bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low back pain care pathways and costs: association with the type of initial contact health care provider. A retrospective cohort study
Authors: Elton David , Kosloff Thomas M. , Zhang Meng , Advani Protima , Guo Yinglong , Shimotsu Scott T. , Sy Sean , Feuer Ari 
Published: June 2022

AbstractBackgroundLow back pain (LBP) is prevalent, management benefits from high-quality clinical practice guidelines, and yet LBP is a common source of low value care. The purpose of this retrospective cohort study was to examine the association between the type of initial contact health care provider (HCP), service utilization, and total episode cost for the management of LBP.MethodsEpisode of care was used to analyze a US national sample of LBP episodes completed in 2017-2019. A combined surgical and non-surgical (pooled) sample and a non-surgical sample were separately analyzed. The primary independent variable was the type of the initial contact HCP. Dependent measures included rate and timing of use of 14 types of health care services and total episode cost. The association between initial contact HCP, total episode cost and rate of prescription opioid and NSAID use was tested using a mixed effects model.ResultsThe study included 616,766 continuously insured individuals aged 18 years and older with 756,631 episodes of LBP involving 386,795 HCPs and incurring $1,010,495,291 in expenditures. A primary care or specialist HCP was initially contacted in 62.0% of episodes, with these episodes associated with early use of low-value services such as imaging, pharmacologic, and interventional services. A non-prescribing HCP was initially contacted in 32.5% of episodes with these episodes associated with early use of guideline recommended first line services.Each type of HCP emphasized different initial services with little indication of a stepped approach to managing LBP. Following adjustment for covariates chiropractors were associated with the lowest total episode cost. As an observational study of associations, numerous confounders may have impacted results.ConclusionsAn individual with LBP has different experiences based on the type of HCP initially contacted. Initial contact with primary care or specialist HCPs is associated with second- and third-line services provided before first line services, with little indication of a guideline recommended stepped approach to managing LBP. Increasing the likelihood of guideline- concordant, high-value care for LBP may require systemic changes to the health care delivery system. In the absence of red flags these changes may include increasing the proportion of individuals receiving early non-pharmacological treatment, either through improving direct access to non-prescribing HCPs or increasing timely referrals from primary care and specialist health care providers.
The evolution of an RNA-based memory of self in the face of genomic conflict
Authors: Pliota Pinelopi , Marvanova Hana , Koreshova Alevtina , Kaufman Yotam , Tikanova Polina , Krogull Daniel , Hagmüller Andreas , Widen Sonya A. , Handler Dominik , Gokcezade Joseph , Duchek Peter , Brennecke Julius , Ben-David Eyal , Burga Alejandro 
Published: June 2022

AbstractDistinguishing endogenous genes from selfish ones is essential for germline integrity. In animals, small regulatory RNAs play a central role in this process; however, the underlying principles are largely unknown. To fill this gap, we studied how selfish toxin-antidote elements (TAs) evade silencing in the nematode Caenorhabditis tropicalis. We found that the slow-1/grow-1 TA is active only when maternally inherited. Surprisingly, this parent-of-origin effect stems from a regulatory role of the toxin’s mRNA: maternal slow-1 mRNA—but not SLOW-1 protein—licenses slow-1 expression in the zygote by counteracting piRNAs. Our results indicate that epigenetic licensing— known to play a role in C. elegans sex-determination—is likely a common mechanism that hinders the spread of selfish genes in wild populations while ensuring a lasting memory of self in the germline.
A Method for Selective 19F-Labeling Absent of Probe Sequestration (SLAPS)
Authors: Dixon Austin D. , Trinidad Jonathan C. , Ziarek Joshua J. 
Published: June 2022

