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Summary: Minerals excavated during industrial activities are stored on the soil surface, exposed to weathering, which leads to the initial development of soil. Plants contribute to soil mineral weathering, mainly by producing acidic or complexing root exudates. In addition, many plants produce antioxidant compounds and phenolic substances that could also contribute to mineral transformation processes, but have rarely been considered in relation to mineral weathering. An incubation experiment was carried out for 2 months under controlled conditions to assess the effects of antioxidant plant metabolites on the weathering processes of a clay mineral. A freshly excavated, sulphur‐rich Callovo‐Oxfordian argillite (COx) sample was artificially leached with three concentrations of three antioxidant compounds (linalool, thymol and carvacrol) or water as a control. The weathering of COx was followed by the analysis of amounts of anions and cations in the leachates. Chlorine, sulphate, nitrate, phosphate, calcium, magnesium and potassium were found in the leachates, whereas iron and aluminium were close to the detection limits. Sulphate leaching reflected oxidation of the pyritic matter contained in COx (mainly fine pyrite particles) by air. Water alone was enough to cause notable leaching of elements such as S and P, but the percentage of leached sulphate increased in the presence of two antioxidant compounds, carvacrol and thymol, and increased to 38% with thymol at 2 mg l−1 compared with the antioxidant‐free control. Thus, antioxidant compounds could contribute to the leaching of elements from COx, depending on their nature and concentration. Highlights: We assessed the effects of leaching with antioxidant plant metabolites on COx clay weathering Sulphate leaching reflected the oxidation of pyritic matter (mainly fine pyrite particles) by air Percentage of sulphate leaching increased to 38% with thymol at 2 mg l−1 Antioxidant compounds contribute to the leaching of elements from COx [ABSTRACT FROM AUTHOR]

In this paper, the Scanning Laser Doppler Vibrometer (SLDV) is used to measure acoustic pressure in small regions of cavities for the study of acoustical localization. It is shown that this optical method leads to interesting information on localized acoustical modes inside irregular cavities, which are very difficult to observe using conventional microphone measurements. Indeed, localization regions are often of comparable size or even smaller than a typical microphone which can make this type of sensor intrusive. The SLDV is used to measure sound pressure after deriving the refracto-vibrometry method from its standard use. Data are obtained in a large area with a high spatial resolution and the method is validated on some cavities. On irregular cavities, localized modes have been measured and visualized precisely, showing a good agreement to numerical simulations. Owing to this tool, the increase of damping induced by irregularities is experimentally demonstrated through the study of the quality factor. The method is also used to estimate the sound absorption coefficient of quarter-wave resonators. The expected application of this work is the use of irregular geometries to dissipate acoustical energy, especially at frequencies at which porous materials are not efficient. [ABSTRACT FROM AUTHOR]

Introduction: The potential impact of targeting different components of an adverse lipid profile in populations with multiple cardiovascular risk factors is not completely clear. This study aims to assess the association between different components of the standard lipid profile with all-cause mortality and hospitalization due to cardiovascular events in a high-risk population. Methods: This prospective registry included high risk adults over 30 years old free of cardiovascular disease (2008–2012). Diagnosis of hypertension, dyslipidemia or diabetes mellitus was inclusion criterion. Lipid biomarkers were evaluated. Primary endpoints were all-cause mortality and hospital admission due to coronary heart disease or stroke. We estimated adjusted rate ratios (aRR), absolute risk differences and population attributable risk associated with adverse lipid profiles. Results: 51,462 subjects were included with a mean age of 62.6 years (47.6% men). During an average follow-up of 3.2 years, 919 deaths, 1666 hospitalizations for coronary heart disease and 1510 hospitalizations for stroke were recorded. The parameters that showed an increased rate for total mortality, coronary heart disease and stroke hospitalization were, respectively, low HDL-Cholesterol: aRR 1.25, 1.29 and 1.23; high Total/HDL-Cholesterol: aRR 1.22, 1.38 and 1.25; and high Triglycerides/HDL-Cholesterol: aRR 1.21, 1.30, 1.09. The parameters that showed highest population attributable risk (%) were, respectively, low HDL-Cholesterol: 7.70, 11.42, 8.40; high Total/HDL-Cholesterol: 6.55, 12.47, 8.73; and high Triglycerides/HDL-Cholesterol: 8.94, 15.09, 6.92. Conclusions: In a population with cardiovascular risk factors, HDL-cholesterol, Total/HDL-cholesterol and triglycerides/HDL-cholesterol ratios were associated with a higher population attributable risk for cardiovascular disease compared to other common biomarkers. [ABSTRACT FROM AUTHOR]

The universal force field (UFF) is a broadly applicable classical force field that contains parameters for almost every atom type of the periodic table. This force field is non-reactive, i.e. the topology of the system under study is considered as fixed and no creation or breaking of covalent bonds is possible. This paper introduces interactive modeling-UFF (IM-UFF), an extension of UFF that combines the possibility to significantly modify molecular structures (as with reactive force fields) with a broad diversity of supported systems thanks to the universality of UFF. Such an extension lets the user easily build and edit molecular systems interactively while being guided by physics based inter-atomic forces. This approach introduces weighted atom types and weighted bonds, used to update topologies and atom parameterizations at every time step of a simulation. IM-UFF has been evaluated on a large set of benchmarks and is proposed as a self-contained implementation integrated in a new module for the SAMSON software platform for computational nanoscience available at http://www.samson-connect.net . [ABSTRACT FROM AUTHOR]

