Characteristics of patients with atrial fibrillation treated with direct oral anticoagulants and new insights into inappropriate dosing: results from the French National Prospective Registry: PAFF.

AIMS: Since the introduction of direct oral anticoagulant (DOAC) for atrial fibrillation (AF) therapy, inappropriate and/or underdosing of these drugs has been a major clinical challenge. We evaluated the characteristics of patients with AF treated with inappropriate and low-dose DOACs. METHODS AND RESULTS: Patients with AF treated with inappropriate and low-dose DOACs from October 2021 to December 2021 were evaluated from the French National Prospective Registry (PAFF). We evaluated 1890 patients with AF receiving DOACs (apixaban 55%, dabigatran 7%, and rivaroxaban 38%). Inappropriate dosing was noted in 18% of the population. Patients with appropriate dosing had less comorbidities: younger age (75 ± 10 vs. 82 ± 8 years old, P < 0.0001), reduced chronic renal failure (26 vs. 61%, P < 0.0001), and lower CHA2DS2VASc and HASBLED scores (3 ± 2 vs. 4 ± 3, P < 0.0001; 2 ±1 vs. 2 ± 2, P < 0.0001), respectively. In multivariate analysis, older age (P < 0.0001) and a higher CHA2DS2VASc score (P = 0.0056) were independently associated with inappropriate DOAC dosing. Among 472 patients (27%) treated with low-dose rivaroxaban or apixaban, 46% were inappropriately underdosed. Patients inappropriately underdosed were younger (82.3 ± 8.4 vs. 85.9 ± 5.9 years, P < 0.0001) with less chronic renal disease (47 vs. 98%, P < 0.0001). However, these patients had higher rates of prior haemorrhagic events (18 vs. 10%, P = 0.01), clopidogrel use (11 vs. 3%, P = 0.0002), and apixaban prescription (74 vs. 50%, P < 0.0001). CONCLUSION: Within this large registry, DOACs were associated with inappropriate dosing in 18% of cases. Independent predictors of inappropriate dosing were high CHA2DS2VASc scores and older age. Moreover, 46% of patients treated with low-dose DOACs were inappropriately underdosed and more frequently in patients treated with apixaban.

[Patients insuffisants cardiaques chroniques rarement adressés à un cardiologue libéral ou régulièrement suivis par un médecin généraliste et un cardiologue libéral : étude descriptive transversale (MIRROR-HF)]. / Patients with chronic heart failure infrequently referred to an officed-based cardiologist or regularly followed by a general practitioner and an officed-based cardiologist : a descriptive, cross-sectional study (MIRROR-HF).

BACKGROUND: French health authorities recommend implementing a strong coordination between general practitioners and office-based cardiologists for the care and management of patients with chronic heart failure. The aim of this study was to describe the characteristics of patients with chronic heart failure who were infrequently referred to an office-based cardiologist (either first time referral or last visit more than 12 months before study inclusion) by a general practitioner or other healthcare professional versus those who were regularly followed by a general practitioner and an office-based cardiologist (at least one visit to an office-based cardiologist in the last 12 months). METHODS: This was a non-interventional, cross-sectional study, conducted among office-based cardiologists in France during a single study visit. Descriptive statistics were performed. RESULTS: 1460 patients were included in the study with 37.1% in the group infrequently referred to an office-based cardiologist and 62.9% in the regularly followed group. The patients who were infrequently referred to an office-based cardiologist had relatively less heart failure with reduced ejection fraction (29.2% versus 36.6%), less prior chronic heart failure hospitalization (15.9% versus 31.4%), and less atrial fibrillation and ischemic heart failure as comorbidities (40.2% versus 50.5% and 39.3% versus 50.1%, respectively) than patients who were regularly followed by an office-based cardiologist and a general practitioner. They also received less clinical exams (25.5% versus 97.4%) and pharmacological (89.3% versus 98.4%) and non-pharmacological (17.3% versus 27.1%) heart failure treatments before the study visit. CONCLUSIONS: This study suggested that patients regularly followed by a general practitioner and an office-based cardiologist had globally a more severe chronic heart failure and a better medical monitoring and follow-up than other patients.

