LLukas22/scidocs huggingface dataset:
Determining the sequence of history

VOLUME 2 | DECEMBER 2004 | 1 Sex-determination mechanisms are famous for their extraordinary diversity and the sequencing revolution promises to untangle the evolutionary events that have fashioned them. Joseph Heitman and colleagues do just this in a recent paper that describes the evolutionary history of the mating-type (MAT) locus of a human fungal pathogen, Cryptococcus neoformans. They also uncover some intriguing parallels between the C. neoformans MAT locus and the human Y chromosome. In fungi, sex only occurs between compatible cell-mating types. Unusually, the C. neoformans MAT locus resembles that of both the Ascomycotina group of fungi — to which Saccharomyces cerevisiae belongs — and members of its own group, the Basidiomycotina. Like S. cerevisiae, C. neoformans has a bipolar mating system with a single MAT locus that contains two alleles, a and α. However, this locus is larger than that of S. cerevisiae and contains gene types that resemble the two unlinked sex-determination loci of some tetrapolar Basidiomycotina fungi. To explore how a complex sex-determining region evolved from simpler loci, the researchers compared the sequences of the MAT loci of two variants of C. neoformans and a sibling species, Cryptococcus gattii. Based on the number of synonymous mutations that have accumulated over time, the researchers found that the genes within the C. neoformans MAT locus could be classified as ‘ancient’, ‘intermediate’ or ‘recent’, according to when they were acquired by the MAT locus during evolution. They suggest that the ancient class represents the two ancestral unlinked sex determination regions — one containing pheromone and pheromone-receptor genes and one containing homeodomain genes. They hypothesize that the pheromone locus expanded to acquire other ancient components of the pheromone-signalling cascade together with some intermediate genes, and that the homeodomain locus acquired other intermediate genes thought to function during meiosis. In one of the two mating types, chromosomal translocation then fused the pheromone and homeodomain clusters together, entrapping the recent category of genes. The resulting tripolar mating system — consisting of the pheromone cluster, the homeodomain cluster and the fused cluster — then collapsed by gene conversion into the bipolar system we see in C. neoformans today. Not only does the C. neoformans MAT locus resemble other fungal sex-determination loci, but Heitman and colleagues also provide tantalizing evidence that it has similar features to the sex chromosomes of animals and plants. Curiously, the human Y chromosome also has four temporal clusters that represent the sequential acquisition of genes. The authors draw on this and other intriguing similarities — such as the palindromic orientation of the pheromone genes – and discuss the future of C. neoformans as a model for understanding sex-chromosome dynamics. Jenny Bangham, Assistant Editor, Nature Reviews
Towards Interpretable Deep Neural Networks by Leveraging Adversarial Examples

Introduction Sometimes it is not enough for a DNN to produce an outcome. For example, in applications such as healthcare, users need to understand the rationale of the decisions. Therefore, it is imperative to develop algorithms to learn models with good interpretability (Doshi-Velez 2017). An important factor that leads to the lack of interpretability of DNNs is the ambiguity of neurons, where a neuron may fire for various unrelated concepts. This work aims to increase the interpretability of DNNs on the whole image space by reducing the ambiguity of neurons. In this paper, we make the following contributions:
Clobetasol propionate, 0.05%, vs hydrocortisone, 1%, for alopecia areata in children: a randomized clinical trial.

IMPORTANCE
Alopecia areata is an idiopathic cause of hair loss with limited therapeutic repertoire.


OBJECTIVE
To compare the efficacy and safety of a high- vs low-potency topical corticosteroid in pediatric patients.


DESIGN, SETTING, AND PARTICIPANTS
This single-center, randomized, blind, 2-arm, parallel-group, superiority trial was carried out over a 24-week period at a tertiary referral academic dermatology clinic at The Hospital for Sick Children in Toronto, Ontario, Canada. Forty-two children attending the outpatients clinic, 2 to 16 years of age with alopecia areata affecting at least 10% of scalp surface area, were eligible; 1 declined to participate. There were no withdrawals from the study. INTERVENTIONS FOR CLINICAL TRIALS: Patients were randomly assigned to receive clobetasol propionate, 0.05% cream, or hydrocortisone, 1%, cream. Patients applied a thin layer of the assigned cream twice daily to the areas of hair loss for 2 cycles of 6 weeks on, 6 weeks off, for a total of 24 weeks.


