bluuebunny/crossref_metadata_2025 huggingface dataset:
Combinatorial Loss of the Enzymatic Activities of Viral Uracil-DNA Glycosylase and Viral dUTPase Impairs Murine Gammaherpesvirus Pathogenesis and Leads to Increased Recombination-Based Deletion in the Viral Genome
Authors: Dong Qiwen , Smith Kyle R. , Oldenburg Darby G. , Shapiro Maxwell , Schutt William R. , Malik Laraib , Plummer Joshua B. , Mu Yunxiang , MacCarthy Thomas , White Douglas W. , McBride Kevin M. , Krug Laurie T.
Published: October 2018

Unrepaired uracils in DNA can lead to mutations and compromise genomic stability. Herpesviruses have hijacked host processes of DNA repair and nucleotide metabolism by encoding a viral UNG that excises uracils and a viral dUTPase that initiates conversion of dUTP to dTTP. To better understand the impact of these processes on gammaherpesvirus pathogenesis, we examined the separate and collaborative roles of vUNG and vDUT upon MHV68 infection of mice. Simultaneous disruption of the enzymatic activities of both vUNG and vDUT led to a severe defect in acute replication and establishment of latency, while also revealing a novel, combinatorial function in promoting viral genomic stability. We propose that herpesviruses require these enzymatic processes to protect the viral genome from damage, possibly triggered by misincorporated uracil. This reveals a novel point of therapeutic intervention to potentially block viral replication and reduce the fitness of multiple herpesviruses.
Helicobacter pylori Biofilm Involves a Multigene Stress-Biased Response, Including a Structural Role for Flagella
Authors: Hathroubi Skander , Zerebinski Julia , Ottemann Karen M.
Published: October 2018

Biofilms, communities of bacteria that are embedded in a hydrated matrix of extracellular polymeric substances, pose a substantial health risk and are key contributors to many chronic and recurrent infections. Chronicity and recalcitrant infections are also common features associated with the ulcer-causing human pathogen
H. pylori
. However, relatively little is known about the role of biofilms in
H. pylori
pathogenesis, as well as the biofilm structure itself and the genes associated with this mode of growth. In the present study, we found that
H. pylori
biofilm cells highly expressed genes related to cell envelope and stress response, as well as those encoding the flagellar apparatus. Flagellar filaments were seen in high abundance in the biofilm. Flagella are known to play a role in initial biofilm formation, but typically are downregulated after that state.
H. pylori
instead appears to have coopted these structures for nonmotility roles, including a role building a robust biofilm.
Gene Essentiality Analyzed by
In Vivo
Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of
Candida albicans
Authors: Segal Ella Shtifman , Gritsenko Vladimir , Levitan Anton , Yadav Bhawna , Dror Naama , Steenwyk Jacob L. , Silberberg Yael , Mielich Kevin , Rokas Antonis , Gow Neil A. R. , Kunze Reinhard , Sharan Roded , Berman Judith
Published: October 2018

Comprehensive understanding of an organism requires that we understand the contributions of most, if not all, of its genes. Classical genetic approaches to this issue have involved systematic deletion of each gene in the genome, with comprehensive sets of mutants available only for very-well-studied model organisms. We took a different approach, harnessing the power of
in vivo
transposition coupled with deep sequencing to identify >500,000 different mutations, one per cell, in the prevalent human fungal pathogen
Candida albicans
and to map their positions across the genome. The transposition approach is efficient and less labor-intensive than classic approaches. Here, we describe the production and analysis (aided by machine learning) of a large collection of mutants and the comprehensive identification of 1,610 
C. albicans
genes that are essential for growth under standard laboratory conditions. Among these
C. albicans
essential genes, we identify those that are also essential in two distantly related model yeasts as well as those that are conserved in all four major human fungal pathogens and that are not conserved in the human genome. This list of genes with functions important for the survival of the pathogen provides a good starting point for the development of new antifungal drugs, which are greatly needed because of the emergence of fungal pathogens with elevated resistance and/or tolerance of the currently limited set of available antifungal drugs.
Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status
Authors: Ren Lili , Zhang Rongbao , Rao Jian , Xiao Yan , Zhang Zhao , Yang Bin , Cao Depan , Zhong Hui , Ning Pu , Shang Ying , Li Mingkun , Gao Zhancheng , Wang Jianwei
Published: October 2018

Recent studies of the microbiome proposed that resident microbes play a beneficial role in maintaining human health. Although lower respiratory tract disease is a leading cause of sickness and mortality, how the lung microbiome interacts with human health remains largely unknown. Here we assessed the association between the lung microbiome and host gene expression, cytokine concentration, and over 20 clinical features. Intriguingly, we found a stratified structure of the active lung microbiome which was significantly associated with bacterial biomass, lymphocyte proportion, human Th17 immune response, and COPD exacerbation frequency. These observations suggest that the microbiome plays a significant role in lung homeostasis. Not only microbial composition but also active functional elements and host immunity characteristics differed among different individuals. Such diversity may partially account for the variation in susceptibility to particular diseases.
Rare extraspinal cause of acute lumbar radiculopathy
Authors: Tieppo Francio Vinicius , Barndt Brandon , Schappell Justin B , Allen Travis , Towery Chris , Davani Saeid
Published: October 2018