Uranium ore waste has led to soil contamination that may affect both environmental and soil health. To analyze the risk of metal transfer, metal bioavailability must be estimated by measuring biological parameters. Kinetic studies allow taking into account the dynamic mechanisms of bioavailability, as well as the steady state concentration in organisms necessary to take into account for relevant risk assessment. In this way, this work aims to model the snail accumulation and excretion kinetics of uranium (U), cesium (Cs) and thorium (Th). Results indicate an absence of Cs and Th accumulation showing the low bioavailability of these two elements and a strong uranium accumulation in snails related to the levels of soil contamination. During the depuration phase, most of the uranium ingested was excreted by the snails. After removing the source of uranium by soil remediation, continued snails excretion of accumulated uranium would lead to the return of their initial internal concentration, thus the potential trophic transfer of this hazardous element would stop. [ABSTRACT FROM AUTHOR]

Background: A new definition of metabolically healthy obesity (MHO) has recently been proposed to stratify the heterogeneous mortality risk of obesity. Metabolomic profiling provides clues to metabolic alterations beyond clinical definition. We aimed to evaluate the association between MHO and cardiovascular events and assess its metabolomic pattern. Methods: This prospective study included Europeans from two population-based studies, the FLEMENGHO and the Hortega study. A total of 2339 participants with follow-up were analyzed, including 2218 with metabolomic profiling. Metabolic health was developed from the third National Health and Nutrition Examination Survey and the UK biobank cohorts and defined as systolic blood pressure < 130 mmHg, no antihypertensive drugs, waist-to-hip ratio < 0.95 for women or 1.03 for men, and the absence of diabetes. BMI categories included normal weight, overweight, and obesity (BMI < 25, 25–30, ≥ 30 kg/m2). Participants were classified into six subgroups according to BMI category and metabolic healthy status. Outcomes were fatal and nonfatal composited cardiovascular events. Results: Of 2339 participants, the mean age was 51 years, 1161 (49.6%) were women, 434 (18.6%) had obesity, 117 (5.0%) were classified as MHO, and both cohorts had similar characteristics. Over a median of 9.2-year (3.7–13.0) follow-up, 245 cardiovascular events occurred. Compared to those with metabolically healthy normal weight, individuals with metabolic unhealthy status had a higher risk of cardiovascular events, regardless of BMI category (adjusted HR: 3.30 [95% CI: 1.73–6.28] for normal weight, 2.50 [95% CI: 1.34–4.66] for overweight, and 3.42 [95% CI: 1.81–6.44] for obesity), whereas those with MHO were not at increased risk of cardiovascular events (HR: 1.11 [95% CI: 0.36–3.45]). Factor analysis identified a metabolomic factor mainly associated with glucose regulation, which was associated with cardiovascular events (HR: 1.22 [95% CI: 1.10–1.36]). Individuals with MHO tended to present a higher metabolomic factor score than those with metabolically healthy normal weight (0.175 vs. -0.057, P = 0.019), and the score was comparable to metabolically unhealthy obesity (0.175 vs. -0.080, P = 0.91). Conclusions: Individuals with MHO may not present higher short-term cardiovascular risk but tend to have a metabolomic pattern associated with higher cardiovascular risk, emphasizing a need for early intervention. [ABSTRACT FROM AUTHOR]

Two short syntheses of benzyl C-glycosides are developed employing oxa-Michael cyclizations of precursors (IIIa,b) or gold-catalyzed cyclization of alkyne (X) as the key step. [ABSTRACT FROM AUTHOR]

The front face fluorescence spectroscopy is often used to quantify chemicals in well-known matrices as it is a rapid and powerful technique, with no sample preparation. However it was not used to investigate extracted organic matter like humic substances. This work aims to fully investigate for the first time front face fluorescence spectroscopy response of a ternary system including boric acid, tryptophan and humic substances, and two binaries system containing quinine sulfate or humic substance in boric acid. Pure chemicals, boric acid, tryptophan, quinine sulfate and humic acid were mixed together in solid pellet at different contents from 0 to 100% in mass. The measurement of excitation emission matrix of fluorescence (3D fluorescence) and laser induced fluorescence were then done in the front face mode. Fluorescence matrices were decomposed using the CP/PARAFAC tools after scattering treatments. Results show that for 3D fluorescence there is no specific component for tryptophan and quinine sulfate, and that humic substances lead to a strong extinction effect for mixture containing quinine sulfate. Laser induced fluorescence gives a very good but non-specific related response for both quinine sulfate and tryptophan. No humic substances fluorescence response was found, but extinction effect is observed as for 3D fluorescence. This effect is stronger for quinine sulfate than for tryptophan. These responses were modeled using a simple absorbance versus emission model. [ABSTRACT FROM AUTHOR]

This paper proposes a new method to generate interpolation paths between two given molecular conformations. It relies on the As-Rigid-As-Possible (ARAP) paradigm used in Computer Graphics to manipulate complex meshes while preserving their essential structural characteristics. The adaptation of ARAP approaches to the case of molecular systems is presented in this contribution. Experiments conducted on a large set of benchmarks show how such a strategy can efficiently compute relevant interpolation paths with large conformational rearrangements. [ABSTRACT FROM AUTHOR]

Air Pollution monitoring and measurement are generally done using sampling techniques and analysis equipment often heavy, complex and expensive. Although these methods offer a high measurement precision which is essential to answer standards requirements, they are not adapted for quality oriented applications where simple information with low precision can be sufficient. The use of semiconductor gas sensors networks can provide the answer for a “low cost” system intended for such applications in air pollution detection fields. Three identical portable autonomous sensors arrays were built, each containing nine commercial semiconductor sensors especially chosen to detect a large range of pollutants usually encountered in ambient air and for a large part of them regulated. In order to overcome the temporal instability and the lack of reproducibility of these sensors, a calibration and normalisation procedure was developed. The obtained systems were used for on-site pollution monitoring in association with the French National Network of Accredited Associations for Air Quality Monitoring (AASQA). Gathered data from sensors systems and network data (NO, NO 2 , CO, PM2,5, …) were treated using nonlinear regression algorithms like Neural Networks with an original “fuzzy logic” type pre-treatment in order to compute a model able to predict the membership degree for three predefined pollution categories: traffic, urban and photochemical pollution, along with a pollution index describing the severity of the predominant pollution. The prediction rate was estimated system per system, and site per site for six sites. It has been shown that it was possible to obtain a quasi-universal model with a success rate over 80%. [ABSTRACT FROM AUTHOR]

