bluuebunny/crossref_metadata_2025 huggingface dataset:
Outpatient parenteral antimicrobial therapy for leishmaniasis: 13 years’ experience at a large UK infectious diseases centre
Authors: Parkash Vivak , Laundy Nicholas , Durojaiye Oyewole Christopher
Published: January 2023

Background

Leishmaniasis is a neglected tropical disease that is imported by travellers returning to the UK. Given the prolonged therapy required, outpatient treatment has been proven to be cost-effective and safe.

Methods

We describe cases of leishmaniasis treated through outpatient parenteral antimicrobial therapy (OPAT) over a 13-y period (March 2006–September 2018) at a large teaching hospital.

Results

A total of 26 episodes of leishmaniasis were treated successfully, with a mean saving of 14.2 bed-days/episode. Sodium stibogluconate was the most used antileishmanial (92%).

Conclusions

Treatment of chronic infections via OPAT is now commonplace and this approach may be considered for other imported infectious diseases.
Conflict resolution between EU law and bilateral investment treaties of the EU Member States in the aftermath of Achmea
Authors: Georgaki Konstantina
Published: January 2023

This article examines how conflicts between European Union (EU) law and Bilateral Investment Treaties (BITs) between EU Member States (intra-EU BITs) are to be tacked following the judgment of the Court of Justice of the EU (CJEU) in Achmea (C-284/16). Starting from an analysis of the CJEU’s ruling and its aftermath (Sections II and III respectively), the article argues that conflicts in the interrelation of EU law with inter se agreements, such as intra-EU BITs, are to be approached as normative conflicts between different sub-systems within the broader system of public international law and resolved in favour of EU law. This argument is based on a two-fold premise, analysed in Section IV: first, that EU law does not constitute a ‘new legal order’, outside of and cut off from international law, but rather a ‘self-contained regime’, operating ‘within’ the broader system of international law. Since EU law is treaty law, conflicts in its relationship with (other) inter se agreements are, therefore, to be addressed using the conflict rules of international law. Against this background, the second premise of the article is that the EU Member States have agreed on a special conflict rule to regulate conflicts between EU law and inter se agreements. That rule is the principle of primacy of EU law. Having established the applicable conflict rule, Section V expands on the consequences of its application to the conflict between EU law and investor-state arbitration clauses in intra-EU BITs affirmed by the CJEU in Achmea.
Phyllosphere Exudates Select for Distinct Microbiome Members in Sorghum Epicuticular Wax and Aerial Root Mucilage
Authors: Mechan-Llontop Marco E. , Mullet John , Shade Ashley
Published: January 2023

Phyllosphere exudates create specialized microhabitats that shape microbial community diversity. We explored the microbiome associated with two sorghum phyllosphere exudates, the epicuticular wax and aerial root mucilage. We assessed the microbiome associated with the wax from sorghum plants over two growth stages, and the root mucilage additionally from nitrogen-fertilized and nonfertilized plants. In parallel, we isolated and characterized hundreds of bacteria from wax and mucilage, and integrated data from cultivation-independent and cultivation-dependent approaches to gain insights into exudate diversity and bacterial phenotypes. We found that Sphingomonadaceae and Rhizobiaceae families were the major taxa in the wax regardless of water availability and plant developmental stage to plants. The cultivation-independent mucilage-associated bacterial microbiome contained the families Erwiniaceae, Flavobacteriaceae, Rhizobiaceae, Pseudomonadaceae, and Sphingomonadaceae, and its structure was strongly influenced by sorghum development but only modestly influenced by fertilization. In contrast, the fungal community structure of mucilage was strongly affected by the year of sampling but not by fertilization or plant developmental stage, suggesting a decoupling of fungal–bacterial dynamics in the mucilage. Our bacterial isolate collection from wax and mucilage had several isolates that matched 100% to detected amplicon sequence variants, and were enriched on media that selected for phenotypes that included phosphate solubilization, putative diazotrophy, resistance to desiccation, capability to grow on methanol as a carbon source, and ability to grow in the presence of linalool and β-caryophyllene (terpenes in sorghum wax). This work expands our understanding of the microbiome of phyllosphere exudates and supports our long-term goal to translate microbiome research to support sorghum cultivation.
Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa
Authors: Alvandi Hosna , Taghavi S. Mohsen , Khojasteh Moein , Rahimi Touraj , Dutrieux Cecile , Taghouti Geraldine , Jacques Marie-Agnes , Portier Perrine , Osdaghi Ebrahim
Published: January 2023

Bacterial leaf streak disease caused by Xanthomonas translucens pv. undulosa is an economically important disease threatening wheat and barley crops around the globe. Thus far, specific PCR-based detection and identification tests for X. translucens pathovars are not available. In this study, we used comparative genomics approach to design a pathovar-specific primer pair for detection of X. translucens pv. undulosa in naturally infected seeds and its differentiation from other pathovars of the species. For this aim, complete genome sequences of strains of different X. translucens pathovars were compared and the specific PCR primer pair XtuF/XtuR was designed. These primers were strictly specific to X. translucens pv. undulosa because the expected 229-bp DNA fragment was not amplified in the closely related pathovars or in other xanthomonads, wheat-pathogenic bacteria, and other plant-pathogenic bacteria. High sensitivity of the primer pair XtuF/XtuR allowed detection of pure DNA of the pathogen in a concentration as low as 4.5 pg/μl. The pathogen was also detected in water suspension at a concentration of 8.6 × 102 CFU/ml. The PCR test was capable of detecting the pathogen in extracts of naturally infected wheat seeds at a concentration of 3.5 × 104 CFU/g while a culture-plate method was able to detect the pathogen at a concentration of 50 × 105 CFU/g of the same seeds. The PCR test developed in this study is a step forward for precise detection and identification of X. translucens pv. undulosa to prevent outbreaks of the bacterial leaf streak disease.
A Multilocus Phylogeny Places Hymenula cerealis (syn. Cephalosporium gramineum) in the Helotiales, Leotiomycetes
Authors: Zhu Zhaoxiang , Dugan Frank , Murray Timothy D.
Published: January 2023

