Human and mouse neuroinflammation markers in Niemann‐Pick disease, type C1

Niemann‐Pick disease, type C1 (NPC1) is an autosomal recessive lipid storage disorder in which a pathological cascade, including neuroinflammation occurs. While data demonstrating neuroinflammation is prevalent in mouse models, data from NPC1 patients is lacking. The current study focuses on identifying potential markers of neuroinflammation in NPC1 from both the Npc1 mouse model and NPC1 patients. We identified in the mouse model significant changes in expression of genes associated with inflammation and compared these results to the pattern of expression in human cortex and cerebellar tissue. From gene expression array analysis, complement 3 (C3) was increased in mouse and human post‐mortem NPC1 brain tissues. We also characterized protein levels of inflammatory markers in cerebrospinal fluid (CSF) from NPC1 patients and controls. We found increased levels of interleukin 3, chemokine (C‐X‐C motif) ligand 5, interleukin 16 and chemokine ligand 3 (CCL3), and decreased levels of interleukin 4, 10, 13 and 12p40 in CSF from NPC1 patients. CSF markers were evaluated with respect to phenotypic severity. Miglustat treatment in NPC1 patients slightly decreased IL‐3, IL‐10 and IL‐13 CSF levels; however, further studies are needed to establish a strong effect of miglustat on inflammation markers. The identification of inflammatory markers with altered levels in the cerebrospinal fluid of NPC1 patients may provide a means to follow secondary events in NPC1 disease during therapeutic trials.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147148/1/jimd0083.pd

Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer

Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations (P<5 × 10−8) with oestrogen receptor (ER)-negative breast cancer and BRCA1-associated breast cancer risk. In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 BRCA1 mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near KLF5, a 2p23.2 locus near WDR43 and a 2q33 locus near PPIL3 that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations (P<0.05) with ER-negative disease. Using functional and eQTL studies we implicate TRMT61B and WDR43 at 2p23.2 and PPIL3 at 2q33 in ER-negative breast cancer aetiology. All ER-negative loci combined account for ∼11% of familial relative risk for ER-negative disease and may contribute to improved ER-negative and BRCA1 breast cancer risk prediction

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Ex-vivo phantom for evaluation of ultrasound speckle tracking in the uterus

Uterine peristaltic movement plays an important role for the success of embryo implantation. This is especially relevant in the context of assisted reproductive technology. Unfortunately, the lack of tools for quantitative analysis limits our understanding of the uterine contractility. Recently, strain analysis by ultrasound speckle tracking has gained attention for the assessment of the uterine contractility. However, the absence of a ground truth hampers the optimization of this technology. This work proposes the first phantom based on a human ex-vivo uterus able to generate controlled tissue motion by sinusoidal (0,05 Hz), linear displacement of a syringe piston, injecting 3-mL water through a balloon catheter inserted into the uterine cavity. This way, controlled, realistic peristaltic movement was generated while maintaining original speckle characteristics. Uterine motion analysis was obtained by US speckle tracking on acquired B-mode imaging data using two block matching techniques, normalized cross-correlation (NCC) and sum of absolute differences (SAD). The proposed phantom based on a human ex-vivo uterus showed its value to assess US speckle tracking techniques providing a realistic ground truth that is fully controlled

Machine learning for prediction of euploidy in human embryos : in search of the best-performing model and predictive features

Objective: To assess the best-performing machine learning (ML) model and features to predict euploidy in human embryos. Design: Retrospective cohort analysis. Setting: Department for reproductive medicine in a university hospital. Patient(s): One hundred twenty-eight infertile couples treated between January 2016 and December 2019. Demographic and clinical data and embryonic developmental and morphokinetic data from 539 embryos (45% euploid, 55% aneuploid) were analyzed. Intervention(s): Random forest classifier (RFC), scikit-learn gradient boosting classifier, support vector machine, multivariate logistic regression, and naive Bayes ML models were trained and used in 9 databases containing either 26 morphokinetic features (as absolute [A1] or interim [A2] times or combined [A3]) alone or plus 19 standard development features [B1, B2, and B3] with and without 40 demographic and clinical characteristics [C1, C2, and C3]. Feature selection and model retraining were executed for the bestperforming combination of model and dataset. Main Outcome Measure(s): The main outcome measures were overall accuracy, precision, recall or sensitivity, F1 score (the weighted average of precision and recall), and area under the receiver operating characteristic curve (AUC) of ML models for each dataset. The secondary outcome measure was ranking of feature importance for the best-performing combination of model and dataset. Result(s): The RFC model had the highest accuracy (71%) and AUC (0.75) when trained and used on dataset C1. The precision, recall or sensitivity, F1 score, and AUC were 66%, 86%, 75%, and 0.75, respectively. The accuracy, recall or sensitivity, and F1 score increased to 72%, 88%, and 76%, respectively, after feature selection and retraining. Morphokinetic features had the highest relative predictive weight. Conclusion(s): The RFC model can predict euploidy with an acceptable accuracy (>70%) using a dataset including embryos' morphokinetics and standard embryonic development and subjects' demographic and clinical features. ((C) 2021 by American Society for Reproductive Medicine.) El resumen esta disponible en Espanol al final del articulo