Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages characterizing protein interaction (ISS) in full text documents. We approached the abstract classification task with a novel, lightweight linear model inspired by spam-detection techniques, as well as an uncertainty-based integration scheme. We also used a Support Vector Machine and the Singular Value Decomposition on the same features for comparison purposes. Our approach to the full text subtasks (protein pair and passage identification) includes a feature expansion method based on word-proximity networks. Our approach to the abstract classification task (IAS) was among the top submissions for this task in terms of the measures of performance used in the challenge evaluation (accuracy, F-score and AUC). We also report on a web-tool we produced using our approach: the Protein Interaction Abstract Relevance Evaluator (PIARE). Our approach to the full text tasks resulted in one of the highest recall rates as well as mean reciprocal rank of correct passages. Our approach to abstract classification shows that a simple linear model, using relatively few features, is capable of generalizing and uncovering the conceptual nature of protein-protein interaction from the bibliome. Since the novel approach is based on a very lightweight linear model, it can be easily ported and applied to similar problems. In full text problems, the expansion of word features with word-proximity networks is shown to be useful, though the need for some improvements is discussed

Interventions to increase the consumption of water among children

The aim of this study was to conduct a systematic review and meta-analysis on the effectiveness of interventions to increase children's water consumption. A systematic literature search was conducted in seven electronic databases. Studies published in English before 18 February 2019 that evaluated any type of intervention that measured change in water consumption among children aged 2 to 12 years by applying any type of design were included. Of the 47 interventions included in the systematic review, 24 reported a statistically significant increase in water consumption. Twenty-four interventions (17 randomized controlled trials and seven studies with other controlled designs) were included in the meta-analysis. On average, children in intervention groups consumed 29 mL/d (confidence interval [CI] = 13–46 mL/d) more water than did children in control groups. This effect was larger in eight interventions focused specifically on diet (MD = 73 mL/d, CI = 20–126 mL/d) than in 16 interventions focused also on other lifestyle factors (MD = 15 mL/d, CI = 1–29 mL/d). Significant subgroup differences were also found by study setting and socioecological level targeted but not by children's age group, intervention strategy, or study design. In conclusion, there is evidence that, on average, lifestyle interventions can lead to small increases in children's daily water consumption. More research is needed to further understand th

Higher COVID-19 pneumonia risk associated with anti-IFN-α than with anti-IFN-ω auto-Abs in children

We found that 19 (10.4%) of 183 unvaccinated children hospitalized for COVID-19 pneumonia had autoantibodies (auto-Abs) neutralizing type I IFNs (IFN-alpha 2 in 10 patients: IFN-alpha 2 only in three, IFN-alpha 2 plus IFN-omega in five, and IFN-alpha 2, IFN-omega plus IFN-beta in two; IFN-omega only in nine patients). Seven children (3.8%) had Abs neutralizing at least 10 ng/ml of one IFN, whereas the other 12 (6.6%) had Abs neutralizing only 100 pg/ml. The auto-Abs neutralized both unglycosylated and glycosylated IFNs. We also detected auto-Abs neutralizing 100 pg/ml IFN-alpha 2 in 4 of 2,267 uninfected children (0.2%) and auto-Abs neutralizing IFN-omega in 45 children (2%). The odds ratios (ORs) for life-threatening COVID-19 pneumonia were, therefore, higher for auto-Abs neutralizing IFN-alpha 2 only (OR [95% CI] = 67.6 [5.7-9,196.6]) than for auto-Abs neutralizing IFN-. only (OR [95% CI] = 2.6 [1.2-5.3]). ORs were also higher for auto-Abs neutralizing high concentrations (OR [95% CI] = 12.9 [4.6-35.9]) than for those neutralizing low concentrations (OR [95% CI] = 5.5 [3.1-9.6]) of IFN-omega and/or IFN-alpha 2

2013 WSES guidelines for management of intra-abdominal infections

Peer reviewe

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

Biomedical article classification using an agent-based model of t-cell cross-regulation

