Miracle-dz/UniFAR-FTUs huggingface dataset:
Glycomic Analysis of Life Stages of the Human Parasite Schistosoma mansoni Reveals Developmental Expression Profiles of Functional and Antigenic Glycan Motifs*

Glycans present on glycoproteins and glycolipids of the major human parasite Schistosoma mansoni induce innate as well as adaptive immune responses in the host. To be able to study the molecular characteristics of schistosome infections it is therefore required to determine the expression profiles of glycans and antigenic glycan-motifs during a range of critical stages of the complex schistosome lifecycle. We performed a longitudinal profiling study covering schistosome glycosylation throughout worm- and egg-development using a mass spectrometry-based glycomics approach. Our study revealed that during worm development N-glycans with Galβ1–4(Fucα1–3)GlcNAc (LeX) and core-xylose motifs were rapidly lost after cercariae to schistosomula transformation, whereas GalNAcβ1–4GlcNAc (LDN)-motifs gradually became abundant and predominated in adult worms. LeX-motifs were present on glycolipids up to 2 weeks of schistosomula development, whereas glycolipids with mono- and multifucosylated LDN-motifs remained present up to the adult worm stage. In contrast, expression of complex O-glycans diminished to undetectable levels within days after transformation. During egg development, a rich diversity of N-glycans with fucosylated motifs was expressed, but with α3-core fucose and a high degree of multifucosylated antennae only in mature eggs and miracidia. N-glycan antennae were exclusively LDN-based in miracidia. O-glycans in the mature eggs were also diverse and contained LeX- and multifucosylated LDN, but none of these were associated with miracidia in which we detected only the Galβ1–3(Galβ1–6)GalNAc core glycan. Immature eggs also exhibited short O-glycan core structures only, suggesting that complex fucosylated O-glycans of schistosome eggs are derived primarily from glycoproteins produced by the subshell envelope in the developed egg. Lipid glycans with multifucosylated GlcNAc repeats were present throughout egg development, but with the longer highly fucosylated stretches enriched in mature eggs and miracidia. This global analysis of the developing schistosome's glycome provides new insights into how stage-specifically expressed glycans may contribute to different aspects of schistosome-host interactions.
Cluster-Based Selection of Statistical Answering Strategies

Question answering (QA) is a highly complex task that brings together classification, clustering, retrieval, and extraction. Question answering systems include various statistical and rule-based components that combine and form multiple strategies for finding answers. However, in real-life scenarios efficiency constraints make it infeasible to simultaneously use all available strategies in a QA system. To address this issue, we present an approach for carefully selecting answering strategies that are likely to benefit individual questions, without significantly reducing performance. We evaluate the impact of strategy selection on question answering performance at several important QA stages: document retrieval, answer extraction, and answer merging. We present strategy selection experiments using a statistical question answering system, and we show significant efficiency improvements. By selecting 10% of the available answering strategies, we obtained similar performance when compared to using all of the strategies combined.
Texture Synthesis Approach Using Cooperative Features

In recent years, a lot of 2D textures have been synthesized from input 2D textures. However, the quality problems still exist for many textures. Further improvements are required to extract more reliable texture features. In this paper, we present a texture synthesis approach using cooperative color and grey-level features. For color feature extraction, we extract appearance vectors to replace RGB color values. For grey-level feature extraction, we extract the statistical features including entropy, contrast, and correlation based on the grey level co-occurrence probabilities (GLCPs). Moreover, we introduce cooperative color and GLCP features for neighborhood matching in the synthesis process. We assign different weights for color and grey-level features according to the characteristics of the input texture. The results show that the proposed approach performs well in terms of the synthesis quality.
Effect of aerobic training on hot flushes and quality of life—a randomized controlled trial

