bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Epidemiology of SARS-CoV-2 in Cyprus
Authors: Richter Jan , Fanis Pavlos , Tryfonos Christina , Koptides Dana , Krashias George , Bashiardes Stavros , Hadjisavvas Andreas , Loizidou Maria , Oulas Anastasis , Alexandrou Denise , Kalakouta Olga , Panayiotidis Mihalis I. , Spyrou George M. , Christodoulou Christina
Published: March 2021

Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.
Pre-pandemic Cognitive Function and COVID-19 Vaccine Hesitancy: Cohort Study
Authors: Batty G. David , Deary Ian J. , Fawns-Ritchie Chloe , Gale Catharine R. , Altschul Drew
Published: March 2021

Background

Whereas several predictors of COVID-19 vaccine hesitancy have been examined, the role of cognitive function following the widely publicised development of an inoculation is unknown.

Objective

To test the association between scores from an array of cognitive function tests and self-reported vaccine hesitancy after the announcement of the successful testing of the Oxford University/AstraZeneca vaccine.

Design, Setting, and Participants

We used individual-level data from a pandemic-focused study (COVID Survey), a prospective cohort study nested within Understanding Society (Main Survey). In the week immediately following the announcement of successful testing of the first efficacious inoculation (November/December 2020), data on vaccine intentionality were collected in 11740 individuals (6702 women) aged 16-95. Pre-pandemic scores on general cognitive function, ascertained from a battery of six tests, were captured in 2011/12 wave of the Main Survey.

Measurements

Self-reported intention to take up a vaccination for COVID-19. To summarise our results, we computed odds ratios with accompanying 95% confidence intervals for general cognitive function adjusted for selected covariates.

Results

Of the study sample, 17.2% (N=1842) indicated they were hesitant about having the vaccine. After adjustment for age, sex, and ethnicity, study members with a lower baseline cognition score were markedly more likely to be vaccine hesitant (odds ratio per standard deviation lower score in cognition; 95% confidence interval: 1.76; 1.62, 1.90). Adjustment for mental and physical health plus household shielding status had no impact on these results, whereas controlling for educational attainment led to partial attenuation but the probability of hesitancy was still elevated (1.52; 1.37, 1.67). There was a linear association for vaccine hesitancy across the full range of cognition scores (p for trend: p<0.0001).

Limitations

Our outcome was based on intention rather than behaviour.

Conclusions

Erroneous social media reports might have complicated personal decision-making, leading to people with lower cognitive ability test scores being vaccine-hesitant. With people with lower cognition also experiencing higher rates of COVID-19 in studies conducted prior to vaccine distribution, these new findings are suggestive of a potential additional disease burden.
The Case for Altruism in Institutional Diagnostic Testing
Authors: Specht Ivan , Sani Kian , Botti-Lodovico Yolanda , Hughes Michael , Heumann Kristin , Bronson Amy , Marshall John , Baron Emily , Parrie Eric , Glennon Olivia , Fry Ben , Colubri Andrés , Sabeti Pardis C.
Published: March 2021

Amid COVID-19, many institutions deployed vast resources to test their members regularly for safe reopening. This self-focused approach, however, not only overlooks surrounding communities but also remains blind to community transmission that could breach the institution. To test the relative merits of a more altruistic strategy, we built an epidemiological model that assesses the differential impact on case counts when institutions instead allocate a proportion of their tests to members’ close contacts in the larger community. We found that testing outside the institution benefits the institution in all plausible circumstances, with the optimal proportion of tests to use externally landing at 45% under baseline model parameters. Our results were robust to local prevalence, secondary attack rate, testing capacity, and contact reporting level, yielding a range of optimal community testing proportions from 18% to 58%. The model performed best under the assumption that community contacts are known to the institution; however, it still demonstrated a significant benefit even without complete knowledge of the contact network.
Degradation of lipid based drug delivery formulations during nebulization
Authors: Klein David M. , Poortinga Albert , Verhoeven Frank M. , Bonn Daniel , Bonnet Sylvestre , van Rijn Cees J.M.
Published: March 2021

Encapsulating pharmaceuticals in protective lipid based nanoparticles, and nebulizing them towards the target area in the body offers a range of clinical advantages. However, the process of nebulization might possibly damage sensitive nanoparticle structures, such as liposomes, resulting in loss of active pharmaceutical ingredients. We compare this loss for two types of lung inhalation devices: high-frequency piezo-actuated vibrating mesh nebulizers and non-actuated continuous jet nebulizers. We find that vibrating mesh nebulizers cause model liposomes to release more than ten times as much encapsulated material as the continuous jet nebulizers because the energies involved in nebulization are much larger. This result highlights the importance of applying a mild nebulization technology when administering shear-sensitive drug formulations such as lipid nanoparticle based drugs to the lungs.
A simple model for how the risk of pandemics from different virus families depends on viral and human traits
Authors: Doelger Julia , Chakraborty Arup K. , Kardar Mehran
Published: March 2021