The soilborne fungus Hymenula cerealis causes Cephalosporium stripe, a vascular wilt disease of wheat and other grasses in the United States and other wheat-producing countries where winter wheat is subjected to snow cover and frozen soil. No sexual stage is known for H. cerealis, and consequently, its phylogenetic position relative to other fungi has been difficult to establish. The purpose of this study was to conduct a multilocus sequence analysis to determine the phylogenetic position of H. cerealis. Sequence data for five genes, the internal transcribed spacer (ITS), partial large subunit nrDNA (LSU), partial RNA polymerase II second largest subunit region (RPB2), β-tubulin gene, and translation elongation factor 1-α (TEF1-α), from a diverse set of C. gramineum isolates and other related fungi was obtained from GenBank or directly from isolates in the Murray lab and used to construct maximum-likelihood and Bayesian trees. Based on phylogenetic analysis of the single LSU and β-tubulin genes, Cephalosporium gramineum is closely related to the Drepanopezizaceae and Ploettnerulaceae of Helotiales. Based on analyses of the DNA sequence of the ITS, RPB2, and TEF1-α genes, as well as the combined five-gene data set, C. gramineum belongs to the family Drepanopezizaceae, which is a sister taxon to the Ploettnerulaceae, and formed a well-supported clade (MLBP/BIPP = 95%/100%). In conclusion, H. cerealis belongs to the Helotiales, Leotiomycetes.
The In Planta Gene Expression of Austropuccinia psidii in Resistant and Susceptible Eucalyptus grandis
Authors: Swanepoel Shae , Visser Erik A. , Shuey Louise S. , Naidoo Sanushka
Published: January 2023

Austropuccinia psidii, commonly known as myrtle rust, is an obligate, biotrophic rust pathogen that causes rust disease in a broad host range of Myrtaceae species. Eucalyptus grandis, a widely cultivated hardwood Myrtaceae species, is susceptible to A. psidii infection, with this pathogen threatening both their natural range and various forest plantations across the world. This study aimed to investigate the A. psidii transcriptomic responses in resistant and susceptible E. grandis at four time points. RNA-seq reads were mapped to the A. psidii reference genome to quantify expressed genes at 12 h postinoculation and 1, 2, and 5 days postinoculation (dpi). A total of eight hundred and ninety expressed genes were found, of which 43 were candidate effector protein genes. These included rust transferred protein 1 ( RTP1), expressed in susceptible hosts at 5 dpi, and a hydrolase protein gene expressed in both resistant and susceptible hosts over time. Functional categorization of expressed genes revealed processes enriched in susceptible hosts, including malate metabolic and malate dehydrogenase activity, implicating oxalic acid in disease susceptibility. These results highlight putative virulence or pathogenicity mechanisms employed by A. psidii to cause disease, and they provide the first insight into the molecular responses of A. psidii in E. grandis over time.
Complete Genome Sequencing of Three Clade-1 Xanthomonads Reveals Genetic Determinants for a Lateral Flagellin and the Biosynthesis of Coronatine-Like Molecules in Xanthomonas
Authors: Peduzzi Chloé , Sagia Angeliki , Burokienė Daiva , Nagy Ildikó Katalin , Fischer-Le Saux Marion , Portier Perrine , Dereeper Alexis , Cunnac Sébastien , Roman-Reyna Veronica , Jacobs Jonathan M. , Bragard Claude , Koebnik Ralf
Published: January 2023

Evolutionarily, early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, as well as Xanthomonas translucens, which infects small-grain cereals and diverse grasses but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches have indicated that this clade likely contains more, yet-undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas campestris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean, and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. Furthermore, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.
Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008-2018
Authors: Polotan Francisco Gerardo M. , Salazar Carl Raymund P. , Morito Hannah Leah E. , Abulencia Miguel Francisco B. , Pantoni Roslind Anne R. , Mercado Edelwisa S. , Hué Stéphane , Ditangco Rossana A.
Published: January 2023

The Philippines has had a rapidly growing HIV epidemic with a shift in the prevalent subtype from B to CRF01_AE. However, the phylodynamic history of CRF01_AE in the Philippines has yet to be reconstructed. We conducted a descriptive retrospective study reconstructing the history of HIV-1 CRF01_AE transmissions in the Philippines through molecular epidemiology. Partial polymerase sequences (n= 1429) collected between 2008 and 2018 from 13 Philippine regions were collated from the RITM drug resistance genotyping database. Subsampling was performed on these Philippine and Los Alamos National Laboratory HIV international sequences followed by estimation of the time to the most recent common ancestor (tMRCA), effective reproductive number (Re), effective viral population size (Ne), relative migration rates and geographic spread of CRF01_AE with BEAST.ReandNewere compared between CRF01_AE and B. Most CRF01_AE sequences formed a single clade with a tMRCA of 1999 [95% HPD: 1996, 2001]. Exponential growth ofNewas observed from 1999 to 2013. TheRereached peaks of 3.71 [95% HPD: 1.71, 6.14] in 2009 and 2.87 [95% HPD: 1.78, 4.22] between 2012 and 2015. A transient decrease to 0.398 [95% HPD: 0.0105, 2.28] occurred between 2010 and 2012. The epidemic most likely started in Luzon in the National Capital Region, which then spread diffusely to the rest of the country. Both CRF01_AE and subtype B exhibited similar but unsynchronized patterns ofReover time. These results characterize the subtype-specific phylodynamic history of the CRF01_AE epidemic in the Philippines, which contextualizes and may inform past, present, and future public health measures toward controlling the HIV epidemic in the Philippines.
A Fresh View at Sports PSM-Systems
Authors: Savostyanov Vladimir , Kobelev Alexander
Published: January 2023