Abstract Background and objective. To estimate whether aerobic training has an effect on frequency of hot flushes or quality of life. Design. A randomized controlled trial. Participants and setting. Symptomatic, sedentary women (n = 176), 43–63 years, no current use of hormone therapy. Intervention. Unsupervised aerobic training for 50 minutes four times per week during 6 months. Outcomes. Hot flushes as measured with Women's Health Questionnaire (WHQ) and Health-Related Quality of Life (HRQoL, SF-36), daily reported hot flushes on phone-based diary, cardiorespiratory fitness (CRF), and body composition. Results. Intervention group had larger decrease in the frequency of night-time hot flushes based on phone diary (P for month × group = 0.012), but not on WHQ scale. Intervention group had less depressed mood (P = 0.01) than control women according to change in WHQ score. Changes in WHQ score in depressed mood (P = 0.03) and menstrual symptoms (P = 0.01) in the intervention group were significantly dependent on frequency of training sessions. HRQoL was improved among the intervention group women in physical functioning (P = 0.049) and physical role limitation (P = 0.017). CRF improved (P = 0.008), and lean muscle mass increased (P = 0.046) significantly in the intervention group as compared to controls. Conclusions. Aerobic training may decrease the frequency of hot flushes and improve quality of life among slightly overweight women.
Frequency planning for cellular network employing carrier aggregation

Carrier aggregation (CA) is an important feature of next-generation cellular networks where multiple component carriers from contiguous or non-contiguous frequency bands are combined to increase the effective transmission bandwidth. In this work, we consider a system which has 2 non-contiguous bands separated by nearly 1 GHz so that the path loss exponent in each band is significantly different. We then derive the coverage probability and average rate in frequency reuse δ by considering two Schemes for CA. Essentially, Scheme 1 uses the carrier with higher path loss exponent for the cell-centre users, and the carrier with the lower path loss exponent for the cell-edge users, and Scheme 2 is the other way. We show that at low SNR for the cell-edge users corresponding to carrier having higher path loss exponent, Scheme 1 may be preferred over Scheme 2. However, at high SNR for the cell-edge users corresponding to carrier having higher path loss exponent, Scheme 2 may be preferred over Scheme 1.
Learning from the users : From Corners to Selective Redundant Interaction Paths

This paper introduces the participatory design of the landing page of the CarePortfolio, an online platform developed within TOPIC, a European Project under the Active and Assisted Living (AAL) Programme that aims to design and develop innovative technologies for elderly informal carers. The project employs a user-centred and participatory design (UCD/PD) approach combined with an evolutionary development process (ED), which entails the involvement of end-users during all phases of the project and affords changes in the system as new requirements are elicited. The paper recounts the challenging process that resulted in the design of the landing page of the platform, highlighting the relevance of constant interaction and communication with the users and iteratively with the design and development teams for the generation of useful and usable technological solutions for the elderly. Hilda Tellioğlu, Aparecido Fabiano Pinatti de Carvalho, Michael Habiger (2016): Alternatives and Redundancy: Interaction Design of the TOPIC CarePortfolio Landing Page. In Markus Garschall, Theo Hamm, Dominik Hornung, Claudia Müller, Katja Neureiter, Marén Schorch, Lex van Velsen (Eds.), International Reports on Socio-Informatics (IRSI), Proceedings of the COOP 2016 Symposium on challenges and experiences in designing for an ageing society. (Vol. 13, Iss. 3, pp. 51-60)
Human T-lymphotropic virus type II RFLP subtypes a0 and b4/b5 are associated with different demographic and geographic characteristics in the United States.