Disentangling the chemistry of Australian plant exudates from a unique historical collection.

For thousands of years, the unique physicochemical properties of plant exudates have defined uses in material culture and practical applications. Native Australian plant exudates, including resins, kinos, and gums, have been used and continue to be used by Aboriginal Australians for numerous technical and cultural purposes. A historic collection of well-preserved native Australian plant exudates, assembled a century ago by plant naturalists, gives a rare window into the history and chemical composition of these materials. Here we report the full hierarchical characterization of four genera from this collection, Xanthorrhoea, Callitris, Eucalyptus, and Acacia, from the local elemental speciation, to functional groups and main molecular markers. We use high-resolution X-ray Raman spectroscopy (XRS) to achieve bulk-sensitive chemical speciation of these plant exudates, including insoluble, amorphous, and cross-linked fractions, without the limitation of invasive and/or surface specific methods. Combinatorial testing of the XRS data allows direct classification of these complex natural species as terpenoid, aromatic, phenolic, and polysaccharide materials. Differences in intragenera chemistry was evidenced by detailed interpretation of the XRS spectral features. We complement XRS with Fourier-transform infrared (FT-IR) spectroscopy, gas chromatography­mass spectrometry (GC-MS), and pyrolysis­GC-MS (Py-GC-MS). This multimodal approach provides a fundamental understanding of the chemistry of these natural materials long used by Aboriginal Australian peoples.

Management of antithrombotics in situations with a gap in evidence: A national French survey focusing on patients with coronary artery disease and atrial fibrillation.

BACKGROUND: If several randomized studies allowed to better apprehend what should be the best antithrombotic strategy in patients with concomitant coronary artery disease (CAD) and atrial fibrillation (AF), there are still several clinical situations with a gap of evidence. METHODS: We conducted a national French survey in September-October 2020 among cardiologists in order to assess what are daily practices regarding the antithrombotic management in several specific clinical settings where no or little scientific evidence is available. The questionnaires were built by a committee of 6 cardiologists routinely involved in the field of CAD and/or AF. RESULTS: Among the 6388 French cardiologists, 483 (7.6%) cardiologists participated to the survey. The rate of participation was rather homogeneous across the country. The mean age of participants was 48 +/- 12.7. There were 134 women (27.7%) and 349 men. Altogether, 181 (37.5%) cardiologists worked in private, 153 (31.7%) in non-universitary public and 83 (17.2%) in universitary public centers. The remaining had shared activity. Among the participants, 150 were interventional (coronary) cardiologists (31.1%). Others were general cardiologists (n = 229), specialists in the field of rhythmology (n = 43), heart failure (n = 17) or imaging (n = 44). The survey consisted of 10 questions pertaining to 2 virtual clinical scenarios. CONCLUSIONS: The present survey is an illustration of how therapeutic decisions may vary in such situations with little or no scientific evidence. Such surveys may help experts to build consensus (answers with little variability) and to target the need for future trials and more research (answers with a lot of variability).

Deciphering the Chemistry of Cultural Heritage: Targeting Material Properties by Coupling Spectral Imaging with Image Analysis.

