Miracle-dz/UniFAR-FTUs huggingface dataset:
Syntactic methods for negation detection in radiology reports in Spanish

Identification of the certainty of events is an important text mining problem. In particular, biomedical texts report medical conditions or findings that might be factual, hedged or negated. Identification of negation and its scope over a term of interest determines whether a finding is reported and is a challenging task. Not much work has been performed for Spanish in this domain. In this work we introduce different algorithms developed to determine if a term of interest is under the scope of negation in radiology reports written in Spanish. The methods include syntactic techniques based in rules derived from PoS tagging patterns, constituent tree patterns and dependency tree patterns, and an adaption of NegEx, a well known rule-based negation detection algorithm (Chapman et al., 2001a). All methods outperform a simple dictionary lookup algorithm developed as baseline. NegEx and the PoS tagging pattern method obtain the best results with 0.92 F1.
Use of the magnitude invariance method for digital emulation of analog controllers

Use of digital computers for controlling physical systems has become more and more popular due to the many advantages of digital control. Because continuous time design tools are abundant and more common with many control engineers, design by emulation is often preferred over direct digital design. Unfortunately, when a controller is mapped from the s-domain to the z-domain using traditional techniques, the magnitude of the resulting discrete-time controller does not match its continuous-time counterpart. In this paper the Magnitude Invariance Method (MIM), which was recently developed in the field of signal processing, is used for digital emulation. This technique produces a discrete time transfer function with a magnitude response nearly the same as its analog prototype. The open-loop frequency and closed-loop step responses of systems designed using this approach are investigated to demonstrate the effectiveness of this approach.
Automatic Analysis of Historical Manuscripts

In this paper a document analysis tool for historical manuscripts is proposed. The goal is to automatically segment layout components of the page, that is text, pictures and decorations. We specifically focused on the pictures, proposing a set of visual features able to identify significant pictures and separating them from all the floral and abstract decorations. The analysis is performed by blocks using a limited set of color and texture features, including a new texture descriptor particularly effective for this task, namely Gradient Spatial Dependency Matrix. The feature vectors are processed by an embedding procedure which allows increased performance in later SVM classification.
STK35L1 Associates with Nuclear Actin and Regulates Cell Cycle and Migration of Endothelial Cells

Background Migration and proliferation of vascular endothelial cells are essential for repair of injured endothelium and angiogenesis. Cyclins, cyclin-dependent kinases (CDKs), and cyclin-dependent kinase inhibitors play an important role in vascular tissue injury and wound healing. Previous studies suggest a link between the cell cycle and cell migration: cells present in the G1 phase have the highest potential to migrate. The molecular mechanism linking these two processes is not understood. Methodology/Principal Findings In this study, we explored the function of STK35L1, a novel Ser/Thr kinase, localized in the nucleus and nucleolus of endothelial cells. Molecular biological analysis identified a bipartite nuclear localization signal, and nucleolar localization sequences in the N-terminal part of STK35L1. Nuclear actin was identified as a novel binding partner of STK35L1. A class III PDZ binding domains motif was identified in STK35L1 that mediated its interaction with actin. Depletion of STK35L1 by siRNA lead to an accelerated G1 to S phase transition after serum-stimulation of endothelial cells indicating an inhibitory role of the kinase in G1 to S phase progression. Cell cycle specific genes array analysis revealed that one gene was prominently downregulated (8.8 fold) in STK35L1 silenced cells: CDKN2A alpha transcript, which codes for p16INK4a leading to G1 arrest by inhibition of CDK4/6. Moreover in endothelial cells seeded on Matrigel, STK35L1 expression was rapidly upregulated, and silencing of STK35L1 drastically inhibited endothelial sprouting that is required for angiogenesis. Furthermore, STK35L1 depletion profoundly impaired endothelial cell migration in two wound healing assays. Conclusion/Significance The results indicate that by regulating CDKN2A and inhibiting G1- to S-phase transition STK35L1 may act as a central kinase linking the cell cycle and migration of endothelial cells. The interaction of STK35L1 with nuclear actin might be critical in the regulation of these fundamental endothelial functions.
Understanding academic attitudes towards the ethical challenges posed by social media research

In this paper, we outline an online survey-based study seeking to understand academic attitudes towards social media research ethics (SMRE). As the exploratory phase of a wider research project, findings are discussed in relation to the responses of 30 participants, spanning multiple faculties and locations at one international university. The paper presents an empirical measure of attitudes towards social media research ethics, reflecting core issues outlined throughout the nascent Internet-mediated research (IMR) literature, in addition to survey questions relating to familiarity with SMRE guidance, and experience of reviewing SMRE proposals from students and/or as part of the university's research ethics committees (RECs). Findings indicate notable variance in academic attitudes towards the ethical challenges of social media research, reflecting the complexity of decision-making within this context and further emphasising the need to understand influencing factors. Future directions are discussed in relation to the tentative findings presented by the current study.
Transtheoretical model of behaviour change in obese

