Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of N-linked Glycoform Profiles of Monoclonal Antibody with Extracellular Metabolites and Two-Step Intracellular Models

Monoclonal antibodies (mAbs) are commonly glycosylated and show varying levels of galactose attachment. A set of experiments in our work showed that the galactosylation level of mAbs was altered by the culture conditions of hybridoma cells. The uridine diphosphate galactose (UDP-Gal) is one of the substrates of galactosylation. Based on that, we proposed a two-step model to predict N-linked glycoform profiles by solely using extracellular metabolites from cell culture. At the first step, the flux level of UDP-Gal in each culture was estimated based on a computational flux balance analysis (FBA); its level was found to be linear with the galactosylation degree on mAbs. At the second step, the glycoform profiles especially for G0F (agalactosylated), G1F (monogalactosylated) and G2F (digalactosylated) were predicted by a kinetic model. The model outputs well matched with the experimental data. Our study demonstrated that the integrated mathematical approach combining FBA and kinetic model is a promising strategy to predict glycoform profiles for mAbs during cell culture processes.
Re: Turning the gaze: racialized nurses’ insights into their nursing education in Canada

Supervisory Committee Dr. Carol McDonald, School of Nursing, University of Victoria Supervisor Dr. Marjorie McIntyre, School of Nursing, University of Victoria Departmental Member Dr. Jo-Anne Lee, Department of Gender Studies, University of Victoria Outside Member Dr. Tania Das Gupta, Department of Equity Studies, York University External Examiner In Canada, nursing education and practice are enacted in the context of a white settler nation-state. As part of their mandates, nursing schools uphold concepts such as multiculturalism, equity, and diversity; however, studies in North America reflect that the reality contradicts these directives and suggest that nursing schools are hegemonic white spaces. This study challenges this white hegemony through the gaze of racialized nurses. Through in-depth interviews, ten self-identified racialized nurses shared narratives looking back at their experiences in nursing school, and their accounts indicate how they faced the complexities of learning within environments where systemic racism is enacted. Using a women of colour feminist approach, this study asked the following question: What are the experiences of racialized nurses in nursing education programs in Canada? Intersectional analysis was used to examine and address the multiplicity of experiences that emerged from the interviews. Racialized nurses’ narratives reveal complex experiences with the following prevailing themes: Othering, the white gaze, navigating white spaces, accent as marker, always proving myself, and racism impacting health. Beyond racism, participants’ experiences were also affected by the intersection
Li isotopes in metal-poor halo dwarfs: a more and more complicated story

Abstract The nuclei of the lithium isotopes are fragile, easily destroyed, so that, at variance with most of the other elements, they cannot be formed in stars through steady hydrostatic nucleosynthesis. The 7Li isotope is synthesized during primordial nucleosynthesis in the first minutes after the Big Bang and later by cosmic rays, by novae and in pulsations of AGB stars (possibly also by the ν process). 6Li is mainly formed by cosmic rays. The oldest (most metal-deficient) warm galactic stars should retain the signature of these processes if, (as it had been often expected) lithium is not depleted in these stars. The existence of a “plateau” of the abundance of 7Li (and of its slope) in the warm metal-poor stars is discussed. At very low metallicity ([Fe/H] < −2.7dex) the star to star scatter increases significantly towards low Li abundances. The highest value of the lithium abundance in the early stellar matter of the Galaxy (logϵ(Li) = A(7Li) = 2.2 dex) is much lower than the the value (logϵ(Li) = 2.72) predicted by the standard Big Bang nucleosynthesis, according to the specifications found by the satellite WMAP. After gathering a homogeneous stellar sample, and analysing its behaviour, possible explanations of the disagreement between Big Bang and stellar abundances are discussed (including early astration and diffusion). On the other hand, possibilities of lower productions of 7Li in the standard and/or non-standard Big Bang nucleosyntheses are briefly evoked. A surprisingly high value (A(6Li)=0.8 dex) of the abundance of the 6Li isotope has been found in a few warm metal-poor stars. Such a high abundance of 6Li independent of the mean metallicity in the early Galaxy cannot be easily explained. But are we really observing 6Li?
TRACKER: a sensor fusion simulator for generalised tracking