A 60-year-old man presented to an outpatient pain management clinic with antalgic gait and left lower extremity (LLE) radiculopathy from an unknown aetiology. A lumbar MRI revealed minimal disc protrusion at L3 and a partially visualised left-sided kidney abnormality. Abdominal and pelvic CT demonstrated severe hydronephrosis of the left kidney compressing the left psoas major. The patient was immediately referred to an outside hospital for nephrology workup, and following nephrostomy tube, his radicular pain resolved. He remained asymptomatic at 4 weeks follow-up. We found two cases of postsurgical, retroperitoneal fluid collection that caused lumbar radiculopathy, but none associated with hydronephrosis. To our knowledge, this is the first case in the literature to report hydronephrosis as the potential aetiology of lumbar radiculopathy, which highlights an important clinical reminder: to consider extraspinal aetiologies in all patients who present with lumbar radiculopathy, when clinical symptoms, examination findings and diagnostic studies present with unusual characteristics.
Acute cholecystitis and gallbladder perforation leading to massive haemoperitoneum in a patient taking rivaroxaban
Authors: Kwok Allan , Chern Tien Yew , Winn Robert
Published: October 2018

We present the case of an 80-year old man taking rivaroxaban for atrial fibrillation who sustained massive intra-abdominal bleeding in the setting of acute cholecystitis. CT scan on admission revealed evidence of active bleeding into the gallbladder lumen and gallbladder perforation. Immediate resuscitation was commenced with intravenous fluids, antibiotics and blood products. Despite attempts to correct coagulopathy, the patient’s haemodynamic status deteriorated and an emergency laparotomy was performed, with open cholecystectomy, washout and haemostasis. The patient had a largely uneventful recovery and was discharged on day 11 of admission. Patients with coagulopathies, whether pharmacological or due to underlying disease processes, are at very high risk of severe haemorrhagic complications and subsequent morbidity. As such, prompt recognition and operative management of haemorrhagic perforated cholecystitis is of crucial importance.
Two-year effectiveness of a stepped-care depression prevention intervention and predictors of incident depression in primary care patients with diabetes type 2 and/or coronary heart disease and subthreshold depression: data from the Step-Dep cluster randomised controlled trial
Authors: Pols Alide Danielle , Adriaanse Marcel C , van Tulder Maurits W , Heymans Martijn W , Bosmans Judith E , van Dijk Susan E , van Marwijk Harm W J
Published: October 2018

Introduction

Major depressive disorders (MDD), diabetes mellitus type 2 (DM2) and coronary heart disease (CHD) are leading contributors to the global burden of disease and often co-occur.

Objectives

To evaluate the 2-year effectiveness of a stepped-care intervention to prevent MDD compared with usual care and to develop a prediction model for incident depression in patients with DM2 and/or CHD with subthreshold depression.

Methods

Data of 236 Dutch primary care patients with DM2/CHD with subthreshold depression (Patient Health Questionnaire 9 (PHQ-9) score ≥6, no current MDD according to the Mini International Neuropsychiatric Interview (Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria)) who participated in the Step-Dep trial were used. A PHQ-9 score of ≥10 at minimally one measurement during follow-up (at 3, 6, 9, 12 and 24 months) was used to determine the cumulative incidence of MDD. Potential demographic and psychological predictors were measured at baseline via web-based self-reported questionnaires and evaluated using a multivariable logistic regression model. Model performance was assessed with the Hosmer-Lemeshow test, Nagelkerke’s R2explained variance and area under the receiver operating characteristic curve (AUC). Bootstrapping techniques were used to internally validate our model.

Results

192 patients (81%) were available at 2-year follow-up. The cumulative incidence of MDD was 97/192 (51%). There was no statistically significant overall treatment effect over 24 months of the intervention (OR 1.37; 95% CI 0.52 to 3.55). Baseline levels of anxiety, depression, the presence of >3 chronic diseases and stressful life events predicted the incidence of MDD (AUC 0.80, IQR 0.79–0.80; Nagelkerke’s R20.34, IQR 0.33–0.36).

Conclusion

A model with 4 factors predicted depression incidence during 2-year follow-up in patients with DM2/CHD accurately, based on the AUC. The Step-Dep intervention did not influence the incidence of MDD. Future depression prevention programmes should target patients with these 4 predictors present, and aim to reduce both anxiety and depressive symptoms.

Trial registration number

NTR3715.
Remediating doctors’ performance to restore patient safety: a realist review protocol
Authors: Price Tristan , Brennan Nicola , Cleland Jennifer , Prescott-Clements Linda , Wanner Amanda , Withers Lyndsey , Wong Geoff , Archer Julian
Published: October 2018

Introduction

Underperformance by doctors poses a risk to patient safety. Remediation is an intervention designed to remedy underperformance and return a doctor to safe practice. Remediation is widely used across healthcare systems globally, and has clear implications for both patient safety and doctor retention. Yet, there is a poor evidence base to inform remediation programmes. In particular, there is a lack of understanding as to why and how a remedial intervention may work to change a doctor’s practice. The aim of this research is to identify why, how, in what contexts, for whom and to what extent remediation programmes for practising doctors work to support patient safety.

