Relation Classification for Bleeding Events From Electronic Health Records Using Deep Learning Systems: An Empirical Study

BACKGROUND: Accurate detection of bleeding events from electronic health records (EHRs) is crucial for identifying and characterizing different common and serious medical problems. To extract such information from EHRs, it is essential to identify the relations between bleeding events and related clinical entities (eg, bleeding anatomic sites and lab tests). With the advent of natural language processing (NLP) and deep learning (DL)-based techniques, many studies have focused on their applicability for various clinical applications. However, no prior work has utilized DL to extract relations between bleeding events and relevant entities. OBJECTIVE: In this study, we aimed to evaluate multiple DL systems on a novel EHR data set for bleeding event-related relation classification. METHODS: We first expert annotated a new data set of 1046 deidentified EHR notes for bleeding events and their attributes. On this data set, we evaluated three state-of-the-art DL architectures for the bleeding event relation classification task, namely, convolutional neural network (CNN), attention-guided graph convolutional network (AGGCN), and Bidirectional Encoder Representations from Transformers (BERT). We used three BERT-based models, namely, BERT pretrained on biomedical data (BioBERT), BioBERT pretrained on clinical text (Bio+Clinical BERT), and BioBERT pretrained on EHR notes (EhrBERT). RESULTS: Our experiments showed that the BERT-based models significantly outperformed the CNN and AGGCN models. Specifically, BioBERT achieved a macro F1 score of 0.842, outperforming both the AGGCN (macro F1 score, 0.828) and CNN models (macro F1 score, 0.763) by 1.4% (P \u3c .001) and 7.9% (P \u3c .001), respectively. CONCLUSIONS: In this comprehensive study, we explored and compared different DL systems to classify relations between bleeding events and other medical concepts. On our corpus, BERT-based models outperformed other DL models for identifying the relations of bleeding-related entities. In addition to pretrained contextualized word representation, BERT-based models benefited from the use of target entity representation over traditional sequence representation

New non-toxic semi-synthetic derivatives from natural diterpenes displaying promising anti-tuberculosis activity

We herein report the synthesis of six diterpene derivatives, three of which are 23 new, generated through known organic chemistry reactions that allowed structural 24 modification of the existing natural products kaurenoic acid (1) and copalic acid (2). The 25 new compounds were fully characterized using high resolution mass spectrometry, infra-26 red spectroscopy, 1H and 13C NMR experiments. We also report the evaluation of the anti-27 tuberculosis potential for all compounds, which showed some promising results for 28 Micobacterium tuberculosis inhibition. Moreover, the toxicity for each of the most active 29 compounds was also assessed

Robust determination of the major merger fraction at z = 0.6 in Groth Strip

(Abridged) We measure the fraction of galaxies undergoing disk-disk major mergers (f_m) at intermediate redshifts (0.35 <= z < 0.85) by studying the asymmetry index A of galaxy images. Results are provided for B- and Ks-band absolute magnitude selected samples from the Groth strip in the GOYA photometric survey. Three sources of systematic error are carefully addressed: (i) we avoid morphological K-corrections, (ii) we measure asymmetries in artificially redshifted to z_d = 0.75 galaxies to lead with loss of morphological information with redshift, and (iii) we take into account the observational errors in z and A, that tend to overestimate the merger fraction, by maximum likelihood techniques. We find: (i) our data allow for a robust merger fraction to be provided for a single redshift bin centered at z=0.6. (ii) Merger fractions have low values: f_m = 0.045 for M_B <= -20 galaxies, and f_m = 0.031 for M_Ks <= -23.5 galaxies. And, (iii) failure to address the effects of the observational errors leads to overestimating f_m by factors of 10%-60%. Combining our results with those on literature, and parameterizing the merger fraction evolution as f_m(z) = f_m(0)(1+z)^m, we obtain that m = 2.9 +- 0.8, and f_m(0) = 0.012 +- 0.004$. Assuming a Ks-band mass-to-light ratio not varying with luminosity, we infer that the merger rate of galaxies with stellar mass M >= 3.5x10^10 M_Sun is R_m = 1.6x10^-4 Mpc^-3 Gyr^-1. When we compare with previous studies at similar redshifts, we find that the merger rate decreases when mass increases.Comment: Accepted for publication in ApJ. 11 pages, 7 figures, 3 tables. Formatted with emulateap

