bluuebunny/crossref_metadata_2025 huggingface dataset:
Pavement markings: identification of relevant covariates and controllable factors of retroreflectivity performance as a road safety measure
Authors: Lee Ho Linda , Bueno Filho Júlio Silvio de Souza , Fujii Walquiria Yumiko , Machado Cláudia A S , Bernucci Liedi Legi Bariani , Quintanilha José Alberto
Published: March 2021

In this paper we present relevant contributions and important features related to the study of the retroreflectivity performance of pavement markings. The contribution of this paper is threefold. First, we propose an artificial scheme to allow some randomization of the treatments owing to several restrictions imposed on the choice of the experimental units. It is an experiment involving one fixed factor (three types of materials) in a randomized block design executed on a high-traffic-volume highway. Under this condition, the traffic volume works as a stress factor and the degradation of the retroreflectivity of pavement markings is faster than the degradation on rural roads or streets. This is related to the second contribution: the possibility of a reduction of experimental time. The current experiment spent 20 weeks to collect the data. And finally a mixed linear model considering three random effects and several fixed effects is fitted and the most relevant effects pointed out. This study can help highway managers to improve road safety by scheduling the maintenance of pavement marks at the appropriate time, choosing adequate material for the pavement markings and applying the proposed artificial scheme in future studies.
Risk of hospitalization and risk of death for healthcare workers with COVID-19 in nine European Union/European Economic Area countries, January 2020–January 2021
Authors: Ferland Lisa , Dias Joana Gomes , Carvalho Carlos , Adlhoch Cornelia , Suetens Carl , Beauté Julien , Kinross Pete , Plachouras Diamantis , Lamb Favelle , Hannila-Handelberg Tuula , Fabiani Massimo , Riccardo Flavia , Mossong Joël , Vergison Anne , van Gageldonk-Lafeber Rianne , Teirlinck Anne , Melillo Jackie , Melillo Tanya , Mook Piers , Pebody Richard , Rehse Ana Paula Coutinho , Monnet Dominique L.
Published: March 2021

We assessed the impact of COVID-19 on healthcare workers (HCWs) from data on 2.9 million cases reported from nine countries in the EU/EEA. Compared to non-HCWs, HCWs had a higher adjusted risk of hospitalization (IRR 3.0 [95% CI 2.2-4.0]), but not death (IRR 0.9, 95% CI 0.4-2.0).

Article Summary Line

Healthcare workers are hospitalized more frequently than non-healthcare workers when adjusting for age, sex, and comorbidities.
Direct detection of microorganisms responsible for the sexually transmitted infection on the mobile real-time PCR device without treating in advance
Authors: Muraoka Masaaki , Sohma Kazunori , Kawaguchi Osamu , Mizukoshi Mikio
Published: March 2021

As WHO reported, four curable STIs-chlamydia, gonorrhoea, syphilis and trichomoniasis occur more than 1 million per each day globally almond 2016. For this reason, it is important to control these STIs, one of which is “to detect”. The general methods in order to detect STIs are nucleic acid amplification tests (NAATs). One of the reasons why NAATs are utilized in many tests is that it is possibly to be more sensitive than other test. However, there needs to treat extraction of nucleic acids in advance and amplify specific regions by NAATs, and hence it must take much labour and much time. In this work, for Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Treponema pallidum (TP) which is each etiological agent of chlamydia, gonorrhoea and syphilis, we evaluate and propose “quicker and simpler” NAATs. Specifically, utilizing mobile real-time PCR device “PCR1100” and PCR reagent kit “KAPA3G Plant PCR Kit”, it was considered whether real-time direct PCR could be performed or not without treating DNA extraction in advance so-called “direct”.

As a result, firstly, we established that real-time direct PCR could be performed in all of CT, NG, and TP, and moreover, each Ct value correlated with the concentration of each organism similarly to detection of genome DNA (each correlation coefficient R2 > 0.95). Moreover, each assay demonstrated a limit of detection (LOD) of the follows; CT was 10^0.86 = 7.24 IFU/reaction, NG was 10^-0.19 = 0.65 CFU/reaction, and TP was 10^1.4 = 25.1 organisms/reaction. However, it appeared the sensitivity was a little low, especially for CT and TP.

Secondly, we found that even as without treating sample in advance, the time of detection was required more less 15 minutes at any of case, which was very quick compared with other current methods for real-time PCR. Additionally, compared with other commercial devices, it was easier to operate the PCR1100 device, for example, start, analysis of Ct value.

In conclusion, the present study has demonstrated that it is possible for real-time direct PCR to perform with combination of the PCR1100 device and the PCR reagent kit in 3 kinds of microorganisms-CT, NG and TP. Furthermore, we propose “quicker and simpler” methods for NAATs, which it would not take labour and time. Further studies are needed in order to contribute to control STIs.
Timing of parental depression on risk of child depression and poor educational outcomes: a population based routine data cohort study from Born in Wales, UK
Authors: Brophy Sinead , Todd Charlotte , Rahman Muhammad A , Kennedy Natasha , Rice Frances
Published: March 2021

Background

Maternal depression is a risk factor for depression in children, though the influence of paternal depression has been less well examined. We examined the association between maternal and paternal depression, and the timing of their depression (before or after the child’s birth) and outcomes for the child including incidence of child depression and poor educational attainment.

Methods

A linked routine data cohort study linking General Practitioner(GP), hospital and education records of young people (aged 0 to 30 years) in Wales. Parental and child diagnosis of depression was identified from GP data. Regression analysis examined the association of maternal and paternal depression with time to diagnosis of depression in the child and odds of attaining educational milestones.

