Mechanistic basis of the dynamic response of TWIK1 ionic selectivity to pH.

Highly selective for K+ at neutral pH, the TWIK1 channel becomes permeable to Na+ upon acidification. Using molecular dynamics simulations, we identify a network of residues involved in this unique property. Between the open and closed states previously observed by electron microscopy, molecular dynamics simulations show that the channel undergoes conformational changes between pH 7.5-6 involving residues His122, Glu235, Lys246 and Phe109. A complex network of interactions surrounding the selectivity filter at high pH transforms into a simple set of stronger interactions at low pH. In particular, His122 protonated by acidification moves away from Lys246 and engages in a salt bridge with Glu235. In addition, stacking interactions between Phe109 and His122, which stabilize the selectivity filter in its K+-selective state at high pH, disappear upon acidification. This leads to dissociation of the Phe109 aromatic side chain from this network, resulting in the Na+-permeable conformation of the channel.

Determinants of non-vaccination against seasonal influenza during pregnancy.

OBJECTIVE: The objective of this study was to identify the determinants of influenza non-vaccination during pregnancy in Canada. METHODS: Biological mothers of children born between December 2018 and March 2019 were surveyed about vaccinations they had received during pregnancy, reasons for non-vaccination, obstetrical history, and demographics. Simple and multiple logistic regression models were used to measure associations between various sociodemographic factors as well as obstetrical history, and non-vaccination against influenza. We analyzed data from 2361 mothers. RESULTS: Factors associated with non-vaccination included being followed during pregnancy by a midwife compared to by an obstetrician-gynecologist (OR 2.02; 95% CI, 1.17‒3.50); having two or more past live births compared to none (OR 1.58; 95% CI, 1.01‒2.49); having an education level below high school diploma compared to a bachelor's degree or above (OR 2.50; 95% CI, 1.06‒5.90); and having a household income below $60,000 (OR 2.46; 95% CI, 1.42‒4.24) or between $60,000 and $99,999 (OR 2.77; 95% CI, 1.70‒4.52) compared to a household income of $140,000 or more. The province or territory of prenatal care proved to be an important factor in non-vaccination, with statistically significant odds ratios for certain provinces: OR 7.50 (95% CI, 1.40‒40.26) for Ontario, 8.23 (95% CI, 1.53‒44.23) for Newfoundland and Labrador, and 11.39 (95% CI, 2.14‒60.60) for Quebec, as compared to the territories. CONCLUSION: Despite universal access to influenza vaccines in Canada during pregnancy, regional variations and socioeconomic disparities in non-vaccination are still observable.

RéSUMé: OBJECTIF: Identifier les déterminants de la non-vaccination contre la grippe pendant la grossesse au Canada. MéTHODES: Notre étude porte sur 2 361 mères biologiques d'enfants nés entre décembre 2018 et mars 2019 qui ont été interrogées sur les vaccins reçus pendant leur grossesse, les raisons de non-vaccination, leurs antécédents obstétricaux, et leurs caractéristiques démographiques. Des modèles de régression logistique simple et multiple ont été utilisés pour mesurer les associations entre divers facteurs sociodémographiques, les antécédents obstétricaux, et la non-vaccination contre l'influenza. RéSULTATS: Les facteurs associés à la non-vaccination comprennent le suivi de grossesse par une sage-femme par rapport à un obstétricien-gynécologue (RC 2,02; IC 95% : 1,17‒3,50); avoir eu deux naissances vivantes ou plus par rapport à aucune (RC 1,58; IC 95% : 1,01‒2,49); avoir une scolarité inférieure au diplôme d'études secondaires par rapport à un baccalauréat ou plus (RC 2,50; IC 95% : 1,06‒5,90); et avoir un revenu du ménage inférieur à 60 000 $ (RC 2,46; IC 95% : 1,42‒4,24) ou entre 60 000 $ et 99 999 $ (RC 2,77; IC 95% : 1,70‒4,52) par rapport à un revenu ménager de 140 000 $ ou plus. La province ou le territoire de soins prénataux s'est avéré un facteur important de la non-vaccination avec des rapports de cote statistiquement significatifs pour certaines provinces : RC 7,50 (IC 95% : 1,40‒40,26) pour l'Ontario, 8,23 (IC 95% : 1,53‒44,23) pour Terre-Neuve-et-Labrador, et 11,39 (IC 95% : 2,14‒60,60) pour le Québec, comparativement aux territoires. CONCLUSION: Malgré l'accès universel aux vaccins antigrippaux au Canada durant la grossesse, des variations régionales et des disparités socioéconomiques en non-vaccination persistent.

