Miracle-dz/UniFAR-FTUs huggingface dataset:
SGM Special Lecture Are dental diseases examples of ecological catastrophes ?

Dental diseases are among the most prevalent and costly diseases affecting industrialized societies, and yet are highly preventable. The microflora of dental plaque biofilms from diseased sites is distinct from that found in health, although the putative pathogens can often be detected in low numbers at normal sites. In dental caries, there is a shift towards community dominance by acidogenic and acid-tolerant Gram-positive bacteria (e.g. mutans streptococci and lactobacilli) at the expense of the acid-sensitive species associated with sound enamel. In contrast, the numbers and proportions of obligately anaerobic bacteria, including Gram-negative proteolytic species, increase in periodontal diseases. Modelling studies using defined consortia of oral bacteria grown in planktonic and biofilm systems have been undertaken to identify environmental factors responsible for driving these deleterious shifts in the plaque microflora. Repeated conditions of low pH (rather than sugar availability per se) selected for mutans streptococci and lactobacilli, while the introduction of novel host proteins and glycoproteins (as occurs during the inflammatory response to plaque), and the concomitant rise in local pH, enriched for Gram-negative anaerobic and asaccharolytic species. These studies emphasized (a) significant properties of dental plaque as both a biofilm and a microbial community, and (b) the dynamic relationship existing between the environment and the composition of the oral microflora. This research resulted in a novel hypothesis (the ‘ecological plaque hypothesis’) to better describe the relationship between plaque bacteria and the host in health and disease. Implicit in this hypothesis is the concept that disease can be prevented not only by directly inhibiting the putative pathogens, but also by interfering with the environmental factors driving the selection and enrichment of these bacteria. Thus, a more holistic approach can be taken in disease control and management strategies.
Integration of new features for telerobotic surgery into the MiroSurge system

Minimally invasive robotic surgery has gained wide acceptance recently. Computer-aided features to assist the surgeon during these interventions may help to develop safer, faster, and more accurate procedures. Especially physiological motion compensation of the beating heart and online soft tissue modelling are promising features that were developed recently. This paper presents the integration of these new features into the minimally invasive robotic surgery platform MiroSurge. A central aim of this research platform is to enable evaluation and comparison of new functionalities for minimally invasive robotic surgery. The system structure of MiroSurge is presented as well as the interfaces for the new functionalities. Some details about the modules for motion tracking and for soft tissue simulation are given. Results are shown with an experimental setup that includes a heart motion simulator and dedicated silicone organ models. Both features are integrated seamlessly and work reliably in the chosen setup. The MiroSurge platform thus shows the potential to provide valuable results in evaluating new functionalities for minimally invasive robotic surgery.
Loss of FMR 2 further emphasizes the link between deregulation of immediate early response genes FOS and JUN and intellectual disability

Loss of FMR2 causes Fragile X E (FRAXE) site-associated intellectual disability (ID). FMR2 regulates transcription, promotes alternative splicing with preference for G-quartet structure harbouring exons and is localized to the nuclear speckles. In primary skin fibroblasts from FRAXE patients (n 5 8), we found a significant reduction in the number, but a significant increase in the size, of nuclear speckles, when compared with the controls (n 5 4). Since nuclear speckles are enriched with factors involved in pre-mRNA processing, we explored the consequence of these defects and the loss of FMR2 on the transcriptome. We performed whole genome expression profiling using total RNA extracted from these cell lines and found 27 genes significantly deregulated by at least 2-fold at P < 0.05 in the patients. Among these genes, FOS was significantly upregulated and was further investigated due to its established role in neuronal cell function. We showed that (i) 30% depletion of Fmr2 in mouse primary cortical neurons led to a 2-fold increase in Fos expression, (ii) overexpression of FMR2 significantly decreased FOS promoter activity in luciferase assays, and (iii) as FOS promoter contains a serum response element, we found that not FOS, but JUN, which encodes for a protein that forms a transcriptional activator complex with FOS, was significantly upregulated in the patients’ cell lines upon mitogen stimulation. These results suggest that FMR2 is an upstream regulator of FOS and JUN, and further link deregulation of the immediate early response genes to the pathology of IDand FRAXE-associated ID in particular.
Modelling inclusive special needs education: insights from Dutch secondary schools

