In Utero Exposures, Infant Growth, and DNA Methylation of Repetitive Elements and Developmentally Related Genes in Human Placenta

BACKGROUND: Fetal programming describes the theory linking environmental conditions during embryonic and fetal development with risk of diseases later in life. Environmental insults in utero may lead to changes in epigenetic mechanisms potentially affecting fetal development. OBJECTIVES: We examined associations between in utero exposures, infant growth, and methylation of repetitive elements and gene-associated DNA in human term placenta tissue samples. METHODS: Placental tissues and associated demographic and clinical data were obtained from subjects delivering at Women and Infants Hospital in Providence, Rhode Island (USA). Methylation levels of long interspersed nuclear element-1 (LINE-1) and the Alu element AluYb8 were determined in 380 placental samples from term deliveries using bisulfite pyrosequencing. Genomewide DNA methylation profiles were obtained in a subset of 184 samples using the Illumina Infinium HumanMethylation27 BeadArray. Multiple linear regression, model-based clustering methods, and gene set enrichment analysis examined the association between birth weight percentile, demographic variables, and repetitive element methylation and gene-associated CpG locus methylation. RESULTS: LINE-1 and AluYb8 methylation levels were found to be significantly positively associated with birth weight percentile (p = 0.01 and p \u3c 0.0001, respectively) and were found to differ significantly among infants exposed to tobacco smoke and alcohol. Increased placental AluYb8 methylation was positively associated with average methylation among CpG loci found in polycomb group target genes; developmentally related transcription factor binding sites were overrepresented for differentially methylated loci associated with both elements. CONCLUSIONS: Our results suggest that repetitive element methylation markers, most notably AluYb8 methylation, may be susceptible to epigenetic alterations resulting from the intrauterine environment and play a critical role in mediating placenta function, and may ultimately inform on the developmental basis of health and disease

Identification of Methylated Genes Associated with Aggressive Bladder Cancer

Approximately 500,000 individuals diagnosed with bladder cancer in the U.S. require routine cystoscopic follow-up to monitor for disease recurrences or progression, resulting in over $2 billion in annual expenditures. Identification of new diagnostic and monitoring strategies are clearly needed, and markers related to DNA methylation alterations hold great promise due to their stability, objective measurement, and known associations with the disease and with its clinical features. To identify novel epigenetic markers of aggressive bladder cancer, we utilized a high-throughput DNA methylation bead-array in two distinct population-based series of incident bladder cancer (n = 73 and n = 264, respectively). We then validated the association between methylation of these candidate loci with tumor grade in a third population (n = 245) through bisulfite pyrosequencing of candidate loci. Array based analyses identified 5 loci for further confirmation with bisulfite pyrosequencing. We identified and confirmed that increased promoter methylation of HOXB2 is significantly and independently associated with invasive bladder cancer and methylation of HOXB2, KRT13 and FRZB together significantly predict high-grade non-invasive disease. Methylation of these genes may be useful as clinical markers of the disease and may point to genes and pathways worthy of additional examination as novel targets for therapeutic treatment

Development of an amplicon-based sequencing approach in response to the global emergence of mpox

The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.This publication was made possible by CTSA Grant Number UL1 TR001863 from the National Center for Advancing Translational Science (NCATS), a component of the National Institutes of Health (NIH) awarded to CBFV. INSA was partially funded by the HERA project (Grant/ 2021/PHF/23776) supported by the European Commission through the European Centre for Disease Control (to VB).info:eu-repo/semantics/publishedVersio

Treatment outcome in early diffuse cutaneous systemic sclerosis: the European Scleroderma Observational Study (ESOS).

OBJECTIVES: The rarity of early diffuse cutaneous systemic sclerosis (dcSSc) makes randomised controlled trials very difficult. We aimed to use an observational approach to compare effectiveness of currently used treatment approaches. METHODS: This was a prospective, observational cohort study of early dcSSc (within three years of onset of skin thickening). Clinicians selected one of four protocols for each patient: methotrexate, mycophenolate mofetil (MMF), cyclophosphamide or 'no immunosuppressant'. Patients were assessed three-monthly for up to 24 months. The primary outcome was the change in modified Rodnan skin score (mRSS). Confounding by indication at baseline was accounted for using inverse probability of treatment (IPT) weights. As a secondary outcome, an IPT-weighted Cox model was used to test for differences in survival. RESULTS: Of 326 patients recruited from 50 centres, 65 were prescribed methotrexate, 118 MMF, 87 cyclophosphamide and 56 no immunosuppressant. 276 (84.7%) patients completed 12 and 234 (71.7%) 24 months follow-up (or reached last visit date). There were statistically significant reductions in mRSS at 12 months in all groups: -4.0 (-5.2 to -2.7) units for methotrexate, -4.1 (-5.3 to -2.9) for MMF, -3.3 (-4.9 to -1.7) for cyclophosphamide and -2.2 (-4.0 to -0.3) for no immunosuppressant (p value for between-group differences=0.346). There were no statistically significant differences in survival between protocols before (p=0.389) or after weighting (p=0.440), but survival was poorest in the no immunosuppressant group (84.0%) at 24 months. CONCLUSIONS: These findings may support using immunosuppressants for early dcSSc but suggest that overall benefit is modest over 12 months and that better treatments are needed. TRIAL REGISTRATION NUMBER: NCT02339441

