Systematic evaluation of benchmark G4 probes and G4 clinical drugs using three biophysical methods: A guideline to evaluate rapidly G4-binding affinity

G-quadruplex DNA structures (G4) are proven to interfere with most genetic and epigenetic processes. Small molecules binding these structures (G4 ligands) are invaluable tools to probe G4-biology and address G4-druggability in various diseases (cancer, viral infections). However, the large number of reported G4 ligands (> 1000) could lead to confusion while selecting one for a given application. Herein we conducted a systematic affinity ranking of 11 popular G4 ligands vs 5 classical G4 sequences using FRET-melting, G4-FID assays and SPR. Interestingly SPR data globally align with the rankings obtained from the two semi-quantitative assays despite discrepancies due to limits and characteristics of each assay. In the whole, PhenDC3 emerges as the most potent binder irrespective of the G4 sequence. Immediately below PDS, PDC-360A, BRACO19, TMPyP4 and RHPS4 feature strong to medium binding again with poor G4 topology discrimination. More strikingly, the G4 drugs Quarfloxin, CX5461 and c-PDS exhibit weak affinity with all G4s studied. Finally, NMM and Cu-ttpy showed heterogeneous behaviors due, in part, to their physicochemical particularities poorly compatible with screening conditions. The remarkable properties of PhenDC3 led us to propose its use for benchmarking FRET-melting and G4-FID assays for rapid G4-affinity evaluation of newly developed ligands.

Remotely sensing potential climate change tipping points across scales

Potential climate tipping points pose a growing risk for societies, and policy is calling for improved anticipation of them. Satellite remote sensing can play a unique role in identifying and anticipating tipping phenomena across scales. Where satellite records are too short for temporal early warning of tipping points, complementary spatial indicators can leverage the exceptional spatial-temporal coverage of remotely sensed data to detect changing resilience of vulnerable systems. Combining Earth observation with Earth system models can improve process-based understanding of tipping points, their interactions, and potential tipping cascades. Such fine-resolution sensing can support climate tipping point risk management across scales.

Unprecedented reactivity of polyamines with aldehydic DNA modifications: structural determinants of reactivity, characterization and enzymatic stability of adducts

Apurinic/apyrimidinic (AP) sites, 5-formyluracil (fU) and 5-formylcytosine (fC) are abundant DNA modifications that share aldehyde-type reactivity. Here, we demonstrate that polyamines featuring at least one secondary 1,2-diamine fragment in combination with aromatic units form covalent DNA adducts upon reaction with AP sites (with concomitant cleavage of the AP strand), fU and, to a lesser extent, fC residues. Using small-molecule mimics of AP site and fU, we show that reaction of secondary 1,2-diamines with AP sites leads to the formation of unprecedented 3'-tetrahydrofuro[2,3,4-ef]-1,4-diazepane ('ribodiazepane') scaffold, whereas the reaction with fU produces cationic 2,3-dihydro-1,4-diazepinium adducts via uracil ring opening. The reactivity of polyamines towards AP sites versus fU and fC can be tuned by modulating their chemical structure and pH of the reaction medium, enabling up to 20-fold chemoselectivity for AP sites with respect to fU and fC. This reaction is efficient in near-physiological conditions at low-micromolar concentration of polyamines and tolerant to the presence of a large excess of unmodified DNA. Remarkably, 3'-ribodiazepane adducts are chemically stable and resistant to the action of apurinic/apyrimidinic endonuclease 1 (APE1) and tyrosyl-DNA phosphoesterase 1 (TDP1), two DNA repair enzymes known to cleanse a variety of 3' end-blocking DNA lesions.

Idiopathic ventricular fibrillation associated with long-coupled Purkinje ectopy

INTRODUCTION

Idiopathic ventricular fibrillation (IVF) is mainly associated with and triggered by short-coupled (R-on-T) ventricular ectopics. However, little is known about the risk of VF associated with long-coupled premature ventricular complexes (LCPVCs).

OBJECTIVE

To examine the prevalence and characteristics of IVF patients presenting with LCPVCs.

METHODS

Consecutive patients with IVF and PVCs from five arrhythmia referral centers were reviewed. We included patients presenting LCPVCs, defined as PVCs falling after the end of the T wave, with a normal QTc interval. We evaluated demographics, medical history, and clinical circumstances associated with PVCs and VF episodes. The origin of PVCs was determined by invasive mapping.

RESULTS

Seventy-nine patients with IVF were reviewed. Among them, 12 (15.2%) met the inclusion criteria (8 women, age 36 ± 14 years). Eleven patients had documented LCPVCs initiating repetitive PVCs or sustained VF, whereas 1 had only documented isolated PVCs. In 10 of 12 patients, PVCs were recorded showing both long and short coupling intervals of 418 ± 46 and 304 ± 33 ms, respectively. Mapping showed that PVCs originated from the left Purkinje in 10 patients, from the right Purkinje in 1 patient, and both in 1 patient. Compared to other patients from the initial cohort, IVF with LCPVCs was associated with a left-sided origin of PVCs (92% in long-coupled IVF vs. 46% of left Purkinje PVCs in short-coupled IVF, p = .004).

CONCLUSION

Long-coupled fascicular PVCs, traditionally recognized as benign, can be associated with IVF in a subset of patients. They can induce IVF by themselves or in association with short-coupled PVCs.