Phosphorylated H2AX (γ-H2AX) is a sensitive marker for DNA double-strand breaks (DSBs), but the variability of H2AX expression in different cell and tissue types makes it difficult to interpret the meaning of the γ-H2AX level. Furthermore, the assays commonly used for γ-H2AX detection utilize laborious and low-throughput microscopy-based methods. We describe here an ELISA assay that measures both phosphorylated H2AX and total H2AX absolute amounts to determine the percentage of γ-H2AX, providing a normalized value representative of the amount of DNA damage. We demonstrate the utility of the assay to measure DSBs introduced by either ionizing radiation or DNA-damaging agents in cultured cells and in xenograft models. Furthermore, utilizing the NCI-60 cancer cell line panel, we show a correlation between the basal fraction of γ-H2AX and cellular mutation levels. This additional application highlights the ability of the assay to measure γ-H2AX levels in many extracts at once, making it possible to correlate findings with other cellular characteristics. Overall, the γ-H2AX ELISA represents a novel approach to quantifying DNA damage, which may lead to a better understanding of mutagenic pathways in cancer and provide a useful biomarker for monitoring the effectiveness of DNA-damaging anticancer agents. [ABSTRACT FROM AUTHOR]

The potential joint influence of metabolites on bone fragility has been rarely evaluated. We assessed the association of plasma metabolic patterns with bone fragility endpoints (primarily, incident osteoporosis-related bone fractures, and, secondarily, bone mineral density BMD) in the Hortega Study participants. Redox balance plays a key role in bone metabolism. We also assessed differential associations in participant subgroups by redox-related metal exposure levels and candidate genetic variants. In 467 participants older than 50 years from the Hortega Study, a representative sample from a region in Spain, we estimated metabolic principal components (mPC) for 54 plasma metabolites from NMR-spectrometry. Metals biomarkers were measured in plasma by AAS and in urine by HPLC-ICPMS. Redox-related SNPs (N = 341) were measured by oligo-ligation assay. The prospective association with incident bone fractures was inverse for mPC1 (non-essential and essential amino acids, including branched-chain, and bacterial co-metabolites, including isobutyrate, trimethylamines and phenylpropionate, versus fatty acids and VLDL) and mPC4 (HDL), but positive for mPC2 (essential amino acids, including aromatic, and bacterial co-metabolites, including isopropanol and methanol). Findings from BMD models were consistent. Participants with decreased selenium and increased antimony, arsenic and, suggestively, cadmium exposures showed higher mPC2-associated bone fractures risk. Genetic variants annotated to 19 genes, with the strongest evidence for NCF4, NOX4 and XDH, showed differential metabolic-related bone fractures risk. Metabolic patterns reflecting amino acids, microbiota co-metabolism and lipid metabolism were associated with bone fragility endpoints. Carriers of redox-related variants may benefit from metabolic interventions to prevent the consequences of bone fragility depending on their antimony, arsenic, selenium, and, possibly, cadmium, exposure levels. • Several metabolic patterns, so-called mPCs, were associated with bone fragility endpoints. • For mPC2, the bone fracture risk was higher with high exposure to Sb, As and, suggestively, Cd, and low Se. • Carriers of genetic variants in NCF4, NOX4 and XDH showed differential metabolic-related bone fracture risk. • Identified gene-environment statistical interactions may be relevant for metabolic bone fragility prevention. [ABSTRACT FROM AUTHOR]

Previous studies focused on the relationships between Serum Uric Acid (SUA) and lipids have found an association mainly with triglycerides. Furthermore, previous studies on adiposity indices have been focused on the evaluation of the Visceral Adiposity Index (VAI). The present study was aimed at providing within the same population a systematic evaluation of lipids and adiposity indices with SUA, employing both the classic cutoff for hyperuricemia and the newly one identified by the Uric Acid Right for Heart Health (URRAH) study. We analyzed data collected in 1892 subjects of the Pressioni Arteriose Monitorate E loro Associazioni (PAMELA) study with available SUA, lipid profile and variables necessary to calculate VAI, Cardio‐Metabolic Index (CMI) and Lipid Accumulation Product (LAP). At linear regression model (corrected for confounders) SUA correlated with all the lipids values (with the strongest β for triglycerides) and adiposity indices. When the two different cutoffs were compared, the URRAH one was significantly related to atherogenic lipids profile (OR 1.207 for LDL and 1.33 for non‐HDL, P < 0.001) while this was not the case for the classic one. Regarding adiposity indices the classic cutoff displays highest OR as compared to the URRAH one. In conclusions, newly reported URRAH cutoff for hyperuricemia better relate to atherogenic lipoprotein (LDL and non‐HDL) when compared to the classic one. The opposite has been found for adiposity indexes where the classic cut‐off seems to present highest performance. Among adiposity indexes, LAP present the highest OR for the relationship with hyperuricemia. [ABSTRACT FROM AUTHOR]