The chemical study of materials from natural history and cultural heritage, which provide information for art history, archeology, or paleontology, presents a series of specific challenges. The complexity of these ancient and historical materials, which are chemically heterogeneous, the product of alteration processes, and inherently not reproducible, is a major obstacle to a thorough understanding of their making and long-term behavior (e.g., fossilization). These challenges required the development of methodologies and instruments coupling imaging and data processing approaches that are optimized for the specific properties of the materials. This Account discusses how these characteristics not only constrain their study but also open up specific innovative avenues for providing key historical information. Synchrotron methods have extensively been used since the late 1990s to study heritage objects, in particular for their potential to provide speciation information from excitation spectroscopies and to image complex heritage objects and samples in two and three dimensions at high resolution. We examine in practice how the identification of key intrinsic chemical specificities has offered fertile ground for the development of novel synchrotron approaches allowing a better stochastic description of the properties of ancient and historical materials. These developments encompass three main aspects: (1) The multiscale heterogeneity of these materials can provide an essential source of information in the development of probes targeting their multiple scales of homogeneity. (2) Chemical alteration can be described in many ways, e.g., by segmenting datasets in a semiquantitative way to jointly inform morphological and chemical transformation pathways. (3) The intrinsic individuality of chemical signatures in artifacts triggers the development of specific strategies, such as those focusing on weak signal detection. We propose a rereading of the advent of these new methodologies for analysis and characterization and examine how they have led to innovative strategies combining materials science, instrument development, history, and data science. In particular, we show that spectral imaging and the search for correlations in image datasets have provided a powerful way to address what archeologists have called the uncertainty and ambiguity of the material record. This approach has implications beyond synchrotron techniques and extends in particular to a series of rapidly developing approaches that couple spectral and spatial information, as in hyperspectral imaging and spatially resolved mass spectrometry. The preeminence of correlations holds promise for the future development of machine learning methods for processing data on historical objects. Beyond heritage, these developments are an original source of inspiration for the study of materials in many related fields, such as environmental, geochemical, or life sciences, which deal with systems whose alteration and heterogeneity cannot be neglected.

Robust framework and software implementation for fast speciation mapping.

One of the greatest benefits of synchrotron radiation is the ability to perform chemical speciation analysis through X-ray absorption spectroscopies (XAS). XAS imaging of large sample areas can be performed with either full-field or raster-scanning modalities. A common practice to reduce acquisition time while decreasing dose and/or increasing spatial resolution is to compare X-ray fluorescence images collected at a few diagnostic energies. Several authors have used different multivariate data processing strategies to establish speciation maps. In this manuscript, the theoretical aspects and assumptions that are often made in the analysis of these datasets are focused on. A robust framework is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. Two fully operational software implementations are provided: a user-friendly implementation within the MicroAnalysis Toolkit software, and a dedicated script developed under the R environment. The procedure is exemplified through the study of a cross section of a typical fossil specimen. The algorithm provides accurate speciation and concentration mapping while decreasing the data collection time by typically two or three orders of magnitude compared with the collection of whole spectra at each pixel. Whereas acquisition of spectral datacubes on large areas leads to very high irradiation times and doses, which can considerably lengthen experiments and generate significant alteration of radiation-sensitive materials, this sparse excitation energy procedure brings the total irradiation dose greatly below radiation damage thresholds identified in previous studies. This approach is particularly adapted to the chemical study of heterogeneous radiation-sensitive samples encountered in environmental, material, and life sciences.

Determinants of Antithrombotic Treatment for Atrial Fibrillation in Octogenarians: Results of the OCTOFA Study.

BACKGROUND AND OBJECTIVE: Atrial fibrillation, the most frequent form of arrhythmia, affects 5-15% individuals aged > 80 years. Stroke is a major risk for atrial fibrillation patients. The benefits of anticoagulant therapy clearly outweigh the risk of hemorrhage, even in the elderly. Despite the efficacy of warfarin, many eligible patients receive no prophylactic antithrombotic therapy. New generation oral anticoagulants compare favorably with vitamin K antagonists in the prevention of thromboembolic events and hemorrhage. These new agents are likely to influence the prescribing habits of anticoagulants in atrial fibrillation. The aim of this study to investigate both the frequency and the determining factors of anticoagulant prescriptions in AF patients aged ≥ 80 years and followed up by private-practice cardiologists in France. METHODS: The OCTOFA (Atrial Fibrillation in Octogenarians) Study assessed the anticoagulant prescribing habits of cardiologists in France. The volunteer cardiologists recruited all consecutive patients fulilling the inclusion criteria. RESULTS: Between June 2013 and September 2016, 89 cardiologists recruited 738 eligible patients: age ≥ 80 years, non-valvular atrial fibrillation, no other compelling indication for anticoagulation therapy, no recent acute coronary syndrome or stroke. Most (90.7%) patients were on oral anticoagulant therapy: vitamin K antagonist or non-vitamin K antagonist oral anticoagulants, low molecular weight heparin (1.4%), aspirin (5.7%), and no antithrombotic treatment (2.2%). Patients on vitamin K antagonists were older (p < 0.001), had lower renal function (p = 0.033), and had a more frequent history of myocardial infarction (p < 0.001), heart failure (p = 0.001), peripheral artery disease (p = 0.033), major hemorrhage (p = 0.025), and falls (p = 0.045). Four determining factors of anticoagulant prescriptions were statistically significant: high CHA2DS2-VASc score (p < 0.001), high HAS-BLED score (p < 0.001), age > 90 years (p = 0.001), and moderate/severe cognitive impairment (p = 0.002). CONCLUSIONS: Most private-practice cardiologists prescribe anticoagulant treatment according to current guidelines in elderly atrial fibrillation patients. Non-vitamin K antagonist oral anticoagulants represent a significant proportion of prescriptions.

