com/igvteam/igv.js under the MIT open-source license. IGV-Web, the end-user application built around igv.js, is available at https://igv.org/app. The source code is available at https://github.com/igvteam/igv-webapp under the MIT open-source license.Supplementary information is available at Bioinformatics online.
TL;DR: In this article, a multilevel logistic regression was used to fit single-pollutant models; quantile g-computation approach was applied to estimate the joint effect of air pollution and PM component mixtures.
TL;DR: In this article , the pseudokinase TRIB1 downstream of the EPAC/RAP2A/PI-PLC pathway was shown to degrade the primary transcriptional activator of Adrb3, CEBPα.
Abstract: The dysregulation of energy homeostasis in obesity involves multihormone resistance. Although leptin and insulin resistance have been well characterized, catecholamine resistance remains largely unexplored. Murine β3-adrenergic receptor expression in adipocytes is orders of magnitude higher compared with that of other isoforms. While resistant to classical desensitization pathways, its mRNA (Adrb3) and protein expression are dramatically downregulated after ligand exposure (homologous desensitization). β3-Adrenergic receptor downregulation also occurs after high-fat diet feeding, concurrent with catecholamine resistance and elevated inflammation. This downregulation is recapitulated in vitro by TNF-α treatment (heterologous desensitization). Both homologous and heterologous desensitization of Adrb3 were triggered by induction of the pseudokinase TRIB1 downstream of the EPAC/RAP2A/PI-PLC pathway. TRIB1 in turn degraded the primary transcriptional activator of Adrb3, CEBPα. EPAC/RAP inhibition enhanced catecholamine-stimulated lipolysis and energy expenditure in obese mice. Moreover, adipose tissue expression of genes in this pathway correlated with body weight extremes in a cohort of genetically diverse mice and with BMI in 2 independent cohorts of humans. These data implicate a signaling axis that may explain reduced hormone-stimulated lipolysis in obesity and resistance to therapeutic interventions with β3-adrenergic receptor agonists.
TL;DR: A comprehensive review of using cell-membrane-coated nanoparticles, namely "cellular nanosponges," as host decoys for a wide range of biological neutralization applications is provided in this paper .
Abstract: Biological neutralization represents a general strategy that deploys therapeutic agents to bind with harmful molecules or infectious pathogens, block their bioactivity, and thus prevent them from causing the diseases. Here, a comprehensive review of using cell-membrane-coated nanoparticles, namely "cellular nanosponges," as host decoys for a wide range of biological neutralization applications is provided. Compared to traditional neutralization strategies, the cellular nanosponges stand out by mimicking susceptible host cells rather than accommodating the structures of the causative agents for the design of therapeutics. As all pathological agents must interact with host cells for bioactivity, nanosponges bypass the diversity of these agents and create function-driven and broad-spectrum neutralization solutions. The review focuses on the recent progress of using this new nanomedicine platform for neutralization against five primary pathological agents, including bacterial toxins, chemical toxicants, inflammatory cytokines, pathological antibodies, and viruses. Existing studies have established cellular nanosponges as versatile tools for biological neutralization. A thorough review of the cellular nanosponge technology is expected to inspire more refined cellular nanosponge designs and unique neutralization applications to address unsolved medical problems.
TL;DR: In this article , the authors proposed to use olfactory receptors in their antennal Olfactory receptor neurons to detect human odors and then integrate these information with the senses of temperature and humidity, as well as vision, processed in the brain into a behavioral output.
TL;DR: In this paper , a nanoscale quantum imaging of low-dimensional ferromagnetic properties in Fe3GeTe2/hBN van der Waals heterostructures is presented.
Abstract: Emergent color centers with accessible spins hosted by van der Waals materials have attracted substantial interest in recent years due to their significant potential for implementing transformative quantum sensing technologies. Hexagonal boron nitride (hBN) is naturally relevant in this context due to its remarkable ease of integration into devices consisting of low-dimensional materials. Taking advantage of boron vacancy spin defects in hBN, we report nanoscale quantum imaging of low-dimensional ferromagnetism sustained in Fe3GeTe2/hBN van der Waals heterostructures. Exploiting spin relaxometry methods, we have further observed spatially varying magnetic fluctuations in the exfoliated Fe3GeTe2 flake, whose magnitude reaches a peak value around the Curie temperature. Our results demonstrate the capability of spin defects in hBN of investigating local magnetic properties of layered materials in an accessible and precise way, which can be extended readily to a broad range of miniaturized van der Waals heterostructure systems.
TL;DR: In this article, the authors proposed a Wi-Fi-based gait recognition method for human identification. But the method is not suitable for the use of wearable sensors and does not work well in outdoor environments.
Abstract: Gait, the walking manner of a person, has been perceived as a physical and behavioral trait for human identification. Compared with cameras and wearable sensors, Wi-Fi-based gait recognition is mor...
14 Jan 2022
TL;DR: In this paper , a dual-color probe (3MBP5) was developed for the simultaneous detection of Mpro and PLpro by fluorescence (or Förster) resonance energy transfer (FRET).
Abstract: The main protease (Mpro ) and papain-like protease (PLpro ) play critical roles in SARS-CoV-2 replication and are promising targets for antiviral inhibitors. The simultaneous visualization of Mpro and PLpro is extremely valuable for SARS-CoV-2 detection and rapid inhibitor screening. However, such a crucial investigation has remained challenging because of the lack of suitable probes. We have now developed a dual-color probe (3MBP5) for the simultaneous detection of Mpro and PLpro by fluorescence (or Förster) resonance energy transfer (FRET). This probe produces fluorescence from both the Cy3 and Cy5 fluorophores that are cleaved by Mpro and PLpro . 3MBP5-activatable specificity was demonstrated with recombinant proteins, inhibitors, plasmid-transfected HEK 293T cells, and SARS-CoV-2-infected TMPRSS2-Vero cells. Results from the dual-color probe first verified the simultaneous detection and intracellular distribution of SARS-CoV-2 Mpro and PLpro . This is a powerful tool for the simultaneous detection of different proteases with value for the rapid screening of inhibitors.