AbstractFluorine (19F) offers several distinct advantages for biomolecular nuclear magnetic resonance (NMR) spectroscopy such as no background signal, 100% natural abundance, high sensitivity, and a large chemical shift range. Exogenous cysteine-reactive 19F-probes have proven especially indispensable for characterizing large, challenging systems that are less amenable to other isotopic labeling strategies such as G protein-coupled receptors (GPCRs). As fluorine linewidths are inherently broad, limiting reactions with offsite cysteines is critical for spectral simplification and accurate deconvolution of component peaks – especially when analyzing systems with intermediate to slow timescale conformational exchange. Here, we uncovered a second source of offsite labeling: non-covalent probe sequestration by detergent micelles. We present a simple four-step protocol for Selective Labeling Absent of Probe Sequestration (SLAPS): physically-disrupt cell membranes in the absence of detergent, incubate membranes with cysteine-reactive 19F-probes, remove excess unreacted 19F-probe molecules via ultracentrifugation, and finally solubilize in the detergent of choice. SLAPS should be broadly applicable to other lipophilic cysteine-reactive probes and membrane protein classes solubilized in detergent micelles or lipid mimetics.
Effects of hydrological change in fire-prone wetland vegetation: an empirical simulation
Authors: Mason Tanya J. , Popovic Gordana C. , McGillycuddy Maeve , Keith David A. 
Published: June 2022

AbstractUpland swamps are peat-accumulating, groundwater-dependent and fire-prone wetland ecosystems. Drying caused by anthropogenic processes such as underground mining, ditching and climate change may disrupt surface and groundwater flows effecting a bottom-up control on wetland expression. Fire is an endogenous, recurring disturbance that drives a top-down consumptive force in many of these systems. When compounded with anthropogenic drying, fire may facilitate permanent community transitions. A dearth of ecological data and temporal lags have hampered our ability to predict risks associated with multiple disturbances in wetland plant communities. We collected intact wetland mesocosms from valley floors and lower slopes of four undisturbed swamp sites. We transferred the mesocosms to a glasshouse and established three different soil moisture availability levels to simulate wetland drainage. After 20 months of the hydrological treatment, we simulated a fire event by sequentially applying biomass removal (clipping), heat and smoke to half of the mesocosms. We monitored species biomass, richness and composition over a 3.5-year time frame. We found evidence of a temporal lag in biomass response to low water availability and synergistic hydrological and fire effects on species richness. In unburnt conditions, richness declined with low water availability but was maintained under high and medium water availability. After simulated fire in medium water availability, however, richness also declined and converged with depauperate low water mesocosm richness. Representation by many obligate swamp species declined in low compared with high water availability mesocosms over time, an effect that was amplified by the fire treatment.SynthesisOur evidence of lagged effects of hydrological change on wetland vegetation and compounding effects of fire should be considered in impact assessments, monitoring programs and ecosystem management to avoid irreversible wetland change in drying environments.
The spatial landscape of Cancer Hallmarks reveals patterns of tumor ecology
Authors: Sibai Mustafa , Cervilla Sergi , Grases Daniela , Musulen Eva , Lazcano Rossana , Mo Chia-Kuei , Davalos Veronica , Fortian Arola , Bernat Adrià , Romeo Margarita , Tokheim Collin , Grande Enrique , Real Francisco , Barretina Jordi , Lazar Alexander J , Ding Li , Esteller Manel , Bailey Matthew H , Porta-Pardo Eduard 
Published: June 2022

AbstractTumors are complex ecosystems with dozens of interacting cell types. The concept of Cancer Hallmarks distills this complexity into a set of underlying principles that govern tumor growth. Here, we exploit this abstraction to explore the physical distribution of Cancer Hallmarks across 63 primary untreated tumors from 10 cancer types using spatial transcriptomics. We show that Hallmark activity is spatially organized–with 7 out of 13 Hallmarks consistently more active in cancer cells than within the non-cancerous tumor microenvironment (TME). The opposite is true for the remaining six Hallmarks. Additionally, we discovered that genomic distance between tumor subclones correlates with differences in Cancer Hallmark activity, even leading to clone-Hallmark specialization in some cases. Finally, we demonstrate interdependent relationships between Cancer Hallmarks at the junctions of TME and cancer compartments. In conclusion, including the spatial dimension, particularly through the lens of Cancer Hallmarks, can improve our understanding of tumor ecology.SignificanceWe explored Cancer Hallmarks in 63 primary untreated tumors from 10 cancer types using spatial transcriptomics. This study unveiled spatial patterns in Hallmark activity, with some being more active in cancer cells and others in the non-cancerous tumor environment. Genomic distance impacted Hallmark activity, and we identified interdependencies at the TME-cancer junctions, improving our understanding of tumor ecology.
scFLUX: a web server for metabolic flux and variation prediction using transcriptomics data
Authors: Zhang Zixuan , Chang Wennan , Alghamdi Norah , Fei Mengyuan , Wan Changlin , Lu Alex , Zang Yong , Xu Ying , Wu Wenzhuo , Cao Sha , Zhang Yu , Zhang Chi 
Published: June 2022