Abstract Inclusive special needs education is prominent on the international education agenda. Research on the characteristics of inclusive education for students with special needs and schools providing this is scarce, however. Our aim in the present study was therefore to further theory-building with regard to inclusive special needs education. On the basis of the relevant literature, we identified three core aspects of inclusivity: the learning environment, the guidance provided by teachers and the general care structure. With the help of exploratory and confirmatory factor analyses conducted on data obtained from school professionals in 79 secondary schools in the Netherlands, we were able to identify 12 underlying characteristics for a conceptual framework to further research on the inclusive nature of schools and education. Multilevel structural equation modelling of the judgments of school professionals at the level of the school also showed that the inclusive special needs education in at least secondary schools can be characterised by two main factors: (1) learning environment and (2) guidance and care. The analyses showed considerable agreement on the important aspects of inclusivity for schools and thus how differences between schools can be explained. The results further showed the work of the care coordinator – which includes cooperation with external partners and teachers with mentoring roles – to be the clearest indicator of the extent of the inclusive special needs education within schools. This finding is interpreted as suggesting that the recommended teaching practices and student care for adequate included special needs education have not yet been integrated into teachers’ thinking and acting. Follow-up research drawing upon the developed framework is therefore called for to not only more generally validate the framework but also determine if the situation in school has changed, now that the policy and practices for inclusive education have become more familiar.
Observational evidence for binary black holes and active double nuclei

I review the observational evidence for the presence of supermassive binary black holes in galaxies and for the presence of active pairs of galaxies. According to hierarchical galaxy merger models, binary black holes should form frequently, and should be common in the cores of galaxies. The presence of massive black hole binaries has been invoked to explain a number of class properties of different types of galaxies, and in triggering various forms of activity. Coalescing massive black hole binaries are powerful emitters of gravitational waves. The search for such binary black holes is therefore of great interest for several topics in astrophysics ranging from galaxy formation to activity in galaxies.
Endemism, palaeoendemism and migration: the case for the ‘European endemic’, Mallomonas intermedia

ABSTRACT The Synurophyceae is a well-supported clade of ecologically important heterokont algae found largely in freshwater planktonic habitats worldwide, whose members have cell coverings consisting of species-specific siliceous scales overlapped in a highly organized manner. Many synurophytes have been described as endemic and are found only in specific regions of the world. A thriving population of the European endemic, Mallomonas intermedia, was discovered in a remote desert pond situated in the Virgin Valley, Nevada, USA and in a stratigraphic sequence from the middle Eocene fossil locality known as Horsefly in British Columbia, Canada. Both North American finds were closely compared with populations from Europe, confirming the identifications. Before these discoveries, this species was recorded from numerous waterbodies exclusively in Europe, but was lacking from hundreds of sites examined from other continents. Its presence in western North America during the warm middle Eocene confirms that historically this species had a significantly wider distribution and may be best classified as a palaeoendemic. Additional species uncovered from a second fossil locality that are closely related to M. intermedia further support the presence of this lineage in North America during the Eocene. The living population in northern Nevada presents an enigma. Does this remote desert population represent a remnant population that has gone undetected until now, or is it a recent arrival from an unknown region by an unknown vector?
UvA-DARE ( Digital Academic Repository ) Tracking moving identities : after attending the right location , the identity does not come for

