bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fis connects two sensory pathways, quorum sensing and surface sensing, to control motility inVibrio parahaemolyticus
Authors: J.G. Tague , Regmi A. , Gregory G.J. , Boyd E.F. 
Published: January 2021

ABSTRACTFis (Factor forInversionStimulation) is a global regulator that is highly expressed during exponential growth and undetectable in stationary growth. Quorum sensing (QS) is a global regulatory mechanism that controls gene expression in response to cell density and growth phase. InV. parahaemolyticus, a marine species and a significant human pathogen, the QS regulatory sRNAs, Qrr1 to Qrr5, negatively regulate the high cell density QS master regulator OpaR. OpaR is a positive regulator of capsule polysaccharide (CPS) formation required for biofilm formation and a repressor of swarming motility. InVibrio parahaemolyticus, we showed, using genetics and DNA binding assays, that Fis bound directly to the regulatory regions of theqrrgenes and was a positive regulator of these genes. In the Δfismutant,opaRexpression was induced and a robust CPS and biofilm was produced, while swarming motility was abolished. Expression analysis and promoter binding assays showed that Fis was a direct activator of both the lateral flagellumlafoperon and the surface sensingscrABCoperon, both required for swarming motility. Inin vitrogrowth competition assays, Δfiswas outcompeted by wild type in minimal media supplemented with intestinal mucus, and we showed that Fis directly modulated catabolism gene expression. Inin vivocolonization competition assays, Δfiswas outcompeted by wild type, indicating Fis is required for fitness. Overall, these data demonstrate a direct role for Fis in QS, motility, and metabolism inV. parahaemolyticus.IMPORTANCEIn this study, we examined the role of Fis in modulating expression of the five-quorum sensing regulatory sRNAs,qrr1toqrr5, and showed that Fis is a direct positive regulator of QS, which oppositely controls CPS and swarming motility inV. parahaemolyticus. The Δfisdeletion mutant was swarming defective due to a requirement for Fis in lateral flagella and surface sensing gene expression. Thus, Fis links QS and surface sensing to control swarming motility and, indirectly, CPS production. Fis was also required for cell metabolism, acting as a direct regulator of several carbon catabolism loci. Bothin vitroandin vivocompetition assays showed that the Δfismutant had a significant defect compared to wild type. Overall, our data demonstrates that Fis plays a critical role inV. parahaemolyticusphysiology that was previously unexamined.
Individual level prediction of emerging suicide events in the pharmacologic treatment of bipolar disorder
Authors: Luo Sean X. , Ciarleglio Adam , Galfalvy Hanga , Grunebaum Michael , Sher Leo , Mann J. John , Oquendo Maria A. 
Published: January 2021

AbstractBackgroundPatients with bipolar disorder have a high lifetime risk of suicide. Predicting, preventing and managing suicidal behavior are major goals in clinical practice. Changes in suicidal thoughts and behavior are common in the course of treatment of bipolar disorder.MethodsUsing a dataset from a randomized clinical trial of bipolar disorder treatment (N=98), we tested predictors of future suicidal behavior identified through a review of literature and applied marginal variable selection and machine learning methods. The performance of the models was assessed using the optimism-adjusted C statistic.ResultsNumber of prior hospitalizations, number of prior suicide attempts, current employment status and Hamilton Depression Scale were identified as predictors and a simple logistic regression model was constructed. This model was compared with a model incorporating interactions with treatment group assignment, and more complex variable selection methods (LASSO and Survival Trees). The best performing models had average optimism-adjusted C-statistics of 0.67 (main effects only) and 0.69 (Survival Trees). Incorporating medication group did not improve prediction performance of the models.ConclusionsThese results suggest that models with a few predictors may yield a clinically meaningful way to stratify risk of emerging suicide events in patients who are undergoing pharmacologic treatment for bipolar disorder.Significance StatementThis study aims to find out whether suicide events that occur during the pharmacological treatment of bipolar disorder, a severe psychiatric disorder that is highly associated with suicide behavior, can be predicted. Using existing methods, we developed and compared several predictive models. We showed that these models performed similarly to predictive models of other outcomes, such as treatment efficacy, in unipolar and bipolar depression. This suggests that suicide events during bipolar disorder may be a feasible target for individualized interventions in the future.
Optimising SARS-CoV-2 pooled testing strategies on social networks for low-resource settings
Authors: Mazzitello K I , Jiang Y , Arizmendi C M 
Published: January 2021