ABSTRACTQuantitative assessment of single cell fluxome is critical for understanding the metabolic heterogeneity in diseases. Unfortunately, single cell fluxomics using laboratory approaches is currently infeasible, and none of the current flux estimation tools could achieve single cell resolution. In light of the natural associations between transcriptomic and metabolomic profiles, it remains both a feasible and urgent task to use the available single cell transcriptomics data for prediction of single cell fluxome. We present scFLUX here, which provides an online platform for prediction of metabolic fluxome and variations using transcriptomics data, on individual cell or sample level. This is in contrast to other flux estimation methods that are only able to model the fluxes for cells of pre-defined groups. The scFLUX webserver implements our in-house single cell flux estimation model, namely scFEA, which integrates a novel graph neural network architecture with a factor graph derived from the complex human metabolic network. To the best of our knowledge, scFLUX is the first and only web-based tool dedicated to predicting individual sample-/cell-metabolic fluxome and variations of metabolites using transcriptomics data. scFLUX is available at http://scflux.org/. The stand-alone tools for using scFLUX locally are available at https://github.com/changwn/scFEA.
Lung endothelium instructs dormancy of susceptible metastatic tumour cells
Authors: Jakab Moritz , Lee Ki Hong , Uvarovskii Alexey , Ovchinnikova Svetlana , Kulkarni Shubhada R , Rostalski Till , Anders Simon , Augustin Hellmut G 
Published: June 2022

AbstractDuring metastasis, cancer cells hijack blood vessels and travel via the circulation to colonize distant sites1,2. Due to the rarity of these events, the immediate cell fate decisions of arrested circulating tumour cells (aCTC) are poorly understood and the role of the endothelium, as the interface of dissemination, remains elusive3,4. Here, we developed a novel strategy to specifically enrich for aCTC subpopulations capturing all cell states of the extravasation process and, in combination with single cell RNA-sequencing, provide a first blueprint of the transcriptional basis of early aCTC decisions. Upon their arrest at the metastatic site, tumour cells either started proliferating intravascularly or extravasated and preferably reached a state of quiescence. Endothelial-derived angiocrine Wnt factors were found to drive this bifurcation by inducing a mesenchymal-like phenotype in aCTCs instructing them to follow the extravasation-dormancy branch. Surprisingly, homogenous tumour cell pools showed an unexpected baseline heterogeneity in Wnt signalling activity and epithelial-to-mesenchyme-transition (EMT) states. This heterogeneity was established at the epigenetic level and served as the driving force of aCTC behaviour. Hypomethylation enabled high baseline Wnt and EMT activity in tumour cells leading them to preferably follow the extravasation-dormancy route, whereas methylated tumour cells had low activity and proliferated intravascularly. The data identify the pre-determined methylation status of disseminated tumour cells as a key regulator of aCTC behaviour in the metastatic niche. While metastatic niche-derived factors per default instruct the acquisition of quiescence, aCTCs unwind a default proliferation program and only deviate from it if hypomethylation in key gene families renders them responsive towards the microenvironment.
Temperature-Sensitive Contacts in Disordered Loops Tune Enzyme I Activity
Authors: Burns Daniel , Singh Aayushi , Venditti Vincenzo , Potoyan Davit A 
Published: June 2022