Synchrotron-Based Phase Mapping in Corroded Metals: Insights from Early Copper-Base Artifacts.

The detailed description of corrosion processes in ancient and historical metal artifacts currently relies on the in-depth study of prepared cross sections. The in-plane elemental and phase distributions can be established from a combination of light and electron microscopy characterization. Here, we show that high-resolution virtual sectioning through synchrotron X-ray microcomputed tomography allows a precise noninvasive 3D description of the distribution of both internal and external mineral phases in whole objects. In fragments of early copper artifacts (third-second millennium BC) from Southern Mesopotamia and the Indus valley, this approach provided essential clues on long-term corrosion processes. Major and minor phases were identified through semiquantitative evaluation of attenuation coefficients using polychromatic X-ray illumination. We found evidence for initially unidentified phases through statistical processing of images. We discuss interpretation of the distribution of these phases. A good correlation between the corrosion phases identified by CT and by invasive BSE-SEM is demonstrated. In addition to the stratigraphy of the copper corrosion compounds, we examine and discuss the variations observed in the attenuation coefficients of Cu(I) phases. Semiquantitative synchrotron X-ray microtomography phase mapping requires no specific sample preparation, in particular polishing or surface finishing, and any material tearing or displacement is avoided. We also provide evidence for the noninvasive observation of phases rapidly altered upon preparation of real cross sections. The method can be applied when cross-sectioning even of minute fragments is impossible.

Intranuclear expression of progesterone receptors in smooth muscle cells of renovascular fibromuscular dysplasia: a pilot study.

BACKGROUND: The pathogenesis of fibromuscular dysplasia (FMD) remains poorly understood. Yet, understanding this mechanism has taken on new urgency after recent evidence indicating that FMD is not as rare as previously thought. We speculated that hormonal receptors in the walls of dysplastic renal arteries were implicated in the pathogenesis of FMD. METHODS: We undertook a pilot prospective case-control study comparing histologic findings from renal arteries that were surgically removed in 2 patient groups. The case group included 6 samples from FMD patients who underwent surgery for stenosis or aneurysm caused by FMD. The control group included 3 FMD-free patients who underwent nephrectomy for nonvascular causes. Surgical specimens were sent to the histology laboratory. FMD was defined preoperatively using conventional radiologic criteria and was confirmed by histologic examination. RESULTS: Immunohistochemical staining detected intense progesterone receptor expression in the nuclei of smooth muscle cells in FMD patients. No progesterone receptor expression was found in the FMD-free patients. Estrogen receptor expression was not noted in the 2 groups. CONCLUSIONS: This preliminary finding may suggest that progesterone plays a key role in the pathogenesis of FMD and opens the fields of genetic and therapeutic approaches.

Trace elemental imaging of rare earth elements discriminates tissues at microscale in flat fossils.