AbstractControlling the COVID-19 pandemic is an urgent global challenge. The rapid geographic spread of SARS-CoV-2 directly reflects the social structure. Before effective vaccines and treatments are widely available, we have to rely on alternative, non-pharmaceutical interventions, including frequency testing, contact tracing, social distancing, mask wearing, and hand-washing, as public health practises to slow down the spread of the disease. However frequent testing is the key in the absence of any alternative. We propose a network approach to determine the optimal low resources setting oriented pool testing strategies that identifies infected individuals in a small number of tests and few rounds of testing, at low prevalence of the virus. We simulate stochastic infection curves on societies under quarantine. Allowing some social interaction is possible to keep the COVID-19 curve flat. However, similar results can be strategically obtained searching and isolating infected persons to preserve a healthier social structure. Here, we analyze which are the best strategies to contain the virus applying an algorithm that combine samples and testing them in groups [1]. A relevant parameter to keep infection curves flat using this algorithm is the dairy frequency of testing at zones where a high infection rate is reported. On the other hand, the algorithm efficiency is low for random search of infected people.
Real-time optical analysis of a colorimetric LAMP assay for SARS-CoV-2 in saliva with a handheld instrument improves accuracy compared to endpoint assessment
Authors: Diaz Lena M. , Johnson Brandon E. , Jenkins Daniel M. 
Published: January 2021

AbstractControlling the course of the COVID-19 pandemic will require widespread deployment of consistent and accurate diagnostic testing of the novel coronavirus SARS-CoV-2. Ideally, tests should detect a minimum viral load, be minimally invasive, and provide a rapid and simple readout. Current FDA-approved RT-qPCR-based standard diagnostic approaches require invasive nasopharyngeal swabs and involve laboratory-based analyses that can delay results. Recently, a loop mediated isothermal nucleic acid amplification (LAMP) test that utilizes colorimetric readout received FDA approval. This approach utilizes a pH indicator dye to detect drop in pH from nucleotide hydrolysis during nucleic acid amplification. This method has only been approved for use with RNA extracted from clinical specimens collected via nasopharyngeal swabs. In this study, we developed a quantitative LAMP-based strategy to detect SARS-CoV-2 RNA in saliva. Our detection system distinguished positive from negative sample types using a handheld instrument that monitors optical changes throughout the LAMP reaction. We used this system in a streamlined LAMP testing protocol that could be completed in less than two hours to directly detect inactivated SARS-CoV-2 in minimally processed saliva that bypassed RNA extraction, with a limit of detection (LOD) of 50 genomes/reaction. The quantitative method correctly detected virus in 100% of contrived clinical samples spiked with inactivated SARS- CoV-2 at either 1X (50 genomes/reaction) or 2X (100 genomes/reaction) of the LOD. Importantly the quantitative method was based on dynamic optical changes during the reaction so was able to correctly classify samples that were misclassified by endpoint observation of color.
Validation of the German version of the Life-Space Assessment LSA-D
Authors: Mümken Sandra A. , Gellert Paul , Stollwerck Malte , O’Sullivan Julie L. , Kiselev Jörn 
Published: January 2021