AbstractHomologous enzymes with identical folds often exhibit different thermal and kinetic behaviors. Understanding how enzyme sequence encodes catalytic activity at functionally optimal temperatures is a fundamental problem in biophysics. Recently it was shown that the residues that tune catalytic activities of thermophilic/mesophilic variants of the C-terminal domain of bacterial Enzyme I (EIC) are largely localized within disordered loops, offering a model system with which to investigate this phenomenon. In this work, we employ molecular dynamics simulations and mutagenesis experiments to reveal a mechanism of sequence-dependent activity tuning of EIC homologs.We find that a network of contacts in the catalytic loops is particularly sensitive to changes in temperature, with some contacts exhibiting distinct linear or non-linear temperature-dependent trends. Moreover, these trends define structurally clustered dynamical modes and can distinguish regions that tend toward order or disorder at higher temperatures. Assaying several thermophilic EIC mutants, we show that complementary mesophilic mutations to the most temperature-sensitive positions exhibit the most enhanced activity while mutations to relatively temperature insensitive positions exhibit the least enhanced activities. These results provide a mechanistic explanation of sequence-dependent temperature tuning and offer a computational method for rational enzyme modification.SignificanceTemperature affects the catalytic rates of all enzymes. The impact of temperature on the catalytic activity of an enzyme, however, is convoluted from contributions of protein sequence, structure, and dynamics. As such, understanding and designing the molecular features of enzymes which tune catalytic rates at different temperatures remains a fundamental challenge in biophysics. In this work we have employed molecular simulations and mutagenesis experiments to reveal the temperature tuning mechanism of mesophilic and thermophilic homologues of the C domain of bacterial Enzyme l. We find that enzymes can be tuned to their physiological temperatures through a network of temperature-sensitive residue contacts localized in the disordered loops. Furthermore, we find that among temperature-sensitive contacts some exhibit linear and others non-linear dependence on temperature. These clues offer a promising physics-based approach for tuning enzyme activity.
Magnetothermal control of temperature-sensitive repressors in superparamagnetic iron nanoparticle-coatedBacillus subtilis
Authors: Greeson Emily M. , Madsen Cody S. , Makela Ashley V. , Contag Christopher H. 
Published: June 2022

AbstractSuperparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents in magnetic resonance imaging (MRI) and magnetic particle imaging (MPI) and resulting images can be used to guide magnetothermal heating. Alternating magnetic fields (AMF) cause local temperature increases in regions with SPIONs, and we investigated the ability of magnetic hyperthermia to regulate temperature-sensitive repressors (TSRs) of bacterial transcription. The TSR, TlpA39, was derived from a Gram-negative bacterium, and used here for thermal control of reporter gene expression in Gram-positive,Bacillus subtilis. In vitroheating ofB. subtiliswith TlpA39 controlling bacterial luciferase expression, resulted in a 14.6-fold (12-hour; h) and 1.8-fold (1-h) increase in reporter transcripts with a 9.0-fold (12-h) and 11.1-fold (1-h) increase in bioluminescence. To develop magnetothermal control,B. subtiliscells were coated with three SPION variations. Electron microscopy coupled with energy dispersive X-ray spectroscopy revealed an external association with, and retention of, SPIONs onB. subtilis. Furthermore, using long duration AMF we demonstrated magnetothermal induction of the TSRs in SPION-coatedB. subtiliswith a maximum of 4.6-fold increases in bioluminescence. After intramuscular injections of SPION-coatedB. subtilis,histology revealed that SPIONs remained in the same locations as the bacteria. Forin vivostudies, 1-h of AMF is the maximum exposure due to anesthesia constraints. Bothin vitroandin vivo, there was no change in bioluminescence after 1-h of AMF treatment. Pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to transcriptional control that expands options for targeted bacteriotherapies.
Systemic silencing and DNA methylation of a host reporter gene induced by a beneficial fungal root endophyte
Authors: Dalakouras Athanasios , Katsaouni Afrodite , Avramidou Marianna , Dadami Elena , Tsiouri Olga , Vasileiadis Sotirios , Makris Athanasios , Georgopoulou Maria Eleni , Papadopoulou Kalliope K. 
Published: June 2022