Methods and analysis

Realist review is an approach to evidence synthesis that seeks to develop programme theories about how an intervention works to produce its effects. The initial search strategy will involve: database and grey literature searching, citation searching and contacting authors. The evidence search will be extended as the review progresses and becomes more focused on the development of specific aspects of the programme theory. The development of the programme theory will involve input from a stakeholder group consisting of professional experts in the remediation process and patient representatives. Evidence synthesis will use a realist logic of analysis to interrogate data in order to develop and refine the initial programme theory into a more definitive realist programme theory of how remediation works. The study will follow and be reported according to Realist And Meta-narrative Evidence Syntheses—Evolving Standards (RAMESES).

Ethics and dissemination

Ethical approval is not required. Our dissemination strategy will include input from our stakeholder group. Customised outputs will be developed using the knowledge-to-action cycle framework, and will be targeted to: policy-makers; education providers and regulators, the National Health Service, doctors and academics.

PROSPERO registration number

CRD42018088779.
Woman with recurrent vomiting
Authors: Liu Ying-Kuo , Kuo Chun-Lin , Hsu Chin-Wang
Published: October 2018

Clinical introduction

A 69-year-old woman presented to the ED with a chief complaint of recurrent vomiting for 3 weeks. She was afebrile, blood pressure was 100/67 mm Hg, HR was 114/min, RR was 19/min and oxygen saturation was 98%. On physical examination, she had mild epigastric tenderness without guarding. Blood tests were normal except for hyponatraemia of 128 mmol/L and hypokalaemia of 2.7 mmol/L. The ECG demonstrated sinus tachycardia with first-degree atrioventricular block. Chest radiograph posteroanterior view (CXR) was performed (figure 1).

Figure 1

Chest radiograph posteroanterior view. The patient presented to the ED with a complaint of recurrent vomiting for 3 weeks.

Question

Due to continuous vomiting of this patient, which of the following is the most appropriate management?

Abdominal ultrasonography.

Chest and abdominal CT.

Barium swallow.

Oesophagogastroduodenoscopy (EGD).

For answer see page 02

For question see page 01
Evidence-based out-of-hours hospital medicine
Authors: McKenzie Gordon Arthur George
Published: October 2018

Out-of-hours (OOH) hospital ward cover is generally provided by junior doctors and is typified by heavy workloads, reduced staff numbers and various non-urgent nurse-initiated requests. The present inefficiencies and management problems with the OOH service are reflected by the high number of quality improvement projects recently published. In this narrative review, five common situations peculiar to the OOH general ward setting are discussed with reference to potential areas of inefficiency and unnecessary management steps: (1) prescription of hypnotics and sedatives; (2) overnight fluid therapy; (3) fever; (4) overnight hypotension and (5) chasing outstanding routine diagnostic tests. It is evident that research and consensus guidelines for many clinical situations in the OOH setting are a neglected arena. Many recommendations made herein are based on expert opinion or first principles. In contrast, the management of significant abnormalities in outstanding blood results is based on well-established guidelines using high-quality systematic reviews.
Transcriptome profiling of rice roots in early response toBacillussubtilis(RR4) colonization
Authors: Rekha Kandaswamy , Kumar Ramasamy Mohan , Ilango K. , Rex Arunraj , Usha Balasundaram
Published: October 2018

Bacillus subtilis, a gram-positive soil bacterium, is widely used as a plant-growth-promoting agent. However, how Bacillus initially colonizes rice roots and evades the plant primary defense mechanisms, and how it influences root secretion of phytochemicals for further colonization remain obscure. To get an insight into how a plant perceives the bacterium upon initial root colonization, a microarray analysis was performed using rice roots treated with a rice rhizosphere isolate, B. subtilis RR4. About 891 transcripts (255 up-regulated and 636 down-regulated) were differentially expressed, indicating that the bacteria reprogram the plant to colonize it. In our experiments, RR4 mainly caused the suppression of transcripts encoding defense response enzymes such as chitinase, cell-wall-modifying enzymes such as pectinesterase, and genes associated with transport/exudation of phytochemicals, signifying that the bacteria modulate the gene expression of the plant to facilitate its colonization. Genes that regulate secondary metabolite production were up-regulated. Although the defense response genes in rice roots were suppressed initially, they were induced gradually at 4 and 10 days post-treatment. This was accompanied by an increased level of salicylic acid in the colonized rice roots. Thus, our results show that B. subtilis alters the transcriptome of rice roots for initial colonization by initially lowering the plants’ defenses, limiting root exudation and active cell growth, but boosting the plants’ defenses at a later stage.
An analysis of spotting distances during the 2017 fire season in the Northern Rockies, USA
Authors: Page Wesley G. , Wagenbrenner Natalie S. , Butler Bret W. , Blunck David L.
Published: October 2018