AbstractObjectivesTo develop a German version of the original University of Alabama at Birmingham (UAB) Study of Aging Life-Space Assessment (LSA-D) for measurement of community mobility in older adults within the past 4 weeks and to evaluate its psychometric properties for urban and rural populations of older adults.DesignCross-sectional validation study.SettingTwo study centres in urban and rural German outpatient hospital settings.ParticipantsIn total N=83 community-dwelling older adults were recruited (n=40 from urban and n=43 from rural areas; mean age was 78.5 (SD=5.4); 49% male).Primary and secondary outcome measuresThe final version of the translated LSA-D was related with questions about activities and instrumental activities of daily living (ADL/iADL; primary hypothesis), Timed-Up&Go-Test (TUG), self-rated health, balance confidence and history of falls, use of transportation, and sociodemographic factors to obtain construct validity. Secondary outcome measures of health included handgrip strength, screening of cognitive function and comorbidities. To assess conduct construct validity, correlations between LSA-D and all health measures were examined for total sample, urban and rural subsamples using bivariate regression and multiple adjusted regression models. Posthoc analyses included different LSA-D scoring methods for each region. All parameters were estimated using non-parametric bootstrapping procedure.ResultsIn the multiple adjusted model for the total sample, number of ADL/iADL limitations (β=-.26; 95%CI=-.42/-.08), TUG (β=-.37; 95%CI=-.68/-.14), living in shared living arrangements (β=.22; 95%CI=.01/.44) and history of falls in the past 6 months (β=-.22; 95%CI=-.41/-.05) showed significant associations with the LSA-D composite score, while living in urban area (β=-.19; 95%CI=-.42/.03) and male gender (β=.15; 95%CI=-.04/.35) were not significant.ConclusionThe LSA-D is a valid tool for measuring life-space mobility in German community-dwelling older adults within the past four weeks in ambulant urban and rural settings.Trial registration numberDRKS00019023Strengths and limitations of this studyGerman validation of the original UAB Life-Space Assessment (LSA-D) for community dwelling older adults in urban and rural settingsUsing bootstrapped bivariate and multiple adjusted regression models to attain construct validity of the LSA-DRecruitment had to be stopped shortly before reaching the calculated sample size due to the decision to restrict in face-to-face research to contain the outbreak of the Covid-19 pandemic in March 2020
Machine learning approach for biopsy-based identification of eosinophilic esophagitis reveals importance of global features
Authors: Czyzewski Tomer , Daniel Nati , Rochman Mark , Caldwell Julie M. , Osswald Garrett A. , Collins Margaret H. , Rothenberg Marc E. , Savir Yonatan 
Published: January 2021

AbstractGoalEosinophilic esophagitis (EoE) is an allergic inflammatory condition characterized by eosinophil accumulation in the esophageal mucosa. EoE diagnosis includes a manual assessment of eosinophil levels in mucosal biopsies—a time-consuming, laborious task that is difficult to standardize. One of the main challenges in automating this process, like many other biopsy-based diagnostics, is detecting features that are small relative to the size of the biopsy.ResultsIn this work, we utilized hematoxylin- and eosin-stained slides from esophageal biopsies from patients with active EoE and control subjects to develop a platform based on a deep convolutional neural network (DCNN) that can classify esophageal biopsies with an accuracy of 85%, sensitivity of 82.5%, and specificity of 87%. Moreover, by combining several downscaling and cropping strategies, we show that some of the features contributing to the correct classification are global rather than specific, local features.ConclusionsWe report the ability of artificial intelligence to identify EoE using computer vision analysis of esophageal biopsy slides. Further, the DCNN features associated with EoE are based on not only local eosinophils but also global histologic changes. Our approach can be used for other conditions that rely on biopsy-based histologic diagnostics.Impact StatementDeep convolutional neural network (DCNN), together with a systematic downscaling approach, can classify esophageal biopsies with high accuracy and reveals a global nature of the histologic features of eosinophilic esophagitis. Our approach of systematic analysis of the image size versus downscaling tradeoff can be used to improve disease classification performance and insight gathering in digital pathology.
Rapid screening of pest resistance genes in maize using a sugarcane mosaic virus vector
Authors: Chung Seung Ho , Bigham Mahdiyeh , Lappe Ryan R. , Chan Barry , Nagalakshmi Ugrappa , Whitham Steven A. , Dinesh-Kumar Savithramma P. , Jander Georg 
Published: January 2021

AbstractSpodoptera frugiperda(fall armyworm) is a notorious pest that threatens maize production world-wide. Current control measures involve the use of chemical insecticides and transgenic maize expressingBacillus thuringiensis(Bt) toxins. Although several additional transgenes have confirmed insecticidal activity in other plants, limited research has been conducted in maize, at least partially due to the technical difficulty of maize transformation. Here, we describe implementation of a sugarcane mosaic virus (SCMV) vector for rapidly testing the efficacy of transgenes for the control ofS. frugiperdain maize. Four categories of proteins were tested using the SCMV vector: (i) maize defense signaling proteins: peptide elicitors (Pep1 and Pep3) and jasmonate acid conjugating enzymes (JAR1a and JAR1b); (ii) maize defensive proteins: the previously identified ribosome-inactivating protein (RIP2) and maize proteinase inhibitor (MPI), and two proteins with predicted but unconfirmed anti-insect activities, an antimicrobial peptide (AMP) and a lectin (JAC1); (iii) lectins from other plant species:Allium cepaagglutinin (ACA) andGalanthus nivalisagglutinin (GNA); and (iv) spider and scorpion toxins: peptides fromUrodacus yaschenkoi(UyCT3 and UyCT5) andHadronyche versuta(Hvt). In most cases,S. frugiperdalarval growth on maize was reduced by transient SCMV-mediated overexpression of genes encoding these proteins. Additionally, experiments with some of the SCMV-expressed genes showed effectiveness against two aphid species,Rhopalosiphum maidis(corn leaf aphid) andMyzus persicae(green peach aphid). Together, these results demonstrate that SCMV vectors can be exploited as a rapid screening method for testing the efficacy and insecticidal activity of candidate genes in maize.
A role for SHARPIN in platelet linear protein ubiquitination and function
Authors: Moore S. F. , Zhao X. , Mallah S. , Poole A.W. , Mundell S. J. , Hutchinson J. L. , Hers I. 
Published: January 2021