Close companions to Brightest Cluster Galaxies: Support for minor mergers and downsizing

We identify close companions of Brightest Cluster Galaxies (BCGs) for the purpose of quantifying the rate at which these galaxies grow via mergers. By exploiting deep photometric data from the CFHTLS, we probe the number of companions per BCG (Nc) with luminosity ratios down to those corresponding to potential minor mergers of 20:1. We also measure the average luminosity in companions per galaxy (Lc). We find that Nc and Lc rise steeply with luminosity ratio for both the BCGs, and a control sample of other bright, red, cluster galaxies. The trend for BCGs rises more steeply, resulting in a larger number of close companions. For companions within 50kpc of a BCG, Nc= 1.38+/-0.14 and Lc=(2.14+/-0.31)x10^(10)L_sun and for companions within 50kpc of a luminosity matched control sample of non-BCGs, Nc=0.87+/-0.08 and Lc=(1.48+/-0.20)x10^(10)L_sun. This suggests that the BCGs are likely to undergo more mergers compared to otherwise comparable luminous galaxies. Additionally, compared to a local sample of luminous red galaxies, the more distant sample presented in this study (with redshifts between 0.15-0.39,) shows a higher Nc, suggesting the younger and smaller BCGs are still undergoing hierarchical formation. Using the Millennium Simulations we model and estimate the level of contamination due to unrelated cluster galaxies. The contamination by interloping galaxies is 50% within projected separations of 50kpc, but within 30kpc, 60% of identified companions are real physical companions. We conclude that the luminosity of bound merger candidates down to luminosity ratios of 20:1 could be adding as much as 10% to the mass of a typical BCG over 0.5Gyr at redshifts of z~0.3.Comment: 10 pages, 7 figures. Accepted and to be published in MNRA

Dynamic neighbour aware power-controlled MAC for multi-hop ad hoc networks

In Ad Hoc networks, resources in terms of bandwidth and battery life are limited; so using a fixed high transmission power limits the durability of a battery life and causes unnecessary high interference while communicating with closer nodes leading to lower overall network throughput. Thus, this paper proposes a new cross layer MAC called Dynamic Neighbour Aware Power-controlled MAC (Dynamic NA -PMAC) for multi-hop Ad Hoc networks that adjust the transmission power by estimating the communication distance based on the overheard signal strength. By dynamically controlling the transmission power based on the receivable signal strength, the probability of concurrent transmission, durability of battery life and bandwidth utilization increases. Moreover, in presence of multiple overlapping signals with different strengths, an optimal transmission power is estimated dynamically to maintain fairness and avoid hidden node issues at the same time. In a given area, since power is controlled, the chances of overlapping the sensing ranges of sources and next hop relay nodes or destination node decreases, so it enhances the probability of concurrent transmission and hence an increased overall throughput. In addition, this paper uses a variable backoff algorithm based on the number of active neighbours, which saves energy and increases throughput when the density of active neighbours is less. The designed mechanism is tested with various random network scenarios using different traffic including CBR, Exponential and TCP in both scenarios (stationary and mobile with high speed) for single as well as multi-hop. Moreover, the proposed model is benchmarked against two variants of power-controlled mechanisms namely Min NA-PMAC and MaxRC-MinDA NA-PMAC to prove that using a fixed minimum transmission power may lead to unfair channel access and using different transmission power for RTS/CTS and Data/ACK leads to lower probability of concurrent transmission respectively

Location based transmission using a neighbour aware with optimized EIFS MAC for ad hoc networks