Cullin-RING ubiquitin E3 ligase (CRLs) composed of four components including cullin scaffolds, adaptors, substrate receptors, and RING proteins mediates the ubiquitination of approximately 20% of cellular proteins that are involved in numerous biological processes. While CRLs deregulation contributes to the pathogenesis of many diseases, including cancer, how CRLs deregulation occurs is yet to be fully investigated. Here, we demonstrate that components of CRL3 and its transcriptional regulators are possible prognosis marker of neuroendocrine (NE) cancer. Analysis of Cancer Cell Line Encyclopedia (CCLE) through the CellMinerCDB portal revealed that expression of CRL3 scaffold Cullin 3 (CUL3) highly correlates with NE signature, and CUL3 silencing inhibited NE cancer proliferation. Moreover, subset of 151 BTB (Bric-a-brac, Tramtrack, Broad complex) domain-containing proteins that have dual roles as substrate receptors and adaptor subunits in CRL3, as well as the expression of transcription factors (TFs) that control the transcription of BTB genes were upregulated in NE cancer. Analysis using published ChIP-sequencing data in small cell lung cancer (SCLC), including NE or non-NE SCLC verified that gene promoter of candidates which show high correlation with NE signature enriched H3K27Ac. These observations suggest that CRL3 is a master regulator of NE cancer and knowledge of specifically regulated CRL3 genes in NE cancer may accelerate new therapeutic approaches. • Cullin 3 is highly expressed in neuroendocrine cancer. • Subgroups of BTBs are highly expressed in neuroendocrine cancer. • Multiple modules in the transcription factors-BTBs-CRL3 axis are promising novel biomarkers in neuroendocrine cancer. [ABSTRACT FROM AUTHOR]

Human heart development is governed by transcription factor (TF) networks controlling dynamic and temporal gene expression alterations. Therefore, to comprehensively characterize these transcriptional regulations, day-to-day transcriptomic profiles were generated throughout the directed cardiac differentiation, starting from three distinct human- induced pluripotent stem cell lines from healthy donors (32 days). We applied an expression-based correlation score to the chronological expression profiles of the TF genes, and clustered them into 12 sequential gene expression waves. We then identified a regulatory network of more than 23,000 activation and inhibition links between 216 TFs. Within this network, we observed previously unknown inferred transcriptional activations linking IRX3 and IRX5 TFs to three master cardiac TFs: GATA4, NKX2-5 and TBX5. Luciferase and co-immunoprecipitation assays demonstrated that these five TFs could (1) activate each other's expression; (2) interact physically as multiprotein complexes; and (3) together, finely regulate the expression of SCN5A, encoding the major cardiac sodium channel. Altogether, these results unveiled thousands of interactions between TFs, generating multiple robust hypotheses governing human cardiac development. [ABSTRACT FROM AUTHOR]

This study describes a new tool for accurate and reliable high-throughput detection of copy number variation in the human genome. We have constructed a large-insert clone DNA microarray covering the entire human genome in tiling path resolution that we have used to identify copy number variation in human populations. Crucial to this study has been the development of a robust array platform and analytic process for the automated identification of copy number variants (CNVs). The array consists of 26,574 clones covering 93.7% of euchromatic regions. Clones were selected primarily from the published "Golden Path," and mapping was confirmed by fingerprinting and BAC-end sequencing. Array performance was extensively tested by a series of validation assays. These included determining the hybridization characteristics of each individual clone on the array by chromosome-specific add-in experiments. Estimation of data reproducibility and false-positive/negative rates was carried out using self--self hybridizations, replicate experiments, and independent validations of CNVs. Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method. [ABSTRACT FROM AUTHOR]

A response by Empar Lurbe and colleagues to several letters to the editor about their article "Increase in Nocturnal Blood Pressure and Progression to Microalbuminuria in Type 1 Diabetes," in the September 12, 2002 issue is presented.

Background: Patients with type 1 diabetes mellitus and microalbuminuria often have elevated blood pressure while they are asleep, but it is not known whether the elevation develops concomitantly with microalbuminuria or precedes it. Methods: We monitored 75 adolescents and young adults who had had type 1 diabetes with normal urinary albumin excretion and blood pressure for more than five years. Ambulatory blood-pressure monitoring was used to assess blood pressure at the initial evaluation and about two years later, at which time all subjects had normal urinary albumin excretion. Subsequently, subjects were monitored for the development of microalbuminuria. Results: Microalbuminuria developed in 14 subjects, whereas the other 61 continued to have normal urinary albumin excretion. The mean (±SD) systolic pressure during sleep increased significantly in the subjects who ultimately had microalbuminuria (from 109.9±11.3 to 114.9±11.7 mm Hg, P=0.01) but not in the subjects with normal albumin excretion (from 106.0±8.8 to 106.4±14.8 mm Hg). The risk of progression to microalbuminuria was examined in relation to the ratio of systolic pressure during sleep to systolic pressure in the daytime. A ratio of 0.9 or lower, used to define a normal fall in nocturnal pressure, had a negative predictive value of 91 percent for the development of microalbuminuria. Moreover, the risk of microalbuminuria was 70 percent lower (95 percent confidence interval, 44 to 110 percent) in subjects with a ratio of 0.9 or less than in those with a ratio higher than 0.9 (P=0.01). Conclusions: In persons with type 1 diabetes, an increase in systolic blood pressure during sleep precedes the development of microalbuminuria. In those whose blood pressure during sleep decreases normally, the progression from normal albumin excretion to microalbuminuria appears to be less likely. (N Engl J Med 2002;347:797-805.) [ABSTRACT FROM AUTHOR]

The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (). We validate both the automatic perception method and the UFF implementation on a series of benchmarks. [ABSTRACT FROM AUTHOR]

