bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vascular inflammation exposes perivascular cells to SARS-CoV-2 infection
Authors: Franca Cristiane Miranda , Mansoorifar Amin , Athirasala Avathamsa , Subbiah Ramesh , Tahayeri Anthony , Bertassoni Luiz 
Published: April 2022

AbstractPericytes stabilize blood vessels and promote vascular barrier function. However, vessels subjected to pro-inflammatory conditions have impaired barrier function, which has been suggested to potentially expose perivascular cells to SARS-CoV-2. To test this hypothesis, we engineered pericyte-supported vascular capillaries on-a-chip, and determined that the extravasation and binding of spike protein (S1) on perivascular cells of inflamed vessels to be significantly higher that in healthy controls, indicating a potential target to understand COVID-19 vascular complications.
KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin
Authors: Campbell Mel , Chantarasrivong Chanikarn , Yanagihashi Yuichi , Inagaki Tomoki , Davis Ryan R. , Nakano Kazushi , Kumar Ashish , Tepper Clifford G. , Izumiya Yoshihiro 
Published: April 2022

AbstractEukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 base pair resolution and constructed a 3D KSHV genomic structural model with 2kb binning. The latent KSHV genome formed very similar genomic architectures in three different naturally infected PEL cell lines and in an experimentally infected epithelial cell line. The majority of the TAD boundaries were occupied by CTCF and SMC1, and the KSHV transactivator was recruited to these sites during reactivation. Triggering KSHV gene expression decreased pre-wired genomic loops within the regulatory unit, while contacts extending outside of regulatory borders increased, leading to formation of a larger regulatory unit with a shift from repressive to active compartments (B to A). The 3D genomic structural model proposes that the immediate-early promoter region is localized on the periphery of the 3D viral genome during latency, while highly inducible non-coding RNA regions moved toward the inner space of the structure, resembling the configuration of a “bird cage” during reactivation. The compartment-like properties of viral episomal chromatin structure and its reorganization during the transition from latency may help coordinate viral gene transcription.ImportanceThe 3D architecture of chromatin allows for efficient arrangement, expression, and replication of genetic material. The genomes of all organisms studied to date have been found to be organized through some form of tiered domain structures. However, the architectural framework of the genomes of large double-stranded DNA viruses such as the herpesvirus family has not been reported. Prior studies with Kaposi’s sarcoma-associated herpesvirus (KSHV) have indicated that the viral chromatin shares many biological properties exhibited by the host cell genome, essentially behaving as a mini human chromosome. Thus, we hypothesized that the KSHV genome may be organized in a similar manner. In this report, we describe the domain structure of the latent and lytic KSHV genome at 500 base pair resolution and present a 3D genomic structural model for KSHV under each condition. These results add new insights into the complex regulation of the viral lifecycle.
Longitudinal lung function assessment of patients hospitalised with COVID-19 using1H and129Xe lung MRI
Authors: Saunders Laura C , Collier Guilhem J , Chan Ho-Fung , Hughes Paul J C , Smith Laurie J , Watson James , Meiring James , Gabriel Zoë , Newman Thomas , Plowright Megan , Wade Phillip , Eaden James A , Bray Jody , Marshall Helen , Capener David J , Armstrong Leanne , Rodgers Jennifer , Brook Martin , Biancardi Alberto M , Rao Madhwesha R , Norquay Graham , Rodgers Oliver , Munro Ryan , Ball James E , Stewart Neil J , Lawrie Allan , Jenkins Gisli , Grist James , Gleeson Fergus , Schulte Rolf F. , Johnson Kevin M , Wilson Frederick , Cahn Anthony , Swift Andrew J , Rajaram Smitha , Mills Gary H , Watson Lisa , Collini Paul J , Lawson Rod , Thompson A A Roger , Wild Jim M 
Published: April 2022