Determinants of parental vaccine hesitancy in Canada: results from the 2017 Childhood National Immunization Coverage Survey.

BACKGROUND: In 2019, the World Health Organization (WHO) designated vaccine hesitancy as one of the ten leading threats to global health. Vaccine hesitancy exists when vaccination services are available and accessible, but vaccine uptake is lower than anticipated. It is often attributed to lack of trust in vaccine safety and effectiveness, or low level of concern about the risk of many vaccine-preventable diseases. This study aimed to examine the sociodemographic factors associated with parental vaccine hesitancy and vaccine refusal in Canada using data from the 2017 Childhood National Immunization Coverage Survey (CNICS). METHOD: The 2017 CNICS was a cross-sectional and nationally representative survey to estimate national vaccine uptake and to collect information about parents' Knowledge, Attitudes and Beliefs (KAB) regarding vaccination. Using the KAB questions, parental vaccine hesitancy (i.e., parental hesitation, delay or refusal of at least one recommended vaccination) and refusal (i.e., unvaccinated children) by sociodemographic factors was estimated using weighted prevalence proportions. A multinomial logistic regression model was fitted to examine associations between parental vaccine hesitancy or refusal and sociodemographic factors among parents of two-year-old children in Canada. Adjusted odds ratios (aOR) of being vaccine-hesitant or vaccine-refusing versus being non-vaccine-hesitant were generated. RESULTS: Both unadjusted and adjusted logistic regressions models showed that parents with lower household income (aOR 1.7, 95% CI 1.2-2.5), and those with a higher number of children in the household (aOR 2.2, 95% CI 1.4-3.5) had higher vaccine hesitancy. Conversely, lower vaccine hesitancy was observed among non-immigrant parents (aOR 0.4, 95% CI 0.3-0.6). In addition, lower household income (aOR 4.0, 95% CI 1.3-12.9), and higher number of children in the household (aOR 6.9, 95% CI 2.1-22.9) were significantly associated with parental vaccine refusal. Regional variations were also observed. CONCLUSION: Several sociodemographic determinants are associated with parental vaccine hesitancy and refusal. The findings of the study could help public health officials and policymakers to develop and implement targeted interventions to improve childhood vaccination programs.

Racial disparities in COVID-19 vaccination in Canada: results from the cross-sectional Canadian Community Health Survey.

BACKGROUND: Racial and ethnic disparities in COVID-19 vaccination coverage have been observed in Canada and in other countries. We aimed to compare vaccination coverage for at least 1 dose of a COVID-19 vaccine between First Nations people living off reserve and Métis, Black, Arab, Chinese, South Asian and White people. METHODS: We used data collected between June 2021 and June 2022 by Statistics Canada's Canadian Community Health Survey, a large, nationally representative cross-sectional study. The analysis included 64 722 participants aged 18 years or older from the 10 provinces. We used a multiple logistic regression model to determine associations between vaccination status and race, controlling for collection period, region of residence, age, gender and education. RESULTS: Nonvaccination against COVID-19 was more frequent in off-reserve First Nations people (adjusted odds ratio [OR] 1.8, 95% confidence interval [CI] 1.2-2.7) and Black people (adjusted OR 1.7, 95% CI 1.1-2.6), and less frequent among South Asian people (adjusted OR 0.3, 95% CI 0.1-0.7) compared to White people. INTERPRETATION: This analysis showed significant inequalities in COVID-19 vaccine uptake between racial/ethnic populations in Canada. Further research is needed to understand the sociocultural, structural and systemic facilitators of and barriers to vaccination across racial groups, and to identify strategies that may improve vaccination uptake among First Nations and Black people.

Pertussis Non-Vaccination During Pregnancy Despite Advice From Prenatal Care Providers.