Outcomes

In adjusted models, the relative risk of offspring developing depression was 1.22 if the mother had depression before the child was born, 1.55 if the mother had depression after the child was born and 1.73 if she had depression both before and after the child was born (chronic depression), compared to those were there was no maternal depression history. For achieving milestones at end of primary school, odds were 0.92, 0.88 and 0.79 respectively. Association of depression in the child was similar if the male living in the household had depression with risk ratios of 1.24 (before), 1.43 (after) and 1.27 (before and after) for child diagnosed depression and 0.85, 0.79 and 0.74 for achieving age 11 milestones.

Interpretation

Children who live with a parent who has depression are more likely to develop depression and not achieve educational milestones, compared to children who live with a parent who has a history of depression (but no active depression in child’s lifetime) and compared to those with no depression. This finding suggests that working closely with families where depression (particularly chronic depression) is present in either parent and treating parental depression to remission is likely to have long-term benefits for children’s mental health and educational attainment.

Funding

This study had no specific funding. The infrastructure to enable the study was funded by Health Care Research Wales (https://healthandcareresearchwales.org/) which funded; the National Centre for Population Health and Wellbeing Research (https://ncphwr.org.uk/) enabling the involvement of SB, CT, MAR, TK, the National Centre for Mental Health Wales (https://www.ncmh.info/), which supported the involvement of FR, and the Secure Anonymised Information Linkage Database (https://saildatabank.com/)
CNBP, REL, and BHLHE40 variants are associated with IL-12 and IL-10 responses and tuberculosis risk
Authors: Shah Javeed A. , Warr Alex J. , Graustein Andrew D. , Saha Aparajita , Dunstan Sarah J. , Thuong Nguyen T.T. , Thwaites Guy E. , Caws Maxine , Thai Phan V.K. , Bang Nguyen D. , Chau Tran T.H. , Nguyen Felicia K. , Hernandez Carlo A. , Jones Madison A. , Sassetti Christopher M. , Fitzgerald Katherine A. , Musvosvi Munyaradzi , Gela Anele , Hanekom Willem A. , Hatherill Mark , Scriba Thomas J. , Hawn Thomas R.
Published: March 2021

Rationale

The major human genes regulating M. tuberculosis (Mtb)-induced immune responses and tuberculosis (TB) susceptibility are poorly understood. Although IL-12 and IL-10 are critical for TB pathogenesis, the genetic factors that regulate their expression are unknown. CNBP, REL, and BHLHE40 are master regulators of IL-12 and IL-10 signaling.

Objectives

To determine whether common human genetic variation in CNBP, REL and BHLHE40 is associated with IL-12 and IL-10 expression, adaptive immune responses to mycobacteria, and susceptibility to TB.

Methods and Main Measurements

We characterized the association between common variants in CNBP, REL, and BHLHE40 and innate immune responses in dendritic cells and monocyte-derived macrophages (MDM), BCG-specific T cell responses, and susceptibility to pediatric and adult TB.

Results

SNP BHLHE40 rs4496464 was associated with increased BHLHE40 expression in MDMs and increased IL-10 from both peripheral blood dendritic cells and MDMs after LPS and TB whole cell lysate stimulation. SNP BHLHE40 rs11130215, in linkage disequilibrium with rs4496464, was associated with increased BCG-specific IL2+CD4+ T cell responses and decreased risk for pediatric TB in South Africa. SNPs REL rs842634 and CNBP rs11709852 were associated with increased IL-12 production from dendritic cells, and SNP REL rs842618, in linkage disequilibrium with rs842634, was associated with increased risk for TB meningitis.

Conclusions

Genetic variation in CNBP, REL, and BHLHE40 is associated with IL-12 and IL-10 cytokine response and TB clinical outcomes. Common human genetic regulation of well-defined intermediate cellular traits provides insights into mechanisms of TB pathogenesis.
Knowledge transfer to enhance the performance of deep learning models for automated classification of B-cell neoplasms
Authors: Mallesh Nanditha , Zhao Max , Meintker Lisa , Höllein Alexander , Elsner Franz , Lüling Hannes , Haferlach Torsten , Kern Wolfgang , Westermann Jörg , Brossart Peter , Krause Stefan W. , Krawitz Peter M.
Published: March 2021

Multi-parameter flow cytometry (MFC) is a cornerstone in clinical decision making for hematological disorders such as leukemia or lymphoma. MFC data analysis requires trained experts to manually gate cell populations of interest, which is time-consuming and subjective. Manual gating is often limited to a two-dimensional space. In recent years, deep learning models have been developed to analyze the data in high-dimensional space and are highly accurate. Such models have been used successfully in histology, cytopathology, image flow cytometry, and conventional MFC analysis. However, current AI models used for subtype classification based on MFC data are limited to the antibody (flow cytometry) panel they were trained on. Thus, a key challenge in deploying AI models into routine diagnostics is the robustness and adaptability of such models. In this study, we present a workflow to extend our previous model to four additional MFC panels. We employ knowledge transfer to adapt the model to smaller data sets. We trained models for each of the data sets by transferring the features learned from our base model. With our workflow, we could increase the model’s overall performance and more prominently, increase the learning rate for very small training sizes.
Cost-Sharing in Medical Care Can Increase Adult Mortality Risk in Lower-Income Countries
Authors: Buitrago Giancarlo , Miller Grant , Vera-Hernández Marcos
Published: March 2021

