bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression QTLs in single-cell sequencing data
Authors: Gewirtz Ariel DH , Townes F William , Engelhardt Barbara E
Published: August 2022

Abstract

Single nucleotide polymorphisms (SNPs) are important drivers of gene expression variation and downstream phenotypes including disease risk. Single-cell RNA-sequencing (scRNA-seq) allows an unprecedented exploration of cell-type specific associations between gene expression levels and genotypes, but current methods rely on pseudobulk approaches that use composite expression values across cells and often use summary statistics within cell types, ignoring information across cell types and assuming cell type labels are accurate. Here, we extend our method, telescoping bimodal latent Dirichlet allocation (TBLDA), that identifies covarying genotypes and gene expression values when the matching from samples to cells is not one-to-one in order to allow cell-type label agnostic discovery of eQTLs in noncomposite scRNA-seq data. In particular, we add GPU-compatibility, sparse priors, and amortization to enable fast inference on large-scale scRNA-seq data. We apply single-cell TBLDA (scTBLDA) to 400K cells from 119 individuals with systemic lupus erythematosus and examine properties of features from each modality across the estimated latent factors. We use linked genes and SNPs to identify 205 cis-eQTLS, 66 trans-eQTLs, and 53 cell type proportion QTLs, which we then compare against prior studies of immune-cell eQTLs. Our results demonstrate the ability of scTBLDA to identify genes involved in cell-type specific regulatory processes associated with SNPs in single-cell data.
Preferential Publication Bias in Nepal’s Medical Journals
Authors: Pant Dipendra Prasad , Acharya Bikram , Kattel Mukunda Raj
Published: August 2022

The article has explored the preferential publication bias of Nepal’s medical journals. To this end, it has reviewed the frequency and proportion of preferential publishing and editorial involvement in endogenous publication practices in six national medical journals registered in the Scopus database system. For the analysis of the data, social network analysis application – VOSviewer for graphical visualisation has been used. Editorial engagement in self-publishing and preferential publishing is found to be common in all journals. The study suggests that as long as the trend of preferential and sequestered publication continues, the integrity and validity generated and disseminated by the journals risks losing trust by the community concerned and the chances of these non-mainstream journals contributing to mainstream journals being slim. And, by way of recommendatory conclusions, it offers the following four questions and areas for further investigation to arrive at the clarity and understanding of some of the issues that have been flagged in the findings and discussions: (a) Why do editors engage in excess self-promotion using the outlet they are supposed to objectively and transparently manage? (b) What is the motivating factor for authors to rely on a particular journal to get published despite having multiple outlets to pick and choose from? (c) Why should the editors and reviewers of scientific contributions maintain the networking silo to include a few in the loop and exclude others from it?
The maternal profile associated with the underlying root cause of neonatal mortality using machine learning and administrative health data
Authors: Beluzo Carlos Eduardo , Carvalho Tiago , Alves Luciana Correia
Published: August 2022

Infant mortality is a reflection of an analysis of biological, socioeconomic, and assistance factors. An analytical analysis of this problem implies the processing of large sets of data from different areas. Data Science approaches have become increasingly widespread to deal with problems that require large datasets to perform deep analysis. Machine learning methods have become popular due to their efficiency and efficacy in discovering knowledge by identifying patterns in feature interactions of large datasets. This work proposes the use of a machine learning approach to evaluate the association between sociodemographic factors and preventable root causes of neonatal mortality. For this, demographic and epidemiological data from Brazilian public health birth and mortality (SINASC and SIM, respectively) information systems were used. Using an unsupervised approach, for instance, the K-Modes clustering algorithm, clusters were created, so we are able to evaluate the socio-demographic profile of each one of the clusters. In this way, it is possible to evaluate the differences between the profiles of each cluster. The profile consists of features such as maternal age, maternal years of schooling, race, number of consultations, type of delivery, public or private hospital, and date of first prenatal consultation. The analysis was performed using data from the period between 2012 and 2018, for the city of São Paulo, one of the richest regions of the country. The data quality for this region is considered to be very high, so there is no need to apply data correction methods. Besides that, the method adapted does not require data assumptions, and it’s suitable for categorical data, which is our case. Considering that this is a data-driven approach, preliminary results indicate that only a few assumptions can be made on profile using these features, although some associations between demographic variables and neonatal mortality by preventable root causes can be identified. We hope to encourage reflection on the newborn in the socioeconomic environment and contribute to public health policies.
The impact of the Covid-19 pandemic on Italian population-based cancer screening activities and test coverage: results from national cross-sectional repeated surveys
Authors: Rossi Paolo Giorgi , Carrozzi Giuliano , Falini Patrizia , Sampaolo Letizia , Gorini Giuseppe , Zorzi Manuel , Armaroli Paola , Senore Carlo , de Bianchi Priscilla Sassoli , Masocco Maria , Zappa Marco , Battisti Francesca , Mantellini Paola
Published: August 2022

Background

In Italy, population-based screening programs for breast, cervical and colorectal cancers are mandatory, and Regions are in charge of their delivery. From March to May 2020, a severe lockdown was imposed due to the Covid-19 pandemic by the Italian Ministry of Health, with the suspension of screening programs. This paper describes the impact of the pandemic on Italian screening activities and test coverage in 2020.