The wildfires that burned in the Northern Rockies region of the USA during the 2017 fire season provided an opportunity to evaluate the suitability of using broadscale and temporally limited infrared data on hot spot locations to determine the influence of several environmental variables on spotting distance. Specifically, correlations between the maximum observed spot fire distance for each unique combination of fire and day and geo-referenced environmental data on wind speed, vegetation, and terrain, along with specific fire characteristics (size, fire perimeter shape, and growth), were assessed. The data were also utilized to evaluate a popular theoretical model developed by Albini (1979) for predicting the maximum spotting distance for single and group tree torching. The results suggested a significant positive correlation between the maximum observed spot fire distance and an interaction between fire growth and wind speed. Significant negative correlations between maximum spotting distance and fire perimeter shape, canopy height, and terrain steepness were also discovered. The evaluation of Albini’s (1979) model suggested that selecting a high estimate of potential wind speed was important to minimize the likelihood of underpredicting maximum spotting distance.
Coulomb scattering in the massless Nelson model II. Regularity of ground states
Authors: Dybalski Wojciech , Pizzo Alessandro
Published: October 2018

For the massless Nelson model, we provide detailed information about the dependence of the normalized ground states [Formula: see text] of the fiber single-electron Hamiltonians [Formula: see text] on the total momentum [Formula: see text] and the infrared cut-off [Formula: see text]. This information is obtained with the help of the iterative analytic perturbation theory. In particular, we derive bounds of the form [Formula: see text] for some constant [Formula: see text] and a function of the maximal admissible coupling constant [Formula: see text] such that [Formula: see text]. These results hold both in the infrared-regular and infrared-singular cases. They are exploited in part I of this series to construct the two-electron scattering states in the infrared-regular massless Nelson model (in the absence of an infrared cut-off) along the lines of the Haag–Ruelle scattering theory. They should also be relevant to the problem of scattering of two infraparticles in the infrared-singular Nelson model, whose solution is the goal of this series of papers. Although a part of a larger investigation, the present work is written in a self-contained fashion.
Assessment of Statistically Significant Command-Following in Pediatric Patients with Disorders of Consciousness, Based on Visual, Auditory and Tactile Event-Related Potentials
Authors: Dovgialo Marian , Chabuda Anna , Duszyk Anna , Zieleniewska Magdalena , Pietrzak Marcin , Różański Piotr , Durka Piotr
Published: October 2018

Disorders of consciousness (DOC) are among the major challenges of contemporary medicine, mostly due to the high rates of misdiagnoses in clinical assessment, based on behavioral scales. This turns our attention to potentially objective neuroimaging methods. Paradigms based on electroencephalography (EEG) are most suited for bedside applications, but sensitive to artifacts. These problems are especially pronounced in pediatric patients.

We present the first study on the assessment of pediatric DOC patients by means of command-following procedures and involving long-latency cognitive event-related potentials. To deal with the above mentioned challenges, we construct a specialized signal processing scheme including artifact correction and rejection, parametrization, classification and final assessment of the statistical significance. To compensate for the possible bias of the tests involved in the final diagnosis, we propose the Monte Carlo evaluation of the processing pipeline. To compensate for possible sensory impairments of DOC patients, for each subject we check command-following responses to the stimuli in the major modalities: visual, tactile, and audio (words and sounds).

We test the scheme on 20 healthy volunteers and present results for 15 patients from a hospital for children with severe brain damage, in relation to their behavioral diagnosis on the Coma Recovery Scale-Revised (CRS-R).
Parametric Description of EEG Profiles for Assessment of Sleep Architecture in Disorders of Consciousness
Authors: Zieleniewska Magdalena , Duszyk Anna , Różański Piotr , Pietrzak Marcin , Bogotko Marta , Durka Piotr
Published: October 2018

We propose a fully parametric approach to the assessment of sleep architecture, based upon the classical electroencephalographic criteria, applicable also to the recordings of patients with disorders of consciousness (DOC). Sleep spindles and slow waves are automatically detected from the matching pursuit decomposition of overnight EEG recordings. Their evolution can be presented in the form of EEG profiles, yielding a continuous description of sleep architecture, compatible with the classical criteria used in sleep staging. We propose assessment of these EEG profiles by five parameters, which can be combined by a linear classifier, assessing the quality of sleep architecture. Proposed methodology is evaluated on 59 overnight EEG recordings from 19 patients from a hospital for children with severe brain damage, in relation to their behavioral diagnosis according to the Coma Recovery Scale-Revised. Presented results indicate robustness of the proposed approach, which may serve as a valuable aid in diagnosis of DOC patients. Complete software environment for computing and presentation of EEG profiles is freely available from http://svarog.pl .
Temporal Modulation of Steady-State Visual Evoked Potentials
Authors: Labecki Maciej , Nowicka Maria Malgorzata , Suffczynski Piotr
Published: October 2018

Electroencephalographic responses to periodic stimulation are termed steady-state visual evoked potentials (SSVEP). Their characteristics in terms of amplitude, frequency and phase are commonly assumed to be stationary. In this work, we tested this assumption in 30 healthy participants submitted to 50 trials of 60[Formula: see text]s flicker stimulation at 15[Formula: see text]Hz frequency. We showed that the amplitude of the first and second harmonic frequency components of SSVEP signals were in general not stable over time. The power (squared amplitude) of the fundamental component was stationary only in 30% the subjects, while the power at the second harmonic frequency was stationary in 66.7% of the group. The phases of both SSVEP frequency components were more stable over time, but could exhibit small drifts. The observed temporal changes were heterogeneous across the subjects, implying that averaging results over participants should be performed carefully. These results may contribute to improved design and analysis of experiments employing prolonged visual stimulation. Our findings offer a novel characterization of the temporal changes of SSVEP that may help to identify their physiological basis.
An ENOB Evaluation Method for an Acquisition Channel
Authors: Liu Xin , Liu Yan , Dong Zengshou
Published: October 2018