Background.The prevalence of obesity is rapidly rising in Croatia as throughout the world. Although physiological and genetic factors may contribute, the increased trend in the prevalence of overweight has primarily been attributed to lifestyle. One theoretical framework, Prochaska and DiClemente's (1983) transtheoretical model of health-related behavior change, has been successful in changing behaviors associated with obesity. The transtheoretical model involves set of constructs: stages of change, decisional balance, self-efficacy and processes of change. Purpose. The main objectives of this study were to apply the transtheoretical model to the area of behavior change focused on weight reduction in an overweight and obese population in Croatia ; to determine relationship among the key constructs of the TTM and to determine the contribution of the processes of change, decisional balance, self-efficacy, age, and the body mass index (BMI) to the stages of change: precontemplation, contemplation, action and maintenance. Method. 294 participants took part in the study, average age 50.64 years (+13.31) and average BMI 33.44 (+ 4.20). Results and conclusions. Almost all correlation coefficients among stages of change, decisional balance, self-efficacy and processes of change are significant. Pros for behavior change is significant predictor for all stages of change and cons for precontemplation, contemplation and action, but not for maintenance stage. It is suggested that in the precontemplation stage, individuals will find more cons of the problem behavior then pros. In the action and maintenance stages, the opposite pattern will occur. Our results support partly this assumption. According to our data, experiential and behavioral processes of change were important both for earlier and latter stages of change. Self-efficacy was significant predictor only for action stage and not for maintenance stage as one could expect. Findings of the present study provide preliminary evidence of the validity of applying TTM to the area of behavior change focused on weight reduction in an overweight and obese population in Croatia. Although our results didn't completely support theory assumptions, the transtheoretical model of behavior change may be appropriate framework for health promotion programs in Croatia.
Leveraging World Knowledge in Chinese Text Classification

In state-of-the-art Text Classification (TC) approaches, only features explicitly mentioned in training set are taken into consideration, but after several decades' endeavor, it seems that these approaches have all reached a plateau. In this paper, we propose an automatic taxonomy mapping algorithm to map from original flat taxonomy to a hierarchical, human-edit on-line taxonomy (ODP), from which we could then synthesize new training samples with common-sense world knowledge by performing a constrained web focus crawling. We show that by leveraging the domain-knowledge which otherwise can't be deduced from training set directly, the text classifier will have better generalization ability. Preliminary Experimental Results on several Chinese data sets confirm the effectiveness of this approach.
Rapid 3D Human Modeling and Animation Based on Sketch and Motion Database

In this paper, a new rapid 3D human modeling and animation method based on sketch and motion database is proposed. This method reconstruct 3D human ball B-Spline model from sketch and implement real-time animation using motion database. We firstly blend all parts of sketch to obtain a new sketch which can represent human by one stroke. Then we triangulate this new sketch and select some circum circle centers of the triangles as key points. Radius information can be evaluated by the circum circle radius of relative triangles. Combine key points and radius information, ball B-Spline character model can be obtained through interpolation method. According to human body topology and skeleton structure described by BVH file in motion database, we can define all animation joint positions. Finally, we implement real time animation using motion data from database by updating control points and control radius of ball B-Spline model.
Good to see you again: engaging users in design

Designers and researchers have been involving users as part of their design processes for some time now. However, there are limited examples of user-driven innovation processes that are conducted and studied in an industrial context. In this paper we present and provide a detailed account of the design process for the Social and Spatial Interactions (SSI) platform. This research project was conducted by systematically involving end users from the very start of and throughout the design process. Some activities conducted as part of this project include a probes study, co-design workshops, and evaluations of prototypes. We describe and illustrate the individual steps of the process, as well as reflect on the overall impact and challenges of introducing and applying user-driven innovation in an industrial research context. In particular, we discuss aspects such as shifting attitudes in different phases of the user engagement, overcoming skepticism in a multidisciplinary research team, and the role and the competence of the facilitator.
Nickel on Mars: Constraints on meteoritic material at the surface

[1] Impact craters and the discovery of meteorites on Mars indicate clearly that there is meteoritic material at the Martian surface. The Alpha Particle X-ray Spectrometers (APXS) on board the Mars Exploration Rovers measure the elemental chemistry of Martian samples, enabling an assessment of the magnitude of the meteoritic contribution. Nickel, an element that is greatly enhanced in meteoritic material relative to samples of the Martian crust, is directly detected by the APXS and is observed to be geochemically mobile at the Martian surface. Correlations between nickel and other measured elements are used to constrain the quantity of meteoritic material present in Martian soil and sedimentary rock samples. Results indicate that analyzed soils samples and certain sedimentary rocks contain an average of 1% to 3% contamination from meteoritic debris.
PlagDetect: a Java programming plagiarism detection tool