AbstractIntroductionMicrovascular abnormalities and impaired gas transfer have been observed in patients with COVID-19. The progression of pathophysiological pulmonary changes during the post-acute period in these patients remains unclear.MethodsPatients who were hospitalised due to COVID-19 pneumonia underwent a pulmonary1H and129Xe MRI protocol at 6, 12, 25 and 51 weeks after hospital admission. The imaging protocol included: ultra-short echo time, dynamic contrast enhanced lung perfusion,129Xe lung ventilation,129Xe diffusion weighted and129Xe 3D spectroscopic imaging of gas exchange.Results9 patients were recruited and underwent MRI at 6 (n=9), 12 (n=9), 25 (n=6) and 51 (n=8) weeks after hospital admission. Patients with signs of interstitial lung damage at 3 months were excluded from this study. At 6 weeks after hospital admission, patients demonstrated impaired129Xe gas transfer (RBC:M) but normal lung microstructure (ADC, LmD). Minor ventilation abnormalities present in four patients were largely resolved in the 6–25 week period. At 12 week follow up, all patients with lung perfusion data available (n=6) showed an increase in both pulmonary blood volume and flow when compared to 6 weeks, though this was not statistically significant. At 12 week follow up, significant improvements in129Xe gas transfer were observed compared to 6-week examinations, however129Xe gas transfer remained abnormally low at weeks 12, 25 and 51. Changes in129Xe gas transfer correlated significantly with changes in pulmonary blood volume and TLCOZ-score.ConclusionsThis study demonstrates that multinuclear MRI is sensitive to functional pulmonary changes in the follow up of patients who were hospitalised with COVID-19. Impairment of xenon transfer may indicate damage to the pulmonary microcirculation.
Combined Infection Control Interventions Protect the Essential Workforce from Occupationally-Acquired SARS-CoV-2 during Produce Production, Harvesting and Processing Activities
Authors: Cooper D. Kane , Sobolik Julia S. , Kovacevic Jovana , Rock Channah M. , Sajewski Elizabeth T. , Guest Jodie L. , Lopman Ben A. , Jaykus Lee-Ann , Leon Juan S. 
Published: April 2022

AbstractEssential food workers experience an elevated risk of SARS-CoV-2 infection due to prolonged occupational exposures (e.g., frequent close contact, enclosed spaces) in food production and processing areas, shared transportation (car or bus), and employer-provided shared housing. The purpose of this study was to evaluate the impact of combined food industry interventions and vaccination on reducing the daily cumulative risk of SARS-CoV-2 infection for produce workers. Six linked quantitative microbial risk assessment models were developed in R to simulate daily scenarios experienced by a worker. Standard industry interventions (2 m physical distancing, handwashing, surface disinfection, universal masking, increased ventilation) and two-dose mRNA vaccinations (86–99% efficacy) were modeled individually and jointly to assess risk reductions. The infection risk for an indoor (0.802, 95% Uncertainty Interval [UI]: 0.472–0.984) and outdoor (0.483, 95% UI: 0.255–0.821) worker was reduced to 0.018 (93% reduction) and 0.060 (87.5% reduction) after implementation of combined industry interventions. Upon integration of these interventions with vaccination, the infection risk for indoor (0.001, 95% UI: 0.0001–0.005) and outdoor (0.004, 95% UI: 0.001–0.016) workers was reduced by ≥99.1%. Food workers face considerable risk of occupationally-acquired SARS-CoV-2 infection without interventions; however, consistent implementation of key infection control measures paired with vaccination effectively mitigates these risks.SynopsisBundled interventions, particularly if they include vaccination, produce significant reductions (>99%) in SARS-CoV-2 infection risk for essential food workers.Graphical Abstract
Risk factors for severe COVID-19 in hospitalized children in Canada: A national prospective study from March 2020–May 2021
Authors: Farrar Daniel S. , Drouin Olivier , Hepburn Charlotte Moore , Baerg Krista , Chan Kevin , Cyr Claude , Donner Elizabeth J. , Embree Joanne E. , Farrell Catherine , Forgie Sarah , Giroux Ryan , Kang Kristopher T. , King Melanie , Thibodeau Melanie Laffin , Orkin Julia , Ouldali Naïm , Papenburg Jesse , Pound Catherine M. , Price Victoria E. , Proulx-Gauthier Jean-Philippe , Purewal Rupeena , Ricci Christina , Sadarangani Manish , Salvadori Marina I. , Thibeault Roseline , Top Karina A. , Viel-Thériault Isabelle , Kakkar Fatima , Morris Shaun K. 
Published: April 2022