In a typical Ad Hoc network, participating nodes have scarce shared bandwidth and limited battery life resources, so resource optimization and enhancing the overall network performance are the primary aims to maintain functionality. This paper proposes a new cross layer Medium Access Control (MAC) algorithm called Location Based Transmission using a Neighbour Aware with optimized Extended Inter-Frame Spacing (EIFS) for Ad Hoc Networks MAC (LBT-NA with optimized-EIFS MAC) that aims to reduce the transmission power when communicating with the next hop receiver based on node’s location which is made available during node deployment. However, node mobility is not taken into account in the study of this paper. According to the algorithm the node dynamically adjusts its transmission power, if there is an active neighbour located beyond the communicating source and destination pair to avoid hidden nodes. The new protocol also defines an optimized EIFS when frame collision, frame error or frame capture takes place, in-order to maintain a fair channel access among the contending nodes. The proposed MAC also uses a modified range of random backoff values, based on the degree of contention unlike IEEE 802.11 series which uses a fixed random backoff value for fresh frames irrespective of the degree of contention. Simulation results indicate that in a random topology with a random source and destination, when the two sources are separated by a minimum distance of 200m, the performance gain of power controlled MAC over IEEE 802.11b ranges from 30% to 70% depending on the type of traffics in the network and the degree of fairness ranges from 62% to 99.99% for a location based MAC with minimum power transmission, whereas LBT-NA with optimized-EIFS MAC secures fairness index ranging from 75% to 99.99%. Communication with a node that is 20m away can save 40% of the battery life in comparison to the traditional transmission power MAC from 802.11b. The validation tests demonstrate that the proposed algorithm increases battery life and reduces the interference impact on shorter distance communication and increases the probability of parallel transmission. The proposed protocol also provides a scope for active nodes to transmit with a higher degree of probability, providing higher degree of overall network throughput in the environment and alleviate the starvation of hidden node by using Dynamic EIFS scheme

Acute response to pathogens in the early human placenta at single-cell resolution

The placenta is a selective maternal-fetal barrier that provides nourishment and protection from infections. However, certain pathogens can attach to and even cross the placenta, causing pregnancy complications with potential lifelong impacts on the child's health. Here, we profiled at the single-cell level the placental responses to three pathogens associated with intrauterine complications—Plasmodium falciparum, Listeria monocytogenes, and Toxoplasma gondii. We found that upon exposure to the pathogens, all placental lineages trigger inflammatory responses that may compromise placental function. Additionally, we characterized the responses of fetal macrophages known as Hofbauer cells (HBCs) to each pathogen and propose that they are the probable niche for T. gondii. Finally, we revealed how P. falciparum adapts to the placental microenvironment by modulating protein export into the host erythrocyte and nutrient uptake pathways. Altogether, we have defined the cellular networks and signaling pathways mediating acute placental inflammatory responses that could contribute to pregnancy complications.</p

Acute response to pathogens in the early human placenta at single-cell resolution

The placenta is a selective maternal-fetal barrier that provides nourishment and protection from infections. However, certain pathogens can attach to and even cross the placenta, causing pregnancy complications with potential lifelong impacts on the child's health. Here, we profiled at the single-cell level the placental responses to three pathogens associated with intrauterine complications—Plasmodium falciparum, Listeria monocytogenes, and Toxoplasma gondii. We found that upon exposure to the pathogens, all placental lineages trigger inflammatory responses that may compromise placental function. Additionally, we characterized the responses of fetal macrophages known as Hofbauer cells (HBCs) to each pathogen and propose that they are the probable niche for T. gondii. Finally, we revealed how P. falciparum adapts to the placental microenvironment by modulating protein export into the host erythrocyte and nutrient uptake pathways. Altogether, we have defined the cellular networks and signaling pathways mediating acute placental inflammatory responses that could contribute to pregnancy complications.</p

Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies

Erratum: J Clin Immunol. 2017 Oct;37(7):693-694. doi: 10.1007/s10875-017-0436-0.In today's global economy and affordable vacation travel, it is increasingly important that visitors to another country and their physician be familiar with emerging infections, infections unique to a specific geographic region, and risks related to the process of travel. This is never more important than for patients with primary immunodeficiency disorders (PIDD). A recent review addressing common causes of fever in travelers provides important information for the general population Thwaites and Day (N Engl J Med 376:548-560, 2017). This review covers critical infectious and management concerns specifically related to travel for patients with PIDD. This review will discuss the context of the changing landscape of infections, highlight specific infections of concern, and profile distinct infection phenotypes in patients who are immune compromised. The organization of this review will address the environment driving emerging infections and several concerns unique to patients with PIDD. The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. Reference tables provide easily accessible information on a broader range of infections than is described in the text.Peer reviewe