bluuebunny/crossref_metadata_2025_split huggingface dataset:
Australian children’s foot, ankle, and leg problems in primary care: a secondary analysis of the Bettering the Evaluation and Care of Health (BEACH) data
Authors: Williams Cylie M. , Menz Hylton B. , Lazzarini Peter A. , Gordon Julie , Harrison Christopher 
Published: February 2022

AbstractObjectivesTo explore children’s foot, ankle and leg consultation patterns and management practices in Australian primary care.DesignCross-sectional, retrospective studySettingAustralia Bettering the Evaluation and Care of Health program dataset.ParticipantsData were extracted for GPs and patients ≤18 years from April 2000 to March 2016 inclusive.Main outcome measuresDemographic characteristics: sex, GP age groups (i.e. <45, 45-54, 55+ years), GP country of training, patient age grouping (0-4, 5-9, 10-14, 15-18 years), postcode, concession card status, Indigenous status, up to three patient encounter reasons, up to four encounter problems/diagnoses, and the clinical management actioned by the GP.ResultsChildren’s foot, ankle or leg problems were managed at a rate of 2.05 (95% CI 1.99 to 2.11) per 100 encounters during 229,137 GP encounters with children. There was a significant increase in the rate of foot, ankle and leg problems managed per 100 children in the population, from 6.1 (95% CI: 5.3-6.8) in 2005-06 to 9.0 (95% CI: 7.9-10.1) in 2015-16. Management of children’s foot, ankle and leg problems were independently associated with male patients (30% more than female), older children (15-18 years were 7.1 times more than <1 years), male GPs (13% more) and younger GPs (<45 years of age 13% more than 55+). The top four most frequently managed problems were injuries (755.9 per 100,000 encounters), infections (458.2), dermatological conditions (299.4) and unspecified pain (176.3). The most frequently managed problems differed according to age grouping.ConclusionsChildren commonly present to GPs for foot, ankle, and leg problems. Presentation frequencies varied according to age. Unexpectedly, conditions presenting commonly in adults, but rarely in children, were also frequently recorded. This data highlights the importance of initiatives supporting contemporary primary care knowledge of diagnoses and management of paediatric lower limb problems to minimise childhood burden of disease.Article SummaryStrengths and limitations of this study-This study examines the full spectrum of childhood foot, ankle, or leg presentations in primary care and how these are managed-This study also provides information about how foot, ankle and leg GP presentations and management patterns differ as children get older-This dataset provides a robust baseline on which future guidelines and implementation studies can measure the outcomes of practice change over time.-This study may be limited by how GPs coded the presentation and management data
The integrated stress response remodels the microtubule organizing center to clear unfolded proteins following proteotoxic stress
Authors: Hurwitz Brian , Guzzi Nicola , Gola Anita , Fiore Vincent F. , Sendoel Ataman , Nikolova Maria , Barrows Douglas , Carroll Thomas S. , Pasolli H. Amalia , Fuchs Elaine 
Published: February 2022

AbstractWhen cells encounter stressful situations, they activate the integrated stress response (ISR), which limits total protein synthesis and redirects translation to proteins that help the cells to cope. The ISR has also been implicated in cancers, but redundancies in the stress-sensing kinases that trigger the ISR have posed hurdles to dissecting physiological relevance. To overcome this challenge, we targeted the regulatory node of these kinases, namely the S51 phosphorylation site of eukaryotic translation initiation factor eIF2α and genetically replaced eIF2α with eIF2α-S51A in squamous cell carcinoma (SCC) stem cells. While inconsequential under normal growth conditions, the vulnerability of this ISR-null state was unveiled when SCC stem cells experienced proteotoxic stress. Seeking mechanistic insights into the protective roles of the ISR, we combined ribosome profiling and functional approaches to identify and probe the functional importance of translational differences between ISR-competent and ISR-null SCC stem cells when exposed to proteotoxic stress. In doing so, we learned that the ISR redirects translation to centrosomal proteins that orchestrate the microtubule dynamics needed to efficiently concentrate unfolded proteins at the microtubule organizing center so that they can be cleared by the perinuclear degradation machinery. Thus, rather than merely maintaining survival during stress, the ISR also functions in promoting cellular recovery once the stress has subsided. This finding exposes a vulnerability to SCC stem cells that could be exploited therapeutically.
Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP
Authors: Manakov Sergei A , Shishkin Alexander A , Yee Brian A , Shen Kylie A , Cox Diana C , Park Samuel S , Foster Heather M , Chapman Karen B , Yeo Gene W , Van Nostrand Eric L 
Published: February 2022