ABSTRACTBackgroundChildren living with chronic comorbid conditions are at increased risk for severe COVID-19, though there is limited evidence regarding the risks associated with specific conditions and which children may benefit from targeted COVID-19 therapies. The objective of this study was to identify factors associated with severe disease among hospitalized children with COVID-19 in Canada.MethodsWe conducted a national prospective study on hospitalized children with microbiologically confirmed SARS-CoV-2 infection via the Canadian Paediatric Surveillance Program from April 2020–May 2021. Cases were reported voluntarily by a network of >2800 paediatricians. Hospitalizations were classified as COVID-19-related, incidental infection, or infection control/social admissions. Severe disease (among COVID-19-related hospitalizations only) was defined as disease requiring intensive care, ventilatory or hemodynamic support, select organ system complications, or death. Risk factors for severe disease were identified using multivariable Poisson regression, adjusting for age, sex, concomitant infections, and timing of hospitalization.FindingsWe identified 544 children hospitalized with SARS-CoV-2 infection, including 60·7% with COVID-19-related disease and 39·3% with incidental infection or infection control/social admissions. Among COVID-19-related hospitalizations (n=330), the median age was 1·9 years (IQR 0·1–13·3) and 43·0% had chronic comorbid conditions. Severe disease occurred in 29·7% of COVID-19-related hospitalizations (n=98/330), most frequently among children aged 2-4 years (48·7%) and 12-17 years (41·3%). Comorbid conditions associated with severe disease included technology dependence (adjusted risk ratio [aRR] 2·01, 95% confidence interval [CI] 1·37-2·95), neurologic conditions (e.g. epilepsy and select chromosomal/genetic conditions) (aRR 1·84, 95% CI 1·32-2·57), and pulmonary conditions (e.g. bronchopulmonary dysplasia and uncontrolled asthma) (aRR 1·63, 95% CI 1·12-2·39).InterpretationWhile severe outcomes were detected at all ages and among patients with and without comorbidities, neurologic and pulmonary conditions as well as technology dependence were associated with increased risk of severe COVID-19. These findings may help guide vaccination programs and prioritize targeted COVID-19 therapies for children.FundingFinancial support for the CPSP was received from the Public Health Agency of Canada.
Impact of the COVID-19 epidemic on mortality in rural coastal Kenya
Authors: Otiende M , Nyaguara A , Bottomley C , Walumbe D , Mochamah G , Amadi D , Nyundo C , Kagucia EW , Etyang AO , Adetifa IMO , Maitha E , Chondo E , Nzomo E , Aman R , Mwangangi M , Amoth P , Kasera K , Ng’ang’a W , Barasa E , Tsofa B , Mwangangi J , Bejon P , Agweyu A , Williams TN , Scott JAG 
Published: April 2022

ABSTRACTBackgroundThe impact of COVID-19 on all-cause mortality in sub-Saharan Africa remains unknown.MethodsWe monitored mortality among 306,000 residents of Kilifi Health and Demographic Surveillance System, Kenya, through four COVID-19 waves from April 2020-September 2021. We calculated expected deaths using negative binomial regression fitted to baseline mortality data (2010-2019) and calculated excess mortality as observed-minus-expected deaths. We excluded deaths in infancy because of under-ascertainment of births during lockdown. In February 2021, after two waves of wild-type COVID-19, adult seroprevalence of anti-SARS-CoV-2 was 25.1%. We predicted COVID-19-attributable deaths as the product of age-specific seroprevalence, population size and global infection fatality ratios (IFR). We examined changes in cause of death by Verbal Autopsy (VA).ResultsBetween April 2020 and February 2021, we observed 1,000 deaths against 1,012 expected deaths (excess mortality -1.2%, 95% PI -6.6%, 5.8%). Based on SARS-CoV-2 seroprevalence, we predicted 306 COVID-19-attributable deaths (a predicted excess mortality of 30.6%) within this period. Monthly mortality analyses showed a significant excess among adults aged ≥45 years in only two months, July-August 2021, coinciding with the fourth (Delta) wave of COVID-19. By September 2021, overall excess mortality was 3.2% (95% PI -0.6%, 8.1%) and cumulative excess mortality risk was 18.7/100,000. By VA, there was a transient reduction in deaths attributable to acute respiratory infections in 2020.ConclusionsNormal mortality rates during extensive transmission of wild-type SARS-CoV-2 through February 2021 suggests that the IFR for this variant is lower in Kenya than elsewhere. We found excess mortality associated with the Delta variant but the cumulative excess mortality risk remains low in coastal Kenya compared to global estimates.
Multiplexed promoter and gene editing in wheat using the virus-based guide RNA delivery system
Authors: Wang Wei , Yu Zitong , He Fei , Bai Guihua , Trick Harold N. , Akhunova Alina , Akhunov Eduard 
Published: April 2022