Patient cost-sharing in medical care constrains total health spending, presumably with little harm to underlying patient health. This paper re-evaluates the link between cost-sharing and health, studying Colombia’s entire formal sector workforce with individual-level health care utilization records linked to payroll data and vital statistics. Given discrete breaks in outpatient cost-sharing imposed at multiple income thresholds by Colombia’s national health system, we use a regression discontinuity design and find that outpatient cost-sharing reduces use of outpatient care, resulting in fewer diagnoses of common chronic diseases and increasing subsequent emergency room visits and hospitalizations. Ultimately, these effects measurably increase mortality, and disproportionately so among the poor – raising the absolute difference in 7-year mortality risk by 0.80 and 0.23 deaths per 1,000 individuals at lower- and higher-income thresholds, respectively. To the best of our knowledge, this study is the first to show a relationship between cost-sharing and adult mortality risk in lower-income countries, a relationship important to incorporate into social welfare analyses of cost-sharing policies.

One Sentence Summary

Outpatient cost-sharing in medical care discourages use – but over time, also increases costly hospital service use and raises mortality risk.
The COVID-19 health equity twindemic: Statewide epidemiologic trends of SARS-CoV-2 outcomes among racial minorities and in rural America
Authors: Dixon Brian E. , Grannis Shaun J. , Lembcke Lauren , Roberts Anna , Embi Peter J.
Published: March 2021

Background

Early studies on COVID-19 identified unequal patterns in hospitalization and mortality in urban environments for racial and ethnic minorities. These studies were primarily single center observational studies conducted within the first few weeks or months of the pandemic. We sought to examine trends in COVID-19 morbidity and mortality over time for minority and rural populations, especially during the U.S. fall surge.

Methods

Statewide cohort of all adult residents in Indiana tested for SARS-CoV-2 infection between March 1 and December 31, 2020, linked to electronic health records. Primary measures were per capita rates of infection, hospitalization, and death. Age adjusted rates were calculated for multiple time periods corresponding to public health mitigation efforts.

Results

Morbidity and mortality increased over time with notable differences among sub-populations. Initially, per capita hospitalizations among racial minorities were 3-4 times higher than whites, and per capita deaths among urban residents were twice those of rural residents. By fall 2020, per capita hospitalizations and deaths in rural areas surpassed those of urban areas, and gaps between black/brown and white populations narrowed. Cumulative morbidity and mortality were highest among minority groups and in rural communities.

Conclusions

Burden of COVID-19 morbidity and mortality shifted over time, creating a twindemic involving disparities in outcomes based on race and geography. Health officials should explicitly measure disparities and adjust mitigation and vaccination strategies to protect vulnerable sub-populations with greater disease burden.
Comparison of clinical course and outcomes of critically ill patients with SARS-CoV2 infection managed in traditional ICU and “Flex” ICU during the surge of the pandemic in the Bronx
Authors: Gutierrez Victor Perez , Carlos Alex , Nino Jessica , Osella Julieta , Dimitrov Vihren , Kasubhai Moiz , Menon Vidya
Published: March 2021

BACKGROUND

As part of the response to increase critical care capacity during the unprecedented surge of COVID-19 infections, NYC Health + Hospital systems identified and resourced areas in the hospital that could deliver critical care as “Flex” ICUs to complement the traditional ICUs to manage the rapid influx of critically ill patients.

OBJECTIVE

Comparison of clinical features and outcomes of mechanically ventilated COVID-19 patients admitted to the traditional and “Flex” ICUs during the surge of the pandemic

METHODS

Retrospective comparative cohort study of patients with confirmed SARS-CoV-2 infection on mechanical ventilation admitted to traditional ICU and ‘Flex’ ICU. Univariate and multivariate analysis to detect factors associated with death from COVID-19 patients in mechanical ventilation were performed with the Cox proportional hazards regression model

RESULTS

Out of the 312 patients on mechanical ventilation, 111 were admitted to the traditional ICU and 201 to the ‘Flex’ ICU. The mortality rate was higher in the ‘Flex’ ICU compared with the traditional ICU, but the adjusted risk model was not significantly associated with increased mortality

CONCLUSION

“Flex” ICUs played a crucial role in the management of critically ill patients during the pandemic. Mortality risk of patients in the “Flex” ICUs were comparable to traditional ICUs in the adjusted analysis. While there is enough evidence for Intensivist managed ICUs to have better outcomes, our study demonstrates the feasibility of non-intensivist led Flex” ICUs during a crisis.
Characterization of patients that can continue conservative treatment for adenomyosis
Authors: Miyagawa Chiho , Murakami Kosuke , Tobiume Takako , Nonogaki Takafumi , Matsumura Noriomi
Published: March 2021

Introduction

Historically, hysterectomy has been the radical treatment for adenomyosis. However, some patients do not wish to hysterectomy. Nevertheless, patients often required hysterectomy during the course of conservative treatment, but the factors involved remain unknown. The purpose of this study was to determine which patients can continue conservative treatment for adenomyosis.

Materials and Methods

We selected women diagnosed with adenomyosis and provided with conservative treatment at the Kindai University Hospital and Osaka Red Cross Hospital. Age at diagnosis, parity, uterine size, subtype of adenomyosis, type of conservative treatment, and timing of hysterectomy for cases with difficulty continuing conservative treatment were examined retrospectively.