Differential Effect of Targeted Temperature Management Between 32 °C and 36 °C Following Cardiac Arrest According to Initial Severity of Illness: Insights From Two International Data Sets

BACKGROUND

Recent guidelines have emphasized actively avoiding fever to improve outcomes in patients who are comatose following resuscitation from cardiac arrest (ie, out-of-hospital cardiac arrest). However, whether targeted temperature management between 32 °C and 36 °C (TTM32-36) can improve neurologic outcome in some patients remains debated.

RESEARCH QUESTION

Is there an association between the use of TTM32-36 and outcome according to severity assessed at ICU admission using a previously derived risk score?

STUDY DESIGN AND METHODS

Data prospectively collected in the Sudden Death Expertise Center (SDEC) registry (France) between May 2011 and December 2017 and in the Resuscitation Outcomes Consortium Continuous Chest Compressions (ROC-CCC) trial (United States and Canada) between June 2011 and May 2015 were used for this study. Severity at ICU admission was assessed through a modified version of the Cardiac Arrest Hospital Prognosis (mCAHP) score, divided into tertiles of severity. The study explored associations between TTM32-36 and favorable neurologic status at hospital discharge by using multiple logistic regression as well as in tertiles of severity for each data set.

RESULTS

A total of 2,723 patients were analyzed in the SDEC data set and 4,202 patients in the ROC-CCC data set. A favorable neurologic status at hospital discharge occurred in 728 (27%) patients in the French data set and in 1,239 (29%) patients in the North American data set. Among the French data set, TTM32-36 was independently associated with better neurologic outcome in the tertile of patients with low (adjusted OR, 1.63; 95% CI, 1.15-2.30; P = .006) and high (adjusted OR, 1.94; 95% CI, 1.06-3.54; P = .030) severity according to mCAHP at ICU admission. Similar results were observed in the North American data set (adjusted ORs of 1.36 [95% CI, 1.05-1.75; P = .020] and 2.42 [95% CI, 1.38-4.24; P = .002], respectively). No association was observed between TTM32-36 and outcome in the moderate groups of the two data sets.

INTERPRETATION

TTM32-36 was significantly associated with a better outcome in patients with low and high severity at ICU admission assessed according to the mCAHP score. Further studies are needed to evaluate individualized temperature control following out-of-hospital cardiac arrest.

Assessment of presumed small-molecule ligands of telomeric i-DNA by biolayer interferometry (BLI)

Biolayer interferometry (BLI) and circular dichroism (CD) spectroscopy were used to investigate the interaction between previously reported i-motif DNA (i-DNA) ligands and folded or unfolded i-DNA in acidic (pH 5.5) and near-neutral (pH 6.5) conditions. We observed that although several ligands, in particular macrocyclic bis-acridine (BisA) and pyridostatin (PDS), showed good affinities for the telomeric i-motif forming sequence, none of the ligands displayed selective interactions with the i-DNA structure nor was able to promote its formation.

Constrained G4 structures unveil topology specificity of known and new G4 binding proteins

G-quadruplexes (G4) are non-canonical secondary structures consisting in stacked tetrads of hydrogen-bonded guanines bases. An essential feature of G4 is their intrinsic polymorphic nature, which is characterized by the equilibrium between several conformations (also called topologies) and the presence of different types of loops with variable lengths. In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures. In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins. Using G-rich single-stranded oligonucleotides that adopt non-controlled G4 conformations, a large number of G4-binding proteins have been identified in vitro, but their specificity towards G4 topology remained unknown. Constrained G4 structures are biomolecular objects based on the use of a rigid cyclic peptide scaffold as a template for directing the intramolecular assembly of the anchored oligonucleotides into a single and stabilized G4 topology. Here, using various constrained RNA or DNA G4 as baits in human cell extracts, we establish the topology preference of several well-known G4-interacting factors. Moreover, we identify new G4-interacting proteins such as the NELF complex involved in the RNA-Pol II pausing mechanism, and we show that it impacts the clastogenic effect of the G4-ligand pyridostatin.

[Fighting against unexplained sudden death]

Sudden cardiac death, mostly related to ventricular arrhythmia, is a major public health issue, with still very poor survival at hospital discharge. Although coronary artery disease remains the leading cause, other etiologies should be systematically investigated. Exhaustive and standardized exploration is required to eventually offer specific therapeutics and management to the patient as well as his/her family members in case of inherited cardiac disease. Identification and establishing direct causality of the detected cardiac anomaly may remain challenging, underlying the need for a multidisciplinary and experimented team.

Catheter ablation in adults with congenital heart disease: A 15-year perspective from a tertiary centre

BACKGROUND

With the growing adult congenital heart disease (ACHD) population, the number of catheter ablation procedures is expected to dramatically increase. Data reporting experience and evolution of catheter ablation in patients with ACHD, over a significant period of time, remain scarce.

AIM

We aimed to describe temporal trends in volume and outcomes of catheter ablation in patients with ACHD.

METHODS

This was a retrospective observational study including all consecutive patients with ACHD undergoing attempted catheter ablation in a large tertiary referral centre over a 15-year period. Acute procedural success rate and freedom from recurrence at 12 and 24 months were analysed.

RESULTS

From November 2004 to November 2019, 302 catheter ablations were performed in 221 patients with ACHD (mean age 43.6±15.0 years; 58.9% male sex). The annual number of catheter ablations increased progressively from four to 60 cases per year (P<0.001). Intra-atrial reentrant tachycardia/focal atrial tachycardia was the most common arrhythmia (n=217, 71.9%). Over the study period, acute procedural success rate increased from 45.0% to 93.4% (P<0.001). Use of irrigated catheters (odds ratio [OR] 4.03, 95% confidence interval [CI] 1.86-8.55), a three-dimensional mapping system (OR 3.70, 95% CI 1.72-7.74), contact force catheters (OR 3.60, 95% CI 1.81-7.38) and high-density mapping (OR 3.69, 95% CI 1.82-8.14) were associated with acute procedural success. The rate of freedom from any recurrence at 12 months increased from 29.4% to 66.2% (P=0.001). Seven (2.3%) non-fatal complications occurred.

CONCLUSIONS

The number of catheter ablation procedures in patients with ACHD has increased considerably over the past 15 years. Growing experience and advances in ablative technologies appear to be associated with a significant improvement in acute and mid-term outcomes.

DiaBLa: a corpus of bilingual spontaneous written dialogues for machine translation

We present a new English–French dataset for the evaluation of Machine Translation (MT) for informal, written bilingual dialogue. The test set contains 144 spontaneous dialogues (5700+ sentences) between native English and French speakers, mediated by one of two neural MT systems in a range of role-play settings. The dialogues are accompanied by fine-grained sentence-level judgments of MT quality, produced by the dialogue participants themselves, as well as by manually normalised versions and reference translations produced a posteriori. The motivation for the corpus is twofold: to provide (i) a unique resource for evaluating MT models, and (ii) a corpus for the analysis of MT-mediated communication. We provide an initial analysis of the corpus to confirm that the participants’ judgments reveal perceptible differences in MT quality between the two MT systems used.

Compared prognostic impact of incident atrial fibrillation versus history of atrial fibrillation in patients with AMI: the FAST-MI programme

Background

History of atrial fibrillation (HxAF) and new onset atrial fibrillation (NOAF) at acute stage of MI are associated with poorer survival. Whether both entities carry an increased risk of stroke is uncertain.

Using data from the FAST-MI 2010 and 2015 registries, we analysed the associations between HxAF and NOAF and risk of 3-year death, nonfatal stroke or combined death or stroke.

Methods

The FAST-MI registries are nationwide French cohorts consecutively including AMI patients admitted over a 1-month period every 5 years. Baseline characteristics, acute management and medications at discharge are collected. Among 9460 patients with STEMI or NSTEMI, 610 (6.4%) had HxAF, and 626 (6.6%) developed NOAF.

Main characteristics

Table 1 Overall, NOAF was associated with larger and more severe AMIs.

Results

In hospital survivors, 3-year death was 8.6% in patients without AF, 23.2% in those with NOAF and 29.2% in those with HxAF. 3-year Kaplan-Meier rates of non-fatal stroke were 1.1%, 0.3% and 3.6%, respectively (Figure).

Compared with no AF, NOAF was not associated with non-fatal stroke (Cox HR, 95% CI: 0.17, 0.02–1.21), while HxAF was (HR, 95% CI 2.04, 1.13–3.66, P=0.017). Risk of death or stroke was increased for both NOAF (HR, 95% CI 1.35, 1.10–1.65, P=0.004) and HxAF (HR 95% CI, 1.37, 1.14–1.65, P=0.001). Risk of all-cause death at 3 years was increased for NOAF (HR, 95% CI 1.32, 1.09–1.60) and HxAF (HR, 95% CI 1.30, 1.09–1.55). The results were concordant in patients not receiving oral anticoagulants at discharge.

Conclusion

Both NOAF and HxAF are associated with increased risk of death at 3 years after AMI. NOAF, however, is not associated with an increased risk of non-fatal stroke.

Figure 1. Non-fatal stroke

Funding Acknowledgement

Type of funding source: Other. Main funding source(s): Pharma companies

Catheter ablation in adults with congenital heart disease: a 15-year perspective from a tertiary center

Background

With the growing population of adults with congenital heart disease (ACHD), the number of catheter ablation procedures is expected to increase over time.

Purpose

We aimed to describe temporal trends in volume and outcomes of catheter ablation procedures in ACHD patients in a large tertiary center.

Methods

Retrospective observational study including all consecutive ACHD patients undergoing catheter ablation in a tertiary reference center over a 15-year period. Acute procedural success rate (including complete success in case of non-inducibility of any arrhythmia at the end of the procedure) as well as freedom from recurrence at 12 months were analyzed.

Results

From November 2004 to November 2019, 302 catheter ablations in 221 ACHD patients (43.6±15.0 years, 58.9% males) were performed. The annual number of catheter ablation increased progressively from 4 to 60 by year (p&lt;0.001). Intra-atrial reentrant tachycardia/focal atrial tachycardia was the most common targeted arrhythmia (n=217, 71.9%). Over the study period, acute procedural success rate increased from 45.0% to 93.3% (p&lt;0.001), including complete acute procedural success from 45.0% to 88.1% (p&lt;0.001) (Figure 1). The use of irrigated catheters (30.0% to 94.8%, p&lt;0.001), 3D-mapping systems (60.0% to 96.3%, p&lt;0.001), contact force catheters (0.0% to 91.9%, &lt;0.001), and high-density mapping (0.0% to 71.9%, p&lt;0.01) increased significantly. Use of irrigated catheters (OR=3.96, 95% CI: 1.79–8.55), 3D-mapping system (OR=3.55, 95% CI: 1.62–7.55), contact force catheters (OR=3.46, 95% CI: 1.71–7.25), and high-density mapping (OR=3.85, 95% CI: 1.60–7.26) were associated with acute procedural success. The rate of freedom from any recurrence at 12 months increased from 29.4% to 66.2% (p=0.001). Seven (2.3%) non-fatal complications occurred.

Conclusions

The number of catheter ablation procedures in ACHD patients has considerably increased over the last 15 years. Advances in ablative technologies appear to be associated with a low rate of complications and a significant improvement in acute and midterm outcomes.

Evolution of acute procedural success

Funding Acknowledgement

Type of funding source: None

Radiotherapy in Patients With a Cardiac Implantable Electronic Device

Recently, the Heart Rhythm Society published recommendations on management of patients with cardiac implantable electronic device (CIED) who require radiotherapy (RT). We aimed to report the experience of a teaching hospital, and discuss our practice in the context of recently published guidelines. We identified all consecutive CIED recipients (12,736 patients) who underwent RT between March 2006 and June 2017. Among them, 90 (1%) patients (78.2 ± 10 years, 73% male) had a CIED: 82 pacemakers and 8 implantable cardioverter-defibrillators. Two patients required CIED extraction prior to RT for ipsilateral breast cancer (no device replacement in 1 patient). Four patients (5%) were considered at high-risk, 35 (39%) at intermediate-risk, and the remaining 50 (56%) at low-risk for CIED dysfunction. Overall, only a minority of patients followed recommended local protocol during RT delivery (31%) and during follow-up (56%). CIED malfunction was detected in 5 patients (6%), mainly back-up mode resetting (80%), with 4 (including 3 pelvic cancer location) patients initially classified as being at intermediate-risk and 1 at low-risk. Four out of the 5 patients with CEID malfunction had received neutron producing beams. In conclusion, our findings underline the lack of rigorous monitoring of patients undergoing RT (though CIED malfunction appears to be rare and relatively benign in nature), and emphasize the interest of considering neutron producing beam for risk stratification as recommended in recent guidelines. Optimization of patient's management requires a close collaboration between both CIED clinicians and radiation oncologists, and more systematic remote CIED monitoring may be helpful.

Idiopathic Ventricular Fibrillation: Role of Purkinje System and Microstructural Myocardial Abnormalities

Idiopathic ventricular fibrillation is diagnosed in patients who survived a ventricular fibrillation episode without any identifiable structural or electrical cause after extensive investigations. It is a common cause of sudden death in young adults. The study reviews the diagnostic value of systematic investigations and the new insights provided by detailed electrophysiological mapping. Recent studies have shown the high incidence of microstructural cardiomyopathic areas, which act as the substrate of ventricular fibrillation re-entries. These subclinical alterations require high-density endo- and epicardial mapping to be identified using electrogram criteria. Small areas are involved and located individually in various sites (mostly epicardial). Their characteristics suggest a variety of genetic or acquired pathological processes affecting cellular connectivity or tissue structure, such as cardiomyopathies, myocarditis, or fatty infiltration. Purkinje abnormalities manifesting as triggering ectopy or providing a substrate for re-entry represent a second important cause. The documentation of ephemeral Purkinje ectopy requires continuous electrocardiography monitoring for diagnosis. A variety of diseases affecting Purkinje cell function or conduction are potentially at play in their pathogenesis. Comprehensive investigations can therefore allow the great majority of idiopathic ventricular fibrillation to ultimately receive diagnoses of a cardiac disease, likely underlain by a mosaic of pathologies. Precise phenotypic characterization has significant implications for interpretation of genetic variants, the risk assessment, and individual therapy. Future improvements in imaging or electrophysiological methods may hopefully allow the identification of the subjects at risk and the development of primary prevention strategies.

Surface plasmon resonance study of the interaction of N-methyl mesoporphyrin IX with G-quadruplex DNA

Surface plasmon resonance (SPR) was used to investigate the interaction between N-methyl mesoporphyrin IX (NMM) and different G-quadruplex (G4) topologies. The study was associated with circular dichroism analysis (CD) to assess the topology of the G4s when they interacted with NMM. We demonstrate the high selectivity of NMM for the parallel G4 structure with a dissociation constant at least ten times lower than those of other G4 topologies. We also confirm the ability of NMM to shift the G4 conformation from both the hybrid and antiparallel topologies toward the parallel structure.

Access to a stabilized i-motif DNA structure through four successive ligation reactions on a cyclopeptide scaffold

Four successive chemical ligations were used for the assembly of a sophisticated biomolecular system allowing the formation of a stabilized i-motif DNA at pH 7.

The Spectrum of Idiopathic Ventricular Fibrillation and J-Wave Syndromes: Novel Mapping Insights

Idiopathic ventricular fibrillation and J-wave syndromes are causes of sudden cardiac death (SCD) without any identified structural cardiac disease after extensive investigations. Recent data show that high-density electrophysiological mapping may ultimately offer diagnoses of subclinical diseases in most patients including those termed "unexplained" SCD. Three major conditions can underlie the occurrence of SCD: (1) localized depolarization abnormalities (due to microstructural myocardial alteration), (2) Purkinje abnormalities manifesting as triggering ectopy and inducible reentry; or (3) repolarization heterogeneities. Each condition may result from a spectrum of pathophysiologic processes with implications for individual therapy.

Extracorporeal cardiopulmonary resuscitation in out-of-hospital cardiac arrest: a registry study

Aims

Out-of-hospital cardiac arrest (OHCA) without return of spontaneous circulation (ROSC) despite conventional resuscitation is common and has poor outcomes. Adding extracorporeal membrane oxygenation (ECMO) to cardiopulmonary resuscitation (extracorporeal-CPR) is increasingly used in an attempt to improve outcomes.

Methods and results

We analysed a prospective registry of 13 191 OHCAs in the Paris region from May 2011 to January 2018. We compared survival at hospital discharge with and without extracorporeal-CPR and identified factors associated with survival in patients given extracorporeal-CPR. Survival was 8% in 525 patients given extracorporeal-CPR and 9% in 12 666 patients given conventional-CPR (P = 0.91). By adjusted multivariate analysis, extracorporeal-CPR was not associated with hospital survival [odds ratio (OR), 1.3; 95% confidence interval (95% CI), 0.8–2.1; P = 0.24]. By conditional logistic regression with matching on a propensity score (including age, sex, occurrence at home, bystander CPR, initial rhythm, collapse-to-CPR time, duration of resuscitation, and ROSC), similar results were found (OR, 0.8; 95% CI, 0.5–1.3; P = 0.41). In the extracorporeal-CPR group, factors associated with hospital survival were initial shockable rhythm (OR, 3.9; 95% CI, 1.5–10.3; P = 0.005), transient ROSC before ECMO (OR, 2.3; 95% CI, 1.1–4.7; P = 0.03), and prehospital ECMO implantation (OR, 2.9; 95% CI, 1.5–5.9; P = 0.002).

Conclusions

In a population-based registry, 4% of OHCAs were treated with extracorporeal-CPR, which was not associated with increased hospital survival. Early ECMO implantation may improve outcomes. The initial rhythm and ROSC may help select patients for extracorporeal-CPR.

Scaffold stabilization of a G-triplex and study of its interactions with G-quadruplex targeting ligands

G-triplex nucleic acid structures (G3) have been conjectured to form in vivo but little is known about their physiological functions. The identification of ligands capable of specific binding to G3 structures is therefore highly appealing but remains elusive. Here we report on the assembly of a DNA conjugate which folds into a stable G3 structure. The structural mimic was used to probe the interactions between a G3 ligand and first-in-class G4 ligands, revealing signification binding promiscuity.

Influence of the SPR Experimental Conditions on the G-Quadruplex DNA Recognition by Porphyrin Derivatives

Surface plasmon resonance (SPR) is a powerful technique to study the interactions of ligands with analytes and therefore a number of biosensor surfaces and injection methods have been developed so far. However, many experimental parameters can affect the interactions and consequently the affinity measurements. In particular, the interactions of positively charged analytes (often used for anionic nucleic acids targets) can be influenced by the sensing surfaces (e.g., negatively charged), leading to significant nonspecific interactions as well as regeneration problems. The aim of the present work is to investigate the effect of different parameters, including ionic strength, SPR biosensor (i.e., nature of the surfaces), and the injection method on the recognition of porphyrin G-quadruplex ligands. We demonstrate that the injection method does not influence the affinity whereas the ionic strength and the nature of the surface impact the recognition properties of the porphyrin for the G-quadruplex DNA. We also found that self-assembled monolayer coating surface presents many advantages in comparison with carboxymethylated dextran surface for SPR studies of G-quadruplex DNA/ligand interactions: (i) the electrostatic interaction with charged analytes is less important, (ii) its structure/composition is less sensitive to the ionic concentration and less prone to unspecific adsorption, (iii) it is easily homemade, and (iv) the cost is approximately 10 times cheaper.

Characteristics and clinical assessment of unexplained sudden cardiac arrest in the real-world setting: focus on idiopathic ventricular fibrillation

Aims

Recent studies have shown that in more than half of apparently unexplained sudden cardiac arrests (SCA), a specific aetiology can be unmasked by a careful evaluation. The characteristics and the extent to which such cases undergo a systematic thorough investigation in real-life practice are unknown.

Methods and results

Data were analysed from an ongoing study, collecting all cases of out-of-hospital cardiac arrest in Paris area. Investigations performed during the index hospitalization or planned after discharge were gathered to evaluate the completeness of assessment of unexplained SCA. Between 2011 and 2016, among the 18 622 out-of-hospital cardiac arrests, 717 survivors (at hospital discharge) fulfilled the definition of cardiac SCA. Of those, 88 (12.3%) remained unexplained after electrocardiogram, echocardiography, and coronary angiography. Cardiac magnetic resonance imaging yielded the diagnosis in 25 (3.5%) cases, other investigations accounted for 14 (2.4%) additional diagnoses, and 49 (6.8%) patients were labelled as idiopathic ventricular fibrillation (IVF) (48.7 ± 15 years, 69.4% male). Among those labelled IVF, only 8 (16.3%) cases benefited from a complete workup (including pharmacological testing). Younger patients [odds ratio (OR) 6.00, 95% confidence interval (CI) 1.80-22.26] and those admitted to university centres (OR 3.60, 95% CI 1.12-12.45) were more thoroughly investigated. Genetic testing and family screening were initiated in only 9 (18.4%) and 12 (24.5%) cases, respectively.

Conclusion

Our findings suggest that complete investigations are carried out in a very low proportion of unexplained SCA. Standardized, systematic approaches need to be implemented to ensure that opportunities for specific therapies and preventive strategies (including relatives) are not missed.

New Ruthenium-Based Probes for Selective G-Quadruplex Targeting

Telomeric regions containing G-quadruplex (G4) structures play a pivotal role in the development of cancers. The development of specific binders for G4s is thus of great interest in order to gain a deeper understanding of the role of these structures, and to ultimately develop new anticancer drug candidates. For several years, Ru^II complexes have been studied as efficient probes for DNA. Interest in these complexes stems mainly from the tunability of their structures and properties, and the possibility of using light excitation as a tool to probe their environment or to selectively trigger their reaction with a biological target. Herein, we report on the synthesis and thorough study of new Ru^II complexes based on a novel dipyrazino[2,3-a:2',3'-h]phenazine ligand (dph), obtained through a Chichibabin-like reaction. Luminescence experiments, surface plasmon resonance (SPR), and computational studies have demonstrated that these complexes behave as selective probes for G-quadruplex structures.

Template-Mediated Stabilization of a DNA G-Quadruplex formed in the HIV-1 Promoter and Comparative Binding Studies

G-rich DNA oligonucleotides derived from the promoter region of the HIV-1 long terminal repeat (LTR) were assembled onto an addressable cyclopeptide platform through sequential oxime ligation, a thiol-iodoacetamide SN2 reaction, and copper-catalyzed azide-alkyne cycloaddition reactions. The resulting conjugate was shown to fold into a highly stable antiparallel G4 architecture as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. The binding affinities of six state-of-the-art G4-binding ligands toward the HIV-G4 structure were compared to those obtained with a telomeric G4 structure and a hairpin structure. Surface plasmon resonance binding analysis provides new insights into the binding mode of broadly exploited G4 chemical probes and further suggests that potent and selective recognition of viral G4 structures of functional significance might be achieved.

Clinical Information Extraction at the CLEF eHealth Evaluation lab 2016

This paper reports on Task 2 of the 2016 CLEF eHealth evaluation lab which extended the previous information extraction tasks of ShARe/CLEF eHealth evaluation labs. The task continued with named entity recognition and normalization in French narratives, as offered in CLEF eHealth 2015. Named entity recognition involved ten types of entities including disorders that were defined according to Semantic Groups in the Unified Medical Language System^® (UMLS^®), which was also used for normalizing the entities. In addition, we introduced a large-scale classification task in French death certificates, which consisted of extracting causes of death as coded in the International Classification of Diseases, tenth revision (ICD10). Participant systems were evaluated against a blind reference standard of 832 titles of scientific articles indexed in MEDLINE, 4 drug monographs published by the European Medicines Agency (EMEA) and 27,850 death certificates using Precision, Recall and F-measure. In total, seven teams participated, including five in the entity recognition and normalization task, and five in the death certificate coding task. Three teams submitted their systems to our newly offered reproducibility track. For entity recognition, the highest performance was achieved on the EMEA corpus, with an overall F-measure of 0.702 for plain entities recognition and 0.529 for normalized entity recognition. For entity normalization, the highest performance was achieved on the MEDLINE corpus, with an overall F-measure of 0.552. For death certificate coding, the highest performance was 0.848 F-measure.

FRET Characterization of Complex Conformational Changes in a Large 16S Ribosomal RNA Fragment Site-Specifically Labeled Using Unnatural Base Pairs

Ribosome assembly has been studied intensively using Förster resonance energy transfer (FRET) with fluorophore-labeled fragments of RNA produced by chemical synthesis. However, these studies are limited by the size of the accessible RNA fragments. We have developed a replicable unnatural base pair (UBP) formed between (d)5SICS and (d)MMO2 or (d)NaM, which efficiently directs the transcription of RNA containing unnatural nucleotides. We now report the synthesis and evaluation of several of the corresponding ribotriphosphates bearing linkers that enable the chemoselective attachment of different functionalities. We found that the RNA polymerase from T7 bacteriophage does not incorporate NaM derivatives but does efficiently incorporate 5SICS(CO), whose linker enables functional group conjugation via Click chemistry, and when combined with the previously identified MMO2(A), whose amine side chains permits conjugation via NHS coupling chemistry, enables site-specific double labeling of transcribed RNA. To study ribosome assembly, we transcribed RNA corresponding to a 243-nt fragment of the central domain of Thermus thermophilus 16S rRNA containing 5SICS(CO) and MMO2(A) at defined locations and then site-specifically attached the fluorophores Cy3 and Cy5. FRET was characterized using single-molecule total internal reflection fluorescence (smTIRF) microscopy in the presence of various combinations of added ribosomal proteins. We demonstrate that each of the fragment's two three-helix junctions exist in open and closed states, with the latter favored by sequential protein binding. These results elucidate early and previously uncharacterized folding events underlying ribosome assembly and demonstrate the applicability of UBPs for biochemical, structural, and functional studies of RNAs.

Templated Formation of Discrete RNA and DNA:RNA Hybrid G-Quadruplexes and Their Interactions with Targeting Ligands

G-rich RNA and DNA oligonucleotides derived from the human telomeric sequence were assembled onto addressable cyclopeptide platforms through oxime ligations and copper-catalyzed azide-alkyne cycloaddition (CuAAc) reactions. The resulting conjugates were able to fold into highly stable RNA and DNA:RNA hybrid G-quadruplex (G4) architectures as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. Whereas rationally designed parallel RNA and DNA:RNA hybrid G4 topologies could be obtained, we could not force the formation of an antiparallel RNA G4 structure, thus supporting the idea that this topology is strongly disfavored. The binding affinities of four representative G4 ligands toward the discrete RNA and DNA:RNA hybrid G4 topologies were compared to the one obtained with the corresponding DNA G4 structure. Surface plasmon resonance (SPR) binding analysis suggests that the accessibility to G4 recognition elements is different among the three structures and supports the idea that G4 ligands might be shaped to achieve structure selectivity in a biological context.

The contribution of co-reference resolution to supervised relation detection between bacteria and biotopes entities

Background

The acquisition of knowledge about relations between bacteria and their locations (habitats and geographical locations) in short texts about bacteria, as defined in the BioNLP-ST 2013 Bacteria Biotope task, depends on the detection of co-reference links between mentions of entities of each of these three types. To our knowledge, no participant in this task has investigated this aspect of the situation. The present work specifically addresses issues raised by this situation: (i) how to detect these co-reference links and associated co-reference chains; (ii) how to use them to prepare positive and negative examples to train a supervised system for the detection of relations between entity mentions; (iii) what context around which entity mentions contributes to relation detection when co-reference chains are provided.

Results

We present experiments and results obtained both with gold entity mentions (task 2 of BioNLP-ST 2013) and with automatically detected entity mentions (end-to-end system, in task 3 of BioNLP-ST 2013). Our supervised mention detection system uses a linear chain Conditional Random Fields classifier, and our relation detection system relies on a Logistic Regression (aka Maximum Entropy) classifier. They use a set of morphological, morphosyntactic and semantic features. To minimize false inferences, co-reference resolution applies a set of heuristic rules designed to optimize precision. They take into account the types of the detected entity mentions, and take advantage of the didactic nature of the texts of the corpus, where a large proportion of bacteria naming is fairly explicit (although natural referring expressions such as "the bacteria" are common). The resulting system achieved a 0.495 F-measure on the official test set when taking as input the gold entity mentions, and a 0.351 F-measure when taking as input entity mentions predicted by our CRF system, both of which are above the best BioNLP-ST 2013 participant system.

Conclusions

We show that co-reference resolution substantially improves over a baseline system which does not use co-reference information: about 3.5 F-measure points on the test corpus for the end-to-end system (5.5 points on the development corpus) and 7 F-measure points on both development and test corpora when gold mentions are used. While this outperforms the best published system on the BioNLP-ST 2013 Bacteria Biotope dataset, we consider that it provides mostly a stronger baseline from which more work can be started. We also emphasize the importance and difficulty of designing a comprehensive gold standard co-reference annotation, which we explain is a key point to further progress on the task.

Construction of anti-parallel G-quadruplexes through sequential templated click

Biologically relevant anti-parallel DNA G-quadruplexes were constrained and stabilised onto addressable cyclopeptide scaffolds through sequential oxime and CuAAc reactions.

Natural language processing of radiology reports for the detection of thromboembolic diseases and clinically relevant incidental findings

Background

Natural Language Processing (NLP) has been shown effective to analyze the content of radiology reports and identify diagnosis or patient characteristics. We evaluate the combination of NLP and machine learning to detect thromboembolic disease diagnosis and incidental clinically relevant findings from angiography and venography reports written in French. We model thromboembolic diagnosis and incidental findings as a set of concepts, modalities and relations between concepts that can be used as features by a supervised machine learning algorithm. A corpus of 573 radiology reports was de-identified and manually annotated with the support of NLP tools by a physician for relevant concepts, modalities and relations. A machine learning classifier was trained on the dataset interpreted by a physician for diagnosis of deep-vein thrombosis, pulmonary embolism and clinically relevant incidental findings. Decision models accounted for the imbalanced nature of the data and exploited the structure of the reports.

Results

The best model achieved an F measure of 0.98 for pulmonary embolism identification, 1.00 for deep vein thrombosis, and 0.80 for incidental clinically relevant findings. The use of concepts, modalities and relations improved performances in all cases.

Conclusions

This study demonstrates the benefits of developing an automated method to identify medical concepts, modality and relations from radiology reports in French. An end-to-end automatic system for annotation and classification which could be applied to other radiology reports databases would be valuable for epidemiological surveillance, performance monitoring, and accreditation in French hospitals.

A semi-synthetic organism with an expanded genetic alphabet

Organisms are defined by the information encoded in their genomes, and since the evolution of life, this information has been encoded using a two base pair genetic alphabet (A-T and G-C). In vitro, the alphabet has been expanded to include several unnatural base pairs (UBPs)^1–3. We have developed a class of UBPs formed between nucleotides bearing hydrophobic nucleobases, exemplified by the pair formed between d5SICS and dNaM (d5SICS-dNaM, Fig. 1a), which is efficiently PCR amplified¹ and transcribed^4,5in vitro, and whose unique mechanism of replication has been characterized^6,7. However, expansion of a organism’s genetic alphabet presents new and unprecedented challenges: the unnatural nucleoside triphosphates must enter the cell; endogenous polymerases must be able to faithfully incorporate the unnatural triphosphates into DNA within the complex cellular milieu; and finally, the UBP must be stable in the presence of pathways that maintain the integrity of DNA. Here we show that an exogenously expressed algal nucleotide triphosphate transporter efficiently imports the triphosphates of both d5SICS and dNaM (d5SICSTP and dNaMTP) into E. coli, and that the endogenous replication machinery uses them to accurately replicate a plasmid containing d5SICS-dNaM. Neither the presence of the unnatural triphosphates nor the replication of the UBP introduces a significant growth burden. Lastly, we find that the UBP is not efficiently excised by DNA repair pathways. Thus, the resulting bacterium is the first organism to stably propagate an expanded genetic alphabet.

Surface-immobilized DNAzyme-type biocatalysis

The structure of the double helix of deoxyribonucleic acid (DNA, also called duplex-DNA) was elucidated sixty years ago by Watson, Crick, Wilkins and Franklin. Since then, DNA has continued to hold a fascination for researchers in diverse fields including medicine and nanobiotechnology. Nature has indeed excelled in diversifying the use of DNA: beyond its canonical role of repository of genetic information, DNA could also act as a nanofactory able to perform some complex catalytic tasks in an enzyme-mimicking manner. The catalytic capability of DNA was termed DNAzyme; in this context, a peculiar DNA structure, a quadruple helix also named quadruplex-DNA, has recently garnered considerable interest since its autonomous catalytic proficiency relies on its higher-order folding that makes it suitable to interact efficiently with hemin, a natural cofactor of many enzymes. Quadruplexes have thus been widely studied for their hemoprotein-like properties, chiefly peroxidase-like activity, i.e., their ability to perform hemin-mediated catalytic oxidation reactions. Recent literature is replete with applications of quadruplex-based peroxidase-mimicking DNAzyme systems. Herein, we take a further leap along the road to biochemical applications, assessing the actual efficiency of catalytic quadruplexes for the detection of picomolar levels of surface-bound analytes in an enzyme-linked immunosorbent (ELISA)-type assay. To this end, we exploit an innovative strategy based on the functionalization of DNA by a multitasking platform named RAFT (for regioselectivity addressable functionalized template), whose versatility enables the grafting of DNA whatever its nature (duplex-DNA, quadruplex-DNA, etc.). We demonstrate that the resulting biotinylated RAFT/quadruplex systems indeed acquire catalytic properties that allow for efficient luminescent detection of picomoles of surface-bound streptavidin. We also highlight some of the pitfalls that have to be faced during optimization, notably demonstrating that highly optimized experimental conditions can make DNA pre-catalysts catalytically competent whatever their secondary structures.

Structural insights into DNA replication without hydrogen bonds

The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.

Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and biotechnology applications

We synthesized a panel of unnatural base pairs whose pairing depends on hydrophobic and packing forces and identify dTPT3-dNaM, which is PCR amplified with a natural base pair-like efficiency and fidelity. In addition, the dTPT3 scaffold is uniquely tolerant of attaching a propargyl amine linker, resulting in the dTPT3(PA)-dNaM pair, which is amplified only slightly less well. The identification of dTPT3 represents significant progress toward developing an unnatural base pair for the in vivo expansion of an organism's genetic alphabet and for a variety of in vitro biotechnology applications where it is used to site-specifically label amplified DNA, and it also demonstrates for the first time that hydrophobic and packing forces are sufficient to mediate natural-like replication.

Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet

A class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM were developed. To explore the use of these pairs to produce site-specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modification of the amplified DNA by Click chemistry is reported. With the d5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the dMMO2 and dDMO analogues, the dMMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether-based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site-selectively attach a biotin tag to the amplified DNA. Finally, we use d5SICS(CO) -dNaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps "evolution" of nanomaterials.

Combining an expert-based medical entity recognizer to a machine-learning system: methods and a case study

Medical entity recognition is currently generally performed by data-driven methods based on supervised machine learning. Expert-based systems, where linguistic and domain expertise are directly provided to the system are often combined with data-driven systems. We present here a case study where an existing expert-based medical entity recognition system, Ogmios, is combined with a data-driven system, Caramba, based on a linear-chain Conditional Random Field (CRF) classifier. Our case study specifically highlights the risk of overfitting incurred by an expert-based system. We observe that it prevents the combination of the 2 systems from obtaining improvements in precision, recall, or F-measure, and analyze the underlying mechanisms through a post-hoc feature-level analysis. Wrapping the expert-based system alone as attributes input to a CRF classifier does boost its F-measure from 0.603 to 0.710, bringing it on par with the data-driven system. The generalization of this method remains to be further investigated.