Although tracking identical moving objects has been studied since the 1980’s, only recently the study into tracking moving objects with distinct identities has started (referred to as Multiple Identity Tracking, MIT). So far, only behavioral studies into MIT have been undertaken. These studies have left a fundamental question regarding MIT unanswered, is MIT a one-stage or a two-stage process? According to the one-stage model, after a location has been attended, the identity is released without effort. However, according to the two-stage model, there are two effortful stages in MIT, attending to a location, and attending to the identity of the object at that location. In the current study we investigated this question by measuring brain activity in response to tracking familiar and unfamiliar targets. Familiarity is known to automate effortful processes, so if attention to identify the object is needed, this should become easier. However, if no such attention is needed, familiarity can only affect other processes (such as memory for the target set). Our results revealed that on unfamiliar trials neural activity was higher in both attentional networks, and visual identification networks. These results suggest that familiarity in MIT automates attentional identification processes, thus suggesting that attentional identification is needed in MIT. This then would imply that MIT is essentially a two-stage process, since after attending the location, the identity does not seem to come for free. Citation: Pinto Y, Scholte HS, Lamme VAF (2012) Tracking Moving Identities: After Attending the Right Location, the Identity Does Not Come for Free. PLoS ONE 7(8): e42929. doi:10.1371/journal.pone. 0042929 Editor: Alessio Avenanti, University of Bologna, Italy Received November 22, 2011; Accepted July 15, 2012; Published August 22, 2012 Copyright: 2012 Pinto et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This research was supported by an advanced investigator grant from the European Research Council (ERC) to Dr. Lamme. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: y.pinto@uva.nl
Distress, Emotional reactivity and Fatigue following Breast Cancer : A Theoretical Approach and a Randomised Intervention Study

Background. Fatigue and emotional reactivity are common among women suffering from breast cancer and might detrimentally affect these women's quality of life. This study evaluates if the stress management delivered either in a group or individual setting would improve fatigue and emotional reactivity among women with a newly diagnosed breast cancer.Material and methods. Participants (n = 304) who reported elevated levels of distress at three-month post-inclusion were randomised between stress management in a group (GSM) (n = 77) or individual (ISM) (n = 78) setting. Participation was declined by 149 women. Participants completed the Multidimensional Fatigue Inventory (MFI-20) and the Everyday Life Stress Scale (ELSS) at the time of inclusion, 3- and 12-month post-inclusion. Analyses were made according to intention to treat and per-protocol principles. Mann-Whitney tests were used to examine differences between the two intervention groups.Results. No significant differences were detected between the GSM and ISM groups on fatigue or emotional reactivity. In addition, there were no changes over time for these outcomes.Conclusions. There were no differences between the two intervention arms with reference to fatigue or emotional reactivity; however, a clinically interesting finding was the low number of women who were interested in participating in a psychosocial intervention. This finding may have clinical implications when psychosocial support is offered to women with a newly diagnosed breast cancer and also in the planning of future studies.
Directly and E � ciently Optimizing Prediction Error and AUC of Linear Classifiers Hiva Ghanbari

The predictive quality of machine learning models is typically measured in terms of their (approximate) expected prediction error or the socalled Area Under the Curve (AUC) for a particular data distribution. However, when the models are constructed by the means of empirical risk minimization, surrogate functions such as the logistic loss are optimized instead. This is done because the empirical approximations of the expected error and AUC functions are nonconvex and nonsmooth, and more importantly have zero derivative almost everywhere. In this work, we show that in the case of linear predictors, and under the assumption that the data has normal distribution, the expected error and the expected AUC are not only smooth, but have closed form expressions, which depend on the first and second moments of the normal distribution. Hence, we derive derivatives of these two functions and use these derivatives in an optimization algorithm to directly optimize the expected error and the AUC. In the case of real data sets, the derivatives can be approximated using empirical moments. We show that even when data is not normally distributed, computed derivatives are sufficiently useful to render an efficient optimization method and high quality solutions. Thus, we propose a gradient-based optimization method for direct optimization of the prediction error and AUC. Moreover, the per-iteration complexity of the proposed algorithm has no dependence on the size of the data set, unlike those for optimizing logistic regression and all other well known empirical risk minimization problems. Lehigh University, Bethlehem, PA, USA. Correspondence to: Hiva Ghanbari <hiva.ghanbari@gmail.com>, Katya Scheinberg <katyascheinberg@gmail.com>.
Consumer Willingness To Pay A Premium For A Functional Food In Ghana 53