Results

A total of 885 patients were diagnosed with adenomyosis, and 124 started conservative treatment. Conservative treatment was continued in 96 patients (77.4%) and hysterectomy was required in 28 patients (22.6%). The cumulative hysterectomy rate was 32.4%, and all women had hysterectomy within 63 months. In the decision tree analysis, 82% (23/28) of women aged 46 years or younger were able to continue conservative treatment when parity was zero or one. If parity was two and over, 95% (20/21) of those aged 39 years and older had hysterectomy.

Conclusions

Patients that continue conservative treatment for approximately 5 years are more likely to have successful preservation of the uterus. Multipara and higher age of diagnosis are factors that contribute to hysterectomy after conservative treatment. Parity and age at diagnosis may be stratifying factor in future clinical trials on hormone therapy.
Digital Health-Enabled Community-Centered Care (D-CCC): A Scalable Model to Empower Future Community Health Workers utilizing Human-in-the-Loop AI
Authors: Rodrigues Sarah M. , Kanduri Anil , Nyamathi Adeline M. , Dutt Nikil , Khargonekar Pramod P. , Rahmani Amir M.
Published: March 2021

Digital Health-Enabled Community-Centered Care (D-CCC) represents a pioneering vision for the future of community-centered care. Utilizing an artificial intelligence-enabled closed-loop digital health platform designed for, and with, community health workers, D-CCC enables timely and individualized delivery of interventions by community health workers to the communities they serve. D-CCC has the potential to transform the current landscape of manual, episodic and restricted community health worker-delivered care and services into an expanded, digitally interconnected and collaborative community-centered health and social care ecosystem which centers around a digitally empowered community health workforce of the future.
Multi-Omic Profiling of Plasma Identify Biomarkers and Pathogenesis of COVID-19 in Children
Authors: Wang Chong , Li Xufang , Ning Wanshan , Gong Sitang , Yang Fengxia , Fang Chunxiao , Gong Yu , Wu Di , Huang Muhan , Gou Yujie , Fu Shanshan , Ren Yujie , Yang Ruyi , Qiu Yang , Xue Yu , Xu Yi , Zhou Xi
Published: March 2021

Although children usually develop less severe disease responding to COVID-19 than adults, little is known about the pathogenesis of COVID-19 in children. Herein, we conducted the plasma proteomic and metabolomic profiling of a cohort of COVID-19 pediatric patients with mild symptoms. Our data show that numerous proteins and metabolites involved in immune as well as anti-inflammatory processes were up-regulated on a larger scale in children than in adults. By developing a machine learning-based pipeline, we prioritized two sets of biomarker combinations, and identified 5 proteins and 5 metabolites as potential children-specific COVID-19 biomarkers. Further study showed that these identified metabolites not only inhibited the expression of pro-inflammatory factors, but also suppressed coronaviral replication, implying that these factors played key roles in protecting pediatric patients from both viral infection and infection-induced inflammation. Together, our study uncovered a protective mechanism responding to COVID-19 in children, and sheds light on potential therapies.

Teaser

Anti-inflammatory metabolites were highly elevated in the plasma of COVID-19 pediatric patients with mild symptoms.
Prevalence of vitamin D is not associated with the COVID-19 epidemic in Europe. A critical update of the existing evidence
Authors: Bakaloudi Dimitra Rafailia , Chourdakis Michail
Published: March 2021

Background

COVID-19 has emerged as a global pandemic, affecting nearly 104 million people worldwide as of February 4th 2021. In previous published studies, the association between the mean Vit D status of each country and COVID-19 infection rate, and mortality among the adult population in European countries was examined. The aim of this study was to re-examine the relationship between the Vit D status of each country and COVID-19 infection, recovery, and mortality using updated data and a different methodological approach.

Methods

Information only form the last decade on Vit D concentration/deficiency for each country was retrieved through literature search on PubMed® database. As of February, 4th 2021, COVID-19 infections and mortalities per one million population as well as total recoveries were extracted from the Worldometer website. The association between vitamin D deficiency and COVID-19 infection, recovery, and mortality were explored using correlation coefficients and scatterplots.

Findings

The prevalence of vitamin D deficiency among European countries ranged from 6.0 (Finland) to 75.5% (Turkey), with several countries facing more than 50% of vitamin D deficiency among their population. Non-significant correlations were observed between the number of COVID-19 infections (r=0.190; p=0.374), recoveries (rs=0.317, p=0.131), and mortalities (r=0.129; p=0.549) per one million population, with the prevalence of vitamin D deficiency.

Interpretation

Prevalence of vitamin D deficiency was not significantly associated with either number of infections, recoveries or mortality rate of COVID-19 among European countries. Thus, it is an important parameter to be considered when implementing preventive measures to face COVID-19.

Funding

None
Comparing the Evidential Strength for Psychotropic Drugs: A Bayesian Meta-Analysis
Authors: Pittelkow Merle-Marie , de Vries Ymkje Anna , Monden Rei , Bastiaansen Jojanneke A. , van Ravenzwaaij Don
Published: March 2021

Objective

Approval and prescription of drugs should be informed by the strength of evidence for efficacy. While there is no formal policy towards different standards for drug approval, the typical strength of evidence might differ for different psychotropic drug groups. Using a Bayesian framework, we examine (1) whether psychotropic drugs are supported by substantial evidence (at the time of Food and Drug Administration [FDA] approval), and (2) whether there are systematic differences across drug groups.