Different virus families, like influenza or corona viruses, exhibit characteristic traits such as typical modes of transmission and replication as well as specific animal reservoirs in which each family of viruses circulate. These traits of genetically related groups of viruses influence how easily an animal virus can adapt to infect humans, how well novel human variants can spread in the population, and the risk of causing a global pandemic. Relating the traits of virus families to their risk of causing future pandemics, and identification of the key time scales within which public health interventions can control the spread of a new virus that could cause a pandemic, are obviously significant. We address these issues using a minimal model whose parameters are related to characteristic traits of different virus families. A key trait of viruses that “spillover” from animal reservoirs to infect humans is their ability to propagate infection through the human population (fitness). We find that the risk of pandemics emerging from virus families characterized by a wide distribution of the fitness of spillover strains is much higher than if such strains were characterized by narrow fitness distributions around the same mean. The dependences of the risk of a pandemic on various model parameters exhibit inflection points. We find that these inflection points define informative thresholds. For example, the inflection point in variation of pandemic risk with time after the spillover represents a threshold time beyond which global interventions would likely be too late to prevent a pandemic.
SARS-CoV-2 prevalence and transmission in swimming activities: results from a retrospective cohort study
Authors: Termansen Martin Brink , Christiansen Ask Vest , Frische Sebastian
Published: March 2021

There is an urgent need for research on the epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing corona virus disease 2019 (COVID-19), as the transmissibility differs between settings and populations. Here we report on a questionnaire-based retrospective cohort study of the prevalence and transmission of SARS-CoV-2 among participants in swimming activities in Denmark in the last five months of 2020 during the COVID-19 pandemic.

Eight of 162 swimming activities with a SARS-CoV-2 positive participant led to transmission to 23 other participants. Overall, the percentage of transmission episodes was 4.9% (competitive swimming 8.9%; recreational swimming 1.3%). Overall, the incidence rate of transmission was 19.5 participants per 100.000 pool activity hours (corresponding values: 43.5 and 4.7 for competitive and recreational swimming, respectively).

Compliance with precautionary restrictions was highest regarding hand hygiene (98.1%) and lowest in distancing personal sports bags (69.9%). Due to low statistical power, the study showed no significant effect of restrictions.

Insight into the risk of transmission of SARS-CoV-2 during indoor swimming is needed to estimate the efficiency of restrictive measures on this and other sports and leisure activities. Only when we know how the virus spreads through various settings, optimal strategies to handle the COVID-19 pandemic can be developed.
Deep clinical phenotyping of Alzheimer’s Disease Patients Leveraging Electronic Medical Records Data Identifies Sex-Specific Clinical Associations
Authors: Tang Alice , Oskotsky Tomiko , Mantyh William , Solsberg Caroline Warly , Zeng Billy , Hu Zicheng , Oskotsky Boris , Dubal Dena , Sirota Marina
Published: March 2021

Alzheimer’s Disease (AD) is a devastating disorder that is still not fully understood. Sex modifies AD vulnerability, but the reasons for this are largely unknown. There has been efforts to understand select comorbidities, covariates, and biomarkers of AD, with and without sex stratification - but there has not yet been an integrative, big data approach to identify clinical and sex specific associations with AD in an unbiased manner. Electronic Medical Records (EMR) contain extensive information on patients, including diagnoses, medications, and lab test results, providing a unique opportunity to apply phenotyping approaches to derive insights into AD clinical associations. Here, we utilize EMRs to perform deep clinical phenotyping and network analysis of AD patients to provide insight into its clinical characteristics and sex-specific clinical associations. We performed embeddings and network representation of patient diagnoses to visualize patient heterogeneity and comorbidity interactions and observe greater connectivity of diagnosis among AD patients compared to controls. We performed enrichment analysis between cases and controls and identified multiple known and new diagnostic and medication associations, such as positive associations with AD and hypertension, hyperlipidemia, anemia, and urinary tract infection - and negative associations with neoplasms and opioids. Furthermore, we performed sex-specific enrichment analyses to identify novel sex-specific associations with AD, such as osteoporosis, depression, cardiovascular risk factors, and musculoskeletal disorders diagnosed in female AD patients and neurological, behavioral, and sensory disorders enriched in male AD patients. We also analyzed lab test results, resulting in clusters of patient phenotype groups, and we observed greater calcium and lower alanine aminotransferase (ALT) in AD, as well as abnormal hemostasis labs in female AD. With this method of phenotyping, we can represent AD complexity, and identify clinical factors that can be followed-up for further temporal and predictive analysis or integrate with molecular data to aid in diagnosis and generate hypotheses about disease mechanisms. Furthermore, the negative associations can help identify factors that may decrease likelihood of AD and help motivate future drug repurposing or therapeutic approaches.
Characterizing Post-Acute Sequelae of SARS-CoV-2 Infection across Claims and Electronic Health Record Databases
Authors: Spotnitz Matthew E. , Hripcsak George , Ryan Patrick B. , Natarajan Karthik
Published: March 2021

Structured Abstract

Importance

Post-acute sequelae of SARS-CoV-2 infection (PASC) is emerging as a major public health issue.

Objective

We characterized the incidence of PASC, or related symptoms and diagnoses, for COVID-19 and influenza patients.

Design

Retrospective cohort study.