MAIN OUTCOMES AND MEASURES
The primary outcome was the change in scalp surface area with hair loss over 24 weeks following enrollment. RESULTS All participants were assessed at 6, 12, 18, and 24 weeks (except 1 participant who missed the 6-week visit). After adjusting for baseline hair loss, the clobetasol group had a statistically significant (P < .001) greater decrease in the surface area with hair loss, compared with the hydrocortisone group at all time points except at 6 weeks. One patient with extensive alopecia areata experienced skin atrophy that resolved spontaneously in 6 weeks. There was no difference observed in the number of patients with abnormal urinary cortisol at the beginning and the end of the study.


CONCLUSIONS AND RELEVANCE
Topical clobetasol propionate, 0.05%, cream is efficacious and safe as a first-line agent for limited patchy childhood alopecia areata. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01453686.
Effect of five genetic variants associated with lung function on the risk of chronic obstructive lung disease, and their joint effects on lung function.

RATIONALE
Genomic loci are associated with FEV1 or the ratio of FEV1 to FVC in population samples, but their association with chronic obstructive pulmonary disease (COPD) has not yet been proven, nor have their combined effects on lung function and COPD been studied.


OBJECTIVES
To test association with COPD of variants at five loci (TNS1, GSTCD, HTR4, AGER, and THSD4) and to evaluate joint effects on lung function and COPD of these single-nucleotide polymorphisms (SNPs), and variants at the previously reported locus near HHIP.


METHODS
By sampling from 12 population-based studies (n = 31,422), we obtained genotype data on 3,284 COPD case subjects and 17,538 control subjects for sentinel SNPs in TNS1, GSTCD, HTR4, AGER, and THSD4. In 24,648 individuals (including 2,890 COPD case subjects and 13,862 control subjects), we additionally obtained genotypes for rs12504628 near HHIP. Each allele associated with lung function decline at these six SNPs contributed to a risk score. We studied the association of the risk score to lung function and COPD.


MEASUREMENTS AND MAIN RESULTS
Association with COPD was significant for three loci (TNS1, GSTCD, and HTR4) and the previously reported HHIP locus, and suggestive and directionally consistent for AGER and TSHD4. Compared with the baseline group (7 risk alleles), carrying 10-12 risk alleles was associated with a reduction in FEV1 (β = -72.21 ml, P = 3.90 × 10(-4)) and FEV1/FVC (β = -1.53%, P = 6.35 × 10(-6)), and with COPD (odds ratio = 1.63, P = 1.46 × 10(-5)).


CONCLUSIONS
Variants in TNS1, GSTCD, and HTR4 are associated with COPD. Our highest risk score category was associated with a 1.6-fold higher COPD risk than the population average score.
A third‐generation wave model for coastal regions: 1. Model description and validation

A third-generation numerical wave model to compute random, short-crested waves in coastal regions with shallow water and ambient currents (Simulating Waves Nearshore (SWAN)) has been developed, implemented, and validated. The model is based on a Eulerian formulation of the discrete spectral balance of action density that accounts for refractive propagation over arbitrary bathymetry and current fields. It is driven by boundary conditions and local winds. As in other third-generation wave models, the processes of wind generation, whitecapping, quadruplet wave-wave interactions, and bottom dissipation are represented explicitly. In SWAN, triad wave-wave interactions and depth-induced wave breaking are added. In contrast to other third-generation wave models, the numerical propagation scheme is implicit, which implies that the computations are more economic in shallow water. The model results agree well with analytical solutions, laboratory observations, and (generalized) field observations.
Detection of driver's drowsiness by means of HRV analysis