Methods

Data from short-term, placebo-controlled phase II/III clinical trials for 15 antipsychotics, 16 antidepressants for depression, nine antidepressants for anxiety, and 20 drugs for ADHD were extracted from FDA reviews evaluating efficacy prior to marketing approval. Bayesian model-averaged meta-analysis was performed and strength of evidence was quantified with the Bayes factor (BFBMA).

Results

We observed substantial variation in strength of evidence and trialling between approved psychotropic drugs: Median evidential strength was extremely strong for ADHD medication (BFBMA= 1820.4), but considerably lower and more frequently classified as weak or moderate for antidepressants for both depression (BFBMA= 94.2) and anxiety (BFBMA= 49.8). Differences might be accounted for by varying median effect sizes (schizophrenia:ESBMA= 0.45, depression:ESBMA= 0.30, anxiety:ESBMA= 0.37, ADHD:ESBMA= 0.72), sample sizes (schizophrenia:N= 324, depression:N= 218, anxiety:N= 254, ADHD:N= 189.5), and numbers of trials (schizophrenia:Nr= 3, depression:Nr= 5.5, anxiety:Nr= 3, ADHD:Nr= 2).

Limitations

The analysis only included pre-marketing studies.

Conclusion

Evidential strength varied across drug groups: Although most psychotropic drugs were supported by strong evidence at the time of approval, some drugs only had moderate or even ambiguous evidence. These results show the need for more systematic quantification and classification of statistical evidence for psychotropic drugs, and for transparent and clear communication of evidential strength toward clinical decision makers.

Registration

https://osf.io/5jn2d
Pharmacological targeting of a PWWP domain demonstrates cooperative control of NSD2 localization
Authors: Dilworth David , Hanley Ronan P. , de Freitas Renato Ferreira , Allali-Hassani Abdellah , Zhou Mengqi , Mehta Naimee , Marunde Matthew R. , Ackloo Suzanne , Marcon Edyta , Li Fengling , Chau Irene , Bolotokova Albina , Qin Su , Lei Ming , Liu Yanli , Szewczyk Magdalena M , Dong Aiping , Kazemzadeh Sina , Abramyan Tigran , Popova Irina K , Hall Nathan W , Meiners Matthew J , Cheek Marcus A , Gibson Elisa , Kireev Dmitri , Greenblatt Jack F. , Keogh Michael-C. , Min Jinrong , Brown Peter J. , Vedadi Masoud , Arrowsmith Cheryl H. , Barsyte-Lovejoy Dalia , James Lindsey I , Schapira Matthieu
Published: March 2021

NSD2 is the primary enzyme responsible for the dimethylation of lysine 36 of histone 3 (H3K36me2), a mark associated with active gene transcription and intergenic DNA methylation. In addition to a methyltransferase domain, NSD2 harbors two PWWP and five PHD domains believed to serve as chromatin reading modules, but their exact function in the regulation of NSD2 activity remains underexplored. Here we report a first-in-class chemical probe targeting the N-terminal PWWP (PWWP1) domain of NSD2.UNC6934binds potently (Kdof 91 ± 8 nM) to PWWP1, antagonizes its interaction with nucleosomal H3K36me2, and selectively engages endogenous NSD2 in cells. Crystal structures show thatUNC6934occupies the canonical H3K36me2-binding pocket of PWWP1 which is juxtaposed to the DNA-binding surface. In cells,UNC6934induces accumulation of endogenous NSD2 in the nucleolus, phenocopying the localization defects of NSD2 protein isoforms lacking PWWP1 as a result of translocations prevalent in multiple myeloma. Mutation of other NSD2 chromatin reader domains also increases NSD2 nucleolar localization, and enhances the effect ofUNC6934. Finally we identified two C-terminal nucleolar localization sequences in NSD2 that appear to drive nucleolar accumulation when one or more chromatin reader domains are disabled. These data support a model in which NSD2 chromatin engagement is achieved in a cooperative manner and subcellular localization is controlled by multiple competitive structural determinants. This chemical probe and the accompanying negative control,UNC7145, will be useful tools in defining NSD2 biology.
Multiplexed VaxArray Immunoassay for Rapid Antigen Quantification in Measles and Rubella Vaccine Manufacturing
Authors: Gillis Jacob H. , Thomas Keely N. , Manoharan Senthilkumar , Panchakshari Mallikarjuna , Taylor Amber W. , Miller David F. , Byrne-Nash Rose T. , Riley Christine , Rowlen Kathy L. , Dawson Erica
Published: March 2021

Measles-containing vaccines (MCV), specifically vaccines against measles and rubella (MR), are extremely effective and critical for the eradication of measles and rubella diseases. In developed countries, vaccination rates are high and vaccines are readily available, but continued high prevalence of both diseases in developing countries and surges in measles deaths in recent years have highlighted the need to expand vaccination efforts. To meet demand for additional vaccines at a globally affordable price, it is highly desirable to streamline vaccine production thereby reducing cost and speeding up time to delivery. MR vaccine characterization currently relies on the 50% cell culture infectious dose (CCID50) assay, an endpoint assay with low reproducibility that requires 10-14 days to complete. For streamlining bioprocess analysis and improving measurement precision relative to CCID50, we developed the VaxArray Measles and Rubella assay kit, which is based on a multiplexed microarray immunoassay with a 5-hour time to result. Here we demonstrate vaccine-relevant sensitivity ranging from 345 – 800 IFU/mL up to 100,000 IFU/mL and specificity that allows simultaneous analysis in bivalent vaccine samples. The assay is sensitive to antigen stability and has minimal interference from common vaccine additives. The assay exhibits high reproducibility and repeatability, with 15% CV, much lower than the typical 0.3 log10error (~65%) observed for the CCID50assay. The intact protein concentration measured by VaxArray is reasonably correlated to, but not equivalent to, CCID50infectivity measurements for harvest samples. However, the measured protein concentration exhibits equivalency to CCID50for more purified samples, including concentrated virus pools and monovalent bulks, making the assay a useful new tool for same-day analysis of vaccine samples for bioprocess development, optimization, and monitoring.
Protein-bound sialic acid in saliva contributes directly to salivary anti-influenza virus activity
Authors: Kobayashi Kaori , Shono Chika , Mori Takuya , Kitazawa Hidefumi , Ota Noriyasu , Kurebayashi Yuki , Suzuki Takashi
Published: March 2021