OBJECTIVE: The purpose of this study was to measure the proportion of non-vaccination for pertussis in mothers in Canada who had been advised by their prenatal care provider to get vaccinated, and to identify sociodemographic factors and beliefs associated with non-vaccination. METHODS: The Survey on Vaccination during Pregnancy (part of childhood National Immunization Coverage Survey) included biological mothers of children born from September 2018 to March 2019. This analysis was restricted to 2657 mothers who had been advised by their prenatal care provider to get vaccinated against pertussis during pregnancy and knew whether or not they had been vaccinated. RESULTS: Of those who had been advised to get vaccinated against pertussis, 21% were not. This rate varied across provinces and territories, ranging from 9% in Prince Edward Island to 32% in Newfoundland and Labrador. Factors independently associated with pertussis non-vaccination included lower household income, having had past live births, and having received prenatal care from an obstetrician-gynecologist or a midwife compared to a family doctor. The risk of pertussis non-vaccination despite prenatal care advice was higher for those who disagreed that the baby would be at greater risk of pertussis if the mother did not get vaccinated. It was also higher for those who disagreed with statements regarding perceived benefits of vaccination. Conversely, disagreement with statements on perceived barriers was negatively associated with pertussis non-vaccination. CONCLUSION: These findings highlight the underlying factors associated with non-vaccination against pertussis despite prenatal care provider recommendation. Some inaccurate beliefs about pertussis and vaccination during pregnancy persist, leading to non-vaccination.

Detection, discrimination and quantification of amphetamine, cathinone and nor-ephedrine regioisomers using benchtop 1 H and 19 F nuclear magnetic resonance spectroscopy.

Amphetamine and cathinone derivatives are abused recreationally due to the sense of euphoria they provide to the user. Methodologies for the rapid detection of the drug derivative present in a seized sample, or an indication of the drug class, are beneficial to law enforcement and healthcare providers. Identifying the drug class is prudent because derivatisation of these drugs, to produce regioisomers, for example, occurs frequently to circumvent global and local drug laws. Thus, newly encountered derivatives might not be present in a spectral library. Employment of benchtop nuclear magnetic resonance (NMR) could be used to provide rapid analysis of seized samples as well as identifying the class of drug present. Discrimination of individual amphetamine-, methcathinone-, N-ethylcathinone and nor-ephedrine-derived fluorinated and methylated regioisomers is achieved herein using qualitative automated 1 H NMR analysis and compared to gas chromatography-mass spectrometry (GC-MS) data. Two seized drug samples, SS1 and SS2, were identified to contain 4-fluoroamphetamine by 1 H NMR (match score median = 0.9933) and GC-MS (RRt = 5.42-5.43 min). The amount of 4-fluoroamphetamine present was 42.8%-43.4% w/w and 48.7%-49.2% w/w for SS1 and SS2, respectively, from quantitative 19 F NMR analysis, which is in agreement with the amount determined by GC-MS (39.9%-41.4% w/w and 49.0%-49.3% w/w). The total time for the qualitative 1 H NMR and quantitative 19 F NMR analysis is ~10 min. This contrasts to ~40 min for the GC-MS method. The NMR method also benefits from minimal sample preparation. Thus, benchtop NMR affords rapid, and discriminatory, analysis of the drug present in a seized sample.

Sociodemographic Disparities in COVID-19 Vaccine Uptake and Vaccination Intent in Canada.

Introduction: This study's objective was to examine sociodemographic disparities in COVID-19 vaccine uptake and vaccination intent in the Canadian provinces by identifying factors associated with vaccine uptake in seniors prioritized for vaccination at the time of the survey and vaccination intent in all adults. Data and methods: A cross-sectional survey of Canadian adults was conducted in all provinces from mid-April to mid-May 2021. In addition to sociodemographic characteristics, respondents (n=10,678) provided information on their COVID-19 vaccination status or their intent to get vaccinated. Logistic regression models were fitted using sociodemographic factors as explanatory variables and vaccination status (unvaccinated vs at least one dose) or vaccination intent (unlikely versus likely or already vaccinated) as outcomes. To account for vaccine prioritization groups, multiple regression models were adjusted for province of residence, age, Indigenous identity and health care worker status. Results: Seniors with a lower household income (less than $60,000) and those living in smaller communities (fewer than 100,000 inhabitants) had higher odds of being unvaccinated. Among Canadian adults, the odds of being unlikely to get vaccinated were higher for males (adjusted odds ratio [AOR] 1.3), individuals younger than 60 (AOR between 3.3 and 5.1), non-health care workers (AOR 3.3), those with less than a high school education (AOR 3.4) or a household income of less than $30,000 (AOR 2.7) and individuals who do not identify as South Asian, Chinese, Black, Filipino, Arab, Latin American, Southeast Asian, West Asian, Korean or Japanese (AOR 1.7). Interpretation: COVID-19 vaccine uptake (80%) and vaccination intent (95%) were high among Canadians; however, relative disparities were observed among specific groups. Continued efforts targeted toward these groups are essential in reducing potential inequity in access or service provision.