Three-parameter and four-parameter sine-wave fitting algorithms are powerful tools for estimating the parameters of the excited single-tone sine-wave for ADC. In the dynamic performance testing processes of instruments, the angle frequency, amplitude, phase and dc component of the input sine-wave are all unknown, so the fitting procedure is nonlinear. This paper proposes and analyzes a test method based on iteration Interpolated Discrete Fourier Transform (IpDFT) and sine-wave fitting method for evaluating the effective number of bit (ENOB) of the acquisition channel. Mathematical expressions of the Least-square fitting residual error and the proposed ENOB evaluation based on iteration IpDFT method are derived. These expressions are then particularized for acquisition circuit output noise composed of single-tone and additive white noise. Simulation results show that the DFT-based golden section searching algorithm (DGSSA) is an effective algorithm under coherent and non-coherent sampling conditions. The accuracy of the derived expressions and estimated parameters are verified through both the computer simulations and experimental results.
Investigation of the elastic and inelastic scattering of 3He from 9Be in the energy range 30–60MeV
Authors: Janseitov D. M. , Lukyanov S. M. , Mendibayev K. , Penionzhkevich Yu. E. , Skobelev N. K. , Sobolev Yu. G. , Kuterbekov K. A. , Valiolda D. S. , Zholdybayev T. K. , Trzaska W. H. , Khlebnikov S. V. , Tyurin G. P. , Urazbekov B. A. , Harakeh M. N. , Burjan V. , Kroha V. , Mrazek J. , Piskoř Š. , Sivaček I. , Glagolev V.
Published: October 2018

We have measured the differential cross-sections for the elastic as well as inelastic scattering populating the 2.43[Formula: see text]MeV [Formula: see text] excited state in [Formula: see text] using [Formula: see text] beams at energies of 30, 40 and 47[Formula: see text]MeV on a [Formula: see text] target. The experimental results for the elastic scattering were analyzed within the framework of the optical model using the Woods–Saxon and double-folding potentials. The theoretical calculations for the concerned excited states were performed using the coupled-channel method. The optimal deformation parameters for the excited states of [Formula: see text] nucleus were extracted.
X-CLE
a
VER
Authors: Lucchese Claudio , Nardini Franco Maria , Orlando Salvatore , Perego Raffaele , Silvestri Fabrizio , Trani Salvatore
Published: October 2018

Learning-to-Rank (LtR) solutions are commonly used in large-scale information retrieval systems such as Web search engines, which have to return highly relevant documents in response to user query within fractions of seconds. The most effective LtR algorithms adopt a gradient boosting approach to build additive ensembles of weighted regression trees. Since the required ranking effectiveness is achieved with very large ensembles, the impact on response time and query throughput of these solutions is not negligible. In this article, we propose X-CLE
a
VER, an iterative meta-algorithm able to build more efficient and effective ranking ensembles. X-CLE
a
VER interleaves the iterations of a given gradient boosting learning algorithm with pruning and re-weighting phases. First, redundant trees are removed from the given ensemble, then the weights of the remaining trees are fine-tuned by optimizing the desired ranking quality metric. We propose and analyze several pruning strategies and we assess their benefits showing that interleaving pruning and re-weighting phases during learning is more effective than applying a single post-learning optimization step. Experiments conducted using two publicly available LtR datasets show that X-CLE
a
VER can be successfully exploited on top of several LtR algorithms as it is effective in optimizing the effectiveness of the learnt ensembles, thus obtaining more compact forests that hence are much more efficient at scoring time.
An Efficient Alternating Newton Method for Learning Factorization Machines
Authors: Chin Wei-Sheng , Yuan Bo-Wen , Yang Meng-Yuan , Lin Chih-Jen
Published: October 2018

To date, factorization machines (FMs) have emerged as a powerful model in many applications. In this work, we study the training of FM with the logistic loss for binary classification, which is a nonlinear extension of the linear model with the logistic loss (i.e., logistic regression). For the training of large-scale logistic regression, Newton methods have been shown to be an effective approach, but it is difficult to apply such methods to FM because of the nonconvexity. We consider a modification of FM that is multiblock convex and propose an alternating minimization algorithm based on Newton methods. Some novel optimization techniques are introduced to reduce the running time. Our experiments demonstrate that the proposed algorithm is more efficient than stochastic gradient algorithms and coordinate descent methods. The parallelism of our method is also investigated for the acceleration in multithreading environments.
Characterizing User Skills from Application Usage Traces with Hierarchical Attention Recurrent Networks
Authors: Yang Longqi , Fang Chen , Jin Hailin , Hoffman Matthew D. , Estrin Deborah
Published: October 2018