Setting

Our data sources were the IBM MarketScan Commercial Claims and Encounters (CCAE), Optum Electronic Health Record (EHR) and Columbia University Irving Medical Center (CUIMC) databases that were transformed to the Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM) and were part of the Observational Health Sciences and Informatics (OHDSI) network.

Participants

The COVID-19 cohort consisted of patients with a diagnosis of COVID-19 or positive lab test of SARS-CoV-2 after January 1st 2020 with a follow up period of at least 30 days. The influenza cohort consisted of patients with a diagnosis of influenza between October 1, 2018 and May 1, 2019 with a follow up period of at least 30 days.

Intervention

Infection with COVID-19 or influenza.

Main Outcomes and Measures

Post-acute sequelae of SARS-CoV-2 infection (PASC), or related diagnoses, for COVID-19 and influenza patients.

Results

In aggregate, we characterized the post-acute experience for over 440,000 patients who were diagnosed with COVID-19 or tested positive for SARS-COV-2. The long term sequelae that had a higher incidence in the COVID-19 compared to Influenza cohorts were altered smell or taste, myocarditis, acute kidney injury, dyspnea and alopecia. Additionally, the long term incidences of respiratory illness, musculoskeletal disease, and psychiatric disorders for the COVID-19 population were higher than expected.

Conclusions and Relevance

The long term sequelae of COVID-19 and influenza may be different. Further characterization of PASC on large scale observational healthcare databases is warranted.
Management of COVID-19-related Arterial Thrombosis Leading to Acute Limb-threatening Ischemia
Authors: Ehsan Omer , Khan Mohammad Iqbal , Raza Muhammad Waqas
Published: March 2021

Objective

Examine the occurrence and clinical outcomes of arterial thrombosis leading to limb-threatening ischemia in patients with coronavirus-2019 (COVID-19).

Study design

Prospective, descriptive case series.

Patients and Methods

Forty-four patients with COVID-19 infection presenting with critical limb ischemia were managed between March 2020 and December 2020. The patients were divided into three groups based on the mode of presentation: 1) those who had been admitted; 2) those presenting in the emergency department; and 3) those presenting to vascular clinics. Clinical evidence suggesting limb ischemia was evaluated with computerized tomographic angiogram. Vascular care was designed according to the need of individual patients, through anticoagulation, revascularization by thrombo-embolectomy, or bypass grafting and amputation.

Results

Ten major amputations and 4 deaths (all in patients admitted) occurred among the 44 patients (9.1%). Most patients (32/44) were males, mean age was 55, and limb ischemia occurred among patients as young as 29. The initial period of ischemia was often not appreciated by patients and physicians. Critical limb ischemia was often not correlated with the severity of COVD symptoms: of 17 patients who presented through the emergency room with limb-threatening ischemia, 10 (58.9%) were asymptomatic for respiratory and general symptoms. Comorbidities were common among all 3 patient groups (26/44; 59%). Anticoagulants did not consistently prevent thromboembolic events since all admitted patients were receiving low molecular weight heparin. The rate of revascularization was lower in this population than in the general population with similar limb ischemia.

Conclusion

Acute limb ischemia in patients with COVID-19 is a vascular emergency that can result in limb loss and even death. The severity of respiratory infection and other symptoms of COVID often are not consistent with the severity and level of vascular involvement. Timely recognition and tailored intervention is needed to save limbs in this population.

What this paper adds to existing knowledge

COVID-19 infection predisposes to arterial and venous thrombosis, but data on arterial thrombosis are sparse. This report describes a series of 44 COVID-19 patients who had arterial thrombosis causing limb-threatening ischemia. Most noteworthy characteristics of the condition are its severity (10 major amputations and 4 deaths); subtle initial expression of the ischemia, which may lead to delayed diagnosis; severity and level of vascular involvement poorly correlated with respiratory symptoms; nearly 60% frequency of comorbidities (diabetes, hypertension, and ischemic heart disease); and low rate of successful revascularization compared with that of usual thromboembolic limb ischemia.
Intra-tumoral epigenetic heterogeneity and aberrant molecular clocks in hepatocellular carcinoma
Authors: Restrepo Paula , Bubie Adrian , Craig Amanda J. , Labgaa Ismail , Schwartz Myron , Thung Swan , Stolovitzky Gustavo , Losic Bojan , Villanueva Augusto
Published: March 2021

There is limited understanding of the epigenetic drivers of tumor evolution in hepatocellular carcinoma (HCC). We quantify epigenetic intra-tumoral heterogeneity (ITH) using regional enhanced reduced-representation bisulfite sequencing (eRRBS) DNA methylation data from 47 early stage, treatment-naive HCC biopsies across 9 patients. Integrating these data with matching RNAseq, targeted DNA sequencing, tumor-infiltrating lymphocyte (TIL) and hepatitis-B viral (HBV) expression, we computed regional differential methylation (DM) ITH signatures across 19,327 promoter regions, and 654,133 CpG islands, while overlapping with known methylation age marker genes (240/354). We found substantial ITH signatures in promoter and enhancer sites across 4/9 patients highlighting novel molecular pathways of tumor progression not otherwise detectable from RNA analysis alone. Additionally, we identify an epigenetic tumoral aging measure that reflects a complex tumor fitness phenotype as a potential proxy for tumor evolution. In order to compute clinical associations with epigenetic tumoral age, we use 450k array data from 377 HCC patients in the TCGA-LIHC single-biopsy cohort to calculate tumoral age and find evidence implying that epigenetically old tumors have lower fitness yet higher TIL burden. Our data reveal a novel, unique epigenetic ITH axis in HCC tumors that furthers our understanding of tumor evolution and may serve as a potential avenue for enhancing patient stratification and treatment.
Neutralization of European, South African, and United States SARS-CoV-2 mutants by a human antibody and antibody domains
Authors: Sun Zehua , Kim Andrew , Sobolewski Michele D , Enick Nathan , Chen Chuan , Adams Cynthia , Jacobs Jana L , McCormick Kevin D , Mellors John W , Dimitrov Dimiter S , Li Wei
Published: March 2021