This paper presents a multisensor, multitarget tracking simulator TRACKER that can be used to demonstrate and evaluate airborne early warning and control surveillance systems. TRACKER is a Level 1 fusion surveillance software package that generates a unified object state vector and its measure of uncertainty for each tracked object based on cluttered multitarget augmented (kinematic and discrete type) measurements from multiple dissimilar sensors. It integrates sensors and other sources of information without requiring synchronism and unifies tracking and identification. The resulting track and identity estimates are of a higher quality than those from algorithm in which tracking and identification are carried out separately. The software package is modular in structure and consists of a tracking and data fusion component written in MATLAB, and a graphical user interface written in Java. The package is equipped with a scenario generator and a set of post-mission analysis tools.
Are Interest Rate Derivatives Spanned by the Term Structure of Interest Rates?

This is an investigation of whether the same finite-dimensional system spans both interest rates (the yield curve) and interest rate options (the implied volatility surface). The options market is found to exhibit factors seemingly independent of the underlying yield curve. While three common factors are adequate to capture the systematic movement of the yield curve, three additional factors are needed to capture the movement of the implied volatility surface. Simulation analysis confirms the robustness of these findings.
Physical Fitness Levels in Korean Adolescents: The National Fitness Award Project

Background Although physical fitness in adolescents has been widely studied, there is the lack of information regarding developmental patterns of various youth fitness components. The LMS (L=skewness, M=median curve, and S=coefficient of variation) statistical method has been utilized to develop growth percentiles for height and weight as well as for fitness in the US and Europe countries. The purpose of this study was to develop age- and sex-specific smoothed percentile curves for fitness using the LMS method in Korean adolescents aged 13–18 years. Methods A sample of 14,794 adolescents (7,688 boys and 7,106 girls) who participated in the National Fitness Award Project in 2013 and 2014 was analyzed. The components were cardiorespiratory fitness (20-m PACER), muscle strength (handgrip strength), muscle endurance (partial curl-up, 30-s endurance jump), and flexibility (sit and reach). Age- and sex-specific smoothed percentile curves were calculated for fitness using the LMS method. Results Age- and sex-specific smoothed percentile curves (5th, 10th, 25th, 50th, 75th, 90th, and 95th) were presented for each fitness component. Except for flexibility, fitness levels were higher in boys than in girls. In general, performance in fitness components, except for partial curl-ups, increased with age in boys. However, in girls, performance in fitness components, except for partial curl-ups, slightly increased or remained stable. Conclusion This study presented age- and sex-specific fitness percentile curves for Korean adolescents aged 13–18 years. This material might be useful in understanding and evaluating the fitness status of Korean adolescents.
Adaptive compressive noncoherent change detection : An AMP-based approach

We propose a turbo approximate message passing (AMP) algorithm to detect spatially clustered changes in signal magnitude, relative to a reference signal, from compressive linear mea surements. We then show how the Gaussian posterior approximations gener ated by this scheme can be used for mutual-information based meas urement kernel adaptation. Numerical simulations show excellent p erformance.
Going Beyond Traditional QA Systems: Challenges and Keys in Opinion Question Answering

The treatment of factual data has been widely studied in different areas of Natural Language Processing (NLP). However, processing subjective information still poses important challenges. This paper presents research aimed at assessing techniques that have been suggested as appropriate in the context of subjective - Opinion Question Answering (OQA). We evaluate the performance of an OQA with these new components and propose methods to optimally tackle the issues encountered. We assess the impact of including additional resources and processes with the purpose of improving the system performance on two distinct blog datasets. The improvements obtained for the different combination of tools are statistically significant. We thus conclude that the proposed approach is adequate for the OQA task, offering a good strategy to deal with opinionated questions.
Mariner Transposons Contain a Silencer: Possible Role of the Polycomb Repressive Complex 2