AbstractThe low efficiency of genetic transformation and gene editing across diverse cultivars hinders the broad application of CRISPR technology for crop improvement. The development of virus-based methods of CRISPR-Cas system delivery into the plant cells holds great promise to overcome these limitations. Here, we applied the barley stripe mosaic virus (BSMV) for delivering guide RNAs (sgRNA) into the Cas9-expressing wheat lines to create targeted deletions in the promoter of a transcription factor and to perform multiplexed editing of agronomic genes. We demonstrate that pooled BSMV-sgRNAs could be used to generate heritable targeted deletions and multiple mutations in the genome. We transferred the high-expressing allele of Cas9 into adapted spring and winter cultivars and successfully performed the BSMV-sgRNA-based editing of two agronomic genes. The strategies presented in our study could be applied to any cultivar for creating new cis-regulatory diversity or targeting multiple genes in biological pathways or QTL regions, opening possibilities for the effective engineering of crop genomes and accelerating gene discovery and trait improvement efforts.
Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes
Authors: Smith-Zaitlik Thomas , Shibu Preetha , McCartney Anne L. , Foster Geoffrey , Hoyles Lesley , Negus David 
Published: April 2022

ABSTRACTHigh levels of antimicrobial resistance among members of theKlebsiella oxytocacomplex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positiveKlebsiella michiganensisstrains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genusSlopekvirus. rpoBgene-based sequence analysis of 108 presumptiveK. oxytocaisolates (n=59 clinical,n=49 veterinary) foundK. michiganensisto be more prevalent (46 % clinical and 43 % veterinary, respectively) thanK. oxytoca(40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several putative homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.
Cryo-EM structure of the diapause chaperone artemin
Authors: Parvate Amar D. , Powell Samantha M. , Brookreson Jory T. , Moser Trevor H. , Novikova Irina V. , Zhou Mowei , Evans James E. 
Published: April 2022

AbstractThe protein artemin constitutes over 10% of all protein in Artemia cysts during diapause and acts as both an RNA and protein chaperone. However, its mechanistic details remain elusive since no high-resolution structure of artemin exists. Here we report the full-length structure of artemin at 2.04 Å resolution. The cryo-EM map contains density for an intramolecular disulfide bond between Cys22-Cys61 and resolves the entire C-terminus extending into the core of the assembled protein cage. We also provide data supporting the role of C-terminal helix F towards stabilizing the dimer form that is believed to be important for its chaperoning activity. We were able to destabilize this effect by placing a tag at the C-terminus to fully pack the internal cavity and cause limited steric hindrance.
Hypoxia-mediated suppression of pyruvate carboxylase drives tumor microenvironment immunosuppression
Authors: Coleman Michael F. , Cotul Eylem Kulkoyluoglu , Pfeil Alexander J. , Devericks Emily N. , Chen Hao , Kiesel Violet A. , Safdar Muhammad H. , Teegarden Dorothy , Hursting Stephen D. , Wendt Michael K. 
Published: April 2022