Human T-lymphotropic virus type II (HTLV-II) prevalence is very low among the general U.S. population, intermediate among American Indians, and high among injecting drug users and their sexual partners. However, the transmission dynamics underlying this distribution are not well described. We obtained blood specimens from 493 blood donors found to be seropositive for HTLV-II at blood centers in five U.S. cities. Nested polymerase chain reaction was used to amplify a 672-bp region of the HTLV-II long terminal repeat region, and restriction fragment length polymorphism (RFLP) analysis was performed to classify each virus into subtypes as defined by Switzer et al. (1995, J. Virol. 69, 621-632). Associations between RFLP subtype and other characteristics were analyzed using multivariable logistic regression. HTLV-II subtype a0 was independently associated with age over 30 years (odds ratio (OR) = 2.12, 95% confidence interval (CI) 1.13-3.99) and with Black race/ethnicity (OR = 2.00, 95% CI 1.10-3.65 versus Hispanic race/ethnicity). Conversely, HTLV-II RFLP subtypes b4 and b5 were significantly more common among American Indian (OR = 3.77, 95% CI 1.23-11.57) and Other race/ethnicity (OR = 4.22, 95% CI 1.25-14.27, both versus Black race/ethnicity) and at the Oklahoma City blood center (OR = 3.57, 95% CI 1.08-11.84 compared to Washington, DC/Baltimore). There may have been at least two transmission foci of HTLV-II in the United States: a modest HTLV-II subtype a0 epidemic of unknown source in the 1960s and 1970s spread predominantly among Black persons in several geographic areas and a smaller focus of HTLV-II subtypes b4/b5 among non-Black individuals in Oklahoma and perhaps in other areas not examined by this study.
Learning Policies with External Memory

In order for an agent to perform well in partially observable domains, it is usually necessary for actions to depend on the history of observations. In this paper, we explore a {\it stigmergic} approach, in which the agent's actions include the ability to set and clear bits in an external memory, and the external memory is included as part of the input to the agent. In this case, we need to learn a reactive policy in a highly non-Markovian domain. We explore two algorithms: SARSA(\lambda), which has had empirical success in partially observable domains, and VAPS, a new algorithm due to Baird and Moore, with convergence guarantees in partially observable domains. We compare the performance of these two algorithms on benchmark problems.
Interactivity in Visual Analytics: Use of Conceptual Frameworks to Support Human-Centered Design of a Decision-Support Tool

Visual analytics (VA) combines the strengths of humans and computers such that joint cognitive systems are formed. To be effective, a VA tool should be designed such that the component parts of the whole system are strongly coupled and function in a harmonious fashion. These components include cognitive and perceptual issues, tasks, algorithms, data models, and other aspects of the systems that contribute to its overall efficacy. The quality of interaction among all of these components can be referred to as interactivity. In the existing visualization literature, not enough focus has been placed on developing our understanding of human-centered aspects of interactivity. We have recently developed some conceptual frameworks to inform and guide the design of visual analytics tools in a systematic, human-centered fashion. In this paper, we describe the design of a tool that supports decision-making and other complex cognitive activities. We discuss how the conceptual frameworks supported systematic design and coherent thinking about the interactivity of the tool. We also discuss some extensions of interactivity into important areas of concern for visual analytics tools.
Music in Therapy: Increasing Possibilities for Action

The article discusses how music therapy, considered as a discipline as well as arenas of different practices and theoretical models, may contribute to our understanding of how music may influence our actions. Among the many models of music therapy the author discusses an ontology of music which is compatible with a contextual understanding of how musical meanings are produced and performed. The article further presents how theories from receptive music therapy (The Bonny Method of Guided Imagery and Music), improvisational music therapy (Creative Music Therapy), Community Music Therapy, and more resource-oriented ways of working may provide new insights into how music in therapy works in giving us new possibilities for action.
SE and EE of Uplink D2D Underlaid Massive MIMO Cellular Networks with Power Control

One of key 5G scenarios is that device-to-device (D2D) and massive multiple-input multiple-output (MIMO) will be co-existed. However, interference in the uplink D2D underlaid massive MIMO cellular networks needs to be coordinated, due to the vast cellular and D2D transmissions. To this end, this paper introduces a spatially dynamic power control solution for mitigating the cellular-to-D2D and D2D-to-cellular interference. In particular, the proposed D2D power control policy is rather flexible including the special cases of no D2D links or using maximum transmit power. Under the considered power control, an analytical approach is developed to evaluate the spectral efficiency (SE) and energy efficiency (EE) in such networks. Thus, the exact expressions of SE and EE for a cellular user or D2D transmitter are derived, which quantify the impacts of key system parameters such as massive MIMO antennas and D2D density. Numerical results corroborate our analysis and show that the proposed power control solution can efficiently mitigate interference between the cellular and D2D tier.
My reading life: towards utilizing eyetracking on unmodified tablets and phones