Interest in functional foods has been growing in sub-Saharan Africa due to consumer concerns with diet and nutrition. This paper analyses consumer awareness, perceptions and effects of the determinants of consumer willingness to pay (WTP) a premium for Moringa bread in Ghana. An ordered probit model is employed. The empirical results indicate that consumer knowledge of the nutritional and health benefits of Moringa bread is what matters most to consumers in respect of their WTP a higher premium for the product. Consumers with knowledge on Moringa products are more willing to pay above 50% price premiums for Moringa bread. Fruitful policy recommendations are made in
IMPROVING THE PERFORMANCE OF SIMILARITY JOINS USING GRAPHICS PROCESSING UNIT

IMPROVING THE PERFORMANCE OF SIMILARITY JOINS USING GRAPHICS PROCESSING UNIT Zeynep Korkmaz M.S. in Computer Engineering Supervisors: Prof. Dr. Cevdet Aykanat and Assoc. Prof. Dr. Hakan Ferhatosmanoğlu November, 2012 The similarity join is an important operation in data mining and it is used in many applications from varying domains. A similarity join operator takes one or two sets of data points and outputs pairs of points whose distances in the data space is within a certain threshold value, ε. The baseline nested loop approach computes the distances between all pairs of objects. When considering large set of objects which yield too long query time for nested loop paradigm, accelerating such operator becomes more important. The computing capability of recent GPUs with the help of a general purpose parallel computing architecture (CUDA) has attracted many researches. With this motivation, we propose two similarity join algorithms for Graphics Processing Unit (GPU). To exploit the advantages of general purpose GPU computing, we first propose an improved nested loop join algorithm (GPU-INLJ) for the specific environment of GPU. Also we present a partitioning-based join algorithm (KMEANS-JOIN) that guarantees each partition can be joined independently without missing any join pair. Our experiments demonstrate massive performance gains and the suitability of our algorithms for large datasets.
Removing Phase Transition in Distributed Spectrum Sharing Games Via Congestion Advertisement

Distributed spectrum sharing has been studied via game theoretical tools. We seek answer to the question that how long does it take to reach good equilibrium in a spectrum sharing game G. Mainly we are motivated to answer the question that given that n secondary users are located on the vertex of a general graph G, whether there exists any scheme to reach the good equilibrium in polynomial (in n) time. Answer to the problem has been provided by establishing the connections with the concepts of maximum entropy correlated equilibria (MECE) and phase transition. A MECE logit-response learning mechanism has been introduced that maps the dynamic of the game to the glauber dynamic of anti-ferromagnetic Ising models. Using this mapping it has been shown that there exists graphs that it is impossible to achieve a good equilibrium within polynomial steps for the game G. It also has been proved that there is a trade off between the capacity of graph G in providing good social welfares and fast convergence properties. It has been shown how base stations can improve the convergence rate by modifying the dynamics of the system through a spectrum congestion advertisement so that independent of the graph G it is possible to obtain the good equilibrium solution in polynomial time. The effect of congestion advertisement on dynamics of network has been verified via simulations. Appropriate advertisement leads to improved price of anarchy and faster convergence.
CARACTERIZAÇÃO SEDIMENTAR E ASSEMBLEIAS DE FORAMINÍFEROS BENTÔNICOS DA PLATAFORMA EXTERNA EQUATORIAL, ADJACENTE AO ESTADO DO RIO GRANDE DO NORTE, BRASIL