COMPARAISON DU VOLUME ET DE LA VALEUR DES BOIS RÉSINEUX ISSUS D’ÉCLAIRCIES PAR LE BAS ET PAR DÉGAGEMENT D’ARBRES-ÉLITES DANS L’EST DU CANADA

Le choix des tiges à récolter lors des interventions d’éclaircies commerciales peut avoir des répercussions sur la quantité et le type de produits forestiers qu’on peut en tirer, de même que sur la structure des peuplements résiduels. L’objectif de cette étude était de comparer l’éclaircie par le bas (ÉCbas) et deux intensités d’éclaircie par dégagement de 50 (AÉ50) ou 100 (AÉ100) arbres-élites à l’hectare. En 2008, quatre peuplements de 30 ans ont été sélectionnés dans des peuplements résineux naturels et plantations d’épinette blanche au Québec pour comparer les effets des modalités d’éclaircie sur la structure diamétrale, le volume/ha, le diamètre quadratique moyen des arbres marchands (dqm), le volume moyen par tige ainsi que la répartition par type de produits (dimensions) du sciage et co-produits (copeaux et sciures) de première transformation, la valeur de la matière ligneuse récoltée par m3 ha-1. Globalement, il n’y a pas de différences significatives dans les attributs dendrométriques entre les modalités d’éclaircie, sauf la surface terrière et le volume prélevés dans les plantations. La transformation par simulation des bois issus de ces éclaircies permet de produire une proportion analogue de pièces de 1x3, 1x4 et 2x3 pouces, mais ÉCbas produit significativement moins de 2x4 et plus de co-produits par rapport à AÉ50 ou AÉ100.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Do employees’ needs moderate their reaction to supervisor’s empowerment practices?

This study tests if three employees’ needs (autonomy, achievement, and affiliation) moderate the relationship between supervisor’s empowerment managerial practices (SEMP) and employees’ behavioral empowerment (BE). Our hypothesis was that employees whose needs were less satisfied would be more receptive to empowering practices allowing them to satisfy their needs. A questionnaire study was conducted (n=370) to test this hypothesis. Results of hierarchical regression analyses indicate that the satisfaction of the three needs considered together as well as the satisfaction of achievement need moderate the relationship between SEMP and BE. Contrary to expectations, SEMP were more related to BE when employees’ needs were more satisfied

[Clinical prediction rule for diagnosing deep vein thrombosis in primary care].

International audiencePatients with suspected deep vein thrombosis (DVT) are often managed on an outpatient basis by primary care physicians. International guidelines recommend anticoagulant treatment for patients with suspected DVT when diagnostic testing is delayed or when clinical probability is high. Our goal was to build a clinical prediction rule specifically for easy use in primary care to help decide about starting anticoagulant therapy while awaiting ultrasound examination. Between January and December 2006, 276 patients with clinically suspected DVT were included in this study by 189 general practitioners from Brittany, France. All patients underwent a standardized clinical assessment and were then referred for ultrasonography. The diagnosis of DVT was confirmed in 103 (37%) patients. The final clinical prediction rule comprises four risk factors for DVT (personal history of venous thromboembolism +1, immobilization in previous month +1, estrogen contraceptive +2, active malignancy +3), one clinical sign (swelling of the calf +1), and the presence of an alternative diagnosis more likely than that of DVT (-3). The proportion of confirmed DVT was 26% in patients classified as at low risk, with a score less than 2 points, and 63% in patients classified at high risk, that is, with a score of 2 points or more. This clinical prediction rule is based on simple history and clinical factors that are routinely collected by GPs from patients with suspected DVT. It could help to decide about the immediate prescription of anticoagulation pending ultrasound. This rule should be externally validated before its use in clinical practice can be recommended

[Validation of a deep vein thrombosis prediction rule in primary care].

International audienceOBJECTIVE: Suspected deep vein thrombosis (DVT) of lower limbs (LL) may require different tools to rule out or confirm the diagnosis. Clinical probability provides help to select useful tests, interpret their results, and decide to treat the patient meanwhile. Clinical prediction rules that risk stratify patients with suspected DVT can be established from inpatients, but no prediction rule not requiring laboratory tests has been established from primary care patients. We previously derived and internally validated such a prediction rule. The aim of this study is to externally validate this score. PATIENTS AND METHODS: The score was applied to Optimev outpatients with suspected LL-DVT, and without suspected pulmonary embolism. Sensitivity and specificity were calculated for proximal and distal DVT, according to each score. The area under the ROC curve was calculated for each kind of DVT, in order to assess the validity of the score on predicting the presence or absence of DVT. RESULTS: Among 3523 outpatients prospectively included in the Optimev study for suspected LL DVT, overall prevalence of DVT was 29.7% (n=1046), ranging from 21.7% in the non-high score probability, to 61.4% in the high score probability. The area under the ROC curve was 0.79 [CI 95%, 0.77-0.80]. With subgroup analysis, the area under curve was 0.83 [CI 95%, 0.82-0.85] for proximal DVT, and 0.75 [CI 95%, 0.73-0.77] for distal DVT. CONCLUSION: This score reliably identifies primary care patients with LL DVT, whether proximal or distal