It is estimated that 10–30% of road fatalities are related to drowsy driving or driver fatigue. Driver's drowsiness detection based on biological and vehicle signals is being studied in preventive car safety. Autonomous Nervous System (ANS) activity, which can be measured non-invasively from the Heart Rate Variability (HRV) signal obtained from surface ECG, presents alterations during stress, ex-trem fatigue and drowsiness episodes. Our hypothesis is that these alterations manifest on HRV. In this work we de-velope an on-line detector of driver's drowsiness based on HRV analysis. Two databases have been analyzed: one of driving simulation in which subjects were sleep deprived, and the other of real situation with no sleep deprivation. An external observer annotated each minute of the recordings as drowsy or awake, and constitutes our reference. The proposed detector classified drowsy minutes with a sensitivity of 0.85 and a predictive positive value of 0.93, using 25 features.
A systematic literature review to identify and classify software requirement errors

Most software quality research has focused on identifying faults (i.e., information is incorrectly recorded in an artifact). Because software still exhibits incorrect behavior, a different approach is needed. This paper presents a systematic literature review to develop taxonomy of errors (i.e., the sources of faults) that may occur during the requirements phase of software lifecycle. This taxonomy is designed to aid developers during the requirement inspection process and to improve overall software quality. The review identified 149 papers from the software engineering, psychology and human cognition literature that provide information about the sources of requirements faults. A major result of this paper is a categorization of the sources of faults into a formal taxonomy that provides a starting point for future research into error-based approaches to improving software quality. 2009 Elsevier B.V. All rights reserved.
Left ventricular remodeling after acute myocardial infarction: the influence of viability and revascularization - an echocardiographic substudy of the VIAMI-trial

BACKGROUND
Viability seems to be important in preventing ventricular remodeling after acute myocardial infarction (AMI). We investigated the influence of viability, as demonstrated with low-dose dobutamine echocardiography, and the role of early revascularization on the process of left ventricular (LV) remodeling after AMI.


METHODS
We retrospectively investigated 224 patients who were initially included in the viability-guided angioplasty after acute myocardial infarction-trial (VIAMI-trial). Patients in the VIAMI-trial did not undergo a primary or rescue percutaneous coronary intervention and were stable in the early in-hospital phase. Patients underwent viability testing within 72 hours after AMI. Patients with viability were randomized to an invasive strategy or an ischemia-guided strategy. Follow-up echocardiography was performed at a mean of 205 days. In this echocardiographic substudy, patients were divided into three new groups: group 1, viable and revascularized before follow-up echocardiogram; group 2, viable, but medically treated; and group 3, non-viable patients.


RESULTS
Group 1 showed preservation of LV volume indices. The ejection fraction (EF) increased significantly from 54.0% to 57.5% (P = 0.047). Group 2 showed a significant increase in LV volume indices with no improvement in EF (53.3% versus 53.0%, P = 0.86). Group 3 showed a significant increase in LV volume indices, with a decrease in EF from 53.5% to 49.1% (P = 0.043). Multivariate logistic regression analysis indicated the number of viable segments and revascularization during follow-up as independent predictors for EF improvement, especially in patients with lower EF at baseline.


CONCLUSION
Viability early after AMI is associated with improvement in LV function after revascularization. When viable myocardium is not revascularized, the LV tends to remodel with increased LV volumes, without improvement of EF. Absence of viability results in ventricular dilatation and deterioration of EF, irrespective of revascularization status.


TRIAL REGISTRATION
NCT00149591 (assigned: 6 September 2005).
Foot Placement and Arm Position Affect the Five Times Sit-to-Stand Test Time of Individuals with Chronic Stroke

OBJECTIVES
To investigate the effect of two foot placements (normal or posterior placement) and three arm positions (hands on the thighs, arms crossed over chest, and augmented arm position with elbow extended) on the five times sit-to-stand (FTSTS) test times of individuals with chronic stroke.


DESIGN
Cross-sectional study. Setting. University-based rehabilitation clinic.


PARTICIPANTS
A convenience sample of community-dwelling individuals with chronic stroke (N = 45).


METHODS
The times in completing the FTSTS with two foot placements and the three arm positions were recorded by stopwatch.