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission with several emerging variants remain uncontrolled in many countries, indicating the pandemic remains severe. Recent studies showed reduction of neutralization against these emerging SARS-CoV-2 variants by vaccine-elicited antibodies. Among those emerging SARS-CoV-2 variants, a panel of amino acid mutations was characterized including those in the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. In the present study, we evaluated our previously identified antibody and antibody domains for binding to these RBD variants with the emerging mutations, and neutralization of pseudo typed viruses carrying spike proteins with such mutations. Our results showed that one previously identified antibody domain, ab6, can bind 32 out of 35 RBD mutants tested in an ELISA assay. All three antibodies and antibody domains can neutralize pseudo typed B.1.1.7 (UK variant), but only the antibody domain ab6 can neutralize the pseudo typed virus with the triple mutation (K417N, E484K, N501Y). This domain and its improvements have potential for therapy of infections caused by SARS-CoV-2 mutants.
Early super-spreader events are a likely determinant of novel SARS-CoV-2 variant predominance
Authors: Goyal Ashish , Reeves Daniel , Schiffer Joshua T.
Published: March 2021

The emergence of multiple new SARS-CoV-2 variants, characterized to varying degrees by increased infectivity, higher virulence and evasion of vaccine and infection-induced immunologic memory, has hampered international efforts to contain the virus. While it is generally believed that these variants first develop in single individuals with poor immunologic control of the virus, the factors governing variant predominance in the population remain poorly characterized. Here we present a mathematical framework for variant emergence accounting for the highly variable number of people secondarily infected by individuals with SARS-CoV-2 infection. Our simulations suggest that threatening new variants probably develop within infected people fairly commonly, but that most die out and do not achieve permanence in the population. Variants that predominate are more likely to be associated with higher infectiousness, but also the occurrence of a super-spreader event soon after introduction into the population.
Evaluation of the ROX index in SARS-CoV-2 Acute Respiratory failure treated with both High-Flow Nasal Oxygen (HFNO) and Continuous Positive Airway Pressure (CPAP)
Authors: Ghani Hakim , Shaw Michael , Pyae Phyoe , Cama Rigers , Prabhakar Meghna , Navarra Alessio , Mogal Rahul , Barlow Andrew , Nordin Nazril , Vancheeswaran Rama , Lee Janice Yu Ji , Chua Felix
Published: March 2021

Background

Non-invasive respiratory support including high-flow nasal oxygen (HFNO), and continuous positive airway pressure (CPAP) have been used to provide therapy in selected SARS-CoV-2 patients with acute respiratory failure (ARF). The value of the ROX index, a validated benchmark for outcomes in HFNO is unknown in CPAP.

Objective

Can the ROX, a validated benchmark in HFNO be used for measuring treatment outcomes of CPAP in SARS-COV-2 ARF?

Study Design and Methods

A non-randomised prospective protocol driven observational non-intensive care unit study in 130 SARS-COV-2 patients with ARF treated with non-invasive therapy from March 2020 to January 2021. The primary end point was failure of therapy (death or escalation). Secondary outcomes included time to failure including invasive mechanical ventilation (IMV) or death, the effect of escalation to CPAP from HFNO and the utility of ROX in ARF.

Results

HFNO was better than CPAP in treating SARS-COV-2 ARF: 17/35 (48.5%) with successful HFNO therapy versus 24/95 (25.2%) with CPAP. The ROX index was more sensitive to outcomes with CPAP compared to HFNO and distinguished treatment failure early at 1, 4, 6, 12, and 24 hours with the highest sensitivity at 24 hours (ROX-24h). The AUC for the ROX-24h was 0.77 for HFNO (P<0.0001), and 0.84 for CPAP (P<0.0001). The ROX-24h cut-points predicted failure with HFNO when < 3.9 (PPV 71%, NPV 75%) and CPAP < 4.3 (PPV 75%, NPV 91%). For success, ROX-24h cut-points of 7.6 for HFNO (PPV 85%, NPV 48%) and 6.1 for CPAP (PPV 88%, NPV 62%) were observed. Escalation from HFNO to CPAP was mostly not successful.

Conclusion

ARF in SARS-COV-2 can be successfully managed by non-invasive support. The ROX index, validated for HFNO, provides a timely, low resource measure for both HFNO and CPAP avoiding delayed intubation.

