Experiments in neural question answering

In this thesis, we apply deep learning methods to tackle the tasks of finding duplicate questions, learning to rank the answers of a Multiple Choice Question (MCQ) and classifying the answers to a question coming from the context of a paragraph. We draw our attention toward the problems related to sentence-sentence similarity. We used siamese architecture for better representation of the question and answers. The basic aim of all the methods proposed in this thesis is to build the word embeddings of question and answers and feed them to a deep neural architecture. We used several such architectures like Long-Short term memory (LSTM) and Convolutional Neural Network (CNN). We have also implemented an attention mechanism to put more focus on the sentence-word relationship. Our goal was to extract a refined representation of the question and answers through different combination of these deep learning techniques. We generated a representation of a sentence according to the context of another sentence for solving our tasks. We provide some simple but efficient deep learning models to solve our tasks. As neural models are data-driven, we train our model extensively by making pairs such as question-question and question-answer over a large-scale real-life dataset. We used three different datasets to solve our three different tasks. The Quora dataset of several question-answer pairs was used for the task of finding duplicate question. The OpenTriviaQA question answering dataset for the ranking of multiple answers. Lastly, we use the SQuAD dataset for the answer classification of reading comprehension task. We evaluate our models based on metrics like accuracy, precision, recall, F1 scores. Our methods and experiments demonstrate some significant improvements over the state-of-the-art methods

Decoding the enigma of antiviral crisis: Does one target molecule regulate all?

Disease fatality associated with Ebola, SARS-CoV and dengue infections in humans is attributed to a cytokine storm that is triggered by excessive pro-inflammatory responses. Interleukin (IL)-6 acts as a mediator between pro- and anti-inflammatory reactivity by initiating trans- and classical-signaling, respectively. Hence, IL-6 is assumed to provide a target for a broad range of antiviral agents. Available immunosuppressive antivirals are directed to control an often exaggerated pro-inflammatory response that gives rise to complex clinical conditions such as lymphocytopenia. It is known that IL-6, via its soluble receptor (sIL-6R), initiates a pro-inflammatory response while an anti-inflammatory response is triggered by the membrane-bound IL-6 receptor (IL-6R). Future antivirals should thus aim to target the mechanism that regulates switching between IL-6 trans- and classical-signaling. In this review, we propose that the tumour necrosis factor-α converting enzyme ADAM-17 could be the master molecule involved in regulating IL-6 class switching and through this in controlling pro- and anti-inflammatory responses to viral antigenic stimuli. Therefore, ADAM-17 should be considered as a potential target molecule for novel antiviral drug discovery that would regulate host reactivity to infection and thereby limit or prevent fatal outcomes

Detecting planning conversations in bug reports

Software developers refer to bug reports as a reliable source of information. However, these bug reports are written in the form of conversations among developers and often become long depending on the complexity of the issue, necessitating a significant amount of time and effort to locate the desired information. Prior work focused on tagging the different types of information in the bug reports. However, their work did not identify Plans. In our work, we focus on retrieving Plans from bug reports and labeling them with a Plan Labeller. First, we analyzed bug reports to identify which section contains Plans. Then we examined three methods to detect Plans. Based on that, we found keywords and key-phrases to be the best approach. We applied lists of keywords and key-phrases iteratively to randomly selected bug reports to construct a list of keywords and key-phrases that can identify Plans in a bug report

A cross-country comparison of intensive care physicians' beliefs about their transfusion behaviour : a qualitative study using the theoretical domains framework

Pub Med ID 22999460 PMCID: PMC3527303Peer reviewedPublisher PD

Exfoliation mechanisms of 2D materials and their applications

Due to the strong in-plane but weak out-of-plane bonding, it is relatively easy to separate nanosheets of two-dimensional (2D) materials from their respective bulk crystals. This exfoliation of 2D materials can yield large 2D nanosheets, hundreds of micrometers wide, that can be as thin as one or a few atomic layers thick. However, the underlying physical mechanisms unique to each exfoliation technique can produce a wide distribution of defects, yields, functionalization, lateral sizes, and thicknesses, which can be appropriate for specific end applications. The five most commonly used exfoliation techniques include micromechanical cleavage, ultrasonication, shear exfoliation, ball milling, and electrochemical exfoliation. In this review, we present an overview of the field of 2D material exfoliation and the underlying physical mechanisms with emphasis on progress over the last decade. The beneficial characteristics and shortcomings of each exfoliation process are discussed in the context of their functional properties to guide the selection of the best technique for a given application. Furthermore, an analysis of standard applications of exfoliated 2D nanosheets is presented including their use in energy storage, electronics, lubrication, composite, and structural applications. By providing detailed insight into the underlying exfoliation mechanisms along with the advantages and disadvantages of each technique, this review intends to guide the reader toward the appropriate batch-scale exfoliation techniques for a wide variety of industrial applications

