Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge-rich temporal relation identification and classification in clinical notes

Motivation: We examine the task of temporal relation classification for the clinical domain. Our approach to this task departs from existing ones in that it is (i) ‘knowledge-rich’, employing sophisticated knowledge derived from discourse relations as well as both domain-independent and domain-dependent semantic relations, and (ii) ‘hybrid’, combining the strengths of rule-based and learning-based approaches. Evaluation results on the i2b2 Clinical Temporal Relations Challenge corpus show that our approach yields a 17–24% and 8–14% relative reduction in error over a state-of-the-art learning-based baseline system when gold-standard and automatically identified temporal relations are used, respectively. Database URL: http://www.hlt. utdallas.edu/~jld082000/temporal-relations/
Anti-IL-17 monoclonal antibodies for the treatment of ankylosing spondylitis

ABSTRACT Introduction: Ankylosing spondylitis is the prototype of spondyloarthritis, a chronic inflammatory disease involving mainly the axial skeleton. The treatment strategy was, until now, restricted to NSAIDs and anti-TNF agents. Targeting Interleukin 17 is an emerging option with a currently available biologic agent, secukinumab. Areas covered: This paper reviews the available data published on secukinumab (and other anti-IL-17 agents) in ankylosing spondylitis, evaluating the effect on clinical outcomes as well as radiological progression and extra articular manifestations and safety. Expert opinion: Secukinumab represents the first anti-IL-17A agent available for the treatment of ankylosing spondylitis, with evidence of efficacy upon signs and symptoms of the disease, even after anti-TNF failure, and acceptable safety profile.
CyKEGGParser: tailoring KEGG pathways to fit into systems

The KEGG pathway database is a widely accepted source for biomolecular pathway maps. In this paper we present the CyKEGGParser app ( ) for Cytoscape 3 that allows http://apps.cytoscape. org/apps/cykeggparser manipulation with KEGG pathway maps. Along with basic functionalities for pathway retrieval, visualization and export in KGML and BioPAX formats, the app provides unique features for computer-assisted adjustment of inconsistencies in KEGG pathway KGML files and generation of tissueand protein-protein interaction specific pathways. We demonstrate that using biological context-specific KEGG pathways created with CyKEGGParser makes systems biology analysis more sensitive and appropriate compared to original pathways. This article is included in the Cytoscape Apps gateway. Arsen Arakelyan ( ) Corresponding author: aarakelyan@sci.am No competing interests were disclosed. Competing interests: This study was funded by research grant from the State Committee of Science of the Ministry of Education and Science of the Grant information: Republic of Armenia, granted to Arsen Arakelyan (N 13Y-1F0022, PI: AA). © 2014 Nersisyan L . This is an open access article distributed under the terms of the , Copyright: et al Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the (CC0 1.0 Public domain dedication). Creative Commons Zero "No rights reserved" data waiver Nersisyan L, Samsonyan R and Arakelyan A. How to cite this article: CyKEGGParser: tailoring KEGG pathways to fit into systems biology F1000Research 2014, :145 ( analysis workflows [version 1; peer review: 1 approved, 1 approved with reservations] 3 ) https://doi.org/10.12688/f1000research.4410. 1 01 Jul 2014, :145 ( ) First published: 3 https://doi.org/10.12688/f1000research.4410. 1 1 2
Quasi‐uniform convergence in dynamical systems generated by an amenable group action

We study the Weyl pseudometric associated with an action of a countable amenable group on a compact metric space. We prove that the topological entropy and the number of minimal subsets of the closure of an orbit are both lower semicontinuous with respect to the Weyl pseudometric. Furthermore, the simplex of invariant measures supported on the orbit closure varies continuously. We apply the Weyl pseudometric to Toeplitz configurations for arbitrary amenable residually finite groups. We introduce the notion of a regular Toeplitz configuration and demonstrate that all regular Toeplitz configurations define minimal and uniquely ergodic systems. We prove that this family is path‐connected in the Weyl pseudometric. This leads to a new proof of a theorem of Krieger, saying that Toeplitz configurations can have arbitrary finite entropy.
Shape-dependent surface-enhanced Raman scattering in gold–Raman-probe–silica sandwiched nanoparticles for biocompatible applications

To meet the requirement of Raman probes (labels) for biocompatible applications, a synthetic approach has been developed to sandwich the Raman-probe (malachite green isothiocyanate, MGITC) molecules between the gold core and the silica shell in gold–SiO2 composite nanoparticles. The gold–MGITC–SiO2 sandwiched structure not only prevents the Raman probe from leaking out but also improves the solubility of the nanoparticles in organic solvents and in aqueous solutions even with high ionic strength. To amplify the Raman signal, three types of core, gold nanospheres, nanorods and nanostars, have been chosen as the substrates of the Raman probe. The effect of the core shape on the surface-enhanced Raman scattering (SERS) has been investigated. The colloidal nanostars showed the highest SERS enhancement factor while the nanospheres possessed the lowest SERS activity under excitation with 532 and 785 nm lasers. Three-dimensional finite-difference time domain (FDTD) simulation showed significant differences in the local electromagnetic field distributions surrounding the nanospheres, nanorods, and nanostars, which were induced by the localized surface plasmon resonance (LSPR). The electromagnetic field was enhanced remarkably around the two ends of the nanorods and around the sharp tips of the nanostars. This local electromagnetic enhancement made the dominant contribution to the SERS enhancement. Both the experiments and the simulation revealed the order nanostars > nanorods > nanospheres in terms of the enhancement factor. Finally, the biological application of the nanostar–MGITC–SiO2 nanoparticles has been demonstrated in the monitoring of DNA hybridization. In short, the gold–MGITC–SiO2 sandwiched nanoparticles can be used as a Raman probe that features high sensitivity, good water solubility and stability, low-background fluorescence, and the absence of photobleaching for future biological applications.
The Effect of Metacognitive Knowledge on Mathematics Performance in Self-Regulated Learning Framework—Multiple Mediation of Self-Efficacy and Motivation

Metacognition, self-efficacy, and motivation are important components of interaction in self-regulated learning (SRL). However, the psychological mechanism underlying the association among them in mathematical learning remained ambiguous. The present study investigated whether the relationship between metacognitive knowledge (MK) and mathematics performance can be mediated by self-efficacy and motivation. The sample comprised 569 students (245 male, Mage = 16.39, SD = 0.63) of Grade 10 in China. The MK in mathematics questionnaire, the self-efficacy questionnaire, the academic motivation scale, Raven advanced progressive matrix, and mathematics tests were used for data collection. Our results suggested that the mathematics performance could be predicted by MK, self-efficacy and intrinsic motivation. Moreover, the association between MK and mathematics performance was mediated by self-efficacy and intrinsic motivation, as revealed by a multiple mediation analysis. Additionally, there were sex differences in MK, self-efficacy and intrinsic motivation. The findings highlight the psychological mechanism in the mathematics of Chinese students and will help teachers to improve students’ mathematical learning in SRL framework more effectively. Implications for education and further studies are discussed.
Sexually dimorphic gene expression and transcriptome evolution provide mixed evidence for a fast‐Z effect in Heliconius

Sex chromosomes have different evolutionary properties compared to autosomes due to their hemizygous nature. In particular, recessive mutations are more readily exposed to selection, which can lead to faster rates of molecular evolution. Here, we report patterns of gene expression and molecular evolution for a group of butterflies. First, we improve the completeness of the Heliconius melpomene reference annotation, a neotropical butterfly with a ZW sex determination system. Then, we analyse RNA from male and female whole abdomens and sequence female ovary and gut tissue to identify sex‐ and tissue‐specific gene expression profiles in H. melpomene. Using these expression profiles, we compare (a) sequence divergence and polymorphism; (b) the strength of positive and negative selection; and (c) rates of adaptive evolution, for Z and autosomal genes between two species of Heliconius butterflies, H. melpomene and H. erato. We show that the rate of adaptive substitutions is higher for Z than autosomal genes, but contrary to expectation, it is also higher for male‐biased than female‐biased genes. Additionally, we find no significant increase in the rate of adaptive evolution or purifying selection on genes expressed in ovary tissue, a heterogametic‐specific tissue. Our results contribute to a growing body of literature from other ZW systems that also provide mixed evidence for a fast‐Z effect where hemizygosity influences the rate of adaptive substitutions.
raiden11@IECSIL-FIRE-2018 : Named Entity Recognition for Indian Languages

This paper presents our solution for the Named Entity Recognition (NER) task for the Information Extractor for Conversational Systems in Indian Languages challenge (IECSIL) [5] of the FIRE 2018 conference. A subset of the Information Extraction (IE) task, NER is a key to extract information and semantics of the text from unstructured data. The objective of NER is the identiﬁcation and classiﬁcation of every word or token in a document into predeﬁned categories such as names of person, location, organization, etc. For this challenge the dataset provided by IECSIL [4] comprised of multilingual text of various Indian languages like Hindi, Tamil, Malayalam, Telugu, and Kannada. We mainly focus on the identiﬁcation and classiﬁcation of named entities belonging to nine categories like Name, Location, Datenum, etc. We tried linear models like Naive Bayes and SVM, and also a simple Neural Network to solve this problem. The best results are achieved by the simple neural network with an accuracy of 90.33% for all languages combined. This indicates that diﬀerent advanced neural networks could be possible solutions to further improve this accuracy.
Flexible Radio-Frequency Identification (RFID) Tag Antenna for Sensor Applications

In this paper, an inkjet-printed flexible Radio-Frequency Identification (RFID) tag antenna is proposed for an ultra-high frequency (UHF) sensor application. The proposed tag antenna facilitates a system-level solution for low-cost and faster mass production of RFID passive tag antenna. The tag antenna consists of a modified meander line radiator with a semi-circular shaped feed network. The structure is printed on photo paper using silver nanoparticle conductive ink. The generic design outline, as well as tag antenna performances for several practical application aspects are investigated. The simulated and measured results verify the coverage of universal UHF RFID band with an omnidirectional radiation pattern and a long-read range of 15 ft. In addition, the read range for different bending angles and lifetimes of the tag antenna are also demonstrated.
Genome-Wide Identification and Analysis of U-Box E3 Ubiquitin-Protein Ligase Gene Family in Banana

The U-box gene family is a family of genes which encode U-box domain-containing proteins. However, little is known about U-box genes in banana (Musa acuminata). In this study, 91 U-box genes were identified in banana based on its genome sequence. The banana U-box genes were distributed across all 12 chromosomes at different densities. Phylogenetic analysis of U-box genes from banana, Arabidopsis, and rice suggested that they can be clustered into seven subgroups (I–VII), and most U-box genes had a closer relationship between banana and rice relative to Arabidopsis. Typical U-box domains were found in all identified MaU-box genes through the analysis of conserved motifs. Four conserved domains were found in major banana U-box proteins. The MaU-box gene family had the highest expression in the roots at the initial fruit developmental stage. The MaU-box genes exhibited stronger response to drought than to salt and low temperatures. To the best of our knowledge, this report is the first to perform genome-wide identification and analysis of the U-box gene family in banana, and the results should provide valuable information for better understanding of the function of U-box in banana.
Fine particle sources and cognitive function in an older Puerto Rican cohort in Greater Boston

Background: Puerto Ricans living in the mainland US have substantially higher rates of impairment to cognitive performance as compared to non-Hispanic Whites, with air pollutant exposures a potential risk factor. We investigated whether exposures to specific air pollution sources were associated with performance across several cognitive domains in a cohort of Puerto Rican older adults. Objectives: To investigate the association between sources of fine particulate matter (PM2.5) and cognitive performance in each of five cognitive domains. Methods: We obtained demographic, health, and cognitive function data for 1500 elderly participants of the Boston Puerto Rican Health Study. Cognitive function was assessed in each of two waves for five domains: verbal memory, recognition, mental processing, and executive and visuospatial function. To these data, we linked concentrations of PM2.5 and its components, black carbon (BC), nickel, sulfur, and silicon, as tracers for PM2.5 from traffic, oil combustion, coal combustion, and resuspended dust, respectively. Associations between each PM2.5 component and cognitive domain were examined using linear mixed models. Results: One year moving average exposures to BC were significantly associated with decreased verbal memory (−0.38; 95% confidence interval [CI] = −0.46, −0.30), recognition (−0.35; 95% CI = −0.46, −0.25), mental processing (−1.14; 95% CI = −1.55, −0.74), and executive function (−0.94; 95% CI = −1.31, −0.56). Similar associations were found for nickel. Associations for sulfur, and silicon, and PM2.5 were generally null, although sulfur (−0.51; 95% CI = −0.75, −0.28), silicon (−0.25; 95% CI = −0.36, −0.13), and PM2.5 (−0.35; 95% CI = −0.57, −0.12) were associated with decreased recognition. Conclusion: Long-term exposures to BC and nickel, tracers of traffic and oil combustion, respectively, were associated with decreased cognitive function across all domains, except visuospatial function.
Continuous non-invasive determination of nocturnal blood pressure variation using photoplethysmographic pulse wave signals: comparison of pulse propagation time, pulse transit time and RR-interval

Objective: Cardiovascular diseases are the leading cause of death, whereas nocturnal ambulatory blood pressure (BP) is the most potent predictor for cardiovascular risk. The volume clamp and pulse transit time (PTT) are common methods for continuous non-invasive BP measurement, but have drawbacks during unsupervised ambulatory use and undisturbed sleep. The pulse propagation time (PPT), defined as the time between pulse wave systolic peak and diastolic peak, provides valid information about the pressure pulse waveform. However, the use of PPT for nocturnal BP variation determination and whether such variation is affected by BP or heart rate (i.e. RR-interval or RRI) has not been investigated. Approach: To assess whether the PPT method is suitable for ubiquitous nocturnal BP monitoring, we compared systolic blood pressure (SBP) estimates derived from PPT, PTT, and RRI signals with parallel recorded BP measurements. The RRI-derived SBP signals were used as a baseline for testing a potential heart rate dependency. This work provides an overview of BP measurements, presents the developed real-time signal analysis, and describes the performance assessment. The signal analysis was validated with data records from 42 subjects acquired from an ergometry and sleep laboratory in equal parts. Main results: The algorithms applied to the ergometry laboratory database achieved a correlation coefficient between reference SBP and estimated SBPPPT of 0.89 (p < 0.001) with bias 0.1 mmHg and limits of agreement (LoA) −29.8 to 30.0 mmHg, SBPPTT of 0.97 (p < 0.001) with bias 0.0 mmHg and LoA −15.2 to 15.3 mmHg, and SBPRRI of 0.96 (p < 0.001) with bias 0.0 mmHg and LoA −19.5 to 19.5 mmHg. For the sleep laboratory database, the correlation coefficient was 0.95 (p < 0.001) with bias 0.2 mmHg and LoA −18.3 to 18.8 mmHg for SBPPPT, 0.88 (p < 0.001) with bias 0.0 mmHg and LoA −25.0 to 24.9 mmHg for SBPPTT, and 0.88 (p < 0.001) with bias of 0.1 mmHg and LoA −23.6 to 23.7 mmHg for SBPRRI. A heart rate dependency of PPT or PTT could not be found. The analysis of variance shows no significant differences between the reference SBP values and the estimated values for either the ergometry (F(3, 627) = 2.27, p = 0.08) or the sleep laboratory (F(3, 327) = 2.28, p = 0.08). Significance: In conclusion, the PPT method seems to be an interesting alternative for continuous determination of SBP during simplified cardiovascular monitoring and sleep screening compared to more expensive devices based on volume clamp or PTT methods.
Evaluation of the Ability of Physical Therapists to Palpate Intrapelvic Motion With the Stork Test on the Support Side

Background and Purpose Clinical indicators of pelvic girdle dysfunction are limited. However, research has shown that the pattern of intrapelvic motion is altered during single-leg support in subjects with pelvic girdle pain (PGP). Functionally, no relative motion should occur within the pelvis during load transfer, whereas anterior rotation of the innominate bone relative to the sacrum occurs during weight bearing in the presence of PGP. The aim of this study was to investigate whether the pattern of intrapelvic motion could be detected reliably during a new clinical assessment test for functional load transfer: the Stork Test on the support side. Subjects and Methods Three physical therapists were randomly assigned to palpate the motion of the innominate bones and sacrum in 33 subjects during the Stork Test on the support side. The direction of bone motion was indicated on 2-point and 3-point scales. Results When a 2-point scale was used, intertherapist agreement on the pattern of intrapelvic motion occurring during load transfer showed good reliability (left κ=.67, right κ=.77), and the percentage of agreement was high (left=91.9%, right=89.9%). A 3-point scale resulted in moderate reliability for both the left and the right sides (left κ=.59, right κ=.59), and the percentage of agreement decreased to 82.8% (left) and 79.8% (right). Discussion and Conclusion The ability of the physical therapists to reliably palpate and recognize an altered pattern of intrapelvic motion during the Stork Test on the support side was substantiated. The ability to distinguish between no relative movement and anterior rotation of the innominate bone during a load-bearing task was good. Further research is needed to determine the validity of this test for detecting pelvic girdle dysfunction.
The Molecular Profiling Lottery: More Accuracy, Less Precision, and No Cost

The concept of complete molecular profiling to select investigational treatment options is appealing, theoretically allowing the matching of patients to investigational drugs specifically targeted to molecular features of each patient's cancer. Although some patients do benefit from such a strategy, the vast majority do not. See related article by Tuxen et al., p. 1239
A systematic review of the adverse events and economic impact associated with oral corticosteroids in asthma

Abstract Background: Oral corticosteroids (OCSs) are often used to achieve asthma control. OCS-related comorbidities increase the burden of disease for patients and healthcare providers. Most studies characterizing OCS use and risk of adverse events (AEs) are in non-asthma patients. We sought to systematically review the literature on the burden of OCS use among adults with asthma. Methods: We systematically reviewed the literature including MEDLINE (1946–May 2017), EMBASE (1974–May 2017), and the Cochrane Library (2005–May 2017) to identify studies that considered AEs due to OCS treatment of adults with asthma, their burden on healthcare utilization, and costs. Results: We retrieved 9,589 citations; and 15 studies were included. AEs were significantly higher among OCS-users compared with non-OCS users with pooled adjusted odds ratio (OR) 1.68 (95% CI 1.15–2.46) for diabetes mellitus and 1.34 (95% CI 1.23–1.46) for hypertension. Among high dose OCS-users (>10 mg) compared with non-OCS users, the pooled adjusted ORs for development of any complication was 3.35 (95% CI 2.94–3.82), and bone and muscle complications 2.30 (95% CI 2.18–2.42). The risk of any complication increased with higher doses of OCS, with pooled adjusted OR from 2 studies of 2.26 (95% CI 1.37–3.72), 2.94 (95% CI 2.62–3.29) and 3.35 (95% CI 2.94–3.82) for low dose (<6 mg), medium dose (5–12 mg) and high dose (>10 mg) respectively compared with no OCS use. Conclusions: The use of OCS in the management of asthma is associated with a higher risk of complications. This risk is higher as the OCS dose increases.
Accurate tooth segmentation with improved hybrid active contour model

In orthodontic diagnosis and oral treatment planning, 3D tooth model constructed by dental computed tomography (CT) images is an essential and useful assisted tool. In virtue of the higher spatial resolution and lower radiation of x-ray, cone beam computed tomography (CBCT) has been widely used in dental application. However, due to lower signal to noise ratio, vague and weak edge between tooth root and sockets as well as intensity inhomogeneity, the tooth root is easy to be under-segmented and appears false boundary. This paper presents a new hybrid active contour model in a variational level set formulation to segment the tooth root accurately. Initial shape and intensity information from the upper layer is used for next layer’s enhancement and shape constraint. The hybrid level set model is constituted by multi-scale local likelihood image fitting (LLIF) energy term, prior shape constraint energy term with adaptive weight and reaction–diffusion (RD) regularization energy term. For detailed interpretation of this hybrid energy model, the intensity information in a narrowband region outside the contour was used to enhance the contrast between tooth dentine and sockets. The LLIF energy term was incorporated into the level set function to overcome the edge fuzziness and intensity inhomogeneity. The shape prior energy term with adaptive weight was used to differentiate the constraint of the contour evolution inside and outside the level set function to improve the capability of curve topology changes. The RD energy term was introduced to effectively regularize the level set evolution. A new measurement for tooth segmentation evaluation was proposed for quantitative validation. The experimental result of the proposed method was compared with two other typical approaches, and was demonstrated to achieve a higher segmentation accuracy.