The oral cavity is an entrance for respiratory viruses, such as influenza. Recently, saliva has been shown to exert both antimicrobial and antiviral activities. Thus, saliva may be a biological factor that contributes to the prevention of influenza infection. However, the actual salivary anti-influenza A virus (IAV) activity in individuals and its determinant factors are unknown. By assessing individual variations in salivary anti-IAV activity in 92 people using an established new high-throughput system in this study, we found that the anti-IAV activity varied widely between individuals and showed a significant positive correlation with protein-bound sialic acid (BSA) level (ρ=0.473;p< 0.001). Furthermore, the anti-IAV activity of saliva with enzymatically reduced BSA content was significantly lower. These results indicate that BSA is a direct regulator of salivary anti-IAV activity and is a determinant of individual differences. Additionally, after comparing the anti-IAV activity across the groups by age, anti-IAV activity in young people (aged 5–19 years) were lower than in adults aged 20–59 years and elderly people aged 60–79 years. Our study suggests that BSA levels in saliva may be important in preventing influenza infection.
Exploration of polyyne biosynthetic gene cluster diversity in bacteria leads to the discovery of thePseudomonaspolyyne protegencin
Authors: Mullins Alex J. , Webster Gordon , Kim Hak Joong , Zhao Jinlian , Petrova Yoana D. , Ramming Christina E. , Jenner Matthew , Murray James A. H. , Connor Thomas R. , Hertweck Christian , Challis Gregory L. , Mahenthiralingam Eshwar
Published: March 2021

Natural products that possess alkyne or polyyne moieties have been isolated from a variety of biological sources. In bacteria their biosynthesis has been defined, however, the distribution of polyyne biosynthetic gene clusters (BGCs), and their evolutionary relationship to alkyne biosynthesis, have not been addressed. We explored the distribution of alkyne biosynthesis gene cassettes throughout bacteria, revealing evidence of multiple horizontal gene transfer events. Investigating the evolutionary connection between alkyne and polyyne biosynthesis identified a monophyletic clade possessing a conserved seven-gene cassette for polyyne biosynthesis. Mapping the diversity of these conserved genes revealed a phylogenetic clade representing a polyyne BGC inPseudomonas, pgn, and subsequent pathway mutagenesis and analytical chemistry characterised the associated metabolite, protegencin. In addition to unifying and expanding our knowledge of polyyne diversity, our results show that alkyne and polyyne biosynthetic gene clusters are promiscuous within bacteria. Systematic mapping of conserved biosynthetic genes across bacterial genomic diversity has proven to be a successful method for discovering natural products.
Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows
Authors: Van Den Bossche Tim , Kunath Benoit J. , Schallert Kay , Schäpe Stephanie S. , Abraham Paul E. , Armengaud Jean , Arntzen Magnus Ø. , Bassignani Ariane , Benndorf Dirk , Fuchs Stephan , Giannone Richard J. , Griffin Timothy J. , Hagen Live H. , Halder Rashi , Henry Céline , Hettich Robert L. , Heyer Robert , Jagtap Pratik , Jehmlich Nico , Jensen Marlene , Juste Catherine , Kleiner Manuel , Langella Olivier , Lehmann Theresa , Leith Emma , May Patrick , Mesuere Bart , Miotello Guylaine , Peters Samantha L. , Pible Olivier , Queiros Pedro T. , Reichl Udo , Renard Bernhard Y. , Schiebenhoefer Henning , Sczyrba Alexander , Tanca Alessandro , Trappe Kathrin , Trezzi Jean-Pierre , Uzzau Sergio , Verschaffelt Pieter , von Bergen Martin , Wilmes Paul , Wolf Maximilian , Martens Lennart , Muth Thilo
Published: March 2021

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear.

Here, we carried out the first community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample.

We observed that variability at the peptide level was predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at the protein group level. While differences were observed for predicted community composition, similar functional profiles were obtained across workflows.

CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
Dysbiotic oral and gut viromes in untreated and treated rheumatoid arthritis patients
Authors: Guo Ruochun , Li Shenghui , Zhang Yu , Zhang Yue , Wang Guangyang , Ma Yufang , Yan Qiulong
Published: March 2021

Background

Rheumatoid arthritis (RA) has been considered to be influenced by bacteria from the oral cavity and gut for many years. Despite potential impact of viruses in RA was mentioned in some studies, specific roles of oral and gut viromes in RA is still unclear.