Trial registration

Study approved by NHS HRAREC (20/HRA/2344;ethics 283888)

KEY MESSAGE

What is the key question?

Can the ROX, a validated benchmark in high-flow nasal oxygen (HFNO) be used for measuring treatment outcomes of continuous positive airway pressure (CPAP) in SARS-COV-2 ARF?

What is the bottom line?

The ROX index, validated for HFNO, provides a timely, low resource measure for both HFNO and CPAP support avoiding delayed intubation.

Why read on?

The present study compares the efficacy of HFNO and CPAP, two common globally used modalities of treatment for SARS-CoV-2 and notes the superior utility of the ROX-24h in CPAP to predict outcome, enabling timely escalation decisions.
Quantitative single cell 5hmC sequencing reveals non-canonical gene regulation by non-CG hydroxymethylation
Authors: Fabyanic Emily B. , Hu Peng , Qiu Qi , Wang Tong , Berríos Kiara N. , Flournoy Jennifer , Connolly Daniel R. , Zhou Zhaolan , Kohil Rahul M. , Wu Hao
Published: March 2021

Oxidative modification of 5-methylcytosine (5mC) generates 5-hydroxymethylcytosine (5hmC), a DNA modification that exhibits unique epigenetic regulatory functions and impacts diverse biological processes. However, standard single-nucleus/cell bisulfite sequencing methods cannot resolve the base ambiguity between 5mC and 5hmC to accurately measure cell-type specific epigenomic patterns and gene regulatory functions of 5hmC or true 5mC. Here, we develop single-nucleus 5hmC sequencing (snhmC-seq) for quantitative and unbiased 5hmC profiling in single cells by harnessing differential deaminase activity of APOBEC3A towards 5mC and chemically protected 5hmC. We used snhmC-seq to profile single nuclei from cryopreserved mouse brain samples to reveal epigenetic heterogeneity of 5hmC at single-cell resolution and uncovered a non-canonical gene regulatory role of genic 5hmC in non-CG context.
Bioinformatic analysis deciphers the molecular toolbox in the endophytic/pathogenic behavior inF. oxysporumf. sp.vanillae-V. planifoliaJacks interaction
Authors: Solano De la Cruz MT , Escobar Hernández EE , Arciniega González JA , Rueda Zozaya RP , Adame García J , Luna – Rodríguez M
Published: March 2021

Background

F. oxysporumas a species complex (FOSC) possesses the capacity to specialize into host-specific pathogens known asformae speciales. This with the help of horizontal gene transfer (HGT) between pathogenic and endophytic individuals of FOSC. From these pathogenicforma specialis, F. oxysporumf. sp.vanillae(Fov) is the causal agent of fusarium wilt producing root and stem rot (RSR) and is positioned as the main phytosanitary problem in vanilla plantations worldwide. Nonetheless, the origin of this forma speciales and the behavioral genetics dictating the endophytic/pathogenicFusariumlifestyles still unknown. To elucidate the underlying molecular mechanisms that establish these behaviors we analyzed the RNA-seq libraries of two-times frames of vanilla-Fov interactions.

Results

Our analyses identified the sets of transcripts corresponding toFovpathogenic strain JAGH3 during the two-times frames of the infection as the sets of the transcripts belonging to endophyticFoxin vanilla. Functional predictions ofde novoannotated transcripts as the enriched GO terms with the overrepresented metabolic pathways, allowed us to identify the processes that establish the pathogenic lifestyle inFovbeing virulence, hypervirulence, sporulation, conidiation, necrosis and fusaric acid related genes with the carbohydrates, amino acids, proteins, glycerophospholipids and autophagy metabolic pathways that are key regulators of spores germination and pathogenicity establishment as the underlying mechanisms behind this behavior. As the absence of these were found in the vanilla endophyticFox.

Conclusions

This work reveals the main players of the behavioral genetics in pathogenicFov/endophyticFoxinV. planifoliaJacks. Its pathogenic strategy allowsFovto infect in a SIX genes-independent manner. As the other pathogenic elements found in this study could be explained by the presence of pathogenicity islands and genomic regions associated with supernumerary chromosomes inFov. These play a central role as carriers of genes involved with pathogenic activity and could be obtained through HGT.
Comparative Multiomic Analysis Reveals Low T Cell Infiltration as the Primary Feature of Tobacco Use in HPV(+) Oropharyngeal Cancer
Authors: Wahle Benjamin M. , Zolkind Paul , Ramirez Ricardo , Skidmore Zachary L. , Mazul Angela , Hayes D. Neil , Sandulache Vlad C. , Thorstad Wade L. , Adkins Douglas , Griffith Obi L. , Griffith Malachi , Zevallos Jose P.
Published: March 2021

Purpose

Tobacco use is an independent adverse prognostic feature in human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC). Despite this, the biologic features associated with tobacco use have not been systematically investigated in this population. We sought to characterize the genomic and immunologic features of HPV(+) OPSCC associated with tobacco use and adverse oncologic outcomes.

Experimental Design

Whole exome sequencing of 47 primary HPV(+) OPSCC tumors was performed to investigate mutational differences associated with tobacco exposure. To characterize the tumor immune microenvironment (TIME), targeted mRNA hybridization was performed and immunohistochemical (IHC) staining was used to validate these findings.