Background/Objectives

The purpose of the proposed study is disclosure of correlations between the dynamics of the Breathe Rate (BR) and Heart Rate (HR) when performing the intermittent physical operation at maximum power on a cycle ergometer.

Methods

The stage on the study of the General functional athlete readiness (GFAR) performed using the sports standard “Red Engine” and the cycle ergometer in 16 volunteers (10 men, 6 women) whose average age was 21±1.17 years. To determine the sports potential of the volunteers in this study, we used own Coefficient of Anaerobic Capacity (CANAC Q, beats). Continuous recording of the heart rate and respiratory rate of volunteers in the maximum power sports test was carried out by the “RheoCardioMonitor” device with an athlete functional readiness module based on the method of Transthoracic electrical impedance rheography (TEIRG).

Results

The degree of correlation of functional indicators (M, HRM, GFAR) with CANAC Q for the group in full (n=80) occurred at a very high level, which confirmed the effectiveness of using the Coefficient of Anaerobic Capacity (CANAC Q) in assessing the general functional athlete readiness of the volunteers.

Conclusions

CANAC Q measured in “beats” of the heart and recorded very accurately using the method of transthoracic electrical impedance rheography (TEIRG). For this reason as promising sports PSM-system, CANAC Q can replace the methods for determining the functional athlete readiness by blood lactate concentration and maximum oxygen consumption.
Sex difference in the associations of socioeconomic status, cognitive function and brain volume with dementia in old adults: Findings from the OASIS study
Authors: Liu Sophia Z , Tahmasebi Ghazaal , Sheng Ying , Dinov Ivo D , Tsilimingras Dennis , Liu Xuefeng
Published: January 2023

Background

Sex differences in the association of cognitive function and imaging measures with dementia have not been fully investigated while sex-based investigation of dementia has been discussed. Understanding sex differences in the dementia-related socioeconomic, cognitive, and imaging measurements is important for uncovering sex-related pathways to dementia and facilitating early diagnosis, family planning, and cost control.

Methods

We selected data from the Open Access Series of Imaging Studies with longitudinal measurements of brain volumes on 150 individuals aged 60 to 96 years. Dementia status was determined using the Clinical Dementia Rating (CDR) scale, and Alzheimer’s disease was diagnosed as a CDR of ≥ 0.5. Generalized estimating equation models were used to estimate the associations of socioeconomic, cognitive and imaging factors with dementia in men and women.

Results

Lower education affected dementia more in women than in men. Age, education, Mini-Mental State Examination (MMSE), and normalized whole-brain volume (nWBV) were associated with dementia in women whereas only MMSE and nWBV were associated with dementia in men. Lower socioeconomic status was associated with a reduced estimated total intracranial volume in men, but not in women. Ageing and lower MMSE scores were associated with reduced nWBV in both men and women.

Conclusions

The association between education and prevalence of dementia differs in men and women. Women may have more risk factors for dementia than men.
The Use of Class Imbalanced Learning Methods on ULSAM Data to Predict the Case-Control Status in Genome-Wide Association Studies
Authors: Öztornaci R. Onur , Syed Hamzah , Morris Andrew P. , Taşdelen Bahar
Published: January 2023

Machine learning (ML) methods for uncovering single nucleotide polymorphisms (SNPs) in genome-wide association study (GWAS) data that can be used to predict disease outcomes are becoming increasingly used in genetic research. Two issues with the use of ML models are finding the correct method for dealing with imbalanced data and data training. This article compares three ML models to identify SNPs that predict type 2 diabetes (T2D) status using the Support vector machine SMOTE (SVM SMOTE), The Adaptive Synthetic Sampling Approach (ADASYN), Random under sampling (RUS) on GWAS data from elderly male participants (165 cases and 951 controls) from the Uppsala Longitudinal Study of Adult Men (ULSAM). It was also applied to SNPs selected by the SMOTE, SVM SMOTE, ADASYN, and RUS clumping method. The analysis was performed using three different ML models: (i) support vector machine (SVM), (ii) multilayer perceptron (MLP) and (iii) random forests (RF). The accuracy of the case-control classification was compared between these three methods. The best classification algorithm was a combination of MLP and SMOTE (97% accuracy). Both RF and SVM achieved good accuracy results of over 90%. Overall, methods used against unbalanced data, all three ML algorithms were found to improve prediction accuracy.
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Authors: Himmelstein Daniel S. , Zietz Michael , Rubinetti Vincent , Kloster Kyle , Heil Benjamin J. , Alquaddoomi Faisal , Hu Dongbo , Nicholson David N. , Hao Yun , Sullivan Blair D. , Nagle Michael W. , Greene Casey S.
Published: January 2023