Transposable elements are driving forces for establishing genetic innovations such as transcriptional regulatory networks in eukaryotic genomes. Here, we describe a silencer situated in the last 300 bp of the Mos1 transposase open reading frame (ORF) which functions in vertebrate and arthropod cells. Functional silencers are also found at similar locations within three other animal mariner elements, i.e. IS630-Tc1-mariner (ITm) DD34D elements, Himar1, Hsmar1 and Mcmar1. These silencers are able to impact eukaryotic promoters monitoring strong, moderate or low expression as well as those of mariner elements located upstream of the transposase ORF. We report that the silencing involves at least two transcription factors (TFs) that are conserved within animal species, NFAT-5 and Alx1. These cooperatively act with YY1 to trigger the silencing activity. Four other housekeeping transcription factors (TFs), neuron restrictive silencer factor (NRSF), GAGA factor (GAF) and GTGT factor (GTF), were also found to have binding sites within mariner silencers but their impact in modulating the silencer activity remains to be further specified. Interestingly, an NRSF binding site was found to overlap a 30 bp motif coding a highly conserved PHxxYSPDLAPxD peptide in mariner transposases. We also present experimental evidence that silencing is mainly achieved by co-opting the host Polycomb Repressive Complex 2 pathway. However, we observe that when PRC2 is impaired another host silencing pathway potentially takes over to maintain weak silencer activity. Mariner silencers harbour features of Polycomb Response Elements, which are probably a way for mariner elements to self-repress their transcription and mobility in somatic and germinal cells when the required TFs are expressed. At the evolutionary scale, mariner elements, through their exaptation, might have been a source of silencers playing a role in the chromatin configuration in eukaryotic genomes.
Successful Reentry of African American Women

African American women have a history of being overlooked in the criminal justice system. Despite this, they are disproportionately represented within prisons in the United States. By acknowledging the disadvantages that African American women face, being at the intersectionality of race and gender, it is important that we understand how different factors of society may impact them differently. In addition to African American women being overlooked in the Criminal Justice System, reentry plays a vital role in understanding incarceration and how it impacts criminal justice involved individuals. It is important that the Criminal Justice System is providing criminal justice involved individuals with the necessary programs to ensure that they are successfully reentering and not falling into an endless cycle of crime. This study examines successful reentry of African American women through a series of interviews in order to analyze differences or similarities with existing literature. The goal of this study is to better understand the reentry process of an overlooked demographic and add to existing literature. AFRICAN AMERICAN WOMEN & SUCCESSFUL REENTRY 3
Multi-Scale Stochastic Simulation of Diffusion-Coupled Agents and Its Application to Cell Culture Simulation

Many biological systems consist of multiple cells that interact by secretion and binding of diffusing molecules, thus coordinating responses across cells. Techniques for simulating systems coupling extracellular and intracellular processes are very limited. Here we present an efficient method to stochastically simulate diffusion processes, which at the same time allows synchronization between internal and external cellular conditions through a modification of Gillespie's chemical reaction algorithm. Individual cells are simulated as independent agents, and each cell accurately reacts to changes in its local environment affected by diffusing molecules. Such a simulation provides time-scale separation between the intra-cellular and extra-cellular processes. We use our methodology to study how human monocyte-derived dendritic cells alert neighboring cells about viral infection using diffusing interferon molecules. A subpopulation of the infected cells reacts early to the infection and secretes interferon into the extra-cellular medium, which helps activate other cells. Findings predicted by our simulation and confirmed by experimental results suggest that the early activation is largely independent of the fraction of infected cells and is thus both sensitive and robust. The concordance with the experimental results supports the value of our method for overcoming the challenges of accurately simulating multiscale biological signaling systems.
Convolutive common audio signal extraction

This paper addresses the extraction of a common signal among several mono audio tracks when this common signal undergoes a track-specific filtering. This problem arises in the extraction of a common music and effects track from a set of soundtracks in different languages. To this aim, a novel approach is proposed. The method is based on the dictionary modeling of track-specific and common signals, and is compared to a previous one proposed by the authors based on geometric considerations. The approach is integrated into a Non-Negative Matrix Factorization framework using the Itakura-Saito divergence. The method is evaluated on a synthetic database composed of filtered music and effects tracks, the filters being track-specific, and track-specific dialogs. The results show that this task becomes tractable, while the previously introduced method could not handle track-specific filtering.
Investigating the Factors That Contribute to African Easterly Wave Intensity Forecast Uncertainty in the ECMWF Ensemble Prediction System

