LLukas22/scidocs huggingface dataset:
Effects of Semantic Features on Machine Learning-Based Drug Name Recognition Systems: Word Embeddings vs. Manually Constructed Dictionaries

Semantic features are very important for machine learning-based drug name recognition (DNR) systems. The semantic features used in most DNR systems are based on drug dictionaries manually constructed by experts. Building large-scale drug dictionaries is a time-consuming task and adding new drugs to existing drug dictionaries immediately after they are developed is also a challenge. In recent years, word embeddings that contain rich latent semantic information of words have been widely used to improve the performance of various natural language processing tasks. However, they have not been used in DNR systems. Compared to the semantic features based on drug dictionaries, the advantage of word embeddings lies in that learning them is unsupervised. In this paper, we investigate the effect of semantic features based on word embeddings on DNR and compare them with semantic features based on three drug dictionaries. We propose a conditional random fields (CRF)-based system for DNR. The skip-gram model, an unsupervised algorithm, is used to induce word embeddings on about 17.3 GigaByte (GB) unlabeled biomedical texts collected from MEDLINE (National Library of Medicine, Bethesda, MD, USA). The system is evaluated on the drug-drug interaction extraction (DDIExtraction) 2013 corpus. Experimental results show that word embeddings significantly improve the performance of the DNR system and they are competitive with semantic features based on drug dictionaries. F-score is improved by 2.92 percentage points when word embeddings are added into the baseline system. It is comparative with the improvements from semantic features based on OPEN ACCESS Information 2015, 6 849 drug dictionaries. Furthermore, word embeddings are complementary to the semantic features based on drug dictionaries. When both word embeddings and semantic features based on drug dictionaries are added, the system achieves the best performance with an Fscore of 78.37%, which outperforms the best system of the DDIExtraction 2013 challenge by 6.87 percentage points.
Printed and Handwritten Kannada Numeral Recognition Using Crack Codes and Fourier Descriptors Plate

Selection of feature extraction method is most important factor in achieving high recognition performance in automatic numeral recognition systems. This paper presents an efficient and novel method for recognition of machine printed and handwritten Kannada numerals using Crack codes and Fourier Descriptors. Printed and handwritten Kannada numerals are scan converted to binary images and normalized to a size of 40 x 40 pixels. Crack code that represents the line between the object pixels and the background (the 'crack') is computed. The code obtained is then represented in complex plane and 10 dimensional Fourier
Short-term effects of physical activity, air pollution and their interaction on the cardiovascular and respiratory system.

Physical activity (PA) in urban environments may lead to increased inhalation of air pollutants. As PA and air pollution (AP) have respectively beneficial and detrimental effects on the cardiorespiratory system, the responses to these exposures can interact. Therefore, we assessed the short-term effects of PA, AP and their interaction on a set of subclinical cardiovascular and respiratory outcomes in a panel of healthy adults: heart rate variability (HRV), retinal vessel diameters, lung function and fractional exhaled nitric oxide (FeNO). One hundred twenty two participants measured their PA level and exposure to black carbon (BC), a marker of AP exposure, with wearable sensors during an unscripted week in three different seasons. The study was part of the PASTA project in three European cities (Antwerp: 41 participants, Barcelona: 41 participants, London: 40 participants). At the end of each measurement week, the health outcomes were evaluated. Responses to PA, BC and their interaction were assessed with mixed effect regression models. Separate models were used to account for a 2-h and 24-h time window. During the 2-h time window, HRV and lung function changed statistically significantly in response to PA (METhours) and logarithmic BC (%change). Changes in HRV marked an increased sympathetic tone with both PA (logarithmic LF/HF: +7%; p < 0.01) and BC (logarithmic HF: -19%; p < 0.05). In addition, PA provoked bronchodilation which was illustrated by a significant increase in lung function (FEV1: +15.63 mL; p < 0.05). While a BC %increase was associated with a significant lung function decrease (PEF: -0.10 mL; p < 0.05), the interaction indicated a potential protective effect of PA (p < 0.05). We did not observe a response of the retinal vessel diameters. Most subclinical outcomes did not change in the 24-h time window (except for a few minor changes in LF/HF, FeNO and PEF). Our results on the separate and combined effects of short-term PA and AP exposure on subclinical markers of the cardiorespiratory system are relevant for public health. We provide insights on the physiological responses of multiple, complementary markers. This may move further research towards elucidating potential pathways to disease and the long-term clinical impact of the observed physiological changes.
Effect of fluvastatin on cardiac outcomes in renal transplant recipients: a multicentre, randomised, placebo-controlled trial

BACKGROUND
Renal transplant recipients are at increased risk of premature cardiovascular disease. Although statins reduce cardiovascular risk in the general population, their efficacy and safety in renal transplant recipients have not been established. We investigated the effects of fluvastatin on cardiac and renal endpoints in this population.


METHODS
We did a multicentre, randomised, double-blind, placebo-controlled trial in 2102 renal transplant recipients with total cholesterol 4.0-9.0 mmol/L. We randomly assigned patients fluvastatin (n=1050) or placebo (n=1052) and follow up was for 5-6 years. The primary endpoint was the occurrence of a major adverse cardiac event, defined as cardiac death, non-fatal myocardial infarction (MI), or coronary intervention procedure. Secondary endpoints were individual cardiac events, combined cardiac death or non-fatal MI, cerebrovascular events, non-cardiovascular death, all-cause mortality, and graft loss or doubling of serum creatinine. Analysis was by intention to treat.


FINDINGS
After a mean follow-up of 5.1 years, fluvastatin lowered LDL cholesterol concentrations by 32%. Risk reduction with fluvastatin for the primary endpoint (risk ratio 0.83 [95% CI 0.64-1.06], p=0.139) was not significant, although there were fewer cardiac deaths or non-fatal MI (70 vs 104, 0.65 [0.48-0.88] p=0.005) in the fluvastatin group than in the placebo group. Coronary intervention procedures and other secondary endpoints did not differ significantly between groups.


INTERPRETATION
Although cardiac deaths and non-fatal MI seemed to be reduced, fluvastatin did not generally reduce rates of coronary intervention procedures or mortality. Overall effects of fluvastatin were similar to those of statins in other populations.
Throughput analysis of the proportional fair scheduler in HSDPA

High speed downlink packet access (HSDPA) provides increased user data rate by introducing additional functionalities at the Node B, such as fast packet scheduling based on the instantaneous radio link quality. One of the algorithms that is able to provide this capability is the proportional fair (P-FR) scheduler. In this paper we describe an approximate analysis method for the mean throughput of the proportional fair scheduler with two traffic classes. We extend the existing results that are based on the assumption of continuous rate distributions to the more realistic discrete distributions. The analysis with discrete distributions entails two problems that do not appear in the continuous case, namely that the priority of several users can be equal with a non-zero probability and that the sample path of throughputs does not always converge to a mean throughput. The proposed approximate method is evaluated with NS2 simulations.
Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics

While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/ .
Provable defenses against adversarial examples via the convex outer adversarial polytope

We propose a method to learn deep ReLU-based classifiers that are provably robust against normbounded adversarial perturbations on the training data. For previously unseen examples, the approach is guaranteed to detect all adversarial examples, though it may flag some non-adversarial examples as well. The basic idea is to consider a convex outer approximation of the set of activations reachable through a norm-bounded perturbation, and we develop a robust optimization procedure that minimizes the worst case loss over this outer region (via a linear program). Crucially, we show that the dual problem to this linear program can be represented itself as a deep network similar to the backpropagation network, leading to very efficient optimization approaches that produce guaranteed bounds on the robust loss. The end result is that by executing a few more forward and backward passes through a slightly modified version of the original network (though possibly with much larger batch sizes), we can learn a classifier that is provably robust to any norm-bounded adversarial attack. We illustrate the approach on a number of tasks to train classifiers with robust adversarial guarantees (e.g. for MNIST, we produce a convolutional classifier that provably has less than 5.8% test error for any adversarial attack with bounded `∞ norm less than = 0.1), and code for all experiments is available at http://github.com/ locuslab/convex_adversarial. Machine Learning Department, Carnegie Mellon University, Pittsburgh PA, 15213, USA Computer Science Department, Carnegie Mellon University, Pittsburgh PA, 15213, USA. Correspondence to: Eric Wong <ericwong@cs.cmu.edu>, J. Zico Kolter <zkolter@cs.cmu.edu>. Proceedings of the 35 th International Conference on Machine Learning, Stockholm, Sweden, PMLR 80, 2018. Copyright 2018 by the author(s).
Phase Transition Temperatures and Piezoelectric Properties of (Bi1/2Na1/2)TiO3-and (Bi1/2K1/2)TiO3-Based Bismuth Perovskite Lead-Free Ferroelectric Ceramics

The phase transition temperatures and the dielectric, ferroelectric, and piezoelectric properties of bismuth perovskite lead-free ferroelectric ceramics such as (Bi<sub>1/2</sub>Na<sub>1/2</sub>)TiO<sub>3</sub> (BNT)- and (Bi<sub>1/2</sub>Na<sub>1/2</sub>)TiO<sub>3</sub> (BKT)-based solid solutions have been reviewed. According to the results obtained by our group, these ceramics can be considered as superior lead-free piezoelectric materials for reducing environmental damage. Perovskite-type ceramics appear to be suitable for actuator and high-power applications that require a large piezoelectric constant d<sub>33</sub> and a high Curie temperature T<sub>C</sub> or a high depolarization temperature T<sub>d</sub> (> 200degC). In this paper, we summarize the relationship between phase transition temperatures and piezoelectric properties. In the case of the BNT-based solid solutions, the highest piezoelectric properties were obtained at the morphotropic phase boundary (MPB) between rhombohedral and tetragonal phases. However, d<sub>33</sub> and T<sub>d</sub> were shown to have a tradeoff relationship. Considering the high T<sub>d</sub> and high d<sub>33</sub>, the tetragonal side of the MPB composition is suitable for piezoelectric actuator application. Meanwhile, the Q<sub>m</sub> values on the rhombohedral side of the MPB composition were better than those on the tetragonal side, and excellent high-power characteristics were obtained for Mn-doped BNT-(Bi<sub>1/2</sub>Na<sub>1/2</sub>)TiO<sub>3</sub>-BKT ternary systems with rhombohedral symmetry. BKT ceramics were prepared by the hot-pressing (HP) method, and their ferroelectric and piezoelectric properties were clarified. BKT ceramics doped with a small amount of Bi have a relatively high remanent polarization of P<sub>r</sub> = 27.6 muC/cm<sup>2</sup> and high piezoelectric properties (k<sub>33</sub> = 0.40 and d<sub>33</sub> = 101 pC/N). In addition, it was clarified that BKT ceramics have a high T<sub>d</sub> of approximately 300degC. The solid solution (1-x)BKT-xBaTiO<sub>3</sub> (BKT-BT100x) exhibited a high T<sub>d</sub> of approximately 300degC at x > 0.4.
Security Attack on CloudBI: Practical privacy-preserving outsourcing of biometric identification in the cloud

Recently, [2] presented a security attack on the privacy-preserving outsourcing scheme for biometric identification proposed in [1]. In [2], the author claims that the scheme CloudBI-II proposed in [1] can be broken under the collusion case. That is, when the cloud server acts as a user to submit a number of identification requests, CloudBI-II is no longer secure. In this technical report, we will explicitly show that the attack method proposed in [2] doesn’t work in fact.
A Quantitative and Qualitative Assessment of Automatic Text Summarization Systems

Text summarization is the process of automatically creating a shorter version of one or more text documents. This paper presents a qualitative and quantitative assessment of the 22 state-of-the-art extractive summarization systems using the CNN corpus, a dataset of 3,000 news articles.
Automated trace signals selection using the RTL descriptions

Pre-silicon verification has been traditionally used for eliminating design bugs before tape-out. However, due to the increasing design complexity and the limited accuracy in circuit modelling, the number of the design errors that escape to silicon continues to grow. This is aggravated by the interactions between multiple clock and power domains in the modern system-on-a-chip devices. As a result, structured methods for post-silicon debugging, which aim to detect and localize the bug escapes in silicon, have gained increasing attention in recent years. However, the existing approaches to aid post-silicon debugging primarily rely on the analysis performed using gate-level circuit descriptions. Since design entry is commonly done at the register transfer-level (RTL), the RTL information can be leveraged for the design of the on-chip debug hardware. In particular, in this paper we investigate how to automatically decide which signals to trace in real-time using the RTL information.
The Burden of Rabies in Tanzania and Its Impact on Local Communities

BACKGROUND
Rabies remains a major public health threat in many parts of the world and is responsible for an estimated 55,000 human deaths annually. The burden of rabies is estimated to be around US$20 million in Africa, with the highest financial expenditure being the cost of post-exposure prophylaxis (PEP). However, these calculations may be substantial underestimates because the costs to households of coping with endemic rabies have not been investigated. We therefore aimed to estimate the household costs, health-seeking behaviour, coping strategies, and outcomes of exposure to rabies in rural and urban communities in Tanzania.


METHODS AND FINDINGS
Extensive investigative interviews were used to estimate the incidence of human deaths and bite exposures. Questionnaires with bite victims and their families were used to investigate health-seeking behaviour and costs (medical and non-medical costs) associated with exposure to rabies. We calculated that an average patient in rural Tanzania, where most people live on less than US$1 per day, would need to spend over US$100 to complete WHO recommended PEP schedules. High costs and frequent shortages of PEP led to poor compliance with PEP regimens, delays in presentation to health facilities, and increased risk of death.


CONCLUSION
The true costs of obtaining PEP were twice as high as those previously reported from Africa and should be considered in re-evaluations of the burden of rabies.
Impairment of the atrial substrates by chronic cigarette smoking in patients with atrial fibrillation.

BACKGROUND
Smoking is a major risk factor for cardiovascular disease. The impact of smoking on the right and left atrial substrates is unknown.


METHODS
This study included 88 patients (age 50 +/- 13 years, M/F = 71/17) who underwent four pulmonary veins isolation (PVI) for paroxysmal atrial fibrillation (AF). The mean voltage and total activation time of the individual atria were obtained by using a NavX mapping system, and were compared between the patients with and without a previous smoking history. The dose effect was evaluated by the smoking intensity-duration, defined as the number of packs per day plus how many years they had been smoking.


RESULTS
The right atrial (RA) mean voltage was lower in the patients with a previous history of smoking than in those without a history of smoking (1.92 +/- 0.49 vs 2.17 +/- 0.56 mV, P < 0.05). The left atrial (LA) mean voltage was similar between the two groups (1.73 +/- 0.67 vs 1.82 +/- 0.48 mV, P = 0.488). Further, the total activation time of the RA was longer in the patients with a previous history of smoking than in those without a history of smoking, but not so for the LA. Furthermore, the voltage reduction in the RA was related to the smoking intensity-duration (Pearson's correlation, r = 0.650, P < 0.001).


CONCLUSIONS
In patients with atrial fibrillation, the RA mean voltage and total activation time were significantly correlated to smoking and had a dose-dependent effect.
Dissociation of cognitive from affective components of theory of mind in schizophrenia