As reading is an integral part of our knowledge lives, we should know more about our reading activities. This paper introduces a reading application for smart phone and tablets that aims at giving user more quantified information about their reading habits. We present our work towards building an open library for eye tracking on unmodified tablets and smart phones to support some of the applications advanced functionality. We implemented already several eye tracking algorithms from previous work, unfortunately all seem not to be robust enough for our application case. We give an overview about our challenges and potential solutions.
At the border: reflections on psychoanalytically oriented counselling in an Italian university setting

This paper analyses the ‘border’ position of counselling services in Italian universities. The concept of ‘border’ has great relevance in the work of psychoanalytically oriented university students’ counsellors. Counselling is part of a continuum of interventions, from befriending to psychotherapy. This closeness encompasses the need for identifying specificities and differences among interventions. Moreover, a university counselling service occupies a ‘marginal’ position, continuously confronted with the risks of rejection and/or assimilation. The concept of ‘border’ is also useful to define the developmental phase of university students, crossing the border between late adolescence and young adulthood, as represented by Conrad's novel The shadow line (1917/1999), recently analysed by Green (2008) as the metaphoric demarcation line between youth and adulthood. Finally, most of the students referring to our counselling service come from families that for the first time crossed the border of university education.
Pseudomonas aeruginosa DesB Promotes Staphylococcus aureus Growth Inhibition in Coculture by Controlling the Synthesis of HAQs

Pseudomonas aeruginosa is a pathogen that can cause serious infections and usually coexists with other pathogens, such as Staphylococcus aureus. Virulence factors are important for maintaining a presence of the organisms in these multispecies environments, and DesB plays an important role in P. aeruginosa virulence. Therefore, we investigated the effect of DesB on S. aureus reduction under competitive situation. Liquid cultures of P. aeruginosa wild type (WT) and its desB mutant were spotted on agar plates containing S. aureus, and the size of the clear zones was compared. In addition, interbacterial competition between P. aeruginosa and S. aureus was observed over time during planktonic coculture. The transcriptional profiles of the WT and desB mutant were compared by qRT-PCR and microarray to determine the role of DesB in S. aureus reduction at the molecular level. As a result, the clear zone was smaller for the desB mutant than for P. aeruginosa PAO1 (WT), and in planktonic coculture, the number of S. aureus cells was reduced in the desB mutant. qRT-PCR and microarray revealed that the expression of MvfR-controlled pqsA-E and phnAB operons was significantly decreased, but the mexEF-oprN operon was highly expressed. The results indicate that intracellular levels of 4-hydroxy-2-heptylquinoline (HHQ), a ligand of MvfR, are reduced due to MexEF-OprN-mediated efflux in desB mutant, resulting in the decrease of MvfR binding to pqsA-E promoter and the reduction of 4-hydroxy-2-alkylquinolines (HAQs) synthesis. Overexpression of mexEF-oprN operon in desB mutant was phenotypically confirmed by observing significantly increased resistance to chloramphenicol. In conclusion, these results suggest that DesB plays a role in the inhibition of S. aureus growth by controlling HAQ synthesis.
Open Source Recommendation Systems for Mobile Application

The aim of Recommender Systems is to suggest useful items to users. Three major techniques can be highlighted in these systems: Collaborative Filtering, Content-Based Filtering and Hybrid Filtering. The collaborative method proposes recommendations based on what a group of users have enjoyed and it is widely used in Open Source Recommender Systems. The work presented in this paper takes place in the context of SoliMobile Project that aims to design, build and implement a package of innovative services focused on the individual in unstable situation (unemployment, homeless, etc.). In this paper, we present a study of open source recommender systems and their usefulness for SoliMobile. The paper also presents how our recommender system is fed by extracting implicit ratings using the techniques of Web Usage Mining.
The XC chemokine receptor 1 is a conserved selective marker of mammalian cells homologous to mouse CD8α+ dendritic cells