Although there have been numerous studies documenting the processes/environments that lead to the intensification of African easterly waves (AEWs), only a few of these studies investigated the effect of those processes or the environment on the predictability of AEWs. Here, the large-scale modulation of AEW intensity predictability is evaluated using the 51-member ECMWF ensemble prediction system (EPS) during an active AEW period (July–September 2011–13). Forecasts are stratified based on the 72-h AEW intensity standard deviation (SD) to evaluate hypotheses for how different processes contribute to large forecast SD. While large and small SD forecasts are associated with similar baroclinic and barotropic energy conversions, forecasts with large SD are characterized by higher relative humidity values downstream of the AEW trough. These areas of higher humidity are also associated with higher precipitation and precipitation SD, suggesting that uncertainty associated with diabatic processes could be linked with large AEW intensity SD. Although water vapor is a strong function of longitude and phase of convectively coupled equatorial waves, the cases with large and small SD are characterized by similar longitude and wave phase, suggesting that AEWs occurring in certain locations or convectively coupled equatorial wave phases are not more or less predictable.
Robust Voice Activity Detection Based on Discrete Wavelet Transform

This paper mainly addresses the problem of determining voice activity in presence of noise, especially in a dynamically varying background noise. The proposed voice activity detection algorithm is based on structure of three-layer wavelet decomposition. Appling auto-correlation function into each subband exploits the fact that intensity of periodicity is more significant in sub-band domain than that in full-band domain. In addition, Teager energy operator (TEO) is used to eliminate the noise components from the wavelet coefficients on each subband. Experimental results show that the proposed wavelet-based algorithm is prior to others and can work in a dynamically varying background noise.
Undergraduate research, learning gain and equity: the impact of final year research projects

Abstract This study evaluates the impact of undergraduate research on student achievement. It analyses graduating students from 2012 to 2016 at a UK university that requires a research project comprising 25% of final-year credits in most subjects, providing a sample of over 5000 students across the natural sciences, social sciences and humanities. It compares project grades to other final-year grades to gauge the ‘research gain’ or impact on students’ achievement. Multiple regression analysis then determines what factors affect this impact. It finds that students achieve better grades on research projects than the average of other modules. This improvement is larger for students with lower prior achievement, women, and students in the natural sciences, though smaller for Asians and students declaring a disability. The implications are that undergraduate research provides a measurable benefit to all students, but this impact is larger for some, though not all, historically underrepresented or underachieving groups of students.
Testing a homogeneity of stochastic processes

The paper concentrates on modeling the data that can be described by a homogeneous or non-homogeneous Poisson process. The goal is to decide whether the intensity of the process is constant or not. In technical practice, e.g., it means to decide whether the reliability of the system remains the same or if it is improving or deteriorating. We assume two situations. First, when only the counts of events are known and, second, when the times between the events are available. Several statistical tests for a detection of a change in an intensity of the Poisson process are described and illustrated by an example. We cover both the case when the time of the change is assumed to be known or unknown.
Toward expressive syndication on the web

Syndication systems on the Web have attracted vast amounts of attention in recent years. As technologies have emerged and matured, there has been a transition to more expressive syndication approaches; that is, subscribers and publishers are provided with more expressive means of describing their interests and published content, enabling more accurate information filtering. In this paper, we formalize a syndication architecture that utilizes expressive Web ontologies and logic-based reasoning for selective content dissemination. This provides finer grained control for filtering and automated reasoning for discovering implicit subscription matches, both of which are not achievable in less expressive approaches. We then address one of the main limitations with such a syndication approach, namely matching newly published information with subscription requests in an efficient and practical manner. To this end, we investigate continuous query answering for a large subset of the Web Ontology Language (OWL); specifically, we formally define continuous queries for OWL knowledge bases and present a novel algorithm for continuous query answering in a large subset of this language. Lastly, an evaluation of the query approach is shown, demonstrating its effectiveness for syndication purposes.
Tag clouds revisited

Tagging has become a very common feature in Web 2.0 applications, providing a simple and effective way for users to freely annotate resources to facilitate their discovery and management. Subsequently, tag clouds have become popular as a summarized representation of a collection of tagged resources. A tag cloud is typically a visualization of the top-k most frequent tags in the underlying collection. In this paper, we revisit tag clouds, to examine whether frequency is the most suitable criterion for tag ranking. We propose alternative tag ranking strategies, based on methods for random walk on graphs, diversification,and rank aggregation. To enable the comparison of different tag selection and ranking methods, we propose a set of evaluation metrics that consider the use of tag clouds for search, navigation and recommendations. We apply these tag ranking methods and evaluation metrics to empirically compare alternative tag clouds in a dataset obtained from Flickr, comprising 488,112 tagged photos organized in 451 groups, and 112,514 distinct tags.