Measuring inequalities in COVID-19 vaccination uptake and intent: results from the Canadian Community Health Survey 2021.

BACKGROUND: By July 2021, Canada had received enough COVID-19 vaccines to fully vaccinate every eligible Canadian. However, despite the availability of vaccines, some eligible individuals remain unvaccinated. Differences in vaccination uptake can be driven by health inequalities which have been exacerbated and amplified by the pandemic. This study aims to assess inequalities in COVID-19 vaccination uptake and intent in adults 18 years or older across Canada by identifying sociodemographic factors associated with non-vaccination and low vaccination intent using data drawn from the June to August 2021 Canadian Community Health Survey (CCHS). METHODS: The CCHS is an annual cross-sectional and nationally representative survey conducted by Statistics Canada, which collects health-related information. Since September 2020, questions about the COVID-19 pandemic are asked. Adjusted logistic regression models were fitted to examine associations between vaccination uptake or intent and sociodemographic and health related variables. Region, age, gender, level of education, Indigenous status, visible minority status, perceived health status, and having a regular healthcare provider were considered as predictors, among other factors. RESULTS: The analysis included 9,509 respondents. The proportion of unvaccinated was 11%. Non-vaccination was associated with less than university education (aOR up to 3.5, 95% CI 2.1-6.1), living with children under 12 years old (aOR 1.6, 95% CI 1.1-2.4), not having a regular healthcare provider (aOR 1.6, 95% CI 1.1-2.2), and poor self-perceived health (aOR 1.8, 95% CI 1.3-2.4). Only 5% of the population had low intention to get vaccinated. Being unlikely to get vaccinated was associated with the Prairies region (aOR 2.2, 95% CI 1.2-4.1), younger age groups (aOR up to 4.0, 95% CI 1.3-12.3), less than university education (aOR up to 3.8, 95% CI 1.9-7.6), not being part of a visible minority group (aOR 3.0, 95% CI 1.4-6.4), living with children under 12 years old (aOR 1.8, 95% CI 1.1-2.9), unattached individuals (aOR 2.6, 95% CI 1.1-6.1), and poor self-perceived health (aOR 2.0, 95% CI 1.3-2.9). CONCLUSIONS: Disparities were observed in vaccination uptake and intent among various sociodemographic groups. Awareness of inequalities in COVID-19 vaccination uptake and intent is needed to determine the vaccination barriers to address in vaccination promotion strategies.

Alkaline-sensitive two-pore domain potassium channels form functional heteromers in pancreatic ß-cells.

Two-pore domain K+ channels (K2P channels), active as dimers, produce inhibitory currents regulated by a variety of stimuli. Among them, TWIK1-related alkalinization-activated K+ channel 1 (TALK1), TWIK1-related alkalinization-activated K+ channel 2 (TALK2), and TWIK1-related acid-sensitive K+ channel 2 (TASK2) form a subfamily of structurally related K2P channels stimulated by extracellular alkalosis. The human genes encoding these proteins are clustered at chromosomal region 6p21 and coexpressed in multiple tissues, including the pancreas. The question whether these channels form functional heteromers remained open. By analyzing single-cell transcriptomic data, we show that these channels are coexpressed in insulin-secreting pancreatic ß-cells. Using in situ proximity ligation assay and electrophysiology, we show that they form functional heterodimers both upon heterologous expression and under native conditions in human pancreatic ß-cells. We demonstrate that heteromerization of TALK2 with TALK1 or with TASK2 endows TALK2 with sensitivity to extracellular alkalosis in the physiological range. We further show that the association of TASK2 with TALK1 and TALK2 increases their unitary conductance. These results provide a new example of heteromerization in the K2P channel family expanding the range of the potential physiological and pathophysiological roles of TALK1/TALK2/TASK2 channels, not only in insulin-secreting cells but also in the many other tissues in which they are coexpressed.

Comparative study of the analysis of seized samples by GC-MS, 1H NMR and FT-IR spectroscopy within a Night-Time Economy (NTE) setting.