RESULTS
Posterior foot placement led to significantly shorter FTSTS times when compared with normal foot placement in all the 3 arm positions (P ≤ 0.001). In addition, hands on thigh position led to significantly longer FTSTS times than the augmented arm position (P = 0.014).


CONCLUSION
Our results showed that foot placement and arm position could influence the FTSTS times of individuals with chronic stroke. Standardizing the foot placement and arm position in the test procedure is essential, if FTSTS test is intended to be used repeatedly on the same subject.
Twitter sentiment analysis using hybrid cuckoo search method

Sentiment analysis is one of the prominent fields of data mining that deals with the identification and analysis of sentimental contents generally available at social media. Twitter is one of such social medias used by many users about some topics in the form of tweets. These tweets can be analyzed to find the viewpoints and sentiments of the users by using clustering-based methods. However, due to the subjective nature of the Twitter datasets, metaheuristic-based clustering methods outperforms the traditional methods for sentiment analysis. Therefore, this paper proposes a novel metaheuristic method (CSK) which is based on K-means and cuckoo search. The proposed method has been used to find the optimum cluster-heads from the sentimental contents of Twitter dataset. The efficacy of proposed method has been tested on different Twitter datasets and compared with particle swarm optimization, differential evolution, cuckoo search, improved cuckoo search, gauss-based cuckoo search, and two n-grams methods. Experimental results and statistical analysis validate that the proposed method outperforms the existing methods. The proposed method has theoretical implications for the future research to analyze the data generated through social networks/medias. This method has also very generalized practical implications for designing a system that can provide conclusive reviews on any social issues. © 2017 Elsevier Ltd. All rights reserved.
TASK PERFORMANCE, PERCEIVED COMPETENCE, AND ATTRIBUTED CAUSES OF PERFORMANCE AS DETERMINANTS OF INTRINSIC MOTIVATION

Volunteer subjects engaged in a task that was highly intrinsically motivating under three conditions: no pay, fixed reward, and performance-contingent reward. Results indicated that extrinsic rewar...
The Tradeoffs Between Open and Traditional Relation Extraction

Traditional Information Extraction (IE) takes a relation name and hand-tagged examples of that relation as input. Open IE is a relationindependent extraction paradigm that is tailored to massive and heterogeneous corpora such as the Web. An Open IE system extracts a diverse set of relational tuples from text without any relation-specific input. How is Open IE possible? We analyze a sample of English sentences to demonstrate that numerous relationships are expressed using a compact set of relation-independent lexico-syntactic patterns, which can be learned by an Open IE system. What are the tradeoffs between Open IE and traditional IE? We consider this question in the context of two tasks. First, when the number of relations is massive, and the relations themselves are not pre-specified, we argue that Open IE is necessary. We then present a new model for Open IE called O-CRF and show that it achieves increased precision and nearly double the recall than the model employed by TEXTRUNNER, the previous stateof-the-art Open IE system. Second, when the number of target relations is small, and their names are known in advance, we show that O-CRF is able to match the precision of a traditional extraction system, though at substantially lower recall. Finally, we show how to combine the two types of systems into a hybrid that achieves higher precision than a traditional extractor, with comparable recall.
Automated electronic reminders to facilitate primary cardiovascular disease prevention: randomised controlled trial.

BACKGROUND
Primary care databases contain cardiovascular disease risk factor data, but practical tools are required to improve identification of at-risk patients.


AIM
To test the effects of a system of electronic reminders (the 'e-Nudge') on cardiovascular events and the adequacy of data for cardiovascular risk estimation.


DESIGN OF STUDY
Randomised controlled trial.


SETTING
Nineteen general practices in the West Midlands, UK.


METHOD
The e-Nudge identifies four groups of patients aged over 50 years on the basis of estimated cardiovascular risk and adequacy of risk factor data in general practice computers. Screen messages highlight individuals at raised risk and prompt users to complete risk profiles where necessary. The proportion of the study population in the four groups was measured, as well as the rate of cardiovascular events in each arm after 2 years.