AbstractSHARPIN (Src homology 3 and multiple ankyrin repeat domains protein (SHANK)- associated RH domain-interacting protein) as part of the linear ubiquitin chain assembly complex (LUBAC) catalyses the addition of linear (Met1-linked) ubiquitin chains to substrates. As part of this complex SHARPIN acts as a multi-functional modulator of immune/inflammatory responses through regulation of NfkB activation. In addition, SHARPIN can act as a negative regulator of integrin function. Despite platelets being anucleate cells several studies have determined potential roles for both ubiquitination and NfkB in regulating platelet function. However, little is known about either linear ubiquitination and/or SHARPIN in mouse platelets. In this study, we evaluated platelet function in mice with impaired SHARPIN expression. We confirmed that SHARPIN was expressed in platelets from wild-type mice but not in mice homozygous for SHARPINcpdmallele (cpdm/cpdm) and that this correlated with a reduction in linear ubiquitination. Platelet function in response to thrombin was unaffected. In contrast, CRP-XL-and U46619-mediated platelet responses and thrombus formation under flow on a collagen-coated surface were significantly reduced in the cpdm/cpdm mice. This was associated with impaired U46619-mediated intracellular signalling as well as a reduction in CRP-mediated ERK phosphorylation. Despite the reported role for NfκB in regulating platelet function, inhibiting IκBα phosphorylation did not recapitulate the cpdm/cpdm phenotype. Together, these data indicate that the lack of SHARPIN and linear ubiquitination results in impaired thrombosis and platelet functional responses to CRP and U46619. This phenotype is independent of NfκB pathway inhibition but may involve alternative signalling pathways regulated by linear ubiquitination.Key PointsSHARPIN plays an essential role in platelet linear protein ubiquitination and CRP and U46619-mediated platelet functionIn vitro thrombosis is significantly impaired in SHARPIN deficient mice
Optimisation and validation of a sensitive bioanalytical method for niclosamide
Authors: Arshad Usman , Pertinez Henry , Box Helen , Tatham Lee , Rajoli Rajith KR , Neary Megan , Sharp Joanne , Valentijn Anthony , Hobson James , Unsworth Catherine , Dwyer Andrew , Savage Alison , Mcdonald Tom O , Rannard Steve P , Curley Paul , Owen Andrew 
Published: January 2021

AbstractThe SARS-CoV-2 pandemic has spread at an unprecedented rate, and repurposing opportunities have been intensively studied with only limited success to date. If successful, repurposing will allow interventions to become more rapidly available than development of new chemical entities. Niclosamide has been proposed as a candidate for repurposing for SARS-CoV-2 based upon the observation that it is amongst the most potent antiviral molecules evaluatedin vitro. To investigate the pharmacokinetics of niclosamide, reliable, reproducible and sensitive bioanalytical assays are required. Here, a liquid chromatography tandem mass spectrometry assay is presented which was linear from 31.25-2000 ng/mL (high dynamic range) and 0.78-100 ng/mL (low dynamic range). Accuracy and precision ranged between 97.2% and 112.5%, 100.4% and 110.0%, respectively. The presented assay should have utility in preclinical evaluation of the exposure-response relationship and may be adapted for later evaluation of niclosamide in clinical trials.
Yolk platelets impede nuclear expansion inXenopusembryos
Authors: Shimogama Sora , Iwao Yasuhiro , Hara Yuki 
Published: January 2021