Em estudos na plataforma continental brasileira com sedimentacao mista carbonatica e siliciclastica tem se utilizado de foraminiferos como bioindicadores de produtividade carbonatica, correntes marinhas, entradas de nutrientes, e saude ambiental. O presente trabalho tem como objetivo investigar a cobertura sedimentar recente da plataforma externa equatorial do Rio Grande do Norte, entre os vales incisos Apodi-Mossoro e Piranhas-Acu, para compreender a distribuicao de nutrientes e producao carbonatica atraves de assembleias de foraminiferos. Foram utilizados metodos estatisticos para os dados bioticos, em valores quantitativos e qualitativos. Analises granulometricas, de teores de CaCO3 e de materia orgânica permitiram o reconhecimento de seis facies sedimentares. A presenca de Globigerina rubra, Quinqueloculina patagonica, e Peneroplis pertussus esta relacionada a intrusao de correntes oceânicas sobre a quebra da plataforma. Alem disso, a presenca de Buccella peruviana, se correlaciona aos altos teores de CaCO3 e materia orgânica. As especies de foraminiferos supracitadas podem indicar ocorrencia de fenomenos oceânicos como giro tropical e ressurgencia. A diversidade de organismos simbiontes e sua correlacao aos abioticos se relacionam a producao carbonatica e ao ambiente plataformal pristino.
Canagliflozin triggers the FGF 23 / 1 , 25-dihydroxyvitamin D / PTH axis in healthy volunteers in a randomized crossover study

BACKGROUND. Sodium glucose cotransporter-2 (SGLT2) inhibitors are the most recently approved class of drugs for type 2 diabetes and provide both glycemic efficacy and cardiovascular risk reduction. A number of safety issues have been identified, including treatment-emergent bone fractures. To understand the overall clinical profile, these safety issues must be balanced against an attractive efficacy profile. Our study was designed to investigate pathophysiological mechanisms mediating treatment-emergent adverse effects on bone health.
HIF-pathway proteins: central regulators of tumor immunology

Low oxygen pressure or hypoxia is often an obstacle in pathological conditions, including during cancer development and metastatic dissemination. The main family of transcription factors involved in the adaptation to inappropriate oxygen levels are the ‘Hypoxia-Inducible Factors’ (HIFs) that together with HIF prolyl hydroxylases (PHDs) regulate many different processes, during physiological as well pathological conditions. Additionally, the entire HIF transcription cascade is involved in the ‘seventh’ hallmark of cancer; tumor promoting inflammation. Previous work revealed that HIF-pathway proteins influence tumor associated immune cells in their action toward proliferation, differentiation, vessel normalization and tumor dissemination. These changes are not necessarily analogous to the role of these proteins in non-tumor related immune responses, where hypoxia often encourages a strong inflammatory response. Recently, Clever et al. demonstrated that T-cell intrinsic inhibition of all three PHDs (PHD1-3) is necessary but sufficient to limit CD4+-regulatory T (T reg ) cell induction and stimulates CD8+ T cell effector function. Interestingly, this resulted in the inhibition of local tolerance in the lung but reduced tumor colonization. In this perspective, we discuss the effect of targeting HIF-pathway proteins in tumor-associated cell lineages, their therapeutic prospective and possible pitfalls.
CMU-RI-TR-1904 Combining Neighborhood-based Heuristics : A Framework and Pilot Study on Baselines December 2018

In this paper, we propose an algorithmic framework for combining multiple neighborhood-based heuristics. An algorithm derived from this framework will function by chaining the heuristics in a pipelined fashion. Conceptually, this framework is an algorithmic template that contains two pieces of changeable components: 1) the policyH for selecting heuristics, and 2) the policy L for choosing the length of the pipeline that chains the selected heuristics. In this paper, we will rst offer a theoretical discussion on the design of the policyL , and provide empirical evidence showing the effectiveness of the derived algorithm. We will then brie y touch on the issue of designing the policyH at the end of this paper, and demonstrate a simple pruning strategy and how it can contribute positively to the performance of the algorithm.