SummaryOur expanding knowledge of the roles small regulatory RNAs play across numerous areas of biology, coupled with the promise of RNA-targeted therapies and small RNA-based medicines, create an urgent need for tools that can accurately identify and quantify small RNA:target interactions at scale. MicroRNAs (miRNA) are a major class of small RNAs in plants and animals. The experimental capture of miRNA:mRNA interactions by ligation into chimeric RNA fragments in chimeric CrossLinking and ImmunoPrecipitation (CLIP) provides a direct readout of miRNA targets with high-throughput sequencing. Despite the power of this approach, widespread adoption of chimeric CLIP has been slow due to both methodological technical complexity as well as limited recovery of chimeric molecules (particularly beyond the most abundant miRNAs). Here we describe chimeric eCLIP, in which we integrate a chimeric ligation step into AGO2 eCLIP to enable chimeric read recovery. We show that removal of the cumbersome polyacrylamide gel and nitrocellulose membrane transfer step common to CLIP techniques can be omitted for chimeric AGO2 eCLIP to create a simplified high throughput version of the assay that maintains high signal- to-noise. With the increased yield of recovered miRNA:mRNA interactions in no-gel chimeric eCLIP, we show that simple enrichment steps using either PCR or on-bead probe capture can be added to chimeric eCLIP in order to target and enrich libraries for chimeric reads specific to one or more miRNAs of interest in both cell lines and tissue samples, resulting in 30- to 175-fold increases in recovery of chimeric reads for miRNAs of interest. We further demonstrate that the same probe-capture approach can be used to recover miRNA interactions for a targeted gene of interest, revealing both distinct miRNA targeting as well as co-targeting by several miRNAs from the same seed family. RNA-seq analysis of gene expression following miRNA overexpression confirmed miRNA-mediated repression of chimeric eCLIP-identified targets and indicated that probe-enriched chimeric eCLIP can provide additional sensitivity to detect regulated targets among genes that either contain or lack computationally predicted miRNA target sites. Thus, we believe that chimeric eCLIP will be a useful tool for quantitative profiling of miRNA targets in varied sample types at scale, and for revealing a deeper picture of regulatory networks for specific miRNAs of biological interest.HighlightsNo-gel chimeric eCLIP improves recovery of miRNA:mRNA interactions by 70-foldProbe- and PCR-enrichment deeply profiles mRNA targets of miRNAs of interestChimeric eCLIP targets experimentally identify non-computationally predicted interactionsIncreased depth recovers ∼6 million miRNA:target chimeras in HEK293T
Saccharibacteria harness light energy using Type-1 rhodopsins that may rely on retinal sourced from microbial hosts
Authors: Jaffe Alexander L. , Konno Masae , Kawasaki Yuma , Kataoka Chihiro , Béjà Oded , Kandori Hideki , Inoue Keiichi , Banfield Jillian F. 
Published: February 2022

ABSTRACTMicrobial rhodopsins are a family of photoreceptive membrane proteins with a wide distribution across the Tree of Life. Within the Candidate Phyla Radiation (CPR), a diverse group of putatively episymbiotic bacteria, the genetic potential to produce rhodopsins appears to be confined to a small clade of organisms from sunlit environments. Here, we characterize the metabolic context and biophysical features of Saccharibacteria Type-1 rhodopsin sequences derived from metagenomic surveys and show that these proteins function as outward proton pumps. This provides one of the only known mechanisms by which CPR can generate a proton gradient for ATP synthesis. Intriguingly, Saccharibacteria do not encode the genetic machinery to produce all-trans-retinal, the chromophore essential for rhodopsin function, but their rhodopsins are able to rapidly uptake this cofactor when provided in experimental assays. We found consistent evidence for the capacity to produce retinal from β-carotene in organisms co-occurring with Saccharibacteria, and this genetic potential was dominated by Actinobacteria, which are known hosts of Saccharibacteria in other habitats. If Actinobacteria serve as hosts for Saccharibacteria in freshwater environments, exchange of retinal for use by rhodopsin may be a feature of their associations.
Characterisation and sequence mapping of large RNA and mRNA therapeutics using mass spectrometry
Authors: Vanhinsbergh C.J. , Criscuola A. , Sutton J. , Murphy K. , Williamson A.J.K , Cook K. , Dickman M.J. 
Published: February 2022