Practical computing courses that involve significant amount of programming assessment tasks suffer from e-Plagiarism. A pragmatic solution for this problem could be by discouraging plagiarism particularly among the beginners in programming. One way to address this is to automate the detection of plagiarized work during the marking phase. Our research in this context involves at first examining various metrics used in plagiarism detection in program codes and secondly selecting an appropriate statistical measure using attribute counting metrics (ATMs) for detecting plagiarism in Java programming assignments. The goal of this investigation is to study the effectiveness of ATMs for detecting plagiarism among assignment submissions of introductory programming courses.
Blind separation of ballistocardiogram from EEG via short-and-long-term linear prediction filtering

In this paper the problem of removing ballistocardiogram (BCG) artifact from EEG signals is addressed. This kind of artifact appears in simultaneous EEG-fMRI recordings. We propose a new Blind source extraction method based on linear prediction technique. The proposed method is a joint short-and-long-term prediction (SLTP) strategy to extract the BCG sources. The main reason of using this technique is to jointly model the temporal structure (short-term prediction) of sources and exploiting the prior information of BCG sources (long-term prediction). The results of extensive experiments on both synthetic and real data confirm the strength of the proposed technique to effectively remove the BCG artifact.
Knockdown of BACE1-AS Nonprotein-Coding Transcript Modulates Beta-Amyloid-Related Hippocampal Neurogenesis

Background. Alzheimer's disease (AD) is a devastating neurological disorder and the main cause of dementia in the elderly population worldwide. Adult neurogenesis appears to be upregulated very early in AD pathogenesis in response to some specific aggregates of beta-amyloid (Aβ) peptides, exhausting the neuronal stem cell pools in the brain. Previously, we characterized a conserved nonprotein-coding antisense transcript for β-secretase-1 (BACE1), a critical enzyme in AD pathophysiology. We showed that the BACE1-antisense transcript (BACE1-AS) is markedly upregulated in brain samples from AD patients and promotes the stability of the (sense) BACE1 transcript. In the current paper, we examine the relationship between BACE1, BACE1-AS, adult neurogenesis markers, and amyloid plaque formation in amyloid precursor protein (APP) transgenic mice (Tg-19959) of various ages. Results. Consistent with previous publications in other APP overexpressing mouse models, we found adult neurogenesis markers to be noticeably upregulated in Tg-19959 mice very early in the development of the disease. Knockdown of either one of BACE1 or BACE1-AS transcripts by continuous infusion of locked nucleic acid- (LNA-) modified siRNAs into the third ventricle over the period of two weeks caused concordant downregulation of both transcripts in Tg-19959 mice. Downregulation of BACE1 mRNA was followed by reduction of BACE1 protein and insoluble Aβ. Modulation of BACE1 and BACE1-AS transcripts also altered oligomeric Aβ aggregation pattern, which was in turn associated with an increase in neurogenesis markers at the RNA and protein level. Conclusion. We found alterations in the RNA and protein concentrations of several adult neurogenesis markers, as well as non-protein-coding BACE1-AS transcripts, in parallel with the course of β-amyloid synthesis and aggregation in the brain of Tg15999 mice. In addition, by knocking down BACE1 or BACE1-AS (thereby reducing Aβ production and plaque deposition), we were able to modulate expression of these neurogenesis markers. Our findings suggest a distortion of adult neurogenesis that is associated with Aβ production very early in amyloid pathogenesis. We believe that these alterations, at the molecular level, could prove useful as novel therapeutic targets and/or as early biomarkers of AD.
Dietary patterns and the risk of CVD and all-cause mortality in older British men