RESULTS
Over 38 000 patients' electronic records were randomised. The intervention led to an increase in the proportion of patients with sufficient data who were identifiably at risk, with a difference of 1.94% compared to the control group (95% confidence interval [CI] = 1.38 to 2.50, P<0.001). A corresponding reduction occurred in the proportion potentially at risk but requiring further data for a risk estimation (difference = -3.68%, 95% CI = -4.53 to -2.84, P<0.001). No significant difference was observed in the incidence of cardiovascular events (rate ratio = 0.96, 95% CI = 0.85 to 1.10, P = 0.59).


CONCLUSION
Automated electronic reminders using routinely collected primary care data can improve the adequacy of cardiovascular risk factor information during everyday practice and increase the visibility of the at-risk population.
Effects of Video Game Training on Behavioral and Electrophysiological Measures of Attention and Memory: Protocol for a Randomized Controlled Trial

BACKGROUND
Neuroplasticity-based approaches seem to offer promising ways of maintaining cognitive health in older adults and postponing the onset of cognitive decline symptoms. Although previous research suggests that training can produce transfer effects, this study was designed to overcome some limitations of previous studies by incorporating an active control group and the assessment of training expectations.


OBJECTIVE
The main objectives of this study are (1) to evaluate the effects of a randomized computer-based intervention consisting of training older adults with nonaction video games on brain and cognitive functions that decline with age, including attention and spatial working memory, using behavioral measures and electrophysiological recordings (event-related potentials [ERPs]) just after training and after a 6-month no-contact period; (2) to explore whether motivation, engagement, or expectations might account for possible training-related improvements; and (3) to examine whether inflammatory mechanisms assessed with noninvasive measurement of C-reactive protein in saliva impair cognitive training-induced effects. A better understanding of these mechanisms could elucidate pathways that could be targeted in the future by either behavioral or neuropsychological interventions.


METHODS
A single-blinded randomized controlled trial with an experimental group and an active control group, pretest, posttest, and 6-month follow-up repeated measures design is used in this study. A total of 75 cognitively healthy older adults were randomly distributed into experimental and active control groups. Participants in the experimental group received 16 1-hour training sessions with cognitive nonaction video games selected from Lumosity, a commercial brain training package. The active control group received the same number of training sessions with The Sims and SimCity, a simulation strategy game.


RESULTS
We have recruited participants, have conducted the training protocol and pretest assessments, and are currently conducting posttest evaluations. The study will conclude in the first semester of 2017. Data analysis will take place during 2017. The primary outcome is transfer of benefit from training to attention and working memory functions and the neural mechanisms underlying possible cognitive improvements.


CONCLUSIONS
We expect that mental stimulation with video games will improve attention and memory both at the behavioral level and in ERP components promoting brain and mental health and extending independence among elderly people by avoiding the negative personal and economic consequences of long-term care.


TRIAL REGISTRATION
Clinicaltrials.gov NCT02796508; https://clinicaltrials.gov/ct2/show/NCT02796508 (archived by WebCite at http://www.webcitation.org/6nFeKeFNB).
Ecological environment protection,prevention and treatment of the mine

The mining may lead to ecological damage,based on the related laws and regulations,and introduced mining environmental protection and pollution control in protection,prevention and treatment.The paper proposed some new ideas in land reclamation,and landscape reconstruction.
Investigation arabic speech recognition using CMU sphinx system

In this paper, Arabic was investigated from the speech recognition problem point of view. We propose a novel approach to build an Arabic automated speech recognition system using Arabic environment. The system, based on the open source CMU Sphinx-4, was trained using Arabic characters.
Global sourcing decisions and firm productivity: evidence from Spain

We investigate the link between productivity of firms and their sourcing behavior. Following Antràs & Helpman (2004) we distinguish between domestic and foreign sourcing, as well as between outsourcing and vertical integration. A firm’s choice is driven by a hold-up problem caused by lack of enforceable contracts. We use Spanish firm-level data to examine the productivity premia associated with the different sourcing strategies. We find strong empirical support for the predictions of the model. JEL-Code: F14, F23, L22, L23.