ABSTRACTLarge RNA including messenger RNA (mRNA) has emerged as an important new class of therapeutic. Recently this has been demonstrated by two highly efficacious vaccines based on mRNA sequences encoding for a modified version of the SARS-CoV-2 spike protein. There is currently significant demand for the development of new and improved analytical methods for the characterization of large RNA including mRNA therapeutics. In this study we have developed an automated, high throughput workflow for the rapid characterisation and direct sequence mapping of large RNA and mRNA therapeutics. Partial RNase digestions using RNase T1 immobilised on magnetic particles was performed in conjunction with high resolution liquid chromatography mass spectrometry analysis. Sequence mapping was performed using automated oligoribonucleotide annotation and identifications based on MS/MS spectra. Using this approach >80% sequence of coverage of a range of large RNAs and mRNA therapeutics including the SARS Co-V2 spike protein was obtained in a single analysis. The analytical workflow, including automated sample preparation can be completed within 90 minutes. The ability to rapidly identify, characterise and sequence map large mRNA therapeutics with high sequence coverage provides important information for identity testing, sequence validation and impurity analysis.
Engineered high-density lipoprotein particles that chaperone bioactive lipid mediators to combat endothelial dysfunction and thromboinflammation
Authors: Swendeman Steven , Lin Daniel , Guo Shihui , Culbertson Alan , Kuo Andrew , Levesque Michel , Cartier Andreane , Seno Takahiro , Schmaier Alec , Galvani Sylvain , Inoue Asuka , Parikh Samir , FitzGerald Garret A. , Liao Maofu , Flaumenhaft Robert , Hla Timothy 
Published: February 2022

AbstractHigh-density lipoprotein (HDL) particles suppress inflammation-induced tissue injury via vascular and myeloid cell-dependent mechanisms. As such, HDL-associated bioactive lipids such as sphingosine 1-phosphate (S1P) and prostacyclin (PGI2) signal via their respective G protein-coupled receptors on target cells to promote vascular endothelial function and suppress platelet and myeloid-dependent pathophysiology. Here we have constructed a fusion protein of apolipoprotein A1 (ApoA1) and apolipoprotein M (ApoM) (A1M) that forms HDL-like particles and chaperones S1P and Iloprost, stable PGI2 analog. The A1M/S1P complex activates S1P receptor-1 (S1PR1) as a Gαi-biased agonist and attenuates the inflammation-induced NFκB pathway while A1M/Iloprost acts via IP receptor to inhibit platelet aggregation and promote endothelial barrier function. In addition to enhancing the endothelial barrier, A1M/S1P suppresses neutrophil influx, oxidative burst and inflammatory mediator secretion in a sterile inflammation model. We propose that A1M could be useful as a therapeutic to induce S1P and PGI2-dependent anti-inflammatory functions and suppress collateral tissue injury.
Microsecond Melting and Revitrification of Cryo Samples – Protein Structure and Beam-Induced Motion
Authors: Harder Oliver F. , Voss Jonathan M. , Olshin Pavel K. , Drabbels Marcel , Lorenz Ulrich J. 
Published: February 2022

AbstractWe have recently introduced a novel approach to time-resolved cryo-electron microscopy (cryo-EM) that involves melting a cryo sample with a laser beam to allow protein dynamics to briefly occur in liquid, before trapping the particles in their transient configurations by rapidly revitrifying the sample. With a time-resolution of just a few microseconds, this approach is notably fast enough to study domain motions that are typically associated with the activity of proteins, but which have previously remained inaccessible. Here, we add crucial details to the characterization of our method. We show that single-particle reconstructions of apoferritin and cowpea chlorotic mottle virus (CCMV) from revitrified samples are indistinguishable from those in conventional samples, demonstrating that melting and revitrification leaves the particles intact and that they do not undergo structural changes within the spatial resolution afforded by our instrument. We also characterize how rapid revitrification affects the properties of the ice, showing that revitrified samples exhibit comparable amounts of beam-induced motion. Our results pave the way for microsecond time-resolved studies of the conformational dynamics of proteins and open up new avenues to study the vitrification process and address beam-induced specimen movement.SynopsisMicrosecond melting and revitrification of cryo samples preserves the structure of embedded particles. The beam-induced motion of revitrified samples is comparable to that of conventional cryo samples.
Arid5a mediates an IL-17-dependent pathway that drives autoimmunity but not antifungal host defense
Authors: Taylor Tiffany C. , Li Yang , Li De-Dong , Majumder Saikat , McGeachy Mandy , Biswas Partha S. , Gingras Sebastien , Gaffen Sarah L. 
Published: February 2022