Low-cost particulate matter (PM) sensors are increasingly used by researchers, public health agencies, and the public to measure spatial and temporal variations in air pollution, which can inform strategies for community air pollution reduction. While low-cost PM sensors provide a valuable measure of harmful fine particulate matter (PM 2.5), a significant portion of ambient PM 2.5 is typically the secondary product of air pollution emitted by varied sources outside of community boundaries. In contrast, concentrations of black carbon (BC), a component of PM 2.5 , are directly emitted by a few specific sources, such as diesel engines within communities. Motivated by community organizations seeking to understand persistent sources of local pollution, this study deployed a suite of custom-built BC sensors alongside a network of low-cost PM sensors for four weeks in two seasons at 50 stationary locations in the adjacent cities of Richmond, North Richmond, and San Pablo, California, east of the San Francisco Bay. Concentrations of BC varied more than PM 2.5 both temporally and spatially. Monthly network-average BC was 3 × higher in winter than late spring, while PM 2.5 was only 10% lower. In both seasons, average PM 2.5 concentrations at two-thirds of sites were within ±10% of the network average, whereas two-thirds of sites had BC levels outside of ±10% of the network-average concentration. The most and least polluted locations were more persistent across seasons for BC than PM 2.5 , and the temporal dynamics of BC at these sites were similar, signifying that they are impacted by the same emission sources. Together, these spatiotemporal trends show that BC is a better indicator of the proximity and activity of local pollution sources than PM 2.5. Thus, including BC in addition to PM 2.5 in community monitoring networks can provide additional insights about local sources of air pollution. [Display omitted] • BC and PM sensors deployed 4 weeks in 2 seasons at 50 sites in an environmental justice community. • Greater spatiotemporal heterogeneity and location persistence of BC compared to PM 2.5 • BC more informative than PM 2.5 of proximity and activity of local emission sources. • Recommend measuring PM 2.5 plus BC for insights to community air protection plans. [ABSTRACT FROM AUTHOR]

Presents an abstract for the article on the use of DNA microarrays in the study of head and neck tumors.

Background: Estimating relatedness is an important step for many genetic study designs. A variety of methods for estimating coefficients of pairwise relatedness from genotype data have been proposed. Both the kinship coefficient φ and the fraternity coefficient ψ for all pairs of individuals are of interest. However, when dealing with low-depth sequencing or imputation data, individual level genotypes cannot be confidently called. To ignore such uncertainty is known to result in biased estimates. Accordingly, methods have recently been developed to estimate kinship from uncertain genotypes. Results: We present new method-of-moment estimators of both the coefficients φ and ψ calculated directly from genotype likelihoods. We have simulated low-depth genetic data for a sample of individuals with extensive relatedness by using the complex pedigree of the known genetic isolates of Cilento in South Italy. Through this simulation, we explore the behaviour of our estimators, demonstrate their properties, and show advantages over alternative methods. A demonstration of our method is given for a sample of 150 French individuals with down-sampled sequencing data. Conclusions: We find that our method can provide accurate relatedness estimates whilst holding advantages over existing methods in terms of robustness, independence from external software, and required computation time. The method presented in this paper is referred to as LowKi (Low-depth Kinship) and has been made available in an R package (https://github.com/genostats/LowKi). [ABSTRACT FROM AUTHOR]

Background: Guidelines recommend physical activity to reduce cardiovascular (CV) events. The association between physical activity and progression of chronic kidney disease (CKD) with and without diabetes is unknown. We assessed the association of self-reported physical activity with renal and CV outcomes in high-risk patients aged ≥ 55 years over a median follow-up of 56 months in post-hoc analysis of a previously randomized trial program. Methods: Analyses were done with Cox regression analysis, mixed models for repeated measures, ANOVA and χ2-test. 31,312 patients, among them 19,664 with and 11,648 without diabetes were analyzed. Results: Physical activity was inversely associated with renal outcomes (doubling of creatinine, end-stage kidney disease (ESRD)) and CV outcomes (CV death, myocardial infarction, stroke, heart failure hospitalization). Moderate activity (at least 2 times/week to every day) was associated with lower risk of renal outcomes and lower incidence of new albuminuria (p < 0.0001 for both) compared to lower exercise levels. Similar results were observed for those with and without diabetes without interaction for renal outcomes (p = 0.097–0.27). Physical activity was associated with reduced eGFR decline with a moderate association between activity and diabetes status (p = 0.05). Conclusions: Moderate physical activity was associated with improved kidney outcomes with a threshold at two sessions per week. The association of physical activity with renal outcomes did not meaningfully differ with or without diabetes but absolute benefit of activity was even greater in people with diabetes. Thus, risks were similar between those with diabetes undertaking high physical activity and those without diabetes but low physical activity. Clinical trial registration: http://clinicaltrials.gov.uniqueidentifier:NCT00153101. [ABSTRACT FROM AUTHOR]

Non-coding RNA (ncRNA)-mediated targeting of various genes regulates the molecular mechanisms of the pathogenesis of hypertension (HTN). However, very few circulating long ncRNAs (lncRNAs) have been reported to be altered in essential HTN. The aim of our study was to identify a lncRNA profile in plasma and plasma exosomes associated with urinary albumin excretion in HTN by next-generation sequencing and to assess biological functions enriched in response to albuminuria using GO and KEGG analysis. Plasma exosomes showed higher diversity and fold change of lncRNAs than plasma, and low transcript overlapping was found between the two biofluids. Enrichment analysis identified different biological pathways regulated in plasma or exosome fraction, which were implicated in fatty acid metabolism, extracellular matrix, and mechanisms of sorting ncRNAs into exosomes, while plasma pathways were implicated in genome reorganization, interference with RNA polymerase, and as scaffolds for assembling transcriptional regulators. Our study found a biofluid specific lncRNA profile associated with albuminuria, with higher diversity in exosomal fraction, which identifies several potential targets that may be utilized to study mechanisms of albuminuria and cardiovascular damage. [ABSTRACT FROM AUTHOR]