Methods

The regional number of subjects invited and of screening tests performed in 2020 were compared with those in 2019. Invitation and examination coverage were also calculated. PASSI surveillance system, through telephone interviews, investigated the population screening test coverage, before and during the pandemic, accordingly to educational attainment, perceived economic difficulties and citizenship.

Results

A reduction of subjects invited and tests performed, with differences among periods and geographic macro areas, was observed in 2020 vs. 2019. The reduction in examination coverage was larger than that in invitation coverage for all screening campaigns. From the second half of 2020, the trend for test coverage showed a decrease in all the macro areas for all the screening campaigns. Compared with the pre-pandemic period, there was a greater difference according to level of education in the odds of having had a test last year vs. never having been screened or not being up to date with screening tests. In addition, foreigners had less access to screening than Italians did.

Conclusions

The lockdown and the ongoing Covid-19 emergency caused an important delay in screening activities. This increased the pre-existing individual and geographical inequalities in access. The opportunistic screening did not mitigate the pandemic impact.

Funding

This study was partially supported by Italian Ministry of Health – Ricerca Corrente Annual Program 2023.
Early estimates of the incidence trend and the reproductive number of the monkeypox epidemic in Brazil
Authors: Schrarstzhaupt Isaac N. , Fontes-Dutra Mellanie , Diaz-Quijano Fredi Alexander
Published: August 2022

Objectives

We aimed to calculate the weekly growth of the incidence and the effective reproductive number (Rt) of the 2022 Monkeypox epidemic during its introduction in Brazil.

Methods

We described the case distribution in the country and calculated the incidence trend and the Rt in the four geographical states with the highest case reports. By using two regression approaches, count model and the Prais-Winsten, we calculated the relative incidence increase. Moreover, we estimated the Rt for the period between the 24th and the 50th days after the first official report, using a serial interval reported in another population and two alternative values (±3 days).

Results

Up to August 22, 3.896 Monkeypox cases were confirmed in Brazil. The weekly incidence increases were between 37.5% (95% CI: 20.7% -56,6%) and 82.1% (95% CI: 59.5% -107.8%), and all estimates of Rt were statistically higher than 1 in the four states analyzed.

Conclusion

The Monkeypox outbreak in Brazil is a significant public health emergency that requires coordinated public health strategies such as testing, contact tracing, and vaccination.
Perfusion imaging heterogeneity during NO inhalation distinguishes pulmonary arterial hypertension (PAH) from healthy subjects and has potential as an imaging biomarker
Authors: Winkler Tilo , Kohli Puja , Kelly Vanessa J , Kehl Ekaterina G. , Witkin Alison S. , Rodriguez-Lopez Josanna , Hibbert Kathryn A. , Kone Mamary , Systrom David M. , Waxman Aaron B. , Venegas Jose G. , Channick Richard , Harris R. Scott
Published: August 2022

Background

Without aggressive treatment, pulmonary arterial hypertension (PAH) has a 5-year mortality of approximately 40%. A patient’s response to vasodilators at diagnosis impacts the therapeutic options and prognosis. We hypothesized that analyzing perfusion images acquired before and during vasodilation could identify characteristic differences between PAH and control subjects.

Methods

We studied 5 controls and 4 subjects with PAH using HRCT and13NN PET imaging of pulmonary perfusion and ventilation. The total spatial heterogeneity of perfusion (CV2Qtotal) and its components in the vertical (CV2Qvgrad) and cranio-caudal (CV2Qzgrad) directions, and the residual heterogeneity (CV2Qr), were assessed at baseline and while breathing oxygen and nitric oxide (O2+iNO). The length scale spectrum of CV2Qrwas determined from 10 to 110 mm, and the response of regional perfusion to O2+iNO was calculated as the mean of absolute differences. Vertical gradients in perfusion (Qvgrad) were derived from perfusion images, and ventilation-perfusion distributions from images of13NN washout kinetics.

Results

O2+iNO significantly enhanced perfusion distribution differences between PAH and controls, allowing differentiation between PAH subjects from controls. During O2+iNO, CV2Qvgradwas significantly higher in controls than in PAH (0.08 (0.055-0.10) vs. 6.7 × 10−3(2×10−4-0.02), p<0.001) with a considerable gap between groups. Qvgradand CV2Qtotalshowed smaller differences: –7.3 vs. -2.5, p = 0.002, and 0.12 vs. 0.06, p = 0.01. CV2Qvgradhad the largest effect size among the primary parameters during O2+iNO. CV2Qr, and its length scale spectrum were similar in PAH and controls. Ventilation-perfusion distributions showed a trend towards a difference between PAH and controls at baseline, but it was not statistically significant.

Conclusions

Perfusion imaging during O2+iNO showed a significant difference in the heterogeneity associated with the vertical gradient in perfusion, distinguishing in this small cohort study PAH subjects from controls.

Trial registration

Not applicable
Lower risks of sodium glucose cotransporter 2 (SGLT2) inhibitors compared to dipeptidyl peptidase-4 (DPP4) inhibitors for new-onset non-alcoholic fatty liver disease and hepatocellular carcinoma in type 2 diabetes mellitus: A population-based study
Authors: Chou Oscar Hou In , Ning Jing , Chiu Chan Raymond Ngai , Chung Cheuk To , Huang Helen , Ng Kenrick , Dee Edward Christopher , Lee Sharen , Kaewdech Apichat , Liu Tong , Jing Fengshi , Yung Cheung Bernard Man , Tse Gary , Zhou Jiandong
Published: August 2022

Background

The association between sodium glucose cotransporter 2 inhibitors (SGLT2I) versus dipeptidyl peptidase-4 inhibitors (DPP4I) and the risks of non-alcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC) are currently unknown.

Methods

This was a retrospective population-based cohort study including type-2 diabetes mellitus (T2DM) patients treated with either SGLT2I or DPP4I between 1stJanuary 2015 and 31stDecember 2019 in Hong Kong. Patients with concurrent DPP4I and SGLT2I usage were excluded. The primary outcomes were NAFLD and HCC. The secondary outcomes included cancer-related mortality and all-cause mortality. Propensity score matching (1:1 ratio) was performed using the nearest neighbour search. Univariable and multivariable Cox regression was applied to identify significant predictors. Competing risks models and multiple approaches using the propensity score were performed.

Results

This cohort included 62699 patients with T2DM, amongst which 22154 patients were on SGLT2I and 40545 patients were on DPP4I. After matching (44308 patients), 1090 patients developed new-onset NAFLD (Incidence: 4.6; 95% Confidence interval [CI]: 4.3-4.9) and 187 patients developed HCC (Incidence: 0.8; 95% CI: 0.7-0.9). Overall, SGLT2I was associated with lower risks of NAFLD (Hazard ratio [HR]: 0.39; 95% CI: 0.34-0.46), and HCC (HR: 0.46; 95% CI: 0.29-0.72) compared to DPP4I after adjustments. SGLT2I was also associated with lower risks of cancer-related mortality (HR: 0.29; 95% CI: 0.23-0.37) and all-cause mortality (HR: 0.28; 95% CI: 0.25-0.31). However, amongst patients with hepatitis B virus infection, SGLT2I was associated with higher risks of HCC (HR: 3.28; 95% CI: 1.21-8.90). The results were consistent in competing risk models and different matching approaches.

Conclusion

SGLT2I was associated with lower risks of NAFLD, and HCC compared to DPP4I after propensity scores matching and adjustments.

Lay summary

The association between two antidiabetic medications, SGLT2I and DPP4I, and the risks of fatty liver disease and liver cancer have not been explored. In our study, SGLT2I was associated with a lower risk of fatty liver disease and liver cancer compared to DPP4I amongst patients with type 2 diabetes. However, DPP4I was associated with lower risks of liver cancer compared to SGLT2I among patients with hepatitis B virus infection

Central illustration
Public health benefits of shifting from inpatient to outpatient TB care in Eastern Europe: optimising TB investments in Belarus, the Republic of Moldova, and Romania
Authors: Kelly Sherrie L , Abou Jaoude Gerard Joseph , Palmer Tom , Skordis Jolene , Haghparast-Bidgoli Hassan , Goscé Lara , Jarvis Sarah J , Kedziora David J , Abeysuriya Romesh , Benedikt Clemens , Fraser-Hurt Nicole , Shubber Zara , Cheikh Nejma , Bivol Stela , Roberts Anna , Wilson David P , Martin-Hughes Rowan
Published: August 2022

Background

High rates of drug-resistant tuberculosis (DR TB) continue to threaten public health, especially in Eastern Europe. Costs for treating DR TB are substantially higher than treating drug-susceptible TB, and higher yet if DR TB services are delivered in hospital. Therefore, countries are encouraged to transition from inpatient to ambulatory-focused TB care, which has been shown to have non-inferior health outcomes.

Methods

Allocative efficiency analyses were conducted for three countries in Eastern Europe, Belarus, the Republic of Moldova, and Romania to minimise a combination of active TB cases, prevalence of active TB, and TB-related deaths by 2035. These mathematical optimisations were carried out using Optima TB, a dynamical compartmental model of TB transmission. The focus of this study was to project the health and financial gains that could be realised if TB service delivery shifted from hospital to ambulatory-based care.

Findings

These analyses show that transitioning from inpatient to ambulatory TB care could reduce treatment costs by 5%−31% or almost 35 million US dollars across these three countries without affecting the quality of care. Improved TB outcomes could be achieved without additional spending by reinvesting these potential savings in cost-effective prevention and diagnosis interventions.

Conclusions

National governments should examine barriers delaying the adoption of outpatient DR TB care and consider the lost opportunities caused by delays in switching to more efficient and effective treatment modes.
E-cigarette aerosol exposure of pulmonary surfactant impairs its surface tension reducing function
Authors: Graham Emma , McCaig Lynda , Lau Gloria Shui-Kei , Tejura Akash , Cao Anne , Zuo Yi Y. , Veldhuizen Ruud
Published: August 2022

E-cigarette (EC) and vaping use continue to remain popular amongst teenage and young adult populations, despite several reports of vaping associated lung injury. This popularity is due in part to the vast variety of appealing flavours and nicotine concentrations easily accessible on the market. One of the first compounds that EC aerosols comes into contact within the lungs during a deep inhalation is pulmonary surfactant. This lipid protein mixture lines the alveoli, reducing surface tension and preventing alveolar collapse. Impairment of surfactant’s critical surface tension reducing activity can contribute to lung dysfunction. Currently, information on how EC aerosols impacts pulmonary surfactant remains limited. We hypothesized that exposure to EC aerosol impairs the surface tension reducing ability of surfactant. Bovine Lipid Extract Surfactant (BLES) was used as a model surfactant in a direct exposure syringe system. BLES (2ml) was placed in a syringe (30ml) attached to an EC. The generated aerosol was drawn into the syringe and then expelled, repeated 30 times. Biophysical analysis after exposure was completed using a constrained drop surfactometer (CDS). Minimum surface tensions increased after exposure to the EC aerosol. Variation in device used, addition of nicotine, or temperature of the aerosol had no additional effect. Two e-liquid flavours, menthol and red wedding, had further detrimental effects, resulting in higher surface tension than the vehicle exposed BLES. Alteration of surfactant properties through interaction with the produced aerosol was observed with a basic e-liquid vehicle, however additional compounds produced by added flavourings appeared to be able to increase inhibition. In conclusion, EC aerosols alter surfactant function through increases in minimum surface tension. This impairment may contribute to lung dysfunction and susceptibility to further injury.
Structural determinants of REMORIN nanodomain formation in anionic membranes
Authors: Legrand Anthony , Cava Daniel G. , Jolivet Marie-Dominique , Decossas Marion , Lambert Olivier , Bayle Vincent , Jaillais Yvon , Loquet Antoine , Germain Véronique , Boudsocq Marie , Habenstein Birgit , Vélez Marisela , Mongrand Sébastien
Published: August 2022

Remorins are a family of multigenic phosphoproteins of the plasma membrane, involved in biotic and abiotic plant interaction mechanisms, partnering in molecular signaling cascades. Signaling activity of remorins depends on their phosphorylation states and subsequent clustering into nano-sized membrane domains. The presence of a coiled-coil domain and a C-terminal domain is crucial to anchor remorins to negatively charged membrane domains, however the exact role of the N-terminal intrinsically disordered domain (IDD) on protein clustering and lipid interactions is largely unknown. Here we combine chemical biology and imaging approaches to study the partitioning of group 1 remorin into anionic model membranes mimicking the inner leaflet of the plant plasma membrane. Using reconstituted membranes containing a mix of saturated and unsaturated PhosphatidylCholine (PC), PhosphatidylInositol Phosphates (PIPs), and sterol, we investigate the clustering of remorins to the membrane and monitor the formation of nano-sized membrane domains. REM1.3 promoted membrane nanodomain organization on the exposed external leaflet of both spherical lipid vesicles and flat supported lipid bilayers. Our results reveal that REM1.3 drives a mechanism allowing lipid reorganization, leading to the formation of remorin-enriched nanodomains. Phosphorylation of the N-terminal IDD by the calcium protein kinase CPK3 influences this clustering and can lead to the formation of smaller and more disperse domains. Our work reveals the phosphate-dependent involvement of the N-terminal IDD in the remorin-membrane interaction process by driving structural rearrangements at lipid-water interfaces.

Summary heading

Using reconstituted membranes, we demonstrated the clustering of the plant protein remorins StREM1.3 to the lipid bilayer external leaflet and monitor the formation of nanodomains of the protein.
Optimization and validation of a Protein Phosphatase inhibition assay for accessible microcystin detection
Authors: Alba Posse JE , Gonzalez C , Carriquiriborde P , Nadra A , Gasulla J
Published: August 2022

The presence of cyanobacterial toxins in freshwater constitutes an increasing public health concern, especially affecting developing countries where the high cost of available methods makes monitoring programs difficult. The phosphatase inhibition assay (PPIAs) is a sensitive method with low instrument requirements that allows the quantification of the most frequent cyanotoxins, microcystins (MC). In this work, we implemented a PPIAs, starting from Protein Phosphatase 1 (PP1) expression up to the validation with samples of algal blooms from Argentina. To do this, we optimized the expression and lyophilization of PP1, and the assay conditions. Also, we included robustness and possible interfering analysis. We evaluated the most widely used cyanobacterial lysis methods and determined that heating for 15 minutes at 95°C is simple and adequate for this assay. Then, we performed MC spikes recovery assays on water samples from three dams from Argentina, resulting in a recovery ranging from 77 to 115%. The limit of detection (LOD) was 0.4 μg/L and the linear range is 0.4 μg/L - 5 μg/L. Finally, we evaluated 64 environmental samples where MC was measured by ELISA test containing from 0 μg/L to 625 μg/L. The PPIA showed excellent correlation (Pearson correlation coefficient = 0.967), no false negative and no false positives above the 1 μg/L WHO guideline (0.11 false positive rate). In conclusion, we optimized and validated a PPIAs to be an effective and accessible alternative to available commercial tests.
Kokiri: Random-Forest-Based Comparison and Characterization of Cohorts
Authors: Eckelt Klaus , Adelberger Patrick , Bauer Markus J. , Zichner Thomas , Streit Marc
Published: August 2022

Abstract

We propose an interactive visual analytics approach to characterizing and comparing patient subgroups (i.e., cohorts). Despite having the same disease and similar demographic characteristics, patients respond differently to therapy. One reason for this is the vast number of variables in the genome that influence a patient’s outcome. Nevertheless, most existing tools do not offer effective means of identifying the attributes that differ most, or look at them in isolation and thus ignore combinatorial effects. To fill this gap, we present Kokiri, a visual analytics approach that aims to separate cohorts based on user-selected data, ranks attributes by their importance in distinguishing between cohorts, and visualizes cohort overlaps and separability. With our approach, users can additionally characterize the homogeneity and outliers of a cohort. To demonstrate the applicability of our approach, we integrated Kokiri into the Coral cohort analysis tool to compare and characterize lung cancer patient cohorts.
Genetic variations in G-Quadruplex forming sequences affect the transcription of human disease-related genes
Authors: Lorenzatti Agustín , Piga Ernesto J. , Gismondi Mauro , Binolfi Andrés , Margarit Ezequiel , Calcaterra Nora B. , Armas Pablo
Published: August 2022

Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4s). G4s folded in proximal promoter regions (PPR) are associated either with positive or negative transcriptional regulation. Given that single nucleotide variants (SNVs) affecting G4 folding (G4-Vars) may alter gene transcription, and that SNVs are associated with the human diseases’ onset, we undertook a comprehensive study of the G4-Vars genome-wide (G4-variome) to find disease-associated G4-Vars located into PPRs. We developed a bioinformatics strategy to find disease-related SNVs located into PPRs simultaneously overlapping with putative G4-forming sequences (PQSs). We studied five G4-Vars disturbing in vitro the folding and stability of the G4s located into PPRs, which had been formerly associated with sporadic Alzheimer’s disease (GRIN2B), a severe familiar coagulopathy (F7), atopic dermatitis (CSF2), myocardial infarction (SIRT1), and deafness (LHFPL5). Results obtained in cellulo for GRIN2B and F7 suggest that the G4 disruption due to the identified G4-Vars affect the transcription and are responsible for the mentioned diseases. Collectively, data suggest that G4-Vars may account for the different susceptibilities to human genetic diseases’ onset, and could be novel targets for diagnosis and drug design in precision medicine.
Concurrent measures of impulsive action and choice are partially related and differentially modulated by dopamine D1- and D2-like receptors in a rat model of impulsivity
Authors: Bellés Lidia , Arrondeau Chloé , Urueña-Méndez Ginna , Ginovart Nathalie
Published: August 2022

Impulsivity is a multidimensional construct, but the relationships between its constructs and their respective underlying dopaminergic underpinnings in the normal population remain unclear. A large cohort of Roman high-(RHA) and low- (RLA) avoidance rats were tested for impulsive action and risky decision-making in the rat gambling task, and then for delay discounting in the delay discounting task to concurrently measure the relationships among the three constructs of impulsivity using a within-subject design. Then, we evaluated the effects of dopaminergic drugs on the three constructs of impulsivity, considering innate differences in impulsive behaviors at baseline. Risky decision-making and delay discounting were positively correlated, indicating that both constructs of impulsive choice are related. Impulsive action positively correlated with risky decision-making but not with delay discounting, suggesting partial overlap between impulsive action and impulsive choice. RHAs showed a more impulsive phenotype in the three constructs of impulsivity compared to RLAs, demonstrating the comorbid nature of impulsivity in a normal population. While amphetamine increased impulsive action and had no effects on risky decision-making regardless of baseline levels of impulsivity, it decreased delay discounting but only in high impulsive RHAs. Conversely, the D1R agonist SKF81297, D3R agonist PD128907 and D2/3R partial agonist aripiprazole decreased impulsive action irrespective of baseline levels of impulsivity, whereas D2/3R agonism with quinpirole decreased it exclusively in high impulsive RHAs. Risky decision-making was increased by SKF81297 and quinpirole but not PD128907 and aripiprazole, with quinpirole producing baseline-dependent effects, increasing risky decision-making only in low impulsive RLAs. Finally, while SKF81297, PD128907 and aripiprazole increased delay discounting irrespective of baseline levels of impulsivity, quinpirole decreased it in low impulsive RLAs only. These findings indicate that the acute effects of dopamine drugs were partially overlapping across dimensions of impulsivity, and that only D2/3R agonism showed baseline-dependent effects on the three constructs of impulsivity.
Social media at metabolic meetings: who is tweeting what and for whom?
Authors: Nurse James
Published: August 2022

BACKGROUND

The social media site Twitter has been widely embraced in medical circles for its ability to connect individuals and support rapid information sharing. Critics say that the messages shared may not accurately reflect what was said and that sharing meeting content could devalue conferences themselves. It is unclear how it is used at SSIEM and what value it may bring.

METHODS

Twitter’s tweetdeck software was used to find all tweets containing the conference ‘hashtag’ #SSIEM2018. All tweets were reviewed to identify the author, see what had been shared and count replies, likes and retweets. Authors were grouped by professional background and tweet content was broken down by type of material shared and theme.

RESULTS

122 relevant tweets were sent during the fortnight at the beginning of September 2018, creating over 400,000 impressions. There were a further 73 replies with approximately 13 engagements (likes, replies or retweets) per tweet. 36 people wrote tweets (rate: 3.4 per person [1-33]). One quarter of the tweets shared poster content and over one third of tweets related to Phenylketonuria materials. 50 of the tweets were produced by just two accounts, both intended to provide information to patients and their families.

DISCUSSION

Tweets where no hashtag was used cannot be identified and restrictions within Twitter prevent certain analyses on tweet data greater than 30 days old. However, Twitter uptake within metabolic medicine is significantly behind other specialities where conference tweets can exceed 20,000. Information shared is typically intended for patients rather than other health professionals; this suggests a different uptake to more mainstream specialities. Presenting teams should be aware that their work may be received directly by patients and families and consider how best to present their messages for all who may receive them.
Bioassay-guided isolation and characterization of anti-bacterial compound fromSonneratia apetalaBuch. Ham leaf, from Maharashtra coast of India
Authors: Dhane-Sarkar Jaimini , Sarkar Chiradeep , Jadhav B.L.
Published: August 2022

Mangroves, collection of plants growing in coastal intertidal zones, are rich source of unique bioactive phytochemicals present in their bark, roots, leaves and fruits. They show anti-diabetic, anti-cancer, anti-hypertensive, anti-malarial, anti-bacterial, anti-inflammatory and anti-oxidant properties. In this study, a bioassay-guided isolation and characterization approach was taken to study the anti-bacterial compound fromSonnerartia apetalaBuch. Ham leaf. Petroleum ether, acetone and water extracts were prepared and tested against eight human pathogenic bacteria. Water and acetone extracts have shown the inhibition of bacteria but the acetone extract was carried forward for further study. The compound was isolated using preparative column chromatography method. The isolated compound was studied for anti-bacterial activity using TLC-bioautography . The bioactive compound was isolated and tested against standard antibiotics and showed positive results againstE. coliandB.subtilis. The isolated pure compound was studied for detection of elements and melting point. Further chacterization was done using UV-Vis spectroscopy and FT-IR spectroscopy indicating absorption in the UV spectrum and presence of aromatic and aliphatic groups. This study validates the importance ofSonneratia apetalaleaves as an important resource in traditional medicine for anti-bacterial remedies aimed at human pathogenic diseases.
A novel batokine Breg controls adipose thermogenesis and glucose homeostasis
Authors: Chen Qingbo , Huang Lei , Pan Dongning , Hu Kai , Li Rui , Zhu Lihua J. , Guertin David A. , Wang Yong-Xu
Published: August 2022

Batokines selectively expressed in brown and beige adipocytes remain to be identified and their potential signaling role in adipose thermogenesis are largely unknown. Here we identified a batokine we named as Breg acting as a key regulator for adipose thermogenesis and glucose homeostasis. Breg expression is adipose-specific and highly brown fat-enriched, and its secretion is stimulated by β3-adrenergic activation. Gain-of-functional studies collectively showed that secreted Breg promotes adipose thermogenesis, lowers glucose level, and protects against obesity. Adipose-specific Breg knockout mice are defective in white fat browning, and are susceptible to high fat diet-induced obesity and hyperglycemia, demonstrating the physiological importance of this batokine in energy metabolism. Mechanistically, Breg binds to a putative receptor on adipocyte surface and activates protein kinase A independently of β-adrenergic signaling. These results establish Breg as a major upstream signaling component in thermogenesis and offer a potential avenue for the treatment of obesity and diabetes.
Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds
Authors: Wamhoff Eike-Christian , Ronsard Larance , Feldman Jared , Knappe Grant A. , Hauser Blake M. , Romanov Anna , Lam Evan , Denis Kerri St. , Boucau Julie , Barczak Amy K , Balazs Alejandro B. , Schmidt Aaron , Lingwood Daniel , Bathe Mark
Published: August 2022

Multivalent antigen display is a well-established principle to enhance humoral immunity. Protein-based virus-like particles (VLPs) are commonly used to spatially organize antigens. However, protein-based VLPs are limited in their ability to control valency on fixed scaffold geometries and are thymus-dependent antigens that elicit neutralizing B cell memory themselves, which can distract immune responses. Here, we investigated DNA origami as an alternative material for multivalent antigen display in vivo, applied to the receptor binding domain (RBD) of SARS-CoV-2 that is the primary antigenic target of neutralizing antibody responses. Icosahedral DNA-VLPs elicited neutralizing antibodies to SARS-CoV-2 in a valency-dependent manner following sequential immunization in mice, quantified by pseudo-and live-virus neutralization assays. Further, induction of B cell memory against the RBD required T cell help, but the immune sera did not contain boosted, class-switched antibodies against the DNA scaffold. This contrasted with protein-based VLP display of the RBD that elicited B cell memory against both the target antigen and the scaffold. Thus, DNA-based VLPs enhance target antigen immunogenicity without generating off-target, scaffold-directed immune memory, thereby offering a potentially important alternative material for particulate vaccine design.
Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations
Authors: Pokorná Pavlína , Krepl Miroslav , Campagne Sébastien , Šponer Jiří
Published: August 2022

RNA-protein complexes use diverse binding strategies, ranging from structurally well-defined interfaces to completely disordered regions. Experimental characterization of flexible segments is challenging and can be aided by atomistic molecular dynamics (MD) simulations. Here we used extended set of microsecond-scale MD trajectories (400 μs in total) to study two FUS-RNA constructs previously characterized by NMR spectroscopy. The FUS protein contains well-structured RNA Recognition Motif domain followed by presumably disordered RGG tail and bind RNA stem-loop hairpins. Our simulations provide several suggestions complementing the experiments but also reveal major methodological difficulties in studies of such complex RNA-protein interfaces. Despite efforts to stabilize the binding via system-specific force-field adjustments, we have observed progressive distortions of the RNA-protein interface inconsistent with experimental data, as in detail documented. We further propose that the dynamics is so rich that its converged description would not be achievable even upon stabilizing the system. Still, after careful analysis of the trajectories, we have made several suggestions regarding the binding. We identify substates in the RNA loops which can explain the NOE data. The RGG tail localized in the minor groove remains disordered, sampling countless transient interactions with the RNA. There are long-range couplings among the different elements contributing to the recognition, which can lead to allosteric communication throughout the system. Overall, the RNA-FUS systems form dynamical ensembles that cannot be fully represented by single static structures. Thus, albeit imperfect, MD simulations represent a viable tool to investigate them.
Estimating sequence diversity of prion protein gene (PRNP) in Portuguese populations of two cervid species: red deer and fallow deer
Authors: Pereira Jorge C. , Gonçalves-Anjo Nuno , Orge Leonor , Pires Maria A. , Rocha Sara , Figueira Luís , Matos Ana C. , Silva João , Mendonça Paula , Carvalho Paulo , Tavares Paula , Lima Carla , Alves Anabela , Esteves Alexandra , Pinto Maria L. , Pires Isabel , Gama Adelina , Sargo Roberto , Silva Filipe , Seixas Fernanda , Vieira-Pinto Madalena , Bastos Estela
Published: August 2022

Among the transmissible spongiform encephalopathies (TSEs), chronic wasting disease (CWD) in cervids is now a rising concern in wildlife within Europe, after the detection of the first case in Norway in 2016, in a wild reindeer and until June 2022 a total of 34 cases were described in Norway, Sweden and Finland. The definite diagnosis is postmortem, performed in target areas of the brain and lymph nodes. Samples are first screened using a rapid test and, if positive, confirmed by immunohistochemistry and Western immunoblotting. The study of the genetics of the prion protein gene, PRNP, has been proved to be a valuable tool for determining the relative susceptibility to TSEs. In the present study, the exon 3 of PRNP gene of 143 samples from red deer (Cervus elaphus) and fallow deer (Dama dama) of Portugal was analyzed. Three single nucleotide polymorphisms (SNPs) were found in red deer – codon A136A, codon T98A, codon Q226E – and no sequence variation was detected in fallow deer. The low genetic diversity found in our samples is compatible with previous studies in Europe. The comparison with results from North America, suggests that the free-ranging deer from our study may present susceptibility to CWD, although lack of experimental data and the necessity of extensive survey are necessary to evaluate these populations.
Multimodal Assessment of Non-Alcoholic Fatty Liver Disease with Transmission-Reflection Optoacoustic Ultrasound
Authors: Lafci Berkan , Hadjihambi Anna , Konstantinou Christos , Herraiz Joaquin L. , Pellerin Luc , Burton Neal C. , Deán-Ben Xosé Luís , Razansky Daniel
Published: August 2022

Non-alcoholic fatty liver disease (NAFLD) is an umbrella term referring to a group of conditions associated to fat deposition and damage of liver tissue. Early detection of fat accumulation is essential to avoid progression of NAFLD to serious pathological stages such as liver cirrhosis and hepatocellular carcinoma. We exploited the unique capabilities of transmission-reflection optoacoustic ultrasound (TROPUS), which combines the advantages of optical and acoustic contrasts, for an early-stage multi-parametric assessment of NAFLD in mice. The multispectral optoacoustic imaging allowed for spectroscopic differentiation of lipid content, as well as the bio-distributions of oxygenated and deoxygenated hemoglobin in liver tissues in vivo. The pulse-echo (reflection) ultrasound (US) imaging further provided a valuable anatomical reference whilst transmission US facilitated the mapping of speed of sound changes in lipid-rich regions, which was consistent with the presence of macrovesicular hepatic steatosis in the NAFLD livers examined with ex vivo histological staining. The proposed multimodal approach facilitates quantification of liver abnormalities at early stages using a variety of optical and acoustic contrasts, laying the ground for translating the TROPUS approach toward diagnosis and monitoring NAFLD in patients.
Regulation of Macrophage IFNγ-Stimulated Gene Expression by the Transcriptional Coregulator CITED1
Authors: Subramani Aarthi , Hite Maria E. L. , Kondee Hursha , Millican Grace E. , McClelland Erin E. , Seipelt-Thiemann Rebecca L. , Nelson David E.
Published: August 2022

Macrophages are highly dynamic innate immune cells that adopt temporary phenotypes, known as polarization states, in response to changing environmental signals to combat microbial infection and contribute to the maintenance of tissue homeostasis. During the early stages of an infection, exposure to interferon-gamma (IFNγ) and microbial ligands induce M1 polarization, a heightened proinflammatory anti-microbial state, by regulating the expression of interferon stimulated genes (ISGs). While this response must be sufficiently vigorous to ensure the successful clearance of invading pathogens, it must also be spatially and temporally restricted to prevent uncontrolled inflammation that could result in tissue damage and disease. This is controlled by a variety of cell-extrinsic and -intrinsic mechanisms, including the expression of CBP/p300-interacting transactivator with glutamic acid/aspartic acid-rich carboxyl-terminal domain 2 (CITED2), a transcriptional coregulator that limits IFNγ-stimulated proinflammatory gene expression by inhibiting STAT1- and IRF1-regulated ISGs. In this study, we show that CITED1, another member of the CITED family of proteins, is itself an ISG and is expressed in a STAT1-dependent manner, and that IFNγ stimulates the nuclear accumulation of fluorescently tagged CITED1 proteins. In contrast to CITED2, ectopic expression of CITED1 enhanced the expression of a subset of ISGs, includingCcl2, Ifit3b, Isg15, andOas2. This effect was reversed in aCited1null cell line produced by CRISPR-based genomic editing. Collectively, these data show that CITED1 helps to maintain proinflammatory gene expression during periods of prolonged IFNγ exposure and suggests a distinct and antagonistic relationship between CITED proteins in the regulation of macrophage inflammatory function.
Systematic transcriptomic analysis and temporal modelling of the senescent human fibroblast
Authors: Scanlan R-L. , Pease L. , O’Keefe H. , Martinez-Guimerá A. , Shanley D , Wordsworth J
Published: August 2022

Cellular senescence is a diverse phenotype characterised by permanent cell cycle arrest and an inflammatory senescence associated secretory phenotype (SASP). Typically, senescent cells are removed by the immune system. This process becomes dysregulated with age and senescent cells accumulate leading to chronic inflammatory signalling. Identifying senescent cells is challenging due to the heterogeneity of senescence, and senotherapy often requires a combinatorial approach. Here we have taken an integrative approach to investigate senescence development at the transcriptomic and protein level. We systematically collected 119 transcriptomic datasets related to human fibroblasts, forming an online database describing the relevant study variables which users can filter to select variables and genes of interest. Our own analysis of the database identified 28 genes significantly up- or downregulated across four senescence types (DNA-damage induced senescence (DDIS), oncogene-induced senescence (OIS), replicative senescence, and bystander induced senescence); 14 genes consistently downregulated, 10 genes consistently upregulated and 4 genes regulation dependent on senescence type. We also found gene expression patterns of conventional senescence markers were highly specific and reliable for different senescence inducers, cell lines, and timepoints. Conclusions of existing studies based on single datasets were supported such as differences in p53 and inflammatory signals between DDIS and OIS. However, contrary to some early observations, both p16 and p21 mRNA levels appeared to rise quickly, depending on senescence type, and persist for at least 8-11 days. Additionally, little evidence was found to support an initial TGF-β-centric SASP. To support our transcriptomic analysis, we computationally modelled temporal protein changes of core senescence proteins in DDIS and OIS, as well as performed knockdown interventions. We conclude that while universal biomarkers of senescence are difficult to identify, conventional senescence markers follow predictable profiles and construction of a workflow for studying senescence could lead to more reproducible data and understanding of senescence heterogeneity.
Alleviating cell lysate-induced inhibition to enable RT-PCR from single cells in picoliter-volume double emulsion droplets
Authors: Khariton Margarita , McClune Conor J. , Brower Kara K. , Klemm Sandy , Sattely Elizabeth S. , Fordyce Polly M. , Wang Bo
Published: August 2022

Microfluidic droplet assays enable single-cell PCR and sequencing assays at unprecedented scale, with most methods encapsulating cells within nanoliter sized single emulsion droplets (water-in-oil). Encapsulating cells within picoliter double emulsion (DE) (water-in-oil-in-water) droplets allows sorting on commercially available FACS machines, making it possible to isolate single cells based on phenotypes of interest for downstream sequencing and PCR analyses. However, DE droplets must be within the range of large cells (<20 pl) for sorting on standard cytometers, posing challenges for molecular biology as prior reports suggest that reverse transcription (RT) and PCR amplification cannot proceed efficiently at volumes below 1 nL due to cell lysate-induced inhibition. To overcome this limitation, we used a plate-based RT-PCR assay designed to mimic reactions in picoliter droplets to systematically quantify and ameliorate the inhibition. We find that RT-PCR is blocked by lysate-induced cleavage of nucleic acid probes and primers, but that this cleavage can be efficiently alleviated through heat lysis that simultaneously inactivates inhibitory lysate components. We further show that the magnitude of RT-PCR inhibition depends strongly on cell type, but that RT-PCR can proceed in low-picoscale reaction volumes for most cell lines tested. Finally, we demonstrate one-step RT-PCR from single cells in 20 pL double emulsion droplets with fluorescence detectable via FACS. These results open up exciting new avenues for improving picoscale droplet RT-PCR reactions and expanding microfluidic droplet based single-cell analysis technologies.