Rapid analysis of surrendered or seized drug samples provides important intelligence for health (e.g. treatment or harm reduction), and custodial services. Herein, three in-situ techniques, GC-MS, 1H NMR and FT-IR spectroscopy, with searchable libraries, are used to analyse 318 samples qualitatively, using technique specific library-based searches, obtained over the period 24th - 29th August 2019. 259 samples were identified as consisting of a single component, of which cocaine was the most prevalent (n = 158). Median match scores for all three techniques were ≥ 0.84 and showed agreement except for metformin (n = 1), oxandrolone (identified as vitamin K by IR (n = 4)), diazepam (identified as zolpidem by FT-IR (n = 2)) and 2-Br-4,5-DMPEA (n = 1), a structural isomer of 2C-B identified as a polymer of cellulose (cardboard) by FT-IR. 51 samples were found to consist of two or more components, of which 49 were adulterated cocaine samples (45 binary and 4 tertiary samples). GC-MS identified all components present in the 49 adulterated cocaine samples, whereas IR identified only cocaine in 88 % of cases (adulterant only = 12 %). The breakdown for 1H NMR spectroscopy was all components identified (51 %), cocaine only (33 %), adulterant only (10 %), cocaine and one adulterant (tertiary mixtures only, 6 %).

Guilty by dissociation: Part A: Development of a rapid Ultra-High Performance Liquid Chromatography (UHPLC)-MS/MS methodology for the analysis of regioisomeric diphenidine-derived Novel Psychoactive Substances (NPS).

This study describes the first reported development of a rapid, generic gradient Ultra-High Performance Liquid Chromatography (UHPLC) methodology with targeted triple quadrupole MS/MS using electrospray positive ionisation to detect and unambiguously confirm the identity of 33 substituted 1, 2-diarylethamine (or diphenidine) derivatives in solid drug samples. The in-house synthesised library included a range of derivatives possessing either electron donating/withdrawing substituents, commonly included in combinatorial libraries, of varying size and lipophilicity on the phenyl ring. These test probes were used to investigate if their order of elution and that of their regioisomers were dependent on the position and type of the substituent on the phenyl ring. In addition, investigations into the retention mechanism of the diphenidines under reverse-phase UHPLC conditions were undertaken. Common adulterants found within seized bulk samples were assessed to prove that the methodology was specific, and the developed UHPLC-MS/MS (tG = 10 min) protocol was applied to confirm the identity of the psychoactive components within four seized bulk samples provided by law enforcement.

Guilty by dissociation: Part B: evaluation of Supercritical Fluid Chromatography (SFC-UV) for the analysis of regioisomeric diphenidine-derived Novel Psychoactive Substances (NPS).

Supercritical Fluid Chromatography (SFC-UV) employing a carbon dioxide (CO2) and 10 mM ammonium acetate in MeOH-water (95:5 v/v) gradient provides a rapid analysis (tG <10 min) of 31 novel, regioisomeric diphenidine-derived psychoactive substances, on a range of stationary phases of differing polarity. Medium to large selectivity differences between regioisomers, were observed on the acidic, neutral and basic SFC phases. For individual substituted ortho-, meta- and para-isomers, the same elution order was observed irrespective of the nature of the stationary phase. The acidic silica stationary phases yielded longer retention of the diphenidines via electrostatic attraction, whereas the basic phases resulted in shorter retention via electrostatic repulsion. SFC effected baseline separation of seven of the eight substituted groups of ortho-, meta- and para-diphenidines evaluated on a range of stationary phases. A simple silica phase achieved baseline separation of six of the regioisomeric substituted diphenidines. As the size of the halo-substituent increased, the resolution between ortho-/meta-isomers decreased, resulting in co-elution of the ortho- and meta-bromodiphenidines. Fluphenidines and chlorodiphenidines generated an elution order of meta- < ortho- < para- whereas an elution order switch was observed for the iodophenidines. This contrasted with RP-UHPLC where the elution order for the fluphenidines and iodophenidines was para- < ortho- < meta- and para- < meta- < ortho- respectively. An orthogonal elution order of diphenidines was demonstrated between the RP-UHPLC and SFC stationary phases due to the polarity differences between the separation modes. In general, hydrophilic compounds, which were poorly retained on a C18 reverse phase column, were well retained on SFC columns.

Exploratory State Representation Learning.