Hetnets, short for “heterogeneous networks”, contain multiple node and relationship types and offer a way to encode biomedical knowledge. One such example, Hetionet connects 11 types of nodes — including genes, diseases, drugs, pathways, and anatomical structures — with over 2 million edges of 24 types. Previous work has demonstrated that supervised machine learning methods applied to such networks can identify drug repurposing opportunities. However, a training set of known relationships does not exist for many types of node pairs, even when it would be useful to examine how nodes of those types are meaningfully connected. For example, users may be curious not only how metformin is related to breast cancer, but also how theGJA1gene might be involved in insomnia. We developed a new procedure, termed hetnet connectivity search, that proposes important paths between any two nodes without requiring a supervised gold standard. The algorithm behind connectivity search identifies types of paths that occur more frequently than would be expected by chance (based on node degree alone). We find that predictions are broadly similar to those from previously described supervised approaches for certain node type pairs. Scoring of individual paths is based on the most specific paths of a given type. Several optimizations were required to precompute significant instances of node connectivity at the scale of large knowledge graphs. We implemented the method on Hetionet and provide an online interface athttps://het.io/search. We provide an open source implementation of these methods in our new Python package namedhetmatpy.
A self-inactivating invertebrate opsin with resistance to retinal depletion optically drives biased signaling toward Gβγ-dependent ion channel modulation
Authors: Tsukamoto Hisao , Kubo Yoshihiro
Published: January 2023

Animal opsins, light-sensitive G protein-coupled receptors (GPCRs), have been utilized for optogenetic tools to control G protein-dependent signaling pathways. Upon G protein activation, the Ga and Gβγ subunits drive different intracellular signaling pathways, leading to complex cellular responses. For some purposes, Ga-, Gβγ-dependent signaling needs to be separately modulated, but these responses are simultaneously evoked due to the 1:1 stoichiometry of Ga and Gβγ. Nevertheless, we show temporal activation of G protein using a self-inactivating invertebrate opsin,Platynereisc-opsin1, drives biased signaling for Gβγ-dependent GIRK channel activation in a light-dependent manner by utilizing the kinetic difference between Gβγ-dependent and Ga-dependent responses. The opsin-induced transient Gi/o activation preferably causes activation of the kinetically-fast Gβγ-dependent GIRK channels rather than slower Gi/oα-dependent adenylyl cyclase inhibition. Although similar Gβγ-biased signaling properties were observed in a selfinactivating vertebrate visual pigment,Platynereisc-opsin1 needs fewer retinal molecules to evoke cellular responses. Furthermore, the Gβγ-biased signaling properties ofPlatynereisc-opsinl are enhanced by genetically fused with RGS8 protein which accelerates G protein inactivation. The self-inactivating invertebrate opsin and its RGS8-fusion protein can function as optical control tools biased for Gβγ-dependent ion channel modulation.
Therapeutic effects of human amnion-derived mesenchymal stem cells on hypercoagulability in a uremic calciphylaxis patient
Authors: Bian Anning , Ye Xiaoxue , Wang Jing , Zeng Ming , Liu Jiayin , Liu Kang , Ning Song , Cui Yugui , Tang Shaowen , Xu Xueqiang , Yuan Yanggang , Su Zhonglan , Lu Yan , Zhou Jing , Ma Xiang , Yang Guang , Huang Yaoyu , Lv Xiaolin , Wang Ling , Zhao Jing , Wang Xiuqin , Liang Ningxia , Xing Changying , Qin Lianju , Wang Ningning
Published: January 2023

Calciphylaxis is a rare cutaneous vascular disease with clinical manifestations of intolerable pains, non-healing skin wounds, histologically characterized by calcification, fibrointimal hyperplasia, and thrombosis in microvessels. Currently, there are no approved guidelines for this disease. High prevalence of thrombophilias and hypercoagulable conditions in calciphylaxis patients have been recognized in recent years. Here, we report a case of uremic calciphylaxis patient whom was refractory to conventional treatments and then received a salvage strategyviahuman amnion-derived mesenchymal stem cell (hAMSC) intravenous combined with local application. In order to investigate the therapeutic mechanism of hMASCs from the novel perspective of hypercoagulability, coagulation-related indicators, wound status and quality of life were followed up. Improvement of hypercoagulable condition involving correction of platelet, D-dimer and plasminogen levels, skin regeneration and pain alleviation were revealed after hAMSC administration for one year. We propose that hypercoagulability is the therapeutic target of calciphylaxis patients which can be improved by hAMSC treatment.
The incidence of COVID-19-related hospitalisation in migrants in the UK: Findings from the Virus Watch prospective community cohort study
Authors: Fong Wing Lam Erica , Nguyen Vincent G , Burns Rachel , Boukari Yamina , Beale Sarah , Braithwaite Isobel , Byrne Thomas E , Geismar Cyril , Fragaszy Ellen , Hoskins Susan , Kovar Jana , Navaratnam Annalan MD , Oskrochi Youssof , Patel Parth , Tweed Sam , Yavlinsky Alexei , Hayward Andrew C , Aldridge Robert W
Published: January 2023

Background

Migrants in the UK may be at higher risk of SARS-CoV-2 exposure; however, little is known about their risk of COVID-19-related hospitalisation during waves 1-3 of the pandemic.

Methods

We analysed secondary care data linked to Virus Watch study data for adults and estimated COVID-19-related hospitalisation incidence rates by migration status. To estimate the total effect of migration status on COVID-19 hospitalisation rates, we ran fixed-effect Poisson regression for wave 1 (01/03/2020-31/08/2020; wildtype), and fixed-effect negative binomial regressions for waves 2 (01/09/2020-31/05/2021; Alpha) and 3 (01/06/2020-31/11/2021; Delta). Results of all models were then meta-analysed.