Results

In this study, we observed the viral community variation in the oral and gut samples, performed a comparative analysis of oral and gut viromes in health controls, untreated and treated RA patients, and constructed interaction networks among viruses, bacteria, and RA-associated clinical indexes to address the potential associations between viral community and RA. The results showed that the viromes could be isolated from dental plaque, saliva, and feces samples, among which the saliva having the highest with in-sample diversity. Meanwhile, remarkable variations of viral diversity and composition in the oral (i.e., dental plaque and saliva) virome could be observed in RA patients and healthy controls yet in untreated and treated RA patients, with a relatively low variability in the gut virome. Distraction of viruses-bacteria interaction network was discovered in three sites of RA patients. In addition, some RA-associated oral taxa, includingLactococcus phage vOTU70, Bacteroides vulgatus, Lactococcus lactis, Escherichia coli, Neisseria elongate, were correlated to the RA-related clinical indexes.

Conclusion

Whole-virome analysis illustrated the potential role of oral and gut viral communities in the development of RA.
A specialized bone marrow microenvironment for fetal haematopoiesis
Authors: Liu Yang , Chen Qi , Jeong Hyun-Woo , Watson Emma C. , Xu Cong , Stehling Martin , Zhou Bin , Adams Ralf H.
Published: March 2021

Local signals provided by cells in specialized niche microenvironments regulate stem cell behaviour in many different organs and species. In adult mammalian bone marrow (BM), leptin receptor-positive (LepR+) reticular cells express secreted factors that control the function of haematopoietic stem and progenitor cells (HSPCs). During fetal development, the developing skeletal system is colonized by c-Kit+ haematopoietic cellsde novoafter a transient phase of liver haematopoiesis. The cellular and molecular mechanisms regulatingde novohaematopoietic cell colonization and expansion remain largely unknown. Here, we report that fetal and adult BM exhibit fundamental differences both in terms of cellular composition and molecular interactions by single cell RNA sequencing (scRNA-seq) analysis. While LepR+ reticular cells are almost completely absent in fetal femur, arterial endothelial cells (AECs) are a source of signals controlling the initial HSPC expansion during BM development. Long-term haematopoietic stem cells (HSCs) and other c-Kit+ HSPCs are reduced when Wnt ligand secretion by AECs is genetically blocked. We identify Wnt2 as an AEC-derived signal that directly activates β-catenin dependent proliferation of fetal HSPCs. Treatment of HSPCsex vivowith Wnt2 promotes their proliferation and improves engraftmentin vivoafter transplantation. Our work reveals a fundamental switch in the cellular organization and molecular regulation of BM niches in the embryonic and adult organism.
Mesenchymal Stromal Cell Aging Impairs the Self-Organizing Capacity of Lung Alveolar Epithelial Stem Cells
Authors: Chanda Diptiman , Rehan Mohammad , Smith Samuel R. , Dsouza Kevin G. , Wang Yong , Bernard Karen , Kurundkar Deepali , Memula Vinayak , Kyoko Kojima , Mobley James A. , Benavides Gloria , Darley-Usmar Victor , Young-il Kim , Zmijewski Jaroslaw W. , Deshane Jessy S. , Thannickal Victor J.
Published: March 2021

Multicellular organisms maintain structure and function of tissues/organs through emergent, self-organizing behavior. In this report, we demonstrate a critical role for lung mesenchymal stromal cell (L-MSC) aging in determining the capacity to form 3-dimentional organoids or “alveolospheres “ with type 2 alveolar epithelial cells (AEC2s). In contrast to L-MSCs from aged mice, young L-MSCs support the efficient formation of alveolospheres when co-cultured with young or aged AEC2s. Aged L-MSCs demonstrated features of cellular senescence, altered bioenergetics, and a senescence-associated secretory profile (SASP). The reactive oxygen species generating enzyme, NADPH oxidase 4 (Nox4), was highly activated in aged L-MSCs and Nox4 downregulation was sufficient to, at least partially, reverse this age-related energy deficit, while restoring the self-organizing capacity of alveolospheres. Together, these data indicate a critical role for cellular bioenergetics and redox homeostasis in an organoid model of self-organization, and supports the concept of thermodynamic entropy in aging biology.
A non-coding RNA network involved in KSHV tumorigenesis
Authors: Naipauer Julián , E. García Solá Martín , Salyakina Daria , Rosario Santas , Williams Sion , Coso Omar , C. Abba Martín , Mesri Enrique A. , Lacunza Ezequiel
Published: March 2021

Regulatory pathways involving non-coding RNAs (ncRNAs) such as microRNAs (miRNAs) and long non-coding RNAs (lncRNA) have gained great relevance due to their role in the control of gene expression modulation. Using RNA sequencing of KSHV Bac36 transfected mouse endothelial cells (mECK36) and tumors, we have analyzed the host and viral transcriptome to uncover the role lncRNA-miRNA-mRNA driven networks in KSHV tumorigenesis. The integration of the differentially expressed ncRNAs, with an exhaustive computational analysis of their experimentally supported targets, led us to dissect complex networks integrated by the cancer-related lncRNAs Malat, Neat1, H19, Meg3 and their associated miRNA-target pairs. These networks would modulate pathways related to KSHV pathogenesis, such as viral carcinogenesis, p53 signaling, RNA surveillance, and Cell cycle control. Finally, the ncRNA-mRNA analysis allowed us to develop signatures that can be used to an appropriate identification of druggable gene or networks defining relevant AIDS-KS therapeutic targets.
Allelic expression imbalance ofPIK3CAmutations is frequent in breast cancer and prognostically significant
Authors: Correia Lizelle , Xavier Joana M. , Magno Ramiro , Almeida Bernardo P. de , Esteves Filipa , Duarte Isabel , Eldridge Matthew , Sun Chong , Bosma Astrid , Mittempergher Lorenza , Marreiros Ana , Bernards Rene , Caldas Carlos , Chin Suet-Feung , Maia Ana-Teresa
Published: March 2021

PIK3CA mutations are the most common in breast cancer, particularly in the estrogen receptor positive cohort, but the benefit of PI3K inhibitors has had limited success compared with approaches targeting other less common mutations. We found allelic imbalances in the expression ofPIK3CAin normal breast tissue and mapped a germline candidate regulatory variant. An imbalance was also frequently observed in the expression of the missense mutant and wild-typePIK3CAalleles in breast tumors from METABRIC and TCGA projects. Moreover, although 60% of tumors preferentially expressed the mutant allele, 10% did preferentially express the wild-type allele. Mechanistically, we show that these imbalances are more frequently due to regulatory variants incisthan altered copy-number and predict that somatic variants have a more significant role than germline ones. We further found that imbalanced allelic expression between mutant and wild-type alleles due tocis-regulatory variants associated with poor prognosis (p=0.0081).

Interestingly, ER+, PR+, and Her2−tumors expressing very low levels of the mutant allele had the poorest prognosis (DSS <7.5yrs for ER+and PR+tumors and <5yrs for Her2−tumors). Hence, our work provides compelling evidence to support the clinical utility ofPIK3CAallelic expression in breast cancer in identifying this cohort of low mutant allele expressing patients of poorer prognosis, who will unlikely benefit from PI3K inhibitors. Furthermore, our work establishes a new model of differential regulation of critical cancer-promoting genes.
Host protease activity on bacterial pathogens promotes complement- and antibiotic-directed killing
Authors: Chen Shaorong , Roberts Alexandria-Jade , Lu Felix , Cannon Carolyn , Qin Qing-Ming , de Figueiredo Paul
Published: March 2021

Our understanding of how the host immune system thwarts bacterial evasive mechanisms remains incomplete. Here, we show that host protease neutrophil elastase acts onAcinetobacter baumanniiandPseudomonas aeruginosato destroy factors that prevent serum-associated, complement-directed killing. The protease activity also enhances bacterial susceptibility to antibiotics in sera. These findings implicate a new paradigm where host protease activity on bacteria acts synergistically with the host complement system and antibiotics to defeat bacterial pathogens.
Nrf2 Regulates β-cell Mass by Suppressing Cell Death and Promoting Proliferation
Authors: Baumel-Alterzon Sharon , Katz Liora S. , Brill Gabriel , Jean-Pierre Clairete , Li Yansui , Biswal Shyam , Garcia-Ocaña Adolfo , Scott Donald K.
Published: March 2021

Finding therapies that can protect and expand functional β-cell mass is a major goal of diabetes research. Here we generated β-cell-specific conditional knockout and gain-of-function mouse models and used human islet transplant experiments to examine how manipulating Nrf2 levels affects β-cell survival, proliferation and mass. Depletion of Nrf2 in β-cells resulted in decreased glucose-stimulated β-cell proliferationex vivoand decreased adaptive β-cell proliferation and β-cell mass expansion after a high fat dietin vivo. Nrf2 protects β-cells from apoptosis after a high fat diet. Nrf2 loss-of-function decreases Pdx1 abundance and insulin content. Activating Nrf2 in a β-cell-specific manner increases β-cell proliferation and β-cell mass. Human islets transplanted under the kidney capsule of immunocompromised mice and treated systemically with CDDO-Me, an Nrf2 activator, display increased β-cell proliferation. Thus, Nrf2 regulates β-cell mass and is an exciting therapeutic target for expanding β-cell mass in diabetes.
Mycobacterium abscessusbiofilms produce an ECM and have a distinct mycolic acid profile
Authors: Dokic Anja , Peterson Eliza , Arrieta-Ortiz Mario L , Pan Min , Di Maio Alessandro , Baliga Nitin , Bhatt Apoorva
Published: March 2021

A non-tuberculous mycobacterium (NTM),Mycobacterium abscessusis an emerging opportunistic pathogen associated with difficult to treat pulmonary infections, particularly in patients suffering from cystic fibrosis. It is capable of forming biofilmsin vitrothat result in an increase of already high levels of antibiotic resistance in this bacterium. Evidence thatM. abscessusforms biofilm-like microcolonies in patient lungs and on medical devices further implicated the need to investigate this biofilm in detail. Therefore, in this study we characterized theM. abscessuspellicular biofilm, formed on a liquid-air interface, by studying its molecular composition, and its transcriptional profile in comparison to planktonic cells. Using scanning electron micrographs and fluorescence microscopy, we showed thatM. abscessusbiofilms produce an extracellular matrix composed of lipids, proteins, carbohydrates and eDNA. Transcriptomic analysis of biofilms revealed an upregulation of pathways involved in the glyoxylate shunt, redox metabolism and mycolic acid biosynthesis. Genes involved in elongation and desaturation of mycolic acids were highly upregulated in biofilms and, mirroring those findings, biochemical analysis of mycolates revealed molecular changes and an increase in mycolic acid chain length. Together these results give us an insight into the complex structure ofM. abscessusbiofilms, the understanding of which may be adapted for clinical use in treatment of biofilm infections, including strategies for dispersing the ECM, allowing antibiotics to gain access to bacteria within the biofilm.