ABSTRACTDuring metazoan early embryogenesis, the intracellular properties of proteins and organelles change dynamically through rapid cleavage. In particular, a change in the nucleus size is known to contribute to embryonic development-dependent cell cycle and gene expression regulation. Here, we compared the nuclear sizes of various blastomeres from developingXenopusembryos and analyzed the mechanisms that control the nuclear expansion dynamics by manipulating the amount of intracellular components in a cell-free system. There was slower nuclear expansion during longer interphase durations in blastomeres from vegetal hemispheres than those from animal hemispheres. Furthermore, upon recapitulating interphase events by manipulating the concentration of yolk platelets, which are originally rich in the vegetal blastomeres, in cell-free cytoplasmic extracts, there was slower nuclear expansion and DNA replication as compared to normal yolk-free conditions. Under these conditions, the supplemented yolk platelets accumulated around the nucleus in a microtubule-dependent manner and impeded organization of the endoplasmic reticulum network. Overall, we propose that yolk platelets around the nucleus reduce membrane supply from the endoplasmic reticulum to the nucleus, resulting in slower nuclear expansion in the yolk-rich vegetal blastomeres.
Reducing phenotypic instabilities of microbial population during continuous cultivation based on cell switching dynamics
Authors: Nguyen Thai Minh , Telek Samuel , Zicler Andrew , Martinez Juan Andres , Zacchetti Boris , Kopp Julian , Slouka Christoph , Herwig Christoph , Grünberger Alexander , Delvigne Frank 
Published: January 2021

AbstractPredicting the fate of a microbial population (i.e., growth, gene expression…) remains a challenge, especially when this population is exposed to very dynamic environmental conditions, such as those encountered during continuous cultivation. Indeed, the dynamic nature of continuous cultivation process implies the potential deviation of the microbial population involving genotypic and phenotypic diversification. This work has been focused on the induction of the arabinose operon inEscherichia colias a model system. As a preliminary step, the GFP level triggered by an arabinose-inducible ParaBADpromoter has been tracked by flow cytometry in chemostat with glucose-arabinose co-feeding. For a large range of glucose-arabinose co-feeding, the simultaneous occurrence of GFP positive and negative subpopulation was observed. In a second set of experiments, continuous cultivation was performed by adding either glucose or arabinose, based on the ability of individual cells for switching from low GFP to high GFP states, according to a technology called segregostat. In segregostat mode of cultivation, on-line flow cytometry analysis was used for adjusting the arabinose/glucose transitions based on the phenotypic switching capabilities of the microbial population. This strategy allowed finding an appropriate arabinose pulsing frequency, leading to a prolonged maintenance of the induction level with limited impact on phenotypic diversity for more than 60 generations. This result suggests that constraining individual cells into a given phenotypic trajectory is maybe not the best strategy for directing cell population. Instead, allowing individual cells switching around a predefined threshold seems to be a robust strategy leading to oscillating, but predictable, cell population behavior.
A conserved uORF regulates APOBEC3G translation and is targeted by HIV-1 Vif protein to repress the antiviral factor
Authors: Libre Camille , Seissler Tanja , Guerrero Santiago , Batisse Julien , Verriez Cédric , Stupfler Benjamin , Gilmer Orian , Cabrera-Rodriguez Romina , Weber Melanie M. , Valenzuela-Fernandez Agustin , Cimarelli Andrea , Etienne Lucie , Marquet Roland , Paillart Jean-Christophe 
Published: January 2021

ABSTRACTThe HIV-1 Vif protein is essential for viral fitness and pathogenicity. Vif decreases expression of cellular restriction factors APOBEC3G (A3G), A3F, A3D and A3H, which inhibit HIV-1 replication by inducing hypermutation during reverse transcription. Vif counteracts A3G at several levels (transcription, translation and protein degradation) that together reduce the levels of A3G in cells and prevent its incorporation into viral particles. How Vif affects A3G translation remains unclear. Here, we uncovered the importance of a short conserved uORF (upstream ORF) located within two critical stem-loop structures of the 5’ untranslated region (5’UTR) of A3G mRNA for this process. A3G translation occurs through a combination of leaky-scanning and translation re-initiation and the presence of an intact uORF decreases the extent of global A3G translation under normal conditions. Interestingly, the uORF is also absolutely required for Vif-mediated translation inhibition and redirection of A3G mRNA into stress granules. Overall, we discovered that A3G translation is regulated by a small uORF conserved in the human population and that Vif uses this specific feature to repress its translation.