Results

Of 30,276 adults in the analyses, 26,492 (87.5%) were UK-born and 3,784 (12.5%) were migrants. COVID-19-related hospitalisation incidence rates for UK-born and migrant individuals across waves 1-3 were 2.7 [95% CI 2.2-3.2], and 4.6 [3.1-6.7] per 1,000 person-years, respectively. Pooled incidence rate ratios across waves suggested increased rate of COVID-19-related hospitalisation in migrants compared to UK-born individuals in unadjusted 1.68 [1.08-2.60] and adjusted analyses 1.35 [0.71-2.60].

Conclusion

Our findings suggest migration populations in the UK have excess risk of COVID-19-related hospitalisations and underscore the need for more equitable interventions particularly aimed at COVID-19 vaccination uptake among migrants.
Who Gets Long COVID and Suffers its Mental Health and Socioeconomic Consequences in the United States? Preliminary Findings from a Large Nationwide Study
Authors: Kim Daniel
Published: January 2023

As the number of confirmed COVID-19 cases now exceeds 100 million cases in the United States and continues to climb, concerns have been increasingly raised over the future public health and economic burden of long COVID including disability and concomitant declines in labor force participation. Only a handful of US population-based studies have explored sociodemographic and socioeconomic characteristics that put people at risk of long COVID or have investigated its mental health and socioeconomic sequelae. Herein, I report findings from the largest multivariable analysis to date using US nationally-representative data on 153,543 adults including 19,985 adults with long COVID to explore key predictors and sequelae of long COVID. An estimated 14.0% of adults aged 18-84 y (35.11 million adults) and 15.5% of working-aged adults aged 18-64 y (30.65 million adults) had developed long COVID by November 2022. Several sociodemographic and socioeconomic factors predicted long COVID including lower household income, being aged 30-49 y, Hispanic, female, gay/lesbian or bisexual, and divorced/separated. Even after accounting for such factors, having long COVID was linked to higher risks of recent unemployment, financial hardship, and anxiety and depressive symptomatology, with evidence of dose-response relationships. Overall, an estimated 27.7 million US adults aged 18-84 y and 24.2 million working-aged adults with long COVID who had been or may still be at risk of adverse socioeconomic and mental health outcomes. Lost work was further calculated to be the equivalent of 3 million workers annually, and the estimated annual lost earnings due to long COVID among working-aged adults totaled $175 billion. These preliminary findings highlight the substantial public health and economic implications of long COVID among Americans and should prompt further inquiry and intervention.
Down-regulation ofMALAT1is a hallmark of tissue and peripheral proliferative T cells in COVID-19
Authors: Dey Shoumit , Ashwin Helen , Milross Luke , Hunter Bethany , Majo Joaquim , Filby Andrew J , Fisher Andrew J , Kaye Paul M. , Lagos Dimitris
Published: January 2023

T cells play key protective but also pathogenic roles in COVID-19. We studied expression of long non-coding RNAs (lncRNAs) in COVID-19 T cell transcriptomes by integrating previously published single-cell RNA sequencing datasets. The long intergenic non-coding RNAMALAT1was the most highly transcribed lncRNA in T cells, with Th1 cells demonstrating the lowest and CD8+ resident memory cells the highestMALAT1expression, amongst CD4+ and CD8+ T cells populations, respectively. We then identified gene signatures that covaried withMALAT1in single T cells. A significantly higher number of transcripts correlated negatively withMALAT1than those that correlated. Enriched functional annotations of theMALAT1-anti-correlating gene signature included processes associated with T cell activation such as cell division, oxidative phosphorylation and response to cytokine. TheMALAT1anti-correlating gene signature shared by both CD4+ and CD8+ T cells marked dividing T cells in both lung and blood of COVID-19 patients. Focussing on the tissue, we used an independent patient cohort of post-mortem COVID-19 lung samples and demonstrated thatMALAT1suppression was indeed a marker of MKI67+ proliferating CD8+ T cells. Our results revealMALAT1suppression and its associated gene signature are a hallmark of human proliferating T cells.
Wastewater and seroprevalence for pandemic preparedness: variant analysis, vaccination effect, and hospitalization forecasting for SARS-CoV-2, in Jefferson County, Kentucky
Authors: Holm Rochelle H. , Rempala Grzegorz A. , Choi Boseung , Brick J. Michael , Amraotkar Alok R. , Keith Rachel J. , Rouchka Eric C. , Chariker Julia H. , Palmer Kenneth E. , Smith Ted , Bhatnagar Aruni
Published: January 2023

Despite wide scale assessments, it remains unclear how large-scale SARS-CoV-2 vaccination affected the wastewater concentration of the virus or the overall disease burden as measured by hospitalization rates. We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and linked vaccination and hospitalization data, from April 2021–August 2021 in Jefferson County, Kentucky (USA). Our susceptible (S), vaccinated (V), variant-specific infected (I1andI2), recovered (R), and seropositive (T) model (SVI2RT) tracked prevalence longitudinally. This was related to wastewater concentration. The 64% county vaccination rate translated into about 61% decrease in SARS-CoV-2 incidence. The estimated effect of SARS-CoV-2 Delta variant emergence was a 24-fold increase of infection counts, which corresponded to an over 9-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration had the strongest correlation (r = 0.95) at 1 week lag. Our study underscores the importance of continued environmental surveillance post-vaccine and provides a proof-of-concept for environmental epidemiology monitoring of infectious disease for future pandemic preparedness.
OmiCrisp: A CRISPR SARS-CoV-2 test with Omicron detection
Authors: Sharma Suruchi , Prakash Manasa Bagur , Gupta Nimisha , Gupta Vaijayanti , Chandru Vijay
Published: January 2023