The objective is to assess the impact of anticoagulant treatment in non-valvular atrial fibrillation (AF) and different categories of renal dysfunction in real world. Electronic Health recordings of patients with diagnosis of AF and renal function collected throughout 5 years and classified according to KDIGO categories. Stroke, transitory ischemic attack (TIA), intracranial hemorrhage and all-cause mortality were identified. Anticoagulant treatments during the study period were classified in untreated (never received therapy), VKA, NOAC and Aspirin. The risk of events was calculated by Cox-proportional hazard models adjusted by confounders. A total of 65,734 patients with AF, mean age 73.3 ± 10.49 years old and 47% females and follow-up of 3.2 years were included. KDIGO classification were: G1 33,903 (51.6%), G2 17,456 (26.6%), G3 8024 (12.2%) and G4 6351 (9.7%). There were 8592 cases of stroke and TIA, 437 intracranial hemorrhage, and 9603 all-cause deaths (incidence 36, 2 and 38 per 103 person/year, respectively). 4.1% of patients with CHA2DS2-VASc Score 2 or higher did not receive anticoagulant therapy. Risk of stroke, TIA, and all-cause mortality increased from G1 to G4 groups. Anticoagulant treatments reduced the risk of events in the four categories, but NOAC seemed to offer significantly better protection. Renal dysfunction increases the risk of events in AF and anticoagulant treatments reduced the risk of stroke and all-cause mortality, although NOAC were better than VKA. Efforts should be done to reduce the variability in the use of anticoagulants even in this high risk group. [ABSTRACT FROM AUTHOR]

BEN domain–containing proteins are emerging rapidly as an important class of factors involved in modulating gene expression, yet the molecular basis of how they regulate chromatin function and transcription remains to be established. BEND3 is a quadruple BEN domain–containing protein that associates with heterochromatin and functions as a transcriptional repressor. We find that BEND3 is highly expressed in pluripotent cells, and the induction of differentiation results in the down-regulation of BEND3. The removal of BEND3 from pluripotent cells results in cells exhibiting upregulation of the differentiation-inducing gene expression signature. We find that BEND3 binds to the promoters of differentiation-associated factors and key cell cycle regulators, including CDKN1A, encoding the cell cycle inhibitor p21, and represses the expression of differentiation-associated genes by enhancing H3K27me3 decoration at these promoters. Our results support a model in which transcription repression mediated by BEND3 is essential for normal development and to prevent differentiation. [ABSTRACT FROM AUTHOR]

A practical and efficient synthesis of 2,4,6,8-tetrasubstituted quinazolines through one-pot chemoselective sequential bis- SNAr/bis-Suzuki-Miyaura reactions under microwave irradiation is presented. The bis-SNAr reaction occurs selectively at the C-2 and C-4 positions of 6,8-dibromo-2,4-dichloroquinazoline and the bis- Suzuki-Miyaura cross-coupling at C-6 and C-8. This procedure affords convergent synthesis of polysubstituted quinazoline derivatives in high yields in very few steps and tolerates a wide range of boronic acids and amines. [ABSTRACT FROM AUTHOR]

Due to its short-lived progeny, including gaseous radon isotopes that can be inhaled and its significant transfer into vegetation, radium poses a substantial concern in radiation risk assessment. Although the transfer of Ra from soil to plants has been previously documented, the distribution and speciation of radium within the plant tissues, particularly within trees, remain unclear. The temporal dimension of Ra transfer is also poorly known. Therefore, the transfer of radium and others alkaline earth cations in beech trees was investigated through the analysis of fine (<2 mm) roots and leaves corresponding to tree organs with a life cycle limited to one season. This study was conducted at the experimental Montiers (INRAE-Andra site, France) and Strengbach watershed (OHGE site, France) beech-forested site. The activity of 226Ra and the isotopic ratio (228Ra/226Ra) were measured in roots and leaves using gamma spectrometry. Additionally, the concentration of alkaline earth cations (Mg, Ca, Sr, and Ba) was measured, to better constraint the mechanism of alkaline earth cation transfer through the xylem. The retention of these cations within the trees increases with the mass of the element, following the order Mg < Ca < Sr ≈ Ba < Ra, i.e.: light alkaline earth cations are more efficiently transferred from roots to leaves than heavy one. Our results suggest that these cations maintain their hydration shell during their ascent in stems and a low pH ion-exchange process rather than a complexation process with carboxylic group occurs. The decay of the (228Ra/226Ra) isotopic ratio over time during transfer within the trees allows us to quantify the slow Ra translocation from roots to the leaves, ranging from 1 to more than 16 years. This duration increases with the age of the trees. Hence, radioactive decay of Ra provides particularly valuable timescale information that is usually difficult to assess for Ca or other alkaline earth cations. [Display omitted] • Light alkaline earth cations are more transferred to leaves than heavy one. • Alkaline earth cations keep their hydration shell during ascent in tree stems. • The 228Ra/226Ra ratio provides a means to determine AE cations transfer time in trees. • The translocation of Ra in trees is really slow. • The residence time of Ra increases with the age and/or the size of the tree. [ABSTRACT FROM AUTHOR]

Background: The contribution of metabolomic factors to the association of healthy lifestyle with type 2 diabetes risk is unknown. We assessed the association of a composite measure of lifestyle with plasma metabolite profiles and incident type 2 diabetes, and whether relevant metabolites can explain the prospective association between healthy lifestyle and incident type 2 diabetes. Methods: A Healthy Lifestyle Score (HLS) (5-point scale including diet, physical activity, smoking status, alcohol consumption and BMI) was estimated in 1016 Hortega Study participants, who had targeted plasma metabolomic determinations at baseline examination in 2001–2003, and were followed-up to 2015 to ascertain incident type 2 diabetes. Results: The HLS was cross-sectionally associated with 32 (out of 49) plasma metabolites (2.5% false discovery rate). In the subset of 830 participants without prevalent type 2 diabetes, the rate ratio (RR) and rate difference (RD) of incident type 2 diabetes (n cases = 51) per one-point increase in HLS was, respectively, 0.69 (95% CI, 0.51, 0.93), and − 8.23 (95% CI, − 16.34, − 0.13)/10,000 person-years. In single-metabolite models, most of the HLS-related metabolites were prospectively associated with incident type 2 diabetes. In probit Bayesian Kernel Machine Regression, these prospective associations were mostly driven by medium HDL particle concentration and phenylpropionate, followed by small LDL particle concentration, which jointly accounted for ~ 50% of the HLS-related decrease in incident type 2 diabetes. Conclusions: The HLS showed a strong inverse association with incident type 2 diabetes, which was largely explained by plasma metabolites measured years before the clinical diagnosis. [ABSTRACT FROM AUTHOR]