AbstractIL-17 contributes to the pathogenesis of certain autoimmune diseases, but conversely is essential for host defense against fungi. Antibody-based biologic drugs that neutralize IL-17 are effective in autoimmunity but can be accompanied by adverse side effects. Candida albicans is a commensal fungus that is the primary causative agent of oropharyngeal and disseminated candidiasis. Defects in IL-17 signaling cause susceptibility to candidiasis in mice and humans. A key facet of IL-17 receptor signaling involves RNA binding proteins (RBP), which orchestrate the fate of target mRNA transcripts. In tissue culture models we showed that the RBP AT-rich interacting protein 5a (Arid5a) promotes the stability and/or translation of multiple IL-17-dependent mRNAs. Moreover, during OPC, Arid5a is elevated within the oral mucosa in an IL-17-dependent manner. However, the contribution of Arid5a to IL-17-driven events in vivo is poorly defined. Here, we used CRISPR/Cas9 to generate mice lacking Arid5a. Arid5a-/- mice were fully resistant to experimental autoimmune encephalomyelitis (EAE), an autoimmune setting in which IL-17 signaling drives pathology. Surprisingly, Arid5a-/- mice were resistant to OPC and systemic candidiasis, similar to immunocompetent WT mice and contrasting with mice defective in IL-17 signaling. Therefore, Arid5a-dependent signals mediate pathology in autoimmunity yet are not required for immunity to candidiasis, indicating that selective targeting of IL-17 signaling pathway components may be a viable strategy for development of therapeutics that spare IL-17-driven host defense.
DE-NOVO HEMATOPOIESIS FROM THE FETAL LUNG
Authors: Yeung Anthony K. , Villacorta-Martin Carlos , Lindstrom-Vautrin Jonathan , Belkina Anna C. , Vanuytsel Kim , Dowrey Todd W. , Ysasi Alexandra B. , Vrbanac Vladimir , Mostoslavsky Gustavo , Balazs Alejandro B. , Murphy George J. 
Published: February 2022

SUMMARYHemogenic endothelial cells (HECs) are specialized cells that undergo endothelial to hematopoietic transition (EHT) to give rise to hematopoietic progenitors. Though not defined as a hematopoietic organ, the lung houses many resident hematopoietic cells, aids in platelet biogenesis, and is a reservoir for hematopoietic stem and progenitor cells (HSPCs), but lung HECs have never been described. Using explant cultures of murine and human fetal lungs, we demonstrate that the fetal lung is a source of HECs that have the functional capacity to undergo EHT to produce de-novo HSPCs. Flow cytometric and functional assessment of fetal lung explants showed the production of HSPCs that expressed key EHT and pre-HSPC markers. scRNA-Seq and small molecule modulation demonstrated that fetal lung EHT is reliant on canonical EHT signaling pathways. These findings suggest that functional HECs are present in the fetal lung, thus establishing this location as a potential extramedullary site of de-novo hematopoiesis.
Characterization of TR-107, a Novel Chemical Activator of the Human Mitochondrial Protease ClpP
Authors: Fennell Emily M. J. , Aponte-Collazo Lucas J. , Wynn Joshua D. , Drizyte-Miller Kristina , Leung Elisa , Greer Yoshimi Endo , Graves Paul R. , Iwanowicz Andrew A. , Ashamalla Hani , Holmuhamedov Ekhson , Lang Henk , Karanewsky Donald S. , Der Channing J. , Houry Walid A. , Lipkowitz Stanley , Iwanowicz Edwin J. , Graves Lee M. 
Published: February 2022