Patients suffering from schizophrenia show impaired emotional and social behavior, such as misinterpretation of social situations and lack of theory of mind. However, there is conflicting evidence regarding their ability to perform on theory of mind tasks. Based on previous findings with patients suffering from prefrontal damage, the present study suggests that the behavioral deficit of schizophrenic patients may be due to impaired 'affective theory of mind' abilities, rather than to a general impairment in theory of mind. To test this hypothesis we assessed the ability of 22 schizophrenic patients and 55 age-matched healthy controls, to judge first and second order affective vs. cognitive mental state attribution, based on eye gaze. The relationships between negative and positive symptoms of schizophrenia, and affective and cognitive theory of mind were also assessed. Results indicated that while healthy controls made fewer errors on affective as compared to cognitive theory of mind conditions, schizophrenic patients showed a less prominent trend. Although the pattern of reaction time did not differ significantly between groups, the patients made significantly more errors in the affective conditions, as compared to controls. Furthermore, correlation analysis indicated that impaired affective theory of mind in these patients correlated with their level of negative symptoms. These results indicate that individuals with high level of negative symptoms of schizophrenia may demonstrate selective impairment in their ability to attribute affective mental states. These findings offer new insight into the affective facets of social behavior that may underlie the profound behavioral disturbances observed in schizophrenia.
A trial of clarithromycin for the treatment of suboptimally controlled asthma.

BACKGROUND
PCR studies have demonstrated evidence of Mycoplasma pneumoniae and Chlamydophila pneumoniae in the lower airways of patients with asthma.


OBJECTIVE
To test the hypothesis that clarithromycin would improve asthma control in individuals with mild-to-moderate persistent asthma that was not well controlled despite treatment with low-dose inhaled corticosteroids.


METHODS
Adults with an Asthma Control Questionnaire score ≥1.5 after a 4-week period of treatment with fluticasone propionate were entered into a PCR-stratified randomized, controlled trial to evaluate the effect of 16 weeks of either clarithromycin or placebo, added to fluticasone, on asthma control in individuals with or without lower airway PCR evidence of M pneumoniae or C pneumoniae.


RESULTS
A total of 92 participants were randomized. Twelve (13%) subjects demonstrated PCR evidence of M pneumoniae or C pneumoniae in endobronchial biopsies; 80 were PCR-negative for both organisms. In PCR-positive participants, clarithromycin yielded a 0.4 ± 0.4 unit improvement in the Asthma Control Questionnaire score, with a 0.1 ± 0.3 unit improvement in those allocated to placebo. This between-group difference of 0.3 ± 0.5 (P = .6) was neither clinically nor statistically significant. In PCR-negative participants, a nonsignificant between-group difference of 0.2 ± 0.2 units (P = .3) was observed. Clarithromycin did not improve lung function or airway inflammation but did improve airway hyperresponsiveness, increasing the methacholine PC(20) by 1.2 ± 0.5 doubling doses (P = .02) in the study population.


CONCLUSION
Adding clarithromycin to fluticasone in adults with mild-to-moderate persistent asthma that was suboptimally controlled by low-dose inhaled corticosteroids alone did not further improve asthma control. Although there was an improvement in airway hyperresponsiveness with clarithromycin, this benefit was not accompanied by improvements in other secondary outcomes.
Cultivating mindfulness: effects on well-being.

There has been great interest in determining if mindfulness can be cultivated and if this cultivation leads to well-being. The current study offers preliminary evidence that at least one aspect of mindfulness, measured by the Mindful Attention and Awareness Scale (MAAS; K. W. Brown & R. M. Ryan, 2003), can be cultivated and does mediate positive outcomes. Further, adherence to the practices taught during the meditation-based interventions predicted positive outcomes. College undergraduates were randomly allocated between training in two distinct meditation-based interventions, Mindfulness Based Stress Reduction (MBSR; J. Kabat-Zinn, 1990; n=15) and E. Easwaran's (1978/1991) Eight Point Program (EPP; n=14), or a waitlist control (n=15). Pretest, posttest, and 8-week follow-up data were gathered on self-report outcome measures. Compared to controls, participants in both treatment groups (n=29) demonstrated increases in mindfulness at 8-week follow-up. Further, increases in mindfulness mediated reductions in perceived stress and rumination. These results suggest that distinct meditation-based practices can increase mindfulness as measured by the MAAS, which may partly mediate benefits. Implications and future directions are discussed.