AbstractA growing body of evidence suggests that RNA interference (RNAi) plays a pivotal role in the communication between plants and pathogenic fungi, where a bi-directional cross-kingdom RNAi is established to the advantage of either the host or the pathogen. Similar mechanisms acting during plant association with non-pathogenic symbiotic microorganisms have been elusive to this date. Here, we report on an RNAi-based mechanism of communication between a beneficial fungal endophyte,Fusarium solanistrain K (FsK) and its host plants. This soil-borne endophyte that confers resistance and/or tolerance to biotic and abiotic stress in tomato and, as shown in this study, promotes plant growth inNicotiana benthamiana, is restricted to the root system in both host plants. We first showed that the fungus has a functional core RNAi machinery; double stranded RNAs (dsRNAs) are processed into short interfering RNAs (siRNAs) of predominantly 21-nt in size, which lead to the degradation of homologous mRNAs. Importantly, by using an RNAi sensor system, we demonstrated that root colonization ofN. benthamianaby FsK led to the induction of systemic silencing and DNA methylation of a host reporter gene.. These data reflect a more general but so far unrecognized mechanism wherein root endophytes systemically translocate RNAi signals to the aboveground tissues of their hosts to modulate gene expression during symbiosis, which may be translated to the beneficial phenotypes.HighlightA root-restricted, beneficial fungal endophyte can induce systemic silencing and epigenetic modifications to its host plant.
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota
Authors: Hoces Daniel , Greter Giorgia , Arnoldini Markus , Moresi Claudia , Berent Sara , Kolinko Isabel , Bansept Florence , Woller Aurore , Häfliger Janine , Martens Eric , Hardt Wolf-Dietrich , Loverdo Claude , Slack Emma 
Published: June 2022

SummaryMany microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. However, we remain largely blind to the quantitative effects of processes determining colonization success. In this study, we used genetically-barcoded Bacteroides thetaiotaomicron (B.theta) strains in combination with mathematical modeling to quantify population bottlenecks experienced by B.theta during gut colonization. Integrating population bottlenecks sizes with careful quantification of net growth rates in vivo and in vitro allows us to build models describing the events during intestinal colonization in the context of gnotobiotic and complex microbiotas. Using these models, we estimated the decrease in niche size for B.theta colonization with increasing microbiota complexity. In addition, our system can be applied to mechanistically dissect colonization defects of mutant strains. As a proof of concept, we demonstrated that the competitive disadvantage of a B.theta mutant lacking capsular polysaccharide is due to a combination of an increased lag-phase before growth initiation in the gut, combined with an increased clearance rate. Crucially, the requirement for the B.theta capsule depended strongly on microbiota composition, suggesting that the dominant role may be protection from bacterial or phage aggression rather than from host-induced bactericidal mechanisms.
Extensive substrate recognition by the streptococcal antibody-degrading enzymes IdeS and EndoS
Authors: Sudol Abigail S. L. , Butler John , Ivory Dylan P. , Tews Ivo , Crispin Max 
Published: June 2022

AbstractEnzymatic cleavage of IgG antibodies is a common strategy used by pathogenic bacteria to ablate immune effector function. The Streptococcus pyogenes bacterium secretes the protease IdeS and the glycosidase EndoS, which specifically catalyse cleavage and deglycosylation of human IgG, respectively. IdeS has received clinical approval for kidney transplantation in hypersensitised individuals, while EndoS has found application in engineering antibody glycosylation. Here, we present crystal structures of both enzymes in complex with their IgG1 Fc substrate, which was achieved using Fc engineering to disfavour preferential Fc crystallisation. The IdeS protease displays extensive Fc recognition and encases the antibody hinge. Conversely, the glycan hydrolase domain in EndoS traps the Fc glycan in a flipped-out conformation, while additional recognition of the Fc peptide is driven by the so-called carbohydrate binding module. Understanding the molecular basis of antibody recognition by bacterial enzymes will facilitate the development of next-generation enzymes for clinical and biotechnological use.