Anesthesiologists' and surgeons' perceptions about routine pre-operative testing in low risk patients: application of the Theoretical Domains Framework to identify factors that influence physicians' decisions to order pre-operative tests

Background Routine pre-operative tests for anesthesia management are often ordered by both anesthesiologists and surgeons for healthy patients undergoing low-risk surgery. The Theoretical Domains Framework (TDF) was developed to investigate determinants of behaviour and identify potential behaviour change interventions. In this study, the TDF is used to explore anaesthesiologists’ and surgeons’ perceptions of ordering routine tests for healthy patients undergoing low-risk surgery. Conclusion We identified key factors that anesthesiologists and surgeons believe influence whether they order pre-operative tests routinely for anesthesia management for a healthy adults undergoing low-risk surgery. These beliefs identify potential individual, team, and organisation targets for behaviour change interventions to reduce unnecessary routine test ordering. Methods Sixteen clinicians (eleven anesthesiologists and five surgeons) throughout Ontario were recruited. An interview guide based on the TDF was developed to identify beliefs about preoperative testing practices. Content analysis of physicians’ statements into the relevant theoretical domains was performed. Specific beliefs were identified by grouping similar utterances of the interview participants. Relevant domains were identified by noting the frequencies of the beliefs reported, presence of conflicting beliefs, and perceived influence on the performance of the behaviour under investigation. Results Seven of the twelve domains were identified as likely relevant to changing clinicians’ behaviour about pre-operative test ordering for anesthesia management. Key beliefs were identified within these domains including: conflicting comments about who was responsible for the test-ordering (Social/professional role and identity); inability to cancel tests ordered by fellow physicians (Beliefs about capabilities and social influences); and the problem with tests being completed before the anesthesiologists see the patient (Beliefs about capabilities and Environmental context and resources). Often, tests were ordered by an anesthesiologist based on who may be the attending anesthesiologist on the day of surgery while surgeons ordered tests they thought anesthesiologists may need (Social influences). There were also conflicting comments about the potential consequences associated with reducing testing, from negative (delay or cancel patients’ surgeries), to indifference (little or no change in patient outcomes), to positive (save money, avoid unnecessary investigations) (Beliefs about consequences). Further, while most agreed that they are motivated to reduce ordering unnecessary tests (Motivation and goals), there was still a report of a gap between their motivation and practice (Behavioural regulation)

Supporting genetics in primary care: investigating how theory can inform professional education

Evidence indicates that many barriers exist to the integration of genetic case finding into primary care. We conducted an exploratory study of the determinants of three specific behaviours related to using breast cancer genetics referral guidelines effectively: 'taking a family history', 'making a risk assessment', and 'making a referral decision'. We developed vignettes of primary care consultations with hypothetical patients, representing a wide range of genetic risk for which different referral decisions would be appropriate. We used the Theory of Planned Behavior to develop a survey instrument to capture data on behavioural intention and its predictors (attitude, subjective norm, and perceived behavioural control) for each of the three behaviours and mailed it to a sample of Canadian family physicians. We used correlation and regression analyses to explore the relationships between predictor and dependent variables. The response rate was 96/125 (77%). The predictor variables explained 38-83% of the variance in intention across the three behaviours. Family physicians' intentions were lower for 'making a risk assessment' (perceived as the most difficult) than for the other two behaviours. We illustrate how understanding psychological factors salient to behaviour can be used to tailor professional educational interventions; for example, considering the approach of behavioural rehearsal to improve confidence in skills (perceived behavioural control), or vicarious reinforcement as where participants are sceptical that genetics is consistent with their role (subjective norm)

A guide to using the Theoretical Domains Framework of behaviour change to investigate implementation problems