The interpretation of flattened fossils remains a major challenge due to compression of their complex anatomies during fossilization, making critical anatomical features invisible or hardly discernible. Key features are often hidden under greatly preserved decay prone tissues, or an unpreparable sedimentary matrix. A method offering access to such anatomical features is of paramount interest to resolve taxonomic affinities and to study fossils after a least possible invasive preparation. Unfortunately, the widely-used X-ray micro-computed tomography, for visualizing hidden or internal structures of a broad range of fossils, is generally inapplicable to flattened specimens, due to the very high differential absorbance in distinct directions. Here we show that synchrotron X-ray fluorescence spectral raster-scanning coupled to spectral decomposition or a much faster Kullback-Leibler divergence based statistical analysis provides microscale visualization of tissues. We imaged exceptionally well-preserved fossils from the Late Cretaceous without needing any prior delicate preparation. The contrasting elemental distributions greatly improved the discrimination of skeletal elements material from both the sedimentary matrix and fossilized soft tissues. Aside content in alkaline earth elements and phosphorus, a critical parameter for tissue discrimination is the distinct amounts of rare earth elements. Local quantification of rare earths may open new avenues for fossil description but also in paleoenvironmental and taphonomical studies.

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.

MOTIVATION: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users. RESULTS: We developed new algorithms to allow automatic rebuilding and remodeling of main chain peptide bonds and side chains in crystallographic electron density maps, and incorporated these and further enhancements in the PDB_REDO procedure. Applying the updated PDB_REDO to the oldest, but also to some of the newest models in the PDB, corrects existing modeling errors and brings these models to a higher quality, as judged by standard validation methods. AVAILABILITY AND IMPLEMENTATION: The PDB_REDO database and links to all software are available at http://www.cmbi.ru.nl/pdb_redo. CONTACT: r.joosten@nki.nl; a.perrakis@nki.nl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS.

The DNA mismatch repair protein MutS recognizes mispaired bases in DNA and initiates repair in an ATP-dependent manner. Understanding of the allosteric coupling between DNA mismatch recognition and two asymmetric nucleotide binding sites at opposing sides of the MutS dimer requires identification of the relevant MutS.mmDNA.nucleotide species. Here, we use native mass spectrometry to detect simultaneous DNA mismatch binding and asymmetric nucleotide binding to Escherichia coli MutS. To resolve the small differences between macromolecular species bound to different nucleotides, we developed a likelihood based algorithm capable to deconvolute the observed spectra into individual peaks. The obtained mass resolution resolves simultaneous binding of ADP and AMP.PNP to this ABC ATPase in the absence of DNA. Mismatched DNA regulates the asymmetry in the ATPase sites; we observe a stable DNA-bound state containing a single AMP.PNP cofactor. This is the first direct evidence for such a postulated mismatch repair intermediate, and showcases the potential of native MS analysis in detecting mechanistically relevant reaction intermediates.

Restenosis is more frequent after carotid stenting than after endarterectomy: the EVA-3S study.

BACKGROUND AND PURPOSE: Carotid angioplasty and stenting (CAS) may be more often associated with residual or recurrent stenosis than carotid endarterectomy (CEA). We compared the rates of restenosis in patients treated with CAS or CEA in the EVA-3S trial. METHODS: Five hundred seven patients (242 treated by CAS and 265 by CEA) had carotid ultrasound follow-up (mean carotid ultrasound follow-up, 2.1 years) according to a predefined protocol. Carotid restenosis of 50% to 69% was diagnosed on planimetry, whereas carotid restenosis of ≥70% or occlusion was diagnosed using either planimetry or velocity criteria. RESULTS: The rate of carotid restenosis of ≥50% or occlusion was significantly higher after CAS (12.5%) than after CEA (5.0%; time ratio, 0.16; 95% CI, 0.03-0.76; P=0.02). The rates of severe restenosis of ≥70% or occlusion were low and did not differ significantly between the 2 groups (3-year rates are 3.3% in the CAS group and 2.8% in the CEA group). Age at baseline was the only vascular risk factor significantly associated with carotid restenosis. Our study could not detect any effect of carotid restenosis on ipsilateral stroke. CONCLUSIONS: The short-term rate of carotid restenosis of ≥50% or occlusion is ≈2.5-times more common after CAS than after CEA, a difference accounted for by an excess risk in moderate restenosis. More data with longer follow-up are needed to assess the rates of late severe restenosis and to determine the relation between restenosis and recurrent stroke over time.