Not having access to compact and meaningful representations is known to significantly increase the complexity of reinforcement learning (RL). For this reason, it can be useful to perform state representation learning (SRL) before tackling RL tasks. However, obtaining a good state representation can only be done if a large diversity of transitions is observed, which can require a difficult exploration, especially if the environment is initially reward-free. To solve the problems of exploration and SRL in parallel, we propose a new approach called XSRL (eXploratory State Representation Learning). On one hand, it jointly learns compact state representations and a state transition estimator which is used to remove unexploitable information from the representations. On the other hand, it continuously trains an inverse model, and adds to the prediction error of this model a k-step learning progress bonus to form the maximization objective of a discovery policy. This results in a policy that seeks complex transitions from which the trained models can effectively learn. Our experimental results show that the approach leads to efficient exploration in challenging environments with image observations, and to state representations that significantly accelerate learning in RL tasks.

Pertussis Vaccination in Canadian Pregnant Women, 2018-2019.

OBJECTIVE: This study was undertaken to measure the uptake of pertussis vaccination during pregnancy in Canada and to identify sociodemographic factors associated with non-vaccination. METHODS: A total of 5091 biological mothers of children born between September 2, 2018, and March 1, 2019, were interviewed about pertussis vaccination during their pregnancy. RESULTS: Among 4607 mothers who recalled whether they had been vaccinated for pertussis, 43% had been vaccinated and 57% had not. The main reason given by mothers for not having been vaccinated was not being aware that pertussis vaccination was recommended. Factors independently associated with non-vaccination were being born outside Canada, lower household income, living in a province or territory where pertussis vaccination was not provided free of charge, having had previous live births, and having received maternity care from a midwife. CONCLUSION: Advice from the maternity care provider is an important driver of pertussis vaccination during pregnancy.

The metabolism of the synthetic cannabinoids ADB-BUTINACA and ADB-4en-PINACA and their detection in forensic toxicology casework and infused papers seized in prisons.

Early warning systems detect new psychoactive substances (NPS), while dedicated monitoring programs and routine drug and toxicology testing identify fluctuations in prevalence. We report the increasing prevalence of the synthetic cannabinoid receptor agonist (SCRA) ADB-BUTINACA (N-[1-amino-3,3-dimethyl-1-oxobutan-2-yl]-1-butyl-1H-indazole-3-carbox-amide). ADB-BUTINACA was first detected in a seizure in Sweden in 2019, and we report its detection in 13 routine Swedish forensic toxicology cases soon after. In January 2021, ADB-BUTINACA was detected in SCRA-infused papers seized in Scottish prisons and has rapidly increased in prevalence, being detected in 60.4% of the SCRA-infused papers tested between January and July 2021. In this work, ADB-BUTINACA was incubated with human hepatocytes (HHeps), and 21 metabolites were identified in vitro, 14 being detected in authentic case samples. The parent drug and metabolites B9 (mono-hydroxylation on the n-butyl tail) and B16 (mono-hydroxylation on the indazole ring) are recommended biomarkers in blood, while metabolites B4 (dihydrodiol formation on the indazole core), B9, and B16 are suitable biomarkers in urine. ADB-4en-PINACA (N-[1-amino-3,3-dimethyl-1-oxobutan-2-yl]-1-[pent-4-en-1-yl]-1H-indazole-3-carboxamide) was detected in Scottish prisons in December 2020, but, unlike ADB-BUTINACA, prevalence has remained low. ADB-4en-PINACA was incubated with HHeps, and 11 metabolites were identified. Metabolites E3 (dihydrodiol formed in the tail moiety) and E7 (hydroxylation on the linked/head group) are the most abundant metabolites in vitro and are suggested as urinary biomarkers. The in vitro potencies of ADB-BUTINACA (EC50 , 11.5 nM and ADB-4en-PINACA (EC50 , 11.6 nM) are similar to that of MDMB-4en-PINACA (EC50 , 4.3 nM). A third tert-leucinamide SCRA, ADB-HEXINACA was also detected in prison samples and warrants further investigation.

Long non-coding RNA exploration for mesenchymal stem cell characterisation.