Abstract Dietary patterns are a major risk factor for cardiovascular morbidity and mortality; however, few studies have examined this relationship in older adults. We examined prospective associations between dietary patterns and the risk of CVD and all-cause mortality in 3226 older British men, aged 60–79 years and free from CVD at baseline, from the British Regional Heart Study. Baseline FFQ data were used to generate thirty-four food groups. Principal component analysis identified dietary patterns that were categorised into quartiles, with higher quartiles representing higher adherence to the dietary pattern. Cox proportional hazards examined associations between dietary patterns and risk of all-cause mortality and cardiovascular outcomes. We identified three interpretable dietary patterns: ‘high fat/low fibre’ (high in red meat, meat products, white bread, fried potato, eggs), ‘prudent’ (high in poultry, fish, fruits, vegetables, legumes, pasta, rice, wholemeal bread, eggs, olive oil) and ‘high sugar’ (high in biscuits, puddings, chocolates, sweets, sweet spreads, breakfast cereals). During 11 years of follow-up, 899 deaths, 316 CVD-related deaths, 569 CVD events and 301 CHD events occurred. The ‘high-fat/low-fibre’ dietary pattern was associated with an increased risk of all-cause mortality only, after adjustment for confounders (highest v. lowest quartile; hazard ratio 1·44; 95 % CI 1·13, 1·84). Adherence to a ‘high-sugar’ diet was associated with a borderline significant trend for an increased risk of CVD and CHD events. The ‘prudent’ diet did not show a significant trend with cardiovascular outcomes or mortality. Avoiding ‘high-fat/low-fibre’ and ‘high-sugar’ dietary components may reduce the risk of cardiovascular events and all-cause mortality in older adults.
Gene expression profiling differentiates autism case–controls and phenotypic variants of autism spectrum disorders: evidence for circadian rhythm dysfunction in severe autism

Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by delayed/abnormal language development, deficits in social interaction, repetitive behaviors and restricted interests. The heterogeneity in clinical presentation of ASD, likely due to different etiologies, complicates genetic/biological analyses of these disorders. DNA microarray analyses were conducted on 116 lymphoblastoid cell lines (LCL) from individuals with idiopathic autism who are divided into three phenotypic subgroups according to severity scores from the commonly used Autism Diagnostic Interview‐Revised questionnaire and age‐matched, nonautistic controls. Statistical analyses of gene expression data from control LCL against that of LCL from ASD probands identify genes for which expression levels are either quantitatively or qualitatively associated with phenotypic severity. Comparison of the significant differentially expressed genes from each subgroup relative to the control group reveals differentially expressed genes unique to each subgroup as well as genes in common across subgroups. Among the findings unique to the most severely affected ASD group are 15 genes that regulate circadian rhythm, which has been shown to have multiple effects on neurological as well as metabolic functions commonly dysregulated in autism. Among the genes common to all three subgroups of ASD are 20 novel genes mostly in putative noncoding regions, which appear to associate with androgen sensitivity and which may underlie the strong 4:1 bias toward affected males.
Adaptive detection of multiple point-like targets with conic acceptance

In this paper we consider the problem of detecting multiple point-like targets in the presence of steering vector mismatches and Gaussian disturbance with unknown covariance matrix. To this end, we first model the actual useful signal as a vector belonging to a proper cone whose axis coincides with the whitened direction of the nominal array response. Then we develop two new robust adaptive detectors resorting to the two-step generalized-likelihood ratio test (GLRT) design procedure without assignment of a distinct set of secondary data. Finally, a performance assessment, conducted by Monte Carlo simulation, show that the proposed detectors achieve a visible performance improvement over their natural counterparts.
Quality of door sounds of passenger cars

It is reported that the sound of a car door closing is one of the main factors to determine the overall impression of the car. Much effort has been made to improve the quality of this sound. In this study, sounds of the closing of the doors of various passenger cars were recorded and presented via headphones in a sound-proof room. Based on these sounds, German and Japanese groups of participants formed mental images of the cars involved. They were also asked to evaluate the quality of the sounds. Generally speaking, though there were some differences, similar results were obtained with both groups of participants. It was found that the impressions of the sound quality varied considerably and that there was a correlation between the impression of the sound and the mental image of the car. It was suggested that the image of a car is related to the sound of the car.
γ‐Secretase Dependent Nuclear Targeting of Dystroglycan

Dystroglycan is frequently lost in adenocarcinoma. α‐dystroglycan is known to become hypoglycosylated due to transcriptional silencing of LARGE, whereas β‐dystroglycan is proteolytically cleaved and degraded. The mechanism and proteases involved in the cleavage events affecting β‐dystroglycan are poorly understood. Using LNCaP prostate cancer cells as a model system, we have investigated proteases and tyrosine phosphorylation affecting β‐dystroglycan proteolysis and nuclear targeting. Cell density or phorbol ester treatment increases dystroglycan proteolysis, whereas furin or γ‐secretase inhibitors decreased dystroglycan proteolysis. Using resveratrol treatment of LNCaP cells cultured at low cell density in order to up‐regulate notch and activate proteolysis, we identified significant increases in the levels of a 26 kDa β‐dystroglycan fragment. These data, therefore, support a cell density‐dependent γ‐secretase and furin mediated proteolysis of β‐dystroglycan, which could be notch stimulated, leading to nuclear targeting and subsequent degradation. 117: 2149–2157, 2016. © 2016 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.