Background: Implementing new practices requires changes in the behaviour of relevant actors, and this is facilitated by understanding of the determinants of current and desired behaviours. The Theoretical Domains Framework (TDF) was developed by a collaboration of behavioural scientists and implementation researchers who identified theories relevant to implementation and grouped constructs from these theories into domains. The collaboration aimed to provide a comprehensive, theory-informed approach to identify determinants of behaviour. The first version was published in 2005, and a subsequent version following a validation exercise was published in 2012. This guide offers practical guidance for those who wish to apply the TDF to assess implementation problems and support intervention design. It presents a brief rationale for using a theoretical approach to investigate and address implementation problems, summarises the TDF and its development, and describes how to apply the TDF to achieve implementation objectives. Examples from the implementation research literature are presented to illustrate relevant methods and practical considerations. Methods: Researchers from Canada, the UK and Australia attended a 3-day meeting in December 2012 to build an international collaboration among researchers and decision-makers interested in the advancing use of the TDF. The participants were experienced in using the TDF to assess implementation problems, design interventions, and/or understand change processes. This guide is an output of the meeting and also draws on the a uthors' collective experience. Examples from the implementation research literature judged by authors to be representative of specific applications of the TDF are included in this guide. Results: We explain and illustrate methods, with a focus on qualitative approaches, for selecting and specifying target behaviours key to implementation, selecting the study design, deciding the sampling strategy, developing study materials, collecting and analysing data, and reporting findings of TDF-based studies. Areas for development include methods for triangulating data, e.g. from interviews, questionnaires and observation and methods for designing interventions based on TDF-based problem analysis. Conclusions: We offer this guide to the implementation community to assist in the application of the TDF to achieve implementation objectives. Benefits of using the TDF include the provision of a theoretical basis for implementation studies, good coverage of potential reasons for slow diffusion of evidence into practice and a method for progressing from theory-based investigation to intervention

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Global, regional, and national burden of disorders affecting the nervous system, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BackgroundDisorders affecting the nervous system are diverse and include neurodevelopmental disorders, late-life neurodegeneration, and newly emergent conditions, such as cognitive impairment following COVID-19. Previous publications from the Global Burden of Disease, Injuries, and Risk Factor Study estimated the burden of 15 neurological conditions in 2015 and 2016, but these analyses did not include neurodevelopmental disorders, as defined by the International Classification of Diseases (ICD)-11, or a subset of cases of congenital, neonatal, and infectious conditions that cause neurological damage. Here, we estimate nervous system health loss caused by 37 unique conditions and their associated risk factors globally, regionally, and nationally from 1990 to 2021.MethodsWe estimated mortality, prevalence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs), with corresponding 95% uncertainty intervals (UIs), by age and sex in 204 countries and territories, from 1990 to 2021. We included morbidity and deaths due to neurological conditions, for which health loss is directly due to damage to the CNS or peripheral nervous system. We also isolated neurological health loss from conditions for which nervous system morbidity is a consequence, but not the primary feature, including a subset of congenital conditions (ie, chromosomal anomalies and congenital birth defects), neonatal conditions (ie, jaundice, preterm birth, and sepsis), infectious diseases (ie, COVID-19, cystic echinococcosis, malaria, syphilis, and Zika virus disease), and diabetic neuropathy. By conducting a sequela-level analysis of the health outcomes for these conditions, only cases where nervous system damage occurred were included, and YLDs were recalculated to isolate the non-fatal burden directly attributable to nervous system health loss. A comorbidity correction was used to calculate total prevalence of all conditions that affect the nervous system combined.FindingsGlobally, the 37 conditions affecting the nervous system were collectively ranked as the leading group cause of DALYs in 2021 (443 million, 95% UI 378–521), affecting 3·40 billion (3·20–3·62) individuals (43·1%, 40·5–45·9 of the global population); global DALY counts attributed to these conditions increased by 18·2% (8·7–26·7) between 1990 and 2021. Age-standardised rates of deaths per 100 000 people attributed to these conditions decreased from 1990 to 2021 by 33·6% (27·6–38·8), and age-standardised rates of DALYs attributed to these conditions decreased by 27·0% (21·5–32·4). Age-standardised prevalence was almost stable, with a change of 1·5% (0·7–2·4). The ten conditions with the highest age-standardised DALYs in 2021 were stroke, neonatal encephalopathy, migraine, Alzheimer's disease and other dementias, diabetic neuropathy, meningitis, epilepsy, neurological complications due to preterm birth, autism spectrum disorder, and nervous system cancer.InterpretationAs the leading cause of overall disease burden in the world, with increasing global DALY counts, effective prevention, treatment, and rehabilitation strategies for disorders affecting the nervous system are needed