Results

Low expression of transcripts in a T cell-inflamed gene expression profile (TGEP) was associated with tobacco use at the time of diagnosis and lower overall and disease-free survival. Tobacco use was associated with an increased proportion of T>C substitutions and a lower proportion of mutational signatures typically observed in HPV(+) OPSCC tumors, but was not associated with increases in mutational burden or the rate of recurrent oncogenic mutations.

Conclusions

In HPV(+) OPSCC, low T cell infiltration of primary tumors is associated with current tobacco use and worse oncologic outcomes. Rather than an increased mutational burden, tobacco’s primary and clinically relevant association is immunosuppression of the primary TIME. An objective clinical assay like the TGEP, which quantifies immune infiltration of the primary TIME, may have value for HPV(+) OPSCC risk stratification in future clinical trials.
Generation of functional ciliated cholangiocytes from human pluripotent stem cells
Authors: Ogawa Mina , Jiang Jia-Xin , Xia Sunny , Yang Donghe , Ding Avrilynn , Laselva Onofrio , Chin Stephanie , Hernandez Marcela , Cui Changyi , Higuchi Yuichiro , Suemizu Hiroshi , Dorrell Craig , Grompe Markus , Bear Christine E , Keller Gordon , Ogawa Shinichiro
Published: March 2021

The derivation of mature functional cholangiocytes from human pluripotent stem cells (hPSCs) would provide a model for studying the pathogenesis of cholangiopathies and for developing novel therapies to treat them. Current differentiation protocols are not efficient and give rise to cholangiocytes that are not fully mature, limiting their therapeutic applications. Here, we describe a new strategy to generate functional hPSC-derived cholangiocytes that display many characteristics of mature bile duct cells including high levels of CFTR and the presence of primary cilia capable of sensing flow. With this level of maturation, these cholangiocytes are amenable for testing the efficacy of new cystic fibrosis drugs and for studying the role of cilia in cholangiocyte development and function. Transplantation studies showed that the mature cholangiocytes generate ductal structures in the liver of immunocompromised mice providing the first indication that it may be possible to develop cell-based therapies to restore bile duct function in patients with biliary disease.
Additive manufactured scaffolds for bone tissue engineering: physical characterization of thermoplastic composites with functional fillers
Authors: Sinha Ravi , Sanchez Alberto , Camara-Torres Maria , Uriszar-Aldaca Iñigo Calderon , Calore Andrea Roberto , Harings Jules , Gambardella Ambra , Ciccarelli Lucia , Vanzanella Veronica , Sisani Michele , Scatto Marco , Wendelbo Rune , Perez Sergio , Villanueva Sara , Matanza Amaia , Patelli Alessandro , Grizzuti Nino , Mota Carlos , Moroni Lorenzo
Published: March 2021

Thermoplastic polymer – filler composites are excellent materials for bone tissue engineering (TE) scaffolds, combining the functionality of fillers with suitable load bearing ability, biodegradability, and additive manufacturing (AM) compatibility of the polymer. Two key determinants of their utility are their rheological behavior in the molten state, determining AM processability, and their mechanical load-bearing properties. We report here the characterization of both these physical properties for four bone TE relevant composite formulations with poly(ethylene oxide terephthalate) / poly(butylene terephthalate (PEOT/PBT) as a base polymer, which is often used to fabricate TE scaffolds. The fillers used were reduced graphene oxide (rGO), hydroxyapatite (HA), gentamycin intercalated in zirconium phosphate (ZrP-GTM) and ciprofloxacin intercalated in MgAl layered double hydroxide (MgAl-CFX). The rheological assessment showed that generally the viscous behavior dominated the elastic behavior (G’’ > G’) for the studied composites, at empirically determined extrusion temperatures. Coupled rheological-thermal characterization of ZrP-GTM and HA composites showed that the fillers increased the solidification temperatures of the polymer melts during cooling. Both these findings have implications for the required extrusion temperatures and bonding between layers. Mechanical tests showed that the fillers generally made the polymer stiffer but more brittle in proportion to the filler fractions. Furthermore, the elastic moduli of scaffolds did not directly correlate with the corresponding bulk material properties, implying composite-specific AM processing effects on the mechanical properties. Lastly, we show computational models to predict multi-material scaffold elastic moduli using measured single material scaffold and bulk moduli. The reported characterizations are essential for assessing the AM processability and ultimately the suitability of the manufactured scaffolds for the envisioned bone regeneration application.
Perturbation of ribosomal subunits dynamics by inhibitors of tRNA translocation
Authors: Belardinelli Riccardo , Sharma Heena , Peske Frank , Rodnina Marina V.
Published: March 2021