Predicting users’ proficiencies is a critical component of AI-powered personal assistants. This article introduces a novel approach for the prediction based on users’ diverse, noisy, and passively generated application usage histories. We propose a novel bi-directional recurrent neural network with hierarchical attention mechanism to extract sequential patterns and distinguish informative traces from noise. Our model is able to attend to the most discriminative actions and sessions to make more accurate and directly interpretable predictions while requiring 50× less training data than the state-of-the-art sequential learning approach. We evaluate our model with two large scale datasets collected from 68K Photoshop users: a digital design skill dataset where the user skill is determined by the quality of the end products and a software skill dataset where users self-disclose their software usage skill levels. The empirical results demonstrate our model’s superior performance compared to existing user representation learning techniques that leverage action frequencies and sequential patterns. In addition, we qualitatively illustrate the model’s significant interpretative power. The proposed approach is broadly relevant to applications that generate user time-series analytics.
Evaluation-as-a-Service for the Computational Sciences
Authors: Hopfgartner Frank , Hanbury Allan , Müller Henning , Eggel Ivan , Balog Krisztian , Brodt Torben , Cormack Gordon V. , Lin Jimmy , Kalpathy-Cramer Jayashree , Kando Noriko , Kato Makoto P. , Krithara Anastasia , Gollub Tim , Potthast Martin , Viegas Evelyne , Mercer Simon
Published: October 2018

Evaluation in empirical computer science is essential to show progress and assess technologies developed. Several research domains such as information retrieval have long relied on systematic evaluation to measure progress: here, the Cranfield paradigm of creating shared test collections, defining search tasks, and collecting ground truth for these tasks has persisted up until now. In recent years, however, several new challenges have emerged that do not fit this paradigm very well: extremely large data sets, confidential data sets as found in the medical domain, and rapidly changing data sets as often encountered in industry. Crowdsourcing has also changed the way in which industry approaches problem-solving with companies now organizing challenges and handing out monetary awards to incentivize people to work on their challenges, particularly in the field of machine learning.

This article is based on discussions at a workshop on Evaluation-as-a-Service (EaaS). EaaS is the paradigm of not providing data sets to participants and have them work on the data locally, but keeping the data central and allowing access via Application Programming Interfaces (API), Virtual Machines (VM), or other possibilities to ship executables. The objectives of this article are to summarize and compare the current approaches and consolidate the experiences of these approaches to outline the next steps of EaaS, particularly toward sustainable research infrastructures.

The article summarizes several existing approaches to EaaS and analyzes their usage scenarios and also the advantages and disadvantages. The many factors influencing EaaS are summarized, and the environment in terms of motivations for the various stakeholders, from funding agencies to challenge organizers, researchers and participants, to industry interested in supplying real-world problems for which they require solutions.

EaaS solves many problems of the current research environment, where data sets are often not accessible to many researchers. Executables of published tools are equally often not available making the reproducibility of results impossible. EaaS, however, creates reusable/citable data sets as well as available executables. Many challenges remain, but such a framework for research can also foster more collaboration between researchers, potentially increasing the speed of obtaining research results.
Anserini
Authors: Yang Peilin , Fang Hui , Lin Jimmy
Published: October 2018

This work tackles the perennial problem of reproducible baselines in information retrieval research, focusing on bag-of-words ranking models. Although academic information retrieval researchers have a long history of building and sharing systems, they are primarily designed to facilitate the publication of research papers. As such, these systems are often incomplete, inflexible, poorly documented, difficult to use, and slow, particularly in the context of modern web-scale collections. Furthermore, the growing complexity of modern software ecosystems and the resource constraints most academic research groups operate under make maintaining open-source systems a constant struggle. However, except for a small number of companies (mostly commercial web search engines) that deploy custom infrastructure, Lucene has become the
de facto
platform in industry for building search applications. Lucene has an active developer base, a large audience of users, and diverse capabilities to work with heterogeneous collections at scale. However, it lacks systematic support for
ad hoc
experimentation using standard test collections. We describe Anserini, an information retrieval toolkit built on Lucene that fills this gap. Our goal is to simplify
ad hoc
experimentation and allow researchers to easily reproduce results with modern bag-of-words ranking models on diverse test collections. With Anserini, we demonstrate that Lucene provides a suitable framework for supporting information retrieval research. Experiments show that our system efficiently indexes large web collections, provides modern ranking models that are on par with research implementations in terms of effectiveness, and supports low-latency query evaluation to facilitate rapid experimentation
Invasive Cereal Aphids of North America: Ecology and Pest Management
Authors: Brewer Michael J. , Peairs Frank B. , Elliott Norman C.
Published: October 2018

Aphid invasions of North American cereal crops generally have started with colonization of a new region or crop, followed by range expansion and outbreaks that vary in frequency and scale owing to geographically variable influences. To improve understanding of this process and management, we compare the invasion ecology of and management response to three cereal aphids: sugarcane aphid, Russian wheat aphid, and greenbug. The region exploited is determined primarily by climate and host plant availability. Once an area is permanently or annually colonized, outbreak intensity is also affected by natural enemies and managed inputs, such as aphid-resistant cultivars and insecticides. Over time, increases in natural enemy abundance and diversity, improved compatibility among management tactics, and limited threshold-based insecticide use have likely increased resilience of aphid regulation. Application of pest management foundational practices followed by a focus on compatible strategies are relevant worldwide. Area-wide pest management is most appropriate to large-scale cereal production systems, as exemplified in the Great Plains of North America.
Statistical Damage Constitutive Model for Cemented Sand considering the Residual Strength and Initial Compaction Phase
Authors: Tan Cai , Yuan Ming-dao , Shi Yong-sheng , Zhou Bing-sheng , Li Hao
Published: October 2018