AbstractMetabolic reprogramming and immune evasion are established hallmarks of the tumor microenvironment (TME). Growing evidence supports tumor metabolic dysregulation as an important mediator of tumor immune evasion. High TME levels of lactate potently suppress antitumor immunity. Pyruvate carboxylase (PC), the enzyme responsible for the anaplerotic conversion of pyruvate to oxaloacetate, is essential for lung metastasis in breast cancer. Moreover, PC may be dispensable in some cells within the TME, and loss of PC expression is associated with immunosuppression. Here we test whether PC suppression alters tumor metabolism and immunosuppression. Using multiple animal models of breast cancer, we identify a dimorphic role for PC expression in mammary cancer cells. Specifically, PC supports metastatic colonization of the lungs, while suppression of PC promotes primary tumor growth and suppresses histological and transcriptomic markers of antitumor immunity. We demonstrate that PC is potently suppressed by hypoxia, and that PC is frequently suppressed in solid tumors, particularly those with higher levels of hypoxia. Using metabolomics, high-resolution respirometry, and extracellular flux analysis, we show that PC-suppressed cells produce more lactate and undergo less oxidative phosphorylation than controls. Finally, we identify lactate metabolism as a targetable dependency of PC-suppressed cells, which is sufficient to restore T cell populations to the TME of PC-suppressed tumors. Taken together, these data demonstrate that elevated lactate following PC suppression by hypoxia may be a key mechanism through which primary tumors limit antitumor immunity. Thus, these data highlight that PC-directed tumor metabolism is a nexus of tumor progression and antitumor immunity.
ViReMaShiny: An Interactive Application for Analysis of Viral Recombination Data
Authors: Yeung Jason , Routh Andrew L 
Published: April 2022

AbstractRecombination is an essential driver of virus evolution and adaption, giving rise to new chimeric viruses, structural variants, sub-genomic RNAs, and Defective-RNAs. Next-Generation Sequencing of virus samples, either from experimental or clinical settings, has revealed a complex distribution of recombination events that contributes to the intrahost diversity. We and others have previously developed alignment tools to discover and map these diverse recombination events in NGS data. However, there is no standard for data visualization to contextualize events of interest and downstream analysis often requires bespoke coding. To address this, we present ViReMaShiny, a web-based application built using the R Shiny framework to allow interactive exploration and point-and-click visualization of viral recombination data provided in BED format generated by computational pipelines such as ViReMa (Viral-Recombination-Mapper).
Modelling the spatial dynamics of oncolytic virotherapy in the presence of virus-resistant tumor cells
Authors: Bhatt Darshak K. , Janzen Thijs , Daemen Toos , Weissing Franz J. 
Published: April 2022

AbstractOncolytic virotherapy is a promising form of cancer treatment that uses native or genetically engineered viruses to target, infect and kill cancer cells. Unfortunately, this form of therapy is not effective in a substantial proportion of cancer patients, partly due to the occurrence of infection-resistant tumor cells. To shed new light on the mechanisms underlying therapeutic failure and to discover strategies that improve therapeutic efficacy we designed a cell-based model of viral infection. The model allows to investigate the dynamics of infection-sensitive and infection-resistant cells in tumor tissue in presence of the virus. To reflect the importance of the spatial configuration of the tumor on the efficacy of virotherapy, we compare three variants of the model: two 2D models of a monolayer of tumor cells and a 3D model. In all model variants, we systematically investigate how the therapeutic outcome is affected by properties of the virus (e.g. the rate of viral spread), the tumor (e.g. production rate of resistant cells, cost of resistance), the healthy stromal cells (e.g. degree of resistance to virus) and the timing of treatment. We find that various therapeutic outcomes are possible when resistant cancer cells arise at low frequency in the tumor. These outcomes depend in an intricate but predictable way on the death rate of infected cells, where faster death leads to rapid virus clearance and cancer persistence. Our simulations reveal three different causes of therapy failure: rapid clearance of the virus, rapid selection of resistant cancer cells, and a low rate of viral spread due to the presence of infection-resistant healthy cells. Our models suggest that improved therapeutic efficacy can be achieved by sensitizing healthy stromal cells to infection, although this remedy has to be weighed against the toxicity induced in the healthy tissue.