Background: Guidelines recommend physical activity to reduce cardiovascular (CV) events. The association between physical activity and progression of chronic kidney disease (CKD) with and without diabetes is unknown. We assessed the association of self-reported physical activity with renal and CV outcomes in high-risk patients aged ≥ 55 years over a median follow-up of 56 months in post-hoc analysis of a previously randomized trial program. Methods: Analyses were done with Cox regression analysis, mixed models for repeated measures, ANOVA and χ2-test. 31,312 patients, among them 19,664 with and 11,648 without diabetes were analyzed. Results: Physical activity was inversely associated with renal outcomes (doubling of creatinine, end-stage kidney disease (ESRD)) and CV outcomes (CV death, myocardial infarction, stroke, heart failure hospitalization). Moderate activity (at least 2 times/week to every day) was associated with lower risk of renal outcomes and lower incidence of new albuminuria (p < 0.0001 for both) compared to lower exercise levels. Similar results were observed for those with and without diabetes without interaction for renal outcomes (p = 0.097–0.27). Physical activity was associated with reduced eGFR decline with a moderate association between activity and diabetes status (p = 0.05). Conclusions: Moderate physical activity was associated with improved kidney outcomes with a threshold at two sessions per week. The association of physical activity with renal outcomes did not meaningfully differ with or without diabetes but absolute benefit of activity was even greater in people with diabetes. Thus, risks were similar between those with diabetes undertaking high physical activity and those without diabetes but low physical activity. Clinical trial registration: http://clinicaltrials.gov.uniqueidentifier:NCT00153101. [ABSTRACT FROM AUTHOR]

Objectives: To asses the prognostic value of diagnostic scales in mortality of community-adquired sepsis and added value of additional parameters.Methods: Prospective observational study of patients with community-adquired sepsis in the Emergency Room of University Hospital. The study population were patients presented in the Emergency Room with confirmed infection and practicians sepsis diagnosis. Demographics, triage vital signs, inhaled oxygen fraction, inflammatory markers, biochemistry, all-cause mortality during hospitalization and three months after were recorded. Prognostic value of qSOFA, NEWS, SOFA, SIRS, and amplified scales were calculated by using logistic regression and ROC curves.Results: 201 patients, 54% male, average age 77±11,2 years were included. Sixty-three (31.5%) died during hospitalization and 24 (12%) three months after discharge. At the time of admission vital signs related with in-hospital mortality were Glasgow Coma Scale <13, respiratory rate ≥22 bpm, temperature, oxygen desaturation, high flow oxygen therapy and heart rate. Patients dead in-hospital had lower PaCO2, higher lactate, glucose and creatinine. Greater predictive capacity of the scales, from higher to lower, was: qSOFA, NEWS2, SOFA and SIRS. Amplified scales with lactate >2mg/dl, glucose, blood level >190mg/dl and PaCO2 <35mmHg improved predictive value.Conclusion: Amplified-qSOFA and amplified-NEWS2 scales at Emergency Department may offer a better prognostic of septic patients mortality. [ABSTRACT FROM AUTHOR]

We present a novel Block-Adaptive Quantum Mechanics (BAQM) approach to interactive quantum chemistry. Although quantum chemistry models are known to be computationally demanding, we achieve interactive rates by focusing computational resources on the most active parts of the system. BAQM is based on a divide-and-conquer technique and constrains some nucleus positions and some electronic degrees of freedom on the fly to simplify the simulation. As a result, each time step may be performed significantly faster, which in turn may accelerate attraction to the neighboring local minima. By applying our approach to the nonself-consistent Atom Superposition and Electron Delocalization Molecular Orbital theory, we demonstrate interactive rates and efficient virtual prototyping for systems containing more than a thousand of atoms on a standard desktop computer. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Bacterial adaptation involves extensive cellular reorganization. In particular, growth rate adjustments are associated with substantial modifications of gene expression and mRNA abundance. In this work we aimed to assess the role of mRNA degradation during such variations. A genome-wide transcriptomic-based method was used to determine mRNA half-lives. The model bacterium Lactococcus lactis was used and different growth rates were studied in continuous cultures under isoleucine-limitation and in batch cultures during the adaptation to the isoleucine starvation. During continuous isoleucine-limited growth, the mRNAs of different genes had different half-lives. The stability of most of the transcripts was not constant, and increased as the growth rate decreased. This half-life diversity was analyzed to investigate determinants of mRNA stability. The concentration, length, codon adaptation index and secondary structures of mRNAs were found to contribute to the determination of mRNA stability in these conditions. However, the growth rate was, by far, the most influential determinant. The respective influences of mRNA degradation and transcription on the regulation of intra-cellular transcript concentration were estimated. The role of degradation on mRNA homeostasis was clearly evidenced: for more than 90% of the mRNAs studied during continuous isoleucine-limited growth of L. lactis, degradation was antagonistic to transcription. Although both transcription and degradation had, opposite effects, the mRNA changes in response to growth rate were driven by transcription. Interestingly, degradation control increased during the dynamic adaptation of bacteria as the growth rate reduced due to progressive isoleucine starvation in batch cultures. This work shows that mRNA decay differs between gene transcripts and according to the growth rate. It demonstrates that mRNA degradation is an important regulatory process involved in bacterial adaptation. However, its impact on the regulation of mRNA levels is smaller than that of transcription in the conditions studied. [ABSTRACT FROM AUTHOR]