Many antibiotics that bind to the ribosome inhibit translation by blocking the movement of tRNAs and mRNA or interfering with ribosome dynamics, which impairs the formation of essential translocation intermediates. Here we show how translocation inhibitors viomycin (Vio), neomycin (Neo), paromomycin (Par), kanamycin (Kan), spectinomycin (Spc), hygromycin B (HygB), and streptomycin (Str, an antibiotic that does not inhibit tRNA translocation), affect principal motions of the small ribosomal subunits (SSU) during EF-G-promoted translocation. Using ensemble kinetics, we studied the SSU body domain rotation and SSU head domain swiveling in real time. We show that although antibiotics binding to the ribosome can favor a particular ribosome conformation in the absence of EF-G, EF-G-induced transition to the rotated/swiveled state of the SSU is hardly affected. The major effect of the antibiotics is observed at the stage when the SSU body and the head domain move backward. Vio, Spc and high concentrations of Neo completely inhibit the backward movements of the SSU body and head domain. Kan, Par, HygB and low concentrations of Neo slow down both movements, but their sequence and coordination are retained. Finally, Str has very little effect on the backward rotation of the SSU body domain, but retards the SSU head movement. The data underscore the importance of ribosome dynamics for tRNA-mRNA translocation and provide new insights into the mechanism of antibiotic action.
DNA replication during acute MEK inhibition drives acquisition of resistance through amplification of theBRAFoncogene
Authors: Channathodiyil Prasanna , Segonds-Pichon Anne , Smith Paul D. , Cook Simon J. , Houseley Jonathan
Published: March 2021

Mutations and gene amplifications that confer drug resistance emerge frequently during chemotherapy, but their mechanism and timing is poorly understood. Here, we investigateBRAFV600Eamplification events that underlie resistance to the MEK inhibitor selumetinib (AZD6244/ARRY-142886) in COLO205 cells, a well-characterised model for reproducible emergence of drug resistance, and show thatde novoamplification ofBRAFis the primary path to resistance irrespective of pre-existing amplifications. Selumetinib causes long-term G1 arrest accompanied by reduced expression of DNA replication and repair genes, but cells stochastically re-enter the cell cycle during treatment despite continued repression of pERK1/2. Most DNA replication and repair genes are re-expressed as cells enter S and G2, however, mRNAs encoding a subset of factors important for error-free replication and chromosome segregation including TIPIN, PLK2 and PLK3 remain at low abundance. This suggests that DNA replication in drug is more error prone and provides an explanation for the DNA damage observed under long-term RAF-MEK-ERK1/2 pathway inhibition. To test the hypothesis that DNA replication in drug promotesde novo BRAFamplification, we exploited the combination of palbociclib and selumetinib. Combined treatment with selumetinib and a dose of palbociclib sufficient to reinforce G1 arrest in selumetinib-sensitive cells, but not to impair proliferation of resistant cells, delays the emergence of resistant colonies, meaning that escape from G1 arrest is critical in the formation of resistant clones. Our findings demonstrate that acquisition of MEK inhibitor resistance often occurs throughde novogene amplification and can be suppressed by impeding cell cycle entry in drug.
Identification, crystallization and epitope determination of public TCR shared and expanded in COVID-19 patients
Authors: Lu Xiuyuan , Hosono Yuki , Ishizuka Shigenari , Nagae Masamichi , Ishikawa Eri , Motooka Daisuke , Ozaki Yuki , Sax Nicolas , Shinnakasu Ryo , Inoue Takeshi , Onodera Taishi , Matsumura Takayuki , Shinkai Masaharu , Sato Takashi , Nakamura Shota , Mori Shunsuke , Kanda Teru , Nakayama Emi E. , Shioda Tatsuo , Kurosaki Tomohiro , Arase Hisashi , Yamashita Kazuo , Takahashi Yoshimasa , Yamasaki Sho
Published: March 2021

T cells play pivotal roles in protective immunity against SARS-CoV-2 infection. Follicular helper T (Tfh) cells mediate the production of antigen-specific antibodies; however, T cell receptor (TCR) clonotypes used by SARS-CoV-2-specific Tfh cells have not been well characterized. Here, we first identified and crystallized public TCR of Tfh clonotypes that are shared and expanded in unhospitalized COVID-19-recovered patients. These clonotypes preferentially recognized SARS-CoV-2 spike (S) protein epitopes which are conserved among emerging SARS-CoV-2 variants. These clonotypes did not react with S proteins derived from common cold human coronaviruses, but cross-reacted with symbiotic bacteria, which might confer the publicity. Among SARS-CoV-2 S epitopes, S864-882, presented by frequent HLA-DR alleles, could activate multiple public Tfh clonotypes in COVID-19-recovered patients. Furthermore, S864-882-loaded HLA tetramer preferentially bound to CD4+T cells expressing CXCR5. In this study, we identified and crystallized public TCR for SARS-CoV-2 that may contribute to the prevention of COVID-19 aggravation.
Avidity observed between a bivalent inhibitor and an enzyme monomer with a single active site
Authors: Lacham-Hartman Shiran , Shmidov Yulia , Radisky Evette S. , Bitton Ronit , Lukatsky David B. , Papo Niv
Published: March 2021