AbstractWe recently described the identification of a new class of small molecule activators of the mitochondrial protease ClpP. These compounds synthesized by Madera Therapeutics showed increased potency of cancer growth inhibition over the related compound ONC201. In this study, we describe chemical optimization and characterization of the next generation of highly potent and selective small molecule ClpP activators (TR compounds) and demonstrate their efficacy against breast cancer models in vitro and in vivo. One of these compounds (TR-107) with excellent potency, specificity and drug-like properties was selected for further evaluation. Examination of TR-107 effects in triple-negative breast cancer (TNBC) cell models showed growth inhibition in the low nanomolar range, equipotent to paclitaxel, in a ClpP-dependent manner. TR-107 reduced specific mitochondrial proteins including OXPHOS and TCA cycle components, in a time, dose and ClpP-dependent manner. Seahorse XF analysis and glucose deprivation experiments confirmed inactivation of OXPHOS and demonstrated an increased dependence on glycolysis following TR-107 exposure. The pharmacokinetic properties of TR-107 were compared to other known ClpP activators including ONC201 and ONC212. TR-107 displayed excellent exposure and serum t1/2 after oral administration. The antitumor response to TR-107 was investigated using human TNBC MDA-MB-231 cell line-induced xenograft tumors. Oral administration of TR-107 resulted in reduction in tumor volume and extension of survival in the treated compared with vehicle control mice. In summary, we describe the identification of highly potent new ClpP agonists with improved efficacy against TNBC, through targeted inactivation of OXPHOS and disruption of mitochondrial metabolism.
Açai (Euterpe oleracea Mart) modulates oxidative stress and inflammation by NF-κB inactivation and Nrf2 up-regulation in experimental diabetes
Authors: de Lima Deyse Yorgos , Marçal Rodrigues Adelson , Mouro Margaret Gori , Muniz Seif Elias Jorge , Punaro Giovana Rita , Suemitsu Higa Elisa Mieko 
Published: February 2022

AbstractTo evaluate the effects of açai extract (EA) on oxidative stress and inflammation induced by high glucose in cultured mouse immortalized mesangial cells (MiMC) and diabetic rats. MiMC cell viability and proliferation were determined by MTT. Extracellular and intracellular nitric oxide (NO) and intracellular ROS were also measured. The cell proteins were extracted for analysis of catalase, Nrf2, p-Nrf2, SOD-1, SOD-2, iNOS, NF-κB, p-NF-κB and TNF-α expression. Male, adult Wistar rats were distributed into 3 groups: control (CTL) and diabetic (DM) rats who received water and DMEA and received 1 mL/day EA (200 mg/kg) via gavage for 8 consecutive weeks. After treatment with EA, metabolic profile, renal function and thiobarbituric acid reactives substances (TBARS) levels were evaluated, and kidneys were collected for qualitative histological analysis. EA maintained cell viability above 90% in all groups; it decreased proliferation in the HG group, both significant. NO levels, ROS generation, iNOS, NF-κB, p-NF-κB and TNF-α expression were reduced significantly after 72 h of EA treatment, with significant increases for all antioxidants studied. DMEA vs DM showed a significant increase in body weight, improved kidney function and reduced TBARS excretion. EA treatment decreased proliferation, oxidative stress and inflammation in MiMC, and although açai did not decrease fasting glucose, it recovered the body weight and delayed the decline of renal function in the diabetic animals, suppressing the signaling of inflammatory mediators via NF-κB inactivation and increasing all antioxidants studied by upregulating the Nrf2 response pathway.
Using axiomatic design approach in preliminary design of a blended wing body aircraft
Authors: Alipour Alireza , Shahi Ashtiani Mohammad Ali , Shahmiri Farid 
Published: February 2022

Purpose
This study aims to present a method for improving the preliminary design process of an aircraft.

Design/methodology/approach
The approach of this paper is using Axiomatic Design (AD) principles in the aircraft preliminary design process. The aircraft design process consists of modules and disciplines, which are loosely coupled that can disrupt designers’ ability. Consequently, designers should define suitable functional requirements (FRs) and design parameters for products to avoid or limit coupling between them. As modular architecture is commonly defined as having a one-to-one mapping from the function domain to the physical domain, the independence axiom in AD could support the modularity of the design process. Therefore, these features guide us to use AD principles at the first steps of the aircraft design process.

Findings
Reduction coupling between different FRs and consequently less repetitive activities and design iteration in the design process by using AD principles are the finding of this paper.

Practical implications
This concept could be used for the design process of every complex product.

Originality/value
Looking at the preliminary design of a Blended Wing Body unmanned aerial vehicle with respect to the AD is a new technique to achieve a modular design process.