Congenital anomalies of inferior vena cava in young patients with iliac deep venous thrombosis.

Venous thromboembolism (VTE) in young patients is frequently associated with hereditary biological thrombophilia, autoimmune disorders, or neoplasia. Advances in venous ultrasound and contrast-enhanced computed tomography have allowed for the identification of inferior vena cava (IVC) anomalies as newly considered etiologic factor. We present two cases of VTE in young patients: the first case involves left IVC in a 22-year-old man and the second involves IVC atresia in a 39-year-old man. IVC anomalies should be identified in young patients with spontaneous VTE involving the iliac veins because they are at a high risk for thrombotic recurrence and adaptation to long periods of antithrombotic therapy.

Identification of the finishing technique of an early eighteenth century musical instrument using FTIR spectromicroscopy.

The study of varnishes from musical instruments presents the difficulty of analysing very thin layers of heterogeneous materials on samples most of which are generally brittle and difficult to prepare. Such study is crucial to the understanding of historical musical instrument varnishing practices since written sources before 1800 are very rare and not precise. Fourier-transform infrared (FTIR) spectroscopy and imaging methods were applied to identify the major chemical components within the build-up of the varnish layers on a cello made by one of the most prominent French violin-makers of the eighteenth century (Jacques Boquay, ca. 1680-1730). Two types of FTIR imaging methods were used: scanning with a synchrotron-based microscope and full-field imaging using a 2D imager with a conventional source. An interpretation of the results obtained from these studies on the Boquay cello is that the maker first applied a proteinaceous layer, probably gelatine-based animal glue. He later applied a second layer based on a mixture of a drying oil and diterpenic resin from Pinaceae sp. From an historical perspective, the results complement previous studies by describing a second technique used for musical instrument finishes at the beginning of the eighteenth century in Europe.

Conservative treatment of spontaneous and isolated dissection of mesenteric arteries.

BACKGROUND: Isolated and spontaneous dissection of mesenteric arteries is a rare entity; a little more than 50 cases have been reported in medical literature. There is no therapeutic consensus concerning this type of lesion. METHODS: In this study, we report the results of our treatment based on a conservative approach. This retrospective study concerns eight patients with dissection of the celiac trunk and/or of the upper mesenteric artery (UMA) who were treated between 2002 and 2006. Because these patients were not presenting with acute intestinal ischemia diagnosed by clinical examination or paraclinical tests (medical imaging/biology) or with vital complications, they were treated with an efficient anticoagulation (heparin followed by anti-vitamin K) for 3 to 6 months. Endovascular or surgical treatment was used as the first option in patients with obvious intestinal ischemia or likely to have an arterial rupture, and also when medical treatment had failed. Clinical and radiological follow-up was at 1 month, 3 months, 6 months, and 1 year and then every year. Seven men and one woman (mean age, 48.2; age range, 38-53 years) were treated. Six patients presented with isolated dissection (celiac trunk=4, UMA=2). One patient had a celiac trunk and a UMA dissection and one had a celiac trunk and a UMA dissection along with a dissection of his two renal arteries. On entering the hospital, a patient was operated on for mesenteric ischemia related to a stenosis of the upper mesenteric artery (upper aortomesenteric bypass); a covered stent was implanted in the celiac trunk of another patient presenting with a contained rupture. RESULTS: Both patients were successfully treated. Six patients were medically treated. One of them required an aortohepatic bypass to treat an aneurysmal evolution of the celiac trunk revealed by a computed tomography scan obtained 1 month after the symptoms had begun. In one patient, the dissection remained stable on imaging. Four patients were cured, with a mean 20.1-month follow-up. CONCLUSION: Conservative treatment of spontaneous dissections of mesenteric arteries is possible when there are no complications, and it gives satisfactory results provided regular clinical and radiological checking is performed.