We have developed a CRISPR based assay that can detect the presence of SARS-CoV-2 in RNA extracted from human samples and also predict if it is an Omicron or non-Omicron variant of the virus. This is a nucleic acid amplification-based test (NAAT). The amplification and detection are carried out in two independent steps in this assay. Amplification is done using a standard one-step RT-PCR method. The detection is done using a method that utilizes the trans-cleavage activity of the Cas12a enzyme. We have evaluated the performance of OmiCrisp in more than 80 clinical samples and observed an agreement of 100% with the sequencing results, in labeling SARS-CoV-2 positive samples as Omicron or non-Omicron. OmiCrisp -like platform can be developed quickly and can potentially complement sequencing for quick and rapid tracking of the transmission of new pathogen variants.
Impact of the COVID-19 pandemic on food safety inspection outcomes in Toronto, Canada: a Bayesian interrupted time series analysis
Authors: Young Ian , Desta Binyam Negussie , Sekercioglu Fatih
Published: January 2023

The coronavirus disease (COVID-19) pandemic resulted in major disruptions to the food service industry and regulatory food inspections. The objective of this study was to conduct an interrupted time series analysis to investigate the impact of the COVID-19 pandemic on food safety inspection trends in Toronto, Canada. Inspection data for restaurants and take-out establishments were obtained from 2017 to 2022 and ordered as a weekly time series. Bayesian segmented regression was conducted to evaluate the impact of the pandemic on weekly infraction and inspection pass rates. On average, a 0.31-point lower weekly infraction rate (95% credible interval [CI]: 0.23, 0.40) and a 2.0% higher probability of passing inspections (95% CI: 1.1%, 3.0%) were predicted in the pandemic period compared to pre-pandemic. Models predicted lower infraction rates and higher pass rates immediately following the pandemic that were regressing back toward pre-pandemic levels in 2022. Seasonal effects were also identified, with infraction rates highest in April and pass rates lowest in August. The COVID-19 pandemic resulted in an initial positive effect on food safety outcomes in restaurants and take-out food establishments in Toronto, but this effect appears to be temporary. Additional research is needed on seasonal and long-term inspection trends post-pandemic.
Development ofEncarsia tabacivora(Viggiani) (Hymenoptera: Aphelinidae) in nymphs ofBemisia tabaci(Gennadius) MEAN 1 (Hemiptera: Aleyrodidae)
Authors: Gamarra Heidy , Sporleder Marc , Supanta Luz , Rodríguez Alexander , Kroschel Jürgen , Kreuze Jan
Published: January 2023

Encarsia tabacivoraViggiani 1985 (Hymenoptera: Aphelinidae), is an endoparasitoid of whiteflies, includingBemisia tabaci(Gennadius) MEAN 1 (Hemiptera: Aleyrodidae), reported from southern USA, Caribbean, and Brazil. In field surveys, the natural occurrence ofE. tabacivorawas confirmed in the Cañete valley of Peru. Its biology and development was studied under laboratory conditions at 20°C and 70-75% RH. The results showed that fertilized females lay their eggs inside nymphs of the 3rdand early 4thinstar ofB. tabaciMEAN 1. The stages of development are egg, three larval instars, prepupa and pupa. Development from egg to adult lasted 19.3 (SE±0.17) days for females. No males were produced, which indicates thatE. tabacivoraexhibits thelytokous parthenogenesis. Parasitized host nymphs exhibited multiple oviposition punctures and several L1-instar wasps were observed in individual host nymphs, indicating superparasitism. However, from the L2-instar onwards only one individual developed to adult stage.E. tabacivoramight be a prospective biological control agent forB. tabaciin sweet potato also for minimizing the spread of whitefly-induced plant viruses in Peru and other regions of the world. The knowledge gained might be helpful in establishing mass rearing protocols ofE. tabacivorafor inoculative releases.
Diverging Parkinson’s Disease Pathology between patient-derivedGBAN370S, LRRK2G2019Sand engineeredSNCAA53TiPSC-derived Dopaminergic Neurons
Authors: Fathi Ali , Bakshy Kiranmayee , Zieghami Lida , Fiene Rebecca , Bradley Robert , Dickerson Sarah , Carlson Coby , Schachtele Scott , Liu Jing
Published: January 2023

Multiple neurodegenerative disorders, including Parkinson’s disease (PD) and Alzheimer’s disease-associated dementia (ADAD), are linked with dopaminergic (DA) neuron death and a resulting reduction in dopamine levels in the brain. DA neuron degeneration and the risk of developing PD is connected to genetic mutations affiliated with lysosomal function and protein degradation. Accessible human cellular models for PD-relevant genetic mutations are needed to investigate mechanisms of DA cell death and define points of therapeutic intervention. Human induced pluripotent stem cell (iPSC)-derived midbrain DA neurons offer a developmentally and physiologically relevantin vitromodel for investigating PD pathogenic mechanisms across genetic backgrounds. In this study, we generated DA neurons using iPSCs from two clinically diagnosed PD patients, one harboring an inheritedGBAN370Smutation and the other a mutation inLRRK2G2019Sand compared pathophysiology against DA neurons from genetically engineeredSNCAA53TiPSCs and its isogenic apparently healthy normal (AHN) iPSCs. Our results present a novel phenotype forGBAN370SandLRRK2G2019Sderived DA neurons, showing that they produced and released significantly more dopamine compared to the AHN andSNCAA53Tmutant DA neurons. All mutant DA neurons developed deficient glucocerebrosidase (GCase) activity, increased mitochondrial stress, aberrant neuronal activity patterns, and increased α-synuclein accumulation. Together these data suggest potentially divergent origins of PD pathogenesis inGBAN370SandLRRK2G2019SDA neurons. In addition, compound screening confirmed that GCase modulators can rescue enzyme activity and impact neural activity across all DA mutant neurons, to varying degrees. These data demonstrate uniquein vitrophenotypes associated with PD and suggest a diversity of underlying mechanisms across different genetic backgrounds. Together, the cell lines used in this study present a valuable tool for new therapeutic discovery.
A multicolor suite for deciphering population coding in calcium and cAMPin vivo
Authors: Yokoyama Tatsushi , Manita Satoshi , Uwamori Hiroyuki , Tajiri Mio , Imayoshi Itaru , Yagishita Sho , Murayama Masanori , Kitamura Kazuo , Sakamoto Masayuki
Published: January 2023

cAMP is a pivotal second messenger regulated by various upstream pathways including Ca2+and G protein-coupled receptors (GPCRs). To decipherin vivocAMP dynamics, we rationally designed cAMPinG1, an ultrasensitive genetically encoded green cAMP indicator that outperformed its predecessors in both dynamic range and cAMP affinity. Two-photon cAMPinG1 imaging detected cAMP transients in the somata and dendritic spines of neurons in the mouse visual cortex on the order of tens of seconds. In addition, multicolor imaging with a highly sensitive new red Ca2+indicator RCaMP3 allowed simultaneous measurement of population patterns in Ca2+and cAMP in hundreds of neurons. We identified Ca2+-induced cAMP responses that represented specific information, such as direction selectivity in vision and locomotion, as well as GPCR-induced cAMP responses. Overall, our multicolor suite revealed that information encoded in Ca2+and GPCRs signaling is integrated and stored as cAMP transients for longer periodsin vivo.

Highlights

Developing an ultrasensitive cAMP indicator, cAMPinG1, for visualizing cAMP transients in somata and dendritic spinesin vivo.

Developing a highly sensitive red Ca2+indicator, RCaMP3, for visualizing Ca2+transients in large neuronal population.

Dual-color Ca2+and cAMP imaging for dissecting Ca2+-induced and GPCR-induced cAMP responses.

Single-cell, single-timepoint cAMP imaging for GRCR biology and drug screening.
Antigen-dependent IL-12 signaling in CAR T cells promotes regional to systemic disease targeting
Authors: Jun Lee Eric Hee , Cullen Cody , Murad John P. , Gumber Diana , Park Anthony K. , Yang Jason , Stern Lawrence A. , Adkins Lauren N. , Dhapola Gaurav , Gittins Brenna , Chung-Chang Wen , Martinez Catalina , Woo Yanghee , Cristea Mihaela , Rodriguez-Rodriguez Lorna , Ishihara Jun , Lee John K. , Forman Stephen J. , Wang Leo D. , Priceman Saul J.
Published: January 2023

Chimeric antigen receptor (CAR) T cell therapeutic responses are hampered by limited T cell trafficking, persistence, and durable anti-tumor activity in solid tumor microenvironments. However, these challenges can be largely overcome by relatively unconstrained synthetic engineering strategies, which are being harnessed to improve solid tumor CAR T cell therapies. Here, we describe fully optimized CAR T cells targeting tumor-associated glycoprotein-72 (TAG72) for the treatment of solid tumors, identifying the CD28 transmembrane domain upstream of the 4-1BB co-stimulatory domain as a driver of potent anti-tumor activity and IFNγ secretion. These findings have culminated into a phase 1 trial evaluating safety, feasibility, and bioactivity of TAG72-CAR T cells for the treatment of patients with advanced ovarian cancer (NCT05225363). Preclinically, we found that CAR T cell-mediated IFNγ production facilitated by IL-12 signaling was required for tumor cell killing, which was recapitulated by expressing an optimized membrane-bound IL-12 (mbIL12) molecule on CAR T cells. Critically, mbIL12 cell surface expression and downstream signaling was induced and sustained only following CAR T cell activation. CAR T cells with mbIL12 demonstrated improved antigen-dependent T cell proliferation and potent cytotoxicity in recursive tumor cell killing assaysin vitroand showed robustin vivoanti-tumor efficacy in human xenograft models of ovarian cancer peritoneal metastasis. Further, locoregional administration of TAG72-CAR T cells with antigen-dependent IL-12 signaling promoted durable anti-tumor responses against both regional and systemic disease in mice and was associated with improved systemic T cell persistence. Our study features a clinically-applicable strategy to improve the overall efficacy of locoregionally-delivered CAR T cells engineered with antigen-dependent immune-modulating cytokines in targeting both regional and systemic disease.
Gene Expression Changes in Cultured Reactive Rat Astrocyte Models and Comparison to Device-Associated Effects in the Brain
Authors: Riggins Ti’Air E. , Whitsitt Quentin A. , Saxena Akash , Hunter Emani , Hunt Bradley , Thompson Cort H. , Moore Michael G. , Purcell Erin K.
Published: January 2023