Abstract. We propose a novel bio-inspired solution for biomedical article classification. Our method draws from an existing model of T-cell cross-regulation in the vertebrate immune system (IS), which is a complex adaptive system of millions of cells interacting to distinguish between harmless and harmful intruders. Analogously, automatic biomedical article classification assumes that the interaction and co-occurrence of thousands of words in text can be used to identify conceptually-related classes of articles—at a minimum, two classes with relevant and irrelevant articles for a given concept (e.g. articles with protein-protein interaction information). Our agent-based method for document classification expands the existing analytical model of Carneiro et al. [1], by allowing us to deal simultaneously with many distinct T-cell features (epitomes) and their collective dynamics using agent based modeling. We already extended this model to develop a bio-inspired spam-detection system [2, 3]. Here we develop our agent-base model further, and test it on a dataset of publicly available full-text biomedical articles provided by the BioCreative challenge [4]. We study several new parameter configurations leading to encouraging results comparable to state-of-the-art classifiers. These results help us understand both T-cell cross-regulation and its applicability to document classification in general. Therefore, we show that our bio-inspired algorithm is a promising novel method for biomedical article classification and for binary document classification in general

Comparative bioavailability study of a matrix versus a reservoir transdermal estradiol patch in healthy postmenopausal women

The single-application bioavailability of estradiol from a new matrix (Climaderm(R)) versus a standard reservoir (Estraderm(R) TTS 50) transdermal therapeutic system was investigated in a prospective, open-label, randomized, two-period crossover study in healthy postmenopausal volunteers. Each system was labeled to deliver approximately 0.05 mg of estradiol per day and was applied to the abdominal area and worn continuously for 4 days; there was a minimum 5-day washout between the two study periods. for each study period, venous blood samples were obtained before patch application, during treatment (20 samples), and after patch removal (3 samples) and assayed for estradiol and estrone. in addition, the samples obtained at 0, 8, 12, 24, 48, 72, 96, and 120 hours after application were assayed for follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Twenty-six women completed both study periods, No differences between the patches were detected with regard to peak concentration and time to peak concentration. Based on area under the curve, the two patches were bioequivalent through 48 hours. From 48 to 96 hours, however, the matrix patch produced a more consistent level of estradiol. Mean values for the levels of estradiol, estrone, FSH, and LH for the entire study period are presented.ESCOLA PAULISTA MED,DEPT GYNECOL & OBSTET,São Paulo,BRAZILESCOLA PAULISTA MED,DEPT PSYCHOBIOL,São Paulo,BRAZILESCOLA PAULISTA MED,CLIN EPIDEMIOL UNIT,São Paulo,BRAZILWYETH AYERST INT,PHILADELPHIA,PAWYETH BRAZIL,São Paulo,BRAZILESCOLA PAULISTA MED,DEPT GYNECOL & OBSTET,São Paulo,BRAZILESCOLA PAULISTA MED,DEPT PSYCHOBIOL,São Paulo,BRAZILESCOLA PAULISTA MED,CLIN EPIDEMIOL UNIT,São Paulo,BRAZILWeb of Scienc

Histomorphometry of the postmenopausal endometrium after oral and transdermal estrogen replacement therapy

We studied the morphological and morphometrical aspects of the endometrium of postmenopausal women treated with oral conjugated estrogens and transdermal 17 beta-estradiol for 28 days. Light microscopy revealed that the endometrial glandular epithelium and stroma were more responsive to stimulation than the surface epithelium. Proliferative changes were more intense in the groups that received 1.25 mg/day of conjugated estrogens and 50 mu g/day of transdermal 17 beta-estradiol in comparison with the group that received 0.625 mg/day of conjugated estrogens. Morphometry indicated that the endometrial gland/stroma ratio was higher in the groups that received 1.25 mg/day of conjugated estrogens and 50 mu g/day of transdermal 17 beta-estradiol, an effect that was significantly greater than that observed in women receiving 0.625 mg/day of conjugated estrogens.Universidade Federal de São Paulo,ESCOLA PAULISTA MED,DEPT MORPHOL,BR-04023900 São Paulo,BRAZILUniversidade Federal de São Paulo,ESCOLA PAULISTA MED,DEPT BIOSTAT,BR-04023900 São Paulo,BRAZILUniversidade Federal de São Paulo,ESCOLA PAULISTA MED,DEPT MORPHOL,BR-04023900 São Paulo,BRAZILUniversidade Federal de São Paulo,ESCOLA PAULISTA MED,DEPT BIOSTAT,BR-04023900 São Paulo,BRAZILWeb of Scienc