Background- Hypertension treatment guidelines recommend that blood pressure (BP) be lowered to <140/90 mm Hg, but that a reduction to <130/80 mm Hg be adopted in patients at high cardiovascular (CV) risk. We investigated the CV and renal benefits associated with these BP targets in the high-CV-risk population of the Ongoing Telmisartan Alone and in Combination With Ramipril Global End Point Trial (ONTARGET). Methods and Results- Patients were divided into 4 groups according to the proportion of in-treatment visits before the occurrence of an event (<25%->75%) in which BP was reduced to <140/90 or <130/80 mm Hg. After adjustment for demographic and clinical variables, a progressive increase in the proportion of visits in which BP was reduced to <140/90 or <130/80 mm Hg was associated with a progressive reduction in the risk of stroke, new onset of microalbuminuria or macroalbuminuria, and return to normoalbuminuria in albuminuric patients. An increased frequency of BP control to either target did not have any consistent effect on the adjusted risk of myocardial infarction and heart failure. The adjusted risk of CV events was reduced by increasing the frequency of BP control to <140/90 mm Hg, but not to <130/80 mm Hg. Similar findings were obtained for the achievement of the BP target in the visit preceding a CV event. Conclusion- The more frequent achievement of the BP targets recommended by guidelines led to cerebrovascular and renal protection, but did not increase cardiac protection. Overall, CV protection was favorably affected by the less tight but not by the tighter BP target. Clinical Trial Registration- URL: http://www.clinicaltrials.gov. Unique identifier: NCT00153101. [ABSTRACT FROM AUTHOR]

Background--Hypertension treatment guidelines recommend that blood pressure (BP) be lowered to <140/90 mm Hg, but that a reduction to <130/80 mm Hg be adopted in patients at high cardiovascular (CV) risk. We investigated the CV and renal benefits associated with these BP targets in the high-CV-risk population of the Ongoing Telmisartan Alone and in Combination With Ramipril Global End Point Trial (ONTARGET). Methods and Results--Patients were divided into 4 groups according to the proportion of in-treatment visits before the occurrence of an event (<25%->75%) in which BP was reduced to <140/90 or <130/80 mm Hg. After adjustment for demographic and clinical variables, a progressive increase in the proportion of visits in which BP was reduced to <140/90 or <130/80 mmHg was associated with a progressive reduction in the risk of stroke, new onset of microalbuminuria or macroalbuminuria, and return to normoalbuminuria in albuminuric patients. An increased frequency of BP control to either target did not have any consistent effect on the adjusted risk of myocardial infarction and heart failure. The adjusted risk of CV events was reduced by increasing the frequency of BP control to <140/90 mm Hg, but not to <130/80 mm Hg. Similar findings were obtained for the achievement of the BP target in the visit preceding a CV event. Conclusion--The more frequent achievement of the BP targets recommended by guidelines led to cerebrovascular and renal protection, but did not increase cardiac protection. Overall, CV protection was favorably affected by the less tight but not by the tighter BP target. [ABSTRACT FROM AUTHOR]

Abstract: The vestibular system contributes to a wide range of functions, from postural and oculomotor reflexes to spatial representation and cognition. Vestibular signals are important to maintain an internal, updated representation of the body position and movement in space. However, it is not clear to what extent they are also necessary to mentally simulate movement in situations that do not involve displacements of the body, as in mental imagery. The present study assessed how vestibular loss can affect object-based mental transformations (OMTs), i.e., imagined rotations or translations of objects relative to the environment. Participants performed one task of mental rotation of 3D-objects and two mental scanning tasks dealing with the ability to build and manipulate mental images that have metric properties. Menière''s disease patients were tested before unilateral vestibular neurotomy and during the recovery period (1 week and 1 month). They were compared to healthy participants tested at similar time intervals and to bilateral vestibular-defective patients tested after the recovery period. Vestibular loss impaired all mental imagery tasks. Performance varied according to the extent of vestibular loss (bilateral patients were frequently the most impaired) and according to the time elapsed after unilateral vestibular neurotomy (deficits were stronger at the early stage after neurotomy and then gradually compensated). These findings indicate that vestibular signals are necessary to perform OMTs and provide the first demonstration of the critical role of vestibular signals in processing metric properties of mental representations. They suggest that vestibular loss disorganizes brain structures commonly involved in mental imagery, and more generally in mental representation. [Copyright &y& Elsevier]

Genetic investigations of X-linked intellectual disabilities have implicated the ARX (Aristaless-related homeobox) gene in a wide spectrum of disorders extending from phenotypes characterised by severe neuronal migration defects such as lissencephaly, to mild or moderate forms of mental retardation without apparent brain abnormalities but with associated features of dystonia and epilepsy. Analysis of Arx spatio-temporal localisation profile in mouse revealed expression in telencephalic structures, mainly restricted to populations of GABAergic neurons at all stages of development. Furthermore, studies of the effects of ARX loss of function in humans and animal models revealed varying defects, suggesting multiple roles of this gene during brain development. However, to date, little is known about how ARX functions as a transcription factor and the nature of its targets. To better understand its role, we combined chromatin immunoprecipitation and mRNA expression with microarray analysis and identified a total of 1006 gene promoters bound by Arx in transfected neuroblastoma (N2a) cells and in mouse embryonic brain. Approximately 24% of Arx-bound genes were found to show expression changes following Arx overexpression or knock-down. Several of the Arx target genes we identified are known to be important for a variety of functions in brain development and some of them suggest new functions for Arx. Overall, these results identified multiple new candidate targets for Arx and should help to better understand the pathophysiological mechanisms of intellectual disability and epilepsy associated with ARX mutations. [ABSTRACT FROM AUTHOR]