"Conditional Restraints": Restraining the Free Atoms in ARP/wARP.

The automated building of a protein model into an electron density map remains a challenging problem. In the ARP/wARP approach, model building is facilitated by initially interpreting a density map with free atoms of unknown chemical identity; all structural information for such chemically unassigned atoms is discarded. Here, this is remedied by applying restraints between free atoms, and between free atoms and a partial protein model. These are based on geometric considerations of protein structure and tentative (conditional) assignments for the free atoms. Restraints are applied in the REFMAC5 refinement program and are generated on an ad hoc basis, allowing them to fluctuate from step to step. A large set of experimentally phased and molecular replacement structures showcases individual structures where automated building is improved drastically by the conditional restraints. The concept and implementation we present can also find application in restraining geometries, such as hydrogen bonds, in low-resolution refinement.

Country-based reference values and impact of cardiovascular risk factors on carotid intima-media thickness in a French population: the 'Paroi Artérielle et Risque Cardio-Vasculaire' (PARC) Study.

AIM: To define reference values for mean common carotid artery intima-media thickness (CCAIMT(mean)) from subjects without conventional cardiovascular risk factors. METHODS: This nationwide study involved cardiologists at 246 centres in France. A total of 5,433 subjects with and without conventional cardiovascular risk factors participated. RESULTS: In subjects without risk factors, CCAIMT(mean) was 0.712 +/- 0.122 mm in men and 0.682 +/- 0.105 mm in women (p < 0.0001). Age explained 27.7% (men) and 33.9% (women) of the variance in CCAIMT(mean). Each 10-year increment in age was associated with a sex-adjusted increase in CCAIMT(mean) of 0.049 mm. In subjects with 1 risk factor, CCAIMT(mean) was 0.765 +/- 0.121 (p < 0.0001 vs. subjects without risk factors). CCAIMT(mean) increased continuously with increasing number of risk factors, irrespective of age group. In multivariable analysis, age, sex and number of cardiovascular risk factors appeared independently associated with CCAIMT(mean). CONCLUSION: CCAIMT(mean) may help to identify the population at intermediate cardiovascular risk. As an integrator of both conventional and genetic cardiovascular risk factors at the individual level, its additive value versus other risk scores must be evaluated, particularly in patients in their fourth and sixth decades.

Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease.

The human LINE-1 endonuclease (L1-EN) contributes in defining the genomic integration sites of the abundant human L1 and Alu retrotransposons. LINEs have been considered as possible vehicles for gene delivery and understanding the mechanism of L1-EN could help engineering them as genetic tools. We tested the in vitro activity of point mutants in three L1-EN residues--Asp145, Arg155, Ile204--that are key for DNA cleavage, and determined their crystal structures. The L1-EN structure remains overall unaffected by the mutations, which change the enzyme activity but leave DNA cleavage sequence specificity mostly unaffected. To better understand the mechanism of L1-EN, we performed molecular dynamics simulations using as model the structures of wild type EN-L1, of two betaB6-betaB5 loop exchange mutants we have described previously to be important for DNA recognition, of the R155A mutant from this study, and of the homologous TRAS1 endonuclease: all confirm a rigid scaffold. The simulations crucially indicate that the betaB6-betaB5 loop shows an anticorrelated motion with the surface loops betaA6-betaA5 and betaB3-alphaB1. The latter loop harbors N118, a residue that alters DNA cleavage specificity in homologous endonucleases, and implies that the plasticity and correlated motion of these loops has a functional importance in DNA recognition and binding. To further explore how these loops are possibly involved in DNA binding, we docked computationally two DNA substrates to our structure, one involving a flipped-out nucleotide downstream the scissile phosphodiester; and one not. The models for both scenarios are feasible and agree with the hypotheses derived from the dynamic simulations. The reduced cleavage activity we have observed for the I204Y mutant above however, favors the flipped out nucleotide model.

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.

ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best-fitting ligand from a 'cocktail'; and finding ordered water molecules. All protocols are easy to handle by a nonexpert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours.