LLukas22/scidocs huggingface dataset:
Clinical Relation Extraction Toward Drug Safety Surveillance Using Electronic Health Record Narratives: Classical Learning Versus Deep Learning

BACKGROUND
Medication and adverse drug event (ADE) information extracted from electronic health record (EHR) notes can be a rich resource for drug safety surveillance. Existing observational studies have mainly relied on structured EHR data to obtain ADE information; however, ADEs are often buried in the EHR narratives and not recorded in structured data.


OBJECTIVE
To unlock ADE-related information from EHR narratives, there is a need to extract relevant entities and identify relations among them. In this study, we focus on relation identification. This study aimed to evaluate natural language processing and machine learning approaches using the expert-annotated medical entities and relations in the context of drug safety surveillance, and investigate how different learning approaches perform under different configurations.


METHODS
We have manually annotated 791 EHR notes with 9 named entities (eg, medication, indication, severity, and ADEs) and 7 different types of relations (eg, medication-dosage, medication-ADE, and severity-ADE). Then, we explored 3 supervised machine learning systems for relation identification: (1) a support vector machines (SVM) system, (2) an end-to-end deep neural network system, and (3) a supervised descriptive rule induction baseline system. For the neural network system, we exploited the state-of-the-art recurrent neural network (RNN) and attention models. We report the performance by macro-averaged precision, recall, and F1-score across the relation types.


RESULTS
Our results show that the SVM model achieved the best average F1-score of 89.1% on test data, outperforming the long short-term memory (LSTM) model with attention (F1-score of 65.72%) as well as the rule induction baseline system (F1-score of 7.47%) by a large margin. The bidirectional LSTM model with attention achieved the best performance among different RNN models. With the inclusion of additional features in the LSTM model, its performance can be boosted to an average F1-score of 77.35%.


CONCLUSIONS
It shows that classical learning models (SVM) remains advantageous over deep learning models (RNN variants) for clinical relation identification, especially for long-distance intersentential relations. However, RNNs demonstrate a great potential of significant improvement if more training data become available. Our work is an important step toward mining EHRs to improve the efficacy of drug safety surveillance. Most importantly, the annotated data used in this study will be made publicly available, which will further promote drug safety research in the community.
Cutis verticis gyrata primitif essentiel, une affection cutanée rare: cas clinique et revue de la littérature

Le cutis verticis gyrata (CVG), du cuir chevelu, est une maladie rare et évolutive de la peau du scalp. Elle est caractérisée par une hypertrophie et une hyperlaxité cutanée formant des plis semblables aux gyri du cortex cérébral. Nous présentons le cas d'une patiente de 21 ans atteinte de CVG primitif essentiel, ayant débuté à l'âge de 8 ans, au niveau du scalp et était d'aggravation progressive. La malade présentait une déformation du scalp avec de nombreux plis longitudinaux et transversaux. Sa demande était motivée par une gêne sociale et esthétique. Une résection chirurgicale de l'excédent cutané dans un plan transversal et longitudinal était réalisée. Le traitement de cette maladie est chirurgical, par l'excision des plis cutanés et remise en tension du scalp. Le nombre et la localisation des incisions doivent préserver la vascularisation des lambeaux de scalp et tenir compte du caractère évolutif de cette pathologie. Pan African Medical Journal. 2014; 19:345 doi:10.11604/pamj.2014.19.345.5729 This article is available online at: http://www.panafrican-med-journal.com/content/article/19/345/full/ © Boukind Samira et al. The Pan African Medical Journal ISSN 1937-8688. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Pan African Medical Journal – ISSN: 19378688 (www.panafrican-med-journal.com) Published in partnership with the African Field Epidemiology Network (AFENET). (www.afenet.net) Case report Open Access
Advanced Technologies in Modern Robotic Applications

This chapter introduces a number of robot platforms and relevant devices used throughout this book, including the humanoid robot platforms such as Baxter robot and iCub robot; visual sensors of Microsoft Kinect, stereo camera Point Grey Bumblebee2 and 3D camera Leap Motion, as well as haptic devices of SensAble Omni and Novint joystick Falcon. Meanwhile, a number of software toolkits useful in robot simulation are also introduced in this chapter, e.g., the MATLAB Robotics Toolbox and the Virtual Robot Experiment Platform (V-REP) simulator. Robot Operating System (ROS) is also briefly introduced by highlighting the ROS characters and ROS level concepts. These devices and toolkits are nowadays becoming more and more popularly used in the study of robotics, as they provide ideal means for the study, design, and test of the robotic technologies.
“So distant and wild a scene”: language, domesticity and difference in Hannah Kilham's writing from West Africa, 1822-1832

Abstract Hannah Kilham (1774-1832), a Sheffield Quaker, was involved in philanthropic, educational and missionary work with women in Britain, Ireland and West Africa in the early nineteenth century. In this article the author focuses upon Hannah Kilham's. engagement in the religious and domestic education of African girls and women in the 1820s and 1830s. Through representations of African women as in need of her ‘civilising influence’, Kilham was able to construct a powerful role for herself, and for other white middle-class British women, in the colonial/missionary enterprise. The article explores the significance of notions of gender, domesticity and the Protestant family to the construction of ideas about Africa's ‘difference’ and, through this, British national identity.
Research on Software Security Testing

Software security testing is an important means to ensure software security and trustiness. This paper first mainly discusses the definition and classification of software security testing, and investigates methods and tools of software security testing widely. Then it analyzes and concludes the advantages and disadvantages of various methods and the scope of application, presents a taxonomy of security testing tools. Finally, the paper points out future focus and development directions of software security testing technology. Keywords—security testing, security functional testing, security vulnerability testing, testing method, testing tool
Is universal prevention against youths' substance misuse really universal? Gender-specific effects in the EU-Dap school-based prevention trial.

BACKGROUND
Studies of effectiveness of school-based prevention of substance misuse have generally overlooked gender differences. The purpose of this work was to analyse gender differences in the effectiveness of a new European school-based curriculum for prevention of substance misuse among adolescents.


METHODS
The European Drug Abuse Prevention (EU-Dap) trial took place in seven European countries during the school year 2004-05. Schools were randomly assigned to either a control group or a 12-session standardised curriculum ("Unplugged") based on a comprehensive social influence model. The analytical sample consisted of 6359 students (3324 boys and 3035 girls). The use of cigarettes, alcohol and illicit drugs, adolescents' knowledge and opinions about substances, as well as social and personal skills were investigated through a self-completed anonymous questionnaire administered at enrollment and 3 months after the end of the programme. Adjusted Prevalence Odds Ratios were calculated as the measure of association between the intervention and behavioural outcomes using multilevel regression modelling.


RESULTS
At enrollment, boys were more likely than girls to have used cannabis and illicit drugs, whereas girls had a higher prevalence of cigarette smoking. At the follow-up survey, a significant association between the programme and a lower prevalence of all behavioural outcomes was found among boys, but not among girls. Age and self-esteem emerged as possible modifiers of these gender differences, but effects were not statistically significant.


CONCLUSIONS
Comprehensive social influence school curricula against substance misuse in adolescence may perform differently among girls and boys, owing to developmental and personality factors.
Factors associated with functional recovery and home discharge in stroke patients admitted to a convalescent rehabilitation ward.

AIMS
This study aimed to determine the predictive factors for functional recovery and home discharge in stroke patients receiving in-hospital rehabilitation.


METHODS
This study included a consecutive series of 174 stroke patients (average age 73.0 ± 10.8) admitted to the convalescent rehabilitation ward at Azumino Red Cross Hospital in Japan after acute rehabilitation. The main outcome measures were functional recovery (functional independence measure [FIM] at discharge and Montebello rehabilitation factor score [MRFS]) and home discharge.


RESULTS
Total FIM improved from 72.6 ± 27.6 to 87.7 ± 29.9 during the hospital stay (P < 0.001). The average MRFS was 0.30 ± 0.28. Of the 174 patients, 151 were discharged home (87%). Age, stroke type, premorbid independence, motor FIM, and cognitive FIM at admission showed a significant association with FIM at discharge, while age, premorbid independence, motor FIM at admission, and cognitive FIM at admission were statistically significant predictors of MRFS. Female sex, not living with family, premorbid independence, and neglect were negatively associated with home discharge.


CONCLUSIONS
Premorbid disability and cognitive dysfunction at admission were both negatively associated with functional recovery and home discharge in patients undergoing inpatient stroke rehabilitation.
Characteristic extraction of machined surface using wavelet transformation

In the development and design of machinery products, product performance and tolerance stack-up analysis are generally calculated using computer software. In these calculations, the product shape is modeled as a set of primitives, which are simple geometrical shapes, such as plane, cylinder and sphere. However, the shape of an actual product is different from these shapes because machining error cannot be avoided. Actual shapes usually exhibit deviations in scales, such as geometric deviations, waviness and surface roughness. Therefore, the error between the result of computer calculation and the actual behavior of the product is caused by the shape simplification. A method of for generation of a pseudo shape is required to reduce the calculation error. In this study, a new method for random generation of skin model shapes, which maintain the surface characteristics in multiscale levels, is proposed. In the method, first, an optimal mother wavelet should be decided because they depend on extracting the surface characteristics. In this paper, eight representative mother wavelets are used in wavelet transformation for comparison. The results are discussed based on the results obtained through a case study, and latent problems are also observed.
Barriers to and facilitators of physical activity program use among older adults.

OBJECTIVE
Regular physical activity (PA) is important for maintaining long-term physical, cognitive, and emotional health. However, few older adults engage in routine PA, and even fewer take advantage of programs designed to enhance PA participation. Though most managed Medicare members have free access to the Silver Sneakers and EnhanceFitness PA programs, the vast majority of eligible seniors do not utilize these programs. The goal of this qualitative study was to better understand the barriers to and facilitators of PA and participation in PA programs among older adults.


DESIGN
This was a qualitative study using focus group interviews.


SETTING
Focus groups took place at three Group Health clinics in King County, Washington.


PARTICIPANTS
Fifty-two randomly selected Group Health Medicare members between the ages of 66 to 78 participated.


METHODS
We conducted four focus groups with 13 participants each. Focus group discussions were audio-recorded, transcribed, and analyzed using an inductive thematic approach and a social-ecological framework.


RESULTS
Men and women were nearly equally represented among the participants, and the sample was largely white (77%), well-educated (69% college graduates), and relatively physically active. Prominent barriers to PA and PA program participation were physical limitations due to health conditions or aging, lack of professional guidance, and inadequate distribution of information on available and appropriate PA options and programs. Facilitators included the motivation to maintain physical and mental health and access to affordable, convenient, and stimulating PA options.


CONCLUSION
Older adult populations may benefit from greater support and information from their providers and health care systems on how to safely and successfully improve or maintain PA levels through later adulthood. Efforts among health care systems to boost PA among older adults may need to consider patient-centered adjustments to current PA programs, as well as alternative methods for promoting overall active lifestyle choices.
Mechanical thrombectomy in acute stroke: prospective pilot trial of the solitaire FR device while under conscious sedation.

BACKGROUND AND PURPOSE
The best approach between general anesthesia and conscious sedation to perform mechanical thrombectomy remains unknown. The goal of our study was to evaluate the feasibility, safety, and efficacy of mechanical thrombectomy under conscious sedation in patients with acute ischemic stroke, using the Solitaire FR device, in a prospective, single-center, single-arm study.


MATERIALS AND METHODS
The study included consecutive patients with acute ischemic stroke due to a large artery occlusion within 6 hours of symptom onset for the anterior circulation, and within 24 hours for the posterior circulation. After intravenous thrombolysis (when no contraindications), thrombectomy was performed with the Solitaire device in patients under conscious sedation. Primary efficacy and safety end points were good functional outcome (mRS ≤2) at 3 months and mortality at 3 months. Secondary end points were recanalization (TICI ≥2) and failure rate.


RESULTS
From May 2010 to July 2011, 36 patients were treated. Median baseline NIHSS score was 17.5. The occlusion site was MCA in 21 patients (58.4%), ICA-MCA tandem occlusion in 9 patients (25.0%), terminal ICA in 2 patients (5.5%), and basilar artery in 4 patients (11.1%). Twenty-three patients (63.9%) received intravenous thrombolysis. Superselective catheterization of the occluded vessel was not feasible in 5/36 cases (13.9%). Successful revascularization was achieved in 28/36 patients (77.8%). After 3 months, 22 patients (61.1%) showed good functional outcome (mRS ≤2) and the median NIHSS score was 8.5. Overall mortality rate at 3 months was 22.2% (8/36).


CONCLUSIONS
In acute ischemic stroke, mechanical thrombectomy while under conscious sedation is feasible in a large percentage of cases (86.1%) and is associated with a short procedure delay and a high percentage of good functional outcomes at 3 months (61.1%).
Comparison of prasugrel and ticagrelor loading doses in ST-segment elevation myocardial infarction patients: RAPID (Rapid Activity of Platelet Inhibitor Drugs) primary PCI study.

OBJECTIVES
This study sought to compare the action of prasugrel and ticagrelor in ST-segment elevation myocardial infarction (STEMI) patients undergoing primary percutaneous coronary intervention (PPCI).


BACKGROUND
It has been documented that prasugrel and ticagrelor are able to provide effective platelet inhibition 2 h after a loading dose (LD). However, the pharmacodynamic measurements after prasugrel and ticagrelor LD have been provided by assessing only healthy volunteers or subjects with stable coronary artery disease.


METHODS
Fifty patients with STEMI undergoing PPCI with bivalirudin monotherapy were randomized to receive 60 mg prasugrel LD (n = 25) or 180 mg ticagrelor LD (n = 25). Residual platelet reactivity was assessed by VerifyNow at baseline and 2, 4, 8, and 12 h after LD.


RESULTS
Platelet reactivity units (PRU) 2 h after the LD (study primary endpoint) were 217 (12 to 279) and 275 (88 to 305) in the prasugrel and ticagrelor groups, respectively (p = NS), satisfying pre-specified noninferiority criteria. High residual platelet reactivity (HRPR) (PRU ≥240) was found in 44% and 60% of patients (p = 0.258) at 2 h. The mean time to achieve a PRU <240 was 3 ± 2 h and 5 ± 4 h in the prasugrel and ticagrelor groups, respectively. The independent predictors of HRPR at 2 h were morphine use (odds ratio: 5.29; 95% confidence interval: 1.44 to 19.49; p = 0.012) and baseline PRU value (odds ratio: 1.014; 95% confidence interval: 1.00 to 1.03; p = 0.046).


CONCLUSIONS
In patients with STEMI, prasugrel showed to be noninferior as compared with ticagrelor in terms of residual platelet reactivity 2 h after the LD. The 2 drugs provide an effective platelet inhibition 2 h after the LD in only a half of patients, and at least 4 h are required to achieve an effective platelet inhibition in the majority of patients. Morphine use is associated with a delayed activity of these agents. (Rapid Activity of Platelet Inhibitor Drugs Study, NCT01510171).
Serum Interleukin-27 Level in Different Clinical Stages of Lung Cancer

BACKGROUND
Advanced lung cancer is indicated with rapid disease development. Interleukin 27 (IL-27) is regarded as a cytokine with anti-tumour activities.


AIM
Since, the impact of type of lung cancer on the level of IL-27 in patient's serum has not yet been investigated; current study evaluated the clinical stages according to American Joint Committee on Cancer (AJCC) criteria, Tumor-Node-Metastasis (TNM) stage and the lung cancer spread (localized or widespread) and it's correlation with serum IL-27.MATERIAL AND METHODS: Thirty patients with confirmed histopathological lung cancer and 30 cancer-free healthy individuals as the control group were included in the current study. Patients group were assigned to either small cell lung cancer group (SCLC) or non-small cell lung cancer (NSCLC) according to the clinical features and the results of lung biopsy specimens. Level of IL-27 was quantified with enzyme-linked immunosorbent assay (ELISA) test in serum samples.


RESULTS
A significant increase in serum IL-27 level was noticed in individuals with lung cancer in comparison with the control group. The level of serum IL-27 in the NSCL squamous carcinoma (NSCLC-Sc) type was significantly greater than in the NSCLC adenocarcinoma (NSCLC-Ad) type, and in both groups, this variable was more than the control group. The serum IL-27 content level was greater in stage III versus stage IV.


CONCLUSION
The current research confirmed the existence of the anti-tumour components in patients with NSCLC. IL-27 can be utilised in diagnosis and screening in early stages of lung cancer along with the management of patients. Different levels of IL-27 in different types of lung cancers in the current study can lead to design more comprehensive studies in the future.
Spectrum of GCDFP-15 expression in human fetal and adult normal tissues

 GCDFP-15, a glycoprotein identified in the cyst fluid of cystic breast disease, is considered to be a marker of apocrine differentiation. Studies on GCDFP-15 localization in adult normal tissues are lacking, and no information on GCDFP-15 expression during fetal development has been reported. We investigated GCDFP-15 expression in a large series of formalin-fixed, paraffin-embedded normal human adult and fetal tissues using the monoclonal antibody BRST-2. In normal adult tissues GCDFP-15 expression was found in all apocrine, lacrimal, ceruminous and Moll’s glands and in numerous serous cells of the submandibular, sublingual and minor salivary glands. The serous cells of nasal and bronchial glands were also positive; parotid and laryngeal glands showed rare immunoreactive cells. GCDFP-15-positive cells were observed in all cutaneous eccrine glands from different body sites. In fetal tissues immunoreactivity was observed in numerous acinous cells of all tracheal, bronchial and submandibular salivary glands. GCDFP-15 positivity was identified in numerous cells of all axillary sweat glands and in rare cells of some sweat glands of the thorax, abdomen, back, leg and arm. In both apocrine and nonapocrine glands GCDFP-15 was always localized in the secretory component. These data suggest that GCDFP-15 is a glandular differentiation marker associated with apocrine secretion; that it is expressed in glands that have phylogenetic origins in common with apocrine glands (submandibular salivary and submucosal bronchial glands); and that eccrine cutaneous glands express GCDFP-15 and thus might be referred to as mixed apocrine-eccrine glands. GCDFP-15 is expressed during fetal development and may represent a common marker of embryologically linked glandular structures.
Resilient or Resigned? Criminal Victimisation and Quality of Life in South Africa.

A victimisation study conducted among 3300 householders in South Africa’s Nelson Mandela Metropolitan Municipality (NMMM) in the Eastern Cape Province aimed to inform a crime prevention strategy for the metropolitan area. The study found that the variables ‘fear of crime’ – measured in terms of perceived likelihood of victimisation – and concern about ‘personal safety’ had greater negative influence on life satisfaction than actual victimisation. Individual crimes against the person had greater negative influence on subjective wellbeing and feelings of personal safety than property and other household crimes. Individuals who perceived themselves to be at risk of becoming a victim of crime also perceived greater risk of other misfortunes. However, materially better-off victims reported higher levels of life satisfaction than non-victims in spite of their crime experience. South Africa has high crime rates by international standards and fighting crime presents the country with one of its major challenges in the second decade of democracy. Nevertheless, findings suggest that the negative impact of crime issues on achieving the good life are overshadowed by issues of racial inequalities and poverty. The conclusion is drawn that residents of Nelson Mandela Metropole are hardy when it comes to living with crime but nonetheless suffer stress in doing so. From a methodological perspective, the discussion considers whether subjective crime issues such as fear of crime and personal safety should be regarded as personal or neighbourhood quality-of-life issues. Based on survey findings, the conclusion is drawn that concern for personal safety is both. However, a crime-as neighbourhood-issue is more likely to attract remedial action on the part of local authorities to better protect citizens and allay their fears of crime.