BACKGROUND: The development of RNA sequencing (RNAseq) and the corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emerging class of transcripts with a potential for high tissue specificity and function. Therefore, we tested the biomarker potential of lncRNAs on Mesenchymal Stem Cells (MSCs), a complex type of adult multipotent stem cells of diverse tissue origins, that is frequently used in clinics but which is lacking extensive characterization. RESULTS: We developed a dedicated bioinformatics pipeline for the purpose of building a cell-specific catalogue of unannotated lncRNAs. The pipeline performs ab initio transcript identification, pseudoalignment and uses new methodologies such as a specific k-mer approach for naive quantification of expression in numerous RNAseq data. We next applied it on MSCs, and our pipeline was able to highlight novel lncRNAs with high cell specificity. Furthermore, with original and efficient approaches for functional prediction, we demonstrated that each candidate represents one specific state of MSCs biology. CONCLUSIONS: We showed that our approach can be employed to harness lncRNAs as cell markers. More specifically, our results suggest different candidates as potential actors in MSCs biology and propose promising directions for future experimental investigations.

Kmerator Suite: design of specific k-mer signatures and automatic metadata discovery in large RNA-seq datasets.

The huge body of publicly available RNA-sequencing (RNA-seq) libraries is a treasure of functional information allowing to quantify the expression of known or novel transcripts in tissues. However, transcript quantification commonly relies on alignment methods requiring a lot of computational resources and processing time, which does not scale easily to large datasets. K-mer decomposition constitutes a new way to process RNA-seq data for the identification of transcriptional signatures, as k-mers can be used to quantify accurately gene expression in a less resource-consuming way. We present the Kmerator Suite, a set of three tools designed to extract specific k-mer signatures, quantify these k-mers into RNA-seq datasets and quickly visualize large dataset characteristics. The core tool, Kmerator, produces specific k-mers for 97% of human genes, enabling the measure of gene expression with high accuracy in simulated datasets. KmerExploR, a direct application of Kmerator, uses a set of predictor gene-specific k-mers to infer metadata including library protocol, sample features or contaminations from RNA-seq datasets. KmerExploR results are visualized through a user-friendly interface. Moreover, we demonstrate that the Kmerator Suite can be used for advanced queries targeting known or new biomarkers such as mutations, gene fusions or long non-coding RNAs for human health applications.

Hyperpolarisation of Mirfentanil by SABRE in the Presence of Heroin.

Mirfentanil, a fentanyl derivative that is a µ-opioid partial agonist, is hyperpolarised via Signal Amplification By Reversible Exchange (SABRE), a para-hydrogen-based technique. [Ir(IMes)(COD)Cl] (IMes=1,3-bis(2,4,6-trimethylphenyl)imidazole-2-ylidene, COD=cyclooctadiene) was employed as the polarisation transfer catalyst. Following polarisation transfer at 6.5 mT, the pyrazine-protons were enhanced by 78-fold (polarisation, P=0.04 %). The complex [Ir(IMes)(H)2 (mirfentanil)2 (MeOH)]+ is proposed to form based on the observation of two hydrides at δ -22.9 (trans to mirfentanil) and -24.7 (trans to methanol). In a mixture of mirfentanil and heroin, the former could be detected using SABRE at concentrations less than 1 % w/w. At the lowest concentration analyzed, the amount of mirfentanil present was 0.18 mg (812 µM) and produced a signal enhancement of -867-fold (P=0.42 %). following polarisation transfer at 6.5 mT.

Hitting the Jackpot - development of gas chromatography-mass spectrometry (GC-MS) and other rapid screening methods for the analysis of 18 fentanyl-derived synthetic opioids.

In recent years, the occurrence of synthetic opioid fentanyl and its derivatives has grown significantly in forensic casework. This study presents the synthesis and analysis of 18 fentalogs, selected based on information received from local law enforcement. This study provides colorimetric tests, thin-layer chromatography (TLC) which can potentially be utilized for presumptive screening of the target compounds, as bulk powders or as trace-level adulterants. The fully validated confirmatory GC-MS method (employing SIM mode) allows the identification of the 18 derivatives, five commonly encountered controlled substances and four adulterants, within 20 minutes. The cross-validated method described herein provides a sensitive screening and quantitation method for the illicit (and potentially harmful) components at trace levels (LOD = 0.007-0.822 µg/mL and LOQ = 0.023-2.742 µg/mL respectively). Spectral data [1 H-NMR, 13 C-NMR, 19 F-NMR, FT-IR, and HRMS] and assignments for the synthesized reference materials are also provided in the Supplementary Information for laboratories engaged in the routine analysis of fentanyl and its derivatives.