Based on continuum damage mechanics and the assumption of volume invariance, a damage constitutive model of cemented sand under triaxial stress was established while considering residual strength. Statistical theory was then introduced into this model. Assuming that the microunit strength of cemented sand obeys a Weibull random distribution, an expression of microunit strength based on the Mohr–Coulomb criterion was derived. Additionally, a damage evolution equation and a statistical damage constitutive model of cemented sand under triaxial stress were established. In order to consider the nonlinear deformation and volume change in the initial pore compaction stage, the critical point reflecting the completion of the initial compaction stage was determined. This was done by applying the volume invariance assumption to the linear portion of the stress and strain curve and performing a coordinate transformation. The nonlinearity of the initial compaction stage was fitted by a quadratic function. A triaxial compression test of cemented sand was then carried out to verify this proposed method. The results show that the calculated values by the damage constitutive model fit well with the actual experimental values and that the calculated results can reflect the stress softening, residual strength, and initial compaction characteristics of cemented sand, which shows the rationality and feasibility of the model.
Clinical Manifestation, Dermoscopy, and Scanning Electron Microscopy in Two Cases of Contagious Ecthyma (Orf Nodule)
Authors: Rezende Ana Laura Rosifini Alves , Bernardes Filho Fred , de Paula Natália Aparecida , Towersey Loan , Hay Roderick , Frade Marco Andrey Cipriani
Published: October 2018

Orf is a highly contagious skin disease commonly seen in goats and sheep that can be transmitted to people who have direct contact with infected animals. Here, we report the clinical manifestation, dermoscopy, and scanning electron microscopy in two women who developed skin lesions on their hands after handling goats with wounds in the udders. Human orf is usually self-limiting and no specific treatment is needed.
An Improved Fuzzy Connectedness Method for Automatic Three-Dimensional Liver Vessel Segmentation in CT Images
Authors: Zhang Rui , Zhou Zhuhuang , Wu Weiwei , Lin Chung-Chih , Tsui Po-Hsiang , Wu Shuicai
Published: October 2018

In this paper, an improved fuzzy connectedness (FC) method was proposed for automatic three-dimensional (3D) liver vessel segmentation in computed tomography (CT) images. The vessel-enhanced image (i.e., vesselness image) was incorporated into the fuzzy affinity function of FC, rather than the intensity image used by traditional FC. An improved vesselness filter was proposed by incorporating adaptive sigmoid filtering and a background-suppressing item. The fuzzy scene of FC was automatically initialized by using the Otsu segmentation algorithm and one single seed generated adaptively, while traditional FC required multiple seeds. The improved FC method was evaluated on 40 cases of clinical CT volumetric images from the 3Dircadb (n=20) and Sliver07 (n=20) datasets. Experimental results showed that the proposed liver vessel segmentation strategy could achieve better segmentation performance than traditional FC, region growing, and threshold level set. Average accuracy, sensitivity, specificity, and Dice coefficient of the improved FC method were, respectively, (96.4 ± 1.1)%, (73.7 ± 7.6)%, (97.4 ± 1.3)%, and (67.3 ± 5.7)% for the 3Dircadb dataset and (96.8 ± 0.6)%, (89.1 ± 6.8)%, (97.6 ± 1.1)%, and (71.4 ± 7.6)% for the Sliver07 dataset. It was concluded that the improved FC may be used as a new method for automatic 3D segmentation of liver vessel from CT images.
Study on Catastrophe Theory of Activation‐Induced Prominence of Faults under Dynamic Disturbance
Authors: Zuo Yujun , Wang Hao , Yu Meilu , Dou Xiaoxiao , Wu Zhonghu , Wang Jian
Published: October 2018

In view of the phenomena of coal and gas outburst induced by fault activation under dynamic disturbance, a mechanical model of faults and surrounding rock mechanics was established based on the theory of fold catastrophe. Moreover, the dynamic disturbance factors were introduced and analyzed to analyze the influencing factors of outburst coal rock outburst. Through theoretical analysis, it shows that the thinner the fault medium is, the more energy the external input is required for system instability, and the external energy can reflect the stability of the system. When the width of fault media is fixed, the stronger the mining disturbance, the less energy the external input is required for system instability; on the contrary, the weaker the mining disturbance is, the more energy the external input is required for system instability. In addition, through the equation of conservation of kinetic energy, it can be seen that the stronger the mining disturbance, the greater the critical value of the surrounding rock thickness. The paper introduces the dynamic disturbance parameters through the catastrophe theory and analyzes the influence of the existence of faults on coal and gas outburst in detail, which provides a new theoretical basis for the prediction and prevention of coal and gas outburst disasters.
A Fuzzy Co-Clustering Algorithm via Modularity Maximization
Authors: Liu Yongli , Chen Jingli , Chao Hao
Published: October 2018

In this paper we propose a fuzzy co-clustering algorithm via modularity maximization, named MMFCC. In its objective function, we use the modularity measure as the criterion for co-clustering object-feature matrices. After converting into a constrained optimization problem, it is solved by an iterative alternative optimization procedure via modularity maximization. This algorithm offers some advantages such as directly producing a block diagonal matrix and interpretable description of resulting co-clusters, automatically determining the appropriate number of final co-clusters. The experimental studies on several benchmark datasets demonstrate that this algorithm can yield higher quality co-clusters than such competitors as some fuzzy co-clustering algorithms and crisp block-diagonal co-clustering algorithms, in terms of accuracy.
Extended Poroelasticity: An Analytical Solution and Its Application to p-Wave Propagation in Cervical Tissues
Authors: Palma Roberto , Callejas Antonio M.
Published: October 2018

This work presents a semianalytical solution based on Laplace transform to study the behaviour of poroelastic materials in the context of the Extended Nonequilibrium Thermodynamics. In this framework, the fluid phase incorporates a relaxation time and, consequently, a frequency-dependence appears. This rheological behaviour could explain the frequency-dependence experimentally observed in biological tissues, which has traditionally attributed to the solid phase of tissues. In particular, the analytical solution is applied to two cases, heaviside and sinusoidal inputs, of a semi-infinite domain, which is filled with a material such as the human cervix. From the results, it is observed that the frequency-dependence of the fluid phase could be relevant to high relaxation times while for null relaxation times the classical poroelastic theory is recovered. Finally, the present analytical solution could be used to validate future computational codes and experimental settings.
3D Instantaneous Reconstruction of Turbulent Industrial Flames Using Computed Tomography of Chemiluminescence (CTC)
Authors: Unterberger A. , Röder M. , Giese A. , Al-Halbouni A. , Kempf A. , Mohri K.
Published: October 2018

Computed Tomography of Chemiluminescence (CTC) was used to reconstruct the instantaneous three-dimensional (3D) chemiluminescence field of a high-power industrial flame, which was made optically accessible, for the first time. The reconstruction used 24 projections that were measured simultaneously, in one plane and equiangularly spaced within a total fan angle of 172.5°. The 3D results were examined by plotting both vertical and horizontal slices, revealing highly wrinkled structures with good clarity. The results presented are one of a series of experimental demonstrations of CTC applications to turbulent gaseous flames. The work reveals the potential to use any kind of luminescence measurement, such as emission from heated particles in coal-fired flames, for analysis of the flame shape directly in 3D.
Gluten-Free Snacks Based on Brown Rice and Amaranth Flour with Incorporation of Cactus Pear Peel Powder: Physical, Nutritional, and Sensorial Properties
Authors: Miranda Dayanne Vigo , Rojas Meliza Lindsay , Pagador Sandra , Lescano Leslie , Sanchez-Gonzalez Jesús , Linares Guillermo
Published: October 2018

An agroindustrial by-product (cactus pear peel) and whole grains flour (brown rice and amaranth) were used to present a gluten-free snack proposal. The effect of 5% (F1), 7% (F2), and 10% (F3) substitution of brown-rice flour for yellow cactus pear peel powder (Opuntia ficus-indica) on the snack physical, sensorial, and nutritional properties was evaluated. In addition, 20% of amaranth flour (Amaranthus caudatus) was used for all formulations. As the percentage of substitution increased, the a⁎ value increased, while the L⁎ decreased. The control snacks presented higher hardness, while the snacks with 10% substitution presented a greater crispness. The sensorial properties (overall liking, colour, crispness, and oiliness) reported that the samples containing cactus pear peel powder were the most accepted. The fat content decreased as the substitution percentage increased. The F3 formulation presented the best physical and sensorial properties and when compared with other commercial snack brands, it presented low fat and an adequate protein and fibre content. Therefore, snacks based on brown rice, amaranth, and cactus pear by-product could be considered as a good option of gluten-free product, contributing to reducing the lack of gluten-free products on the markets.
Facial Pain Expression Recognition in Real-Time Videos
Authors: Dutta Pranti , M Nachamai
Published: October 2018

Recognition of pain in patients who are incapable of expressing themselves allows for several possibilities of improved diagnosis and treatment. Despite the advancements that have already been made in this field, research is still lacking with respect to the detection of pain in live videos, especially under unfavourable conditions. To address this gap in existing research, the current study proposed a hybrid model that allowed for efficient pain recognition. The hybrid, which consisted of a combination of the Constrained Local Model (CLM), Active Appearance Model (AAM), and Patch-Based Model, was applied in conjunction with image algebra. This contributed to a system that enabled the successful detection of pain from a live stream, even with poor lighting and a low-resolution recording device. The final process and output allowed for memory for storage that was reduced up to 40%–55% and an improved processing time of 20%–25%. The experimental system met with success and was able to detect pain for the 22 analysed videos with an accuracy of 55.75%–100.00%. To increase the fidelity of the proposed technique, the hybrid model was tested on UNBC‐McMaster Shoulder Pain Database as well.