Although myriad protein–protein interactions in nature use polyvalent binding, in which multiple ligands on one entity bind to multiple receptors on another, to date an affinity advantage of polyvalent binding has been demonstrated experimentally only in cases where the target receptor molecules are clustered prior to complex formation. Here, we demonstrate cooperativity in binding affinity (i.e., avidity) for a protein complex in which an engineered dimer of the amyloid precursor protein inhibitor (APPI), possessing two fully functional inhibitory loops, interacts with mesotrypsin, a soluble monomeric protein that does not self-associate or cluster spontaneously. We found that each inhibitory loop of the purified APPI homodimer was over three-fold more potent than the corresponding loop in the monovalent APPI inhibitor. This observation is consistent with a suggested mechanism whereby the two APPI loops in the homodimer simultaneously and reversibly bind two corresponding mesotrypsin monomers to mediate mesotrypsin dimerization. We propose a simple model for such dimerization that quantitatively explains the observed cooperativity in binding affinity. Binding cooperativity in this system reveals that the valency of ligands may affect avidity in protein–protein interactions including those of targets that are not surface-anchored and do not self-associate spontaneously. In this scenario, avidity may be explained by the enhanced concentration of ligand binding sites in proximity to the monomeric target, which may favor rebinding of the multiple ligand binding sites with the receptor molecules upon dissociation of the protein complex.

Impact statement

Lacham-Hartmanet al. demonstrate enhancement of binding affinity through avidity in a complex between a bivalent ligand and a soluble monomeric target with a single binding site. Avidity effects have previously been demonstrated only for clustered receptor molecules presenting multiple binding sites. Our model may explain how polyvalent ligands can agonize or antagonize biological interactions involving nonclustered target molecules that are crucial for intra- and extracellular structural, metabolic, signaling, and regulatory pathways.
Immune StimulationviaWounding Alters Chemical Profiles of AdultTribolium castaneum
Authors: Lo Lai Ka , Reshma R , Tewes Lisa Johanna , Milutinović Barbara , Müller Caroline , Kurtz Joachim
Published: March 2021

Group-living individuals experience immerse risk of disease transmission and parasite infection. Especially in social, but also in some non-social insects, disease control with immunomodulation takes place not onlyviaindividual immune defenses, but alsoviainfochemicals such as contact cues and (defensive) volatiles to mount a group level immunity. However, little is known about whether an activation of the immune system leads to changes in chemical phenotypes, which may mediate these responses. We here asked whether individual immune experience resulting from wounding or injection of heat-killedBacillus thuringiensisleads to changes in the chemical profiles of female and male adult red flour beetles (Tribolium castaneum), which are non-social but gregarious. We analyzed insect extracts using GC-FID to study the chemical composition of (1) cuticular hydrocarbons (CHCs) as candidates for the transfer of immunity-related information between individualsviacontact, and (2) stink gland secretions, with target analysis of benzoquinones as main active compounds regulating ‘external immunity’. Despite a pronounced sexual dimorphism in CHC profiles, wounding stimulation led to similar profile changes in males and females with increases in the proportion of methyl-branched alkanes compared to naïve beetles. While changes in the overall secretion profiles were less pronounced, absolute amounts of benzoquinones were transiently elevated in wounded compared to naïve females. We suggest that the changes in different infochemicals may mediate immune status signaling in the context of both internal and external immune responses in groups of this non-social insect, thus showing parallels to social immunity.
Phospholipidosis is a shared mechanism underlying thein vitroantiviral activity of many repurposed drugs against SARS-CoV-2
Authors: Tummino Tia A. , Rezelj Veronica V. , Fischer Benoit , Fischer Audrey , O’Meara Matthew J. , Monel Blandine , Vallet Thomas , Zhang Ziyang , Alon Assaf , O’Donnell Henry R. , Lyu Jiankun , Schadt Heiko , White Kris M , Krogan Nevan J. , Urban Laszlo , Shokat Kevan M. , Kruse Andrew C. , García-Sastre Adolfo , Schwartz Olivier , Moretti Francesca , Vignuzzi Marco , Pognan Francois , Shoichet Brian K.
Published: March 2021

Repurposing drugs as treatments for COVID-19 has drawn much attention. A common strategy has been to screen for established drugs, typically developed for other indications, that are antiviral in cells or organisms. Intriguingly, most of the drugs that have emerged from these campaigns, though diverse in structure, share a common physical property: cationic amphiphilicity. Provoked by the similarity of these repurposed drugs to those inducing phospholipidosis, a well-known drug side effect, we investigated phospholipidosis as a mechanism for antiviral activity. We tested 23 cationic amphiphilic drugs—including those from phenotypic screens and others that we ourselves had found—for induction of phospholipidosis in cell culture. We found that most of the repurposed drugs, which included hydroxychloroquine, azithromycin, amiodarone, and four others that have already progressed to clinical trials, induced phospholipidosis in the same concentration range as their antiviral activity; indeed, there was a strong monotonic correlation between antiviral efficacy and the magnitude of the phospholipidosis. Conversely, drugs active against the same targets that did not induce phospholipidosis were not antiviral. Phospholipidosis depends on the gross physical properties of drugs, and does not reflect specific target-based activities, rather it may be considered a confound in early drug discovery. Understanding its role in infection, and detecting its effects rapidly, will allow the community to better distinguish between drugs and lead compounds that more directly impact COVID-19 from the large proportion of molecules that manifest this confounding effect, saving much time, effort and cost.

One Sentence Summary

Drug-induced phospholipidosis is a single mechanism that may explain thein vitroefficacy of a wide-variety of therapeutics repurposed for COVID-19.