Human BDCA3+ dendritic cells (DCs) were suggested to be homologous to mouse CD8α+ DCs. We demonstrate that human BDCA3+ DCs are more efficient than their BDCA1+ counterparts or plasmacytoid DCs (pDCs) in cross-presenting antigen and activating CD8+ T cells, which is similar to mouse CD8α+ DCs as compared with CD11b+ DCs or pDCs, although with more moderate differences between human DC subsets. Yet, no specific marker was known to be shared between homologous DC subsets across species. We found that XC chemokine receptor 1 (XCR1) is specifically expressed and active in mouse CD8α+, human BDCA3+, and sheep CD26+ DCs and is conserved across species. The mRNA encoding the XCR1 ligand chemokine (C motif) ligand 1 (XCL1) is selectively expressed in natural killer (NK) and CD8+ T lymphocytes at steady-state and is enhanced upon activation. Moreover, the Xcl1 mRNA is selectively expressed at high levels in central memory compared with naive CD8+ T lymphocytes. Finally, XCR1−/− mice have decreased early CD8+ T cell responses to Listeria monocytogenes infection, which is associated with higher bacterial loads early in infection. Therefore, XCR1 constitutes the first conserved specific marker for cell subsets homologous to mouse CD8α+ DCs in higher vertebrates and promotes their ability to activate early CD8+ T cell defenses against an intracellular pathogenic bacteria.
Genome Sequence Analysis of In Vitro and In Vivo Phenotypes of Bunyamwera and Ngari Virus Isolates from Northern Kenya

Biological phenotypes of tri-segmented arboviruses display characteristics that map to mutation/s in the S, M or L segments of the genome. Plaque variants have been characterized for other viruses displaying varied phenotypes including attenuation in growth and/or pathogenesis. In order to characterize variants of Bunyamwera and Ngari viruses, we isolated individual plaque size variants; small plaque (SP) and large plaque (LP) and determined in vitro growth properties and in vivo pathogenesis in suckling mice. We performed gene sequencing to identify mutations that may be responsible for the observed phenotype. The LP generally replicated faster than the SP and the difference in growth rate was more pronounced in Bunyamwera virus isolates. Ngari virus isolates were more conserved with few point mutations compared to Bunyamwera virus isolates which displayed mutations in all three genome segments but majority were silent mutations. Contrary to expectation, the SP of Bunyamwera virus killed suckling mice significantly earlier than the LP. The LP attenuation may probably be due to a non-synonymous substitution (T858I) that mapped within the active site of the L protein. In this study, we identify natural mutations whose exact role in growth and pathogenesis need to be determined through site directed mutagenesis studies.
A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells

The predominant morphotype of mycobacteriophage virions has a DNA‐containing capsid attached to a long flexible non‐contractile tail, features characteristic of the Siphoviridae. Within these phage genomes the tape measure protein (tmp) gene can be readily identified due to the well‐established relationship between the length of the gene and the length of the phage tail – because these phages typically have long tails, the tmp gene is usually the largest gene in the genome. Many of these mycobacteriophage Tmp's contain small motifs with sequence similarity to host proteins. One of these motifs (motif 1) corresponds to the Rpf proteins that have lysozyme activity and function to stimulate growth of dormant bacteria, while the others (motifs 2 and 3) are related to proteins of unknown function, although some of the related proteins of the host are predicted to be involved in cell wall catabolism. We show here that motif 3‐containing proteins have peptidoglycan‐hydrolysing activity and that while this activity is not required for phage viability, it facilitates efficient infection and DNA injection into stationary phase cells. Tmp's of mycobacteriophages may thus have acquired these motifs in order to avoid a selective disadvantage that results from changes in peptidoglycan in non‐growing cells.