Implanted microelectrode arrays hold immense therapeutic potential for many neurodegenerative diseases. However, a foreign body response limits long-term device performance. Recent literature supports the role of astrocytes in the response to damage to the central nervous system (CNS) and suggests that reactive astrocytes exist on a spectrum of phenotypes, from beneficial to neurotoxic. The goal of our study was to gain insight into the subtypes of reactive astrocytes responding to electrodes implanted in the brain. In this study, we tested the transcriptomic profile of two reactive astrocyte culture models (cytokine cocktail or lipopolysaccharide, LPS) utilizing RNA sequencing, which we then compared to differential gene expression surrounding devices inserted into rat motor cortex via spatial transcriptomics. We interpreted changes in the genetic expression of the culture models to that of 24 hour, 1 week and 6 week rat tissue samples at multiple distances radiating from the injury site. We found overlapping expression of up to ∼250 genes betweenin vitromodels andin vivoeffects, depending on duration of implantation. Cytokine-induced cells shared more genes in common with chronically implanted tissue (≥1 week) in comparison to LPS-exposed cells. We revealed localized expression of a subset of these intersecting genes (e.g.,Serping1, Chi3l1, and Cyp7b1)in regions of device-encapsulating, glial fibrillary acidic protein (GFAP)-expressing astrocytes identified with immunohistochemistry. We applied a factorization approach to assess the strength of the relationship between reactivity markers and the spatial distribution of GFAP-expressing astrocytesin vivo. We also provide lists of hundreds of differentially expressed genes between reactive culture models and untreated controls, and we observed 311 shared genes between the cytokine induced model and the LPS-reaction induced control model. Our results show that comparisons of reactive astrocyte culture models with spatial transcriptomics data can reveal new biomarkers of the foreign body response to implantable neurotechnology. These comparisons also provide a strategy to assess the development ofin vitromodels of the tissue response to implanted electrodes.
Identification of common sequence motifs shared exclusively among selectively packed exosomal pathogenic microRNAs during rickettsial infections
Authors: Bei Jiani , Qiu Yuan , Cockrell Diane , Chang Qing , Husseinzadeh Sorosh , Zhou Changcheng , Gaitas Angelo , Fang Xiang , Jin Yang , Khanipov Kamil , Saito Tais B. , Gong Bin
Published: January 2023

We previously reported that microRNA (miR)23a and miR30b are selectively sorted into rickettsia-infected, endothelial cell-derived exosomes (R-ECExos). Yet, the mechanism remains unknown. The number of cases of spotted fever rickettsioses has been increasing in recent years, and infections with these bacteria cause life-threatening diseases by targeting brain and lung tissues. Therefore, the aim of the present study is to continue to dissect the molecular mechanism underlyingR-ECExos-induced barrier dysfunction of normal recipient microvascular endothelial cells (MECs), depending on their exosomal RNA cargos. Rickettsiae are transmitted to human hosts by the bite of an infected tick into the skin. In the present study we demonstrate that treatment withR-ECExos, which were derived from spotted fever groupR parkeriinfected human dermal MECs, induced disruptions of the paracellular adherens junctional protein VE-cadherin and breached the paracellular barrier function in recipient pulmonary MECs (PMECs) in an exosomal RNA-dependent manner. Similarly, we did not detect different levels of miRs in parent dermal MECs following rickettsial infections. However, we demonstrated that the microvasculopathy-relevant miR23a-27a-24 cluster and miR30b are selectively enriched inR-ECExos. Bioinformatic analysis revealed that common sequence motifs are shared exclusively among the exosomal, selectively-enriched miR23a cluster and miR30b at different levels. Taken together, these data warrant further functional identification and characterization of a single, bipartition, or tripartition among ACA, UCA, and CAG motifs that guide recognition of microvasculopathy-relevant miR23a-27a-24 and miR30b, and subsequently results in their selective enrichments inR-ECExos.
Integrated analysis of canine soft tissue sarcomas identifies recurrent mutations inTP53, KMTgenes andPDGFBfusions
Authors: Das Sunetra , Idate Rupa , Lana Susan E. , Regan Daniel P. , Duval Dawn L.
Published: January 2023

Canine soft tissue sarcomas (STS) are a heterogenous group of malignant tumors arising from mesenchymal cells of soft tissues. This simplified collective of tumors most commonly arise from subcutaneous tissues, are treated similar clinically, and conventionally exclude other sarcomas with more definitive anatomical, histological, or biological features. Histologically, canine STS sub-types are difficult to discern at the light microscopic level due to their overlapping features. Thus, genomic, and transcriptomic profiling of canine STS may prove valuable in differentiating the diverse sub-types of mesenchymal neoplasms within this group. To this purpose we sought to characterize the transcript expression and genomic mutation profiles of canine STS. To delineate transcriptomic sub-types, hierarchical clustering was used to identify 4 groups with district expression profiles. Using the RNAseq data, we identified three samples carrying driver fusions of platelet derived growth factor B (PDGFB) and collagen genes. Sensitivity to imatinib was evaluated in a canine STS cell line also bearing aPDGFBfusion. Using whole exome sequencing, recurrent driver variants were identified in the cancer genesKMT2D(21% of the samples) andTP53(21%) along with copy number losses of RB1 and CDKN2A. Gene amplifications and resulting transcript increases were identified in genes on chromosomes 13, 14, and 36. A subset of STS was identified with high T-cell infiltration. This multi-omics approach has defined canine STS sub-types at a molecular level for comparison to their human counterparts, to improve diagnosis, and may provide additional targets for therapy.