Miracle-dz/UniFAR-FTUs huggingface dataset:
Scalable Modeling of Conversational-role based Self-presentation Characteristics in Large Online Forums

Online discussion forums are complex webs of overlapping subcommunities (macrolevel structure, across threads) in which users enact different roles depending on which subcommunity they are participating in within a particular time point (microlevel structure, within threads). This sub-network structure is implicit in massive collections of threads. To uncover this structure, we develop a scalable algorithm based on stochastic variational inference and leverage topic models (LDA) along with mixed membership stochastic block (MMSB) models. We evaluate our model on three large-scale datasets, Cancer-ThreadStarter (22K users and 14.4K threads), Cancer-NameMention(15.1K users and 12.4K threads) and StackOverFlow (1.19 million users and 4.55 million threads). Qualitatively, we demonstrate that our model can provide useful explanations of microlevel and macrolevel user presentation characteristics in different communities using the topics discovered from posts. Quantitatively, we show that our model does better than MMSB and LDA in predicting user reply structure within threads. In addition, we demonstrate via synthetic data experiments that the proposed active sub-network discovery model is stable and recovers the original parameters of the experimental setup with high probability.
Complex and photo-realistic scene representation based on range planar segmentation and model fusion

We present an efficient 3D scene representation method from a set of 3D range scans captured from a large-scale indoor or outdoor scene based on range planar segmentation and model fusion. In our method, range images are partitioned into planar patches and non-planar regions. We first partition the range image into a set of rectangle blocks and fit a planar patch to all points of each block. Blocks that are not successfully fitted as planar patches, are iteratively partitioned into sub-blocks until reaching a minimum size. Second, we iteratively merge the planar patches and identify unclassified rectangle blocks or points. The segmentation is then refined by relabelling the boundary points of fitted planar patches with respect to the neighbouring planar patches. We further simplify the scene model representation by fusing range scans and welding neighbouring planar patches with clean straight boundaries. An efficient texture mapping approach is proposed to automatically map the reflectance/colour images onto the fused scene model composed of a set of planar patches. Finally we successfully demonstrate the performance of our algorithms on several challenging range data sets.
Draft Genome Sequence of Turicella otitidis ATCC 51513, Isolated from Middle Ear Fluid from a Child with Otitis Media

ABSTRACT Turicella otitidis is an unusual corynebacterium with a controversial role in otitis media in children. Metabolic capabilities deduced from the draft genome indicate its adaptation to habitats on the human skin and in the intestine. The lack of candidate virulence factors implies that T. otitidis has a low pathogenic potential.
Applied Visual Exploration on Real-time News Feeds using Polarity and Geo-spatial Analysis

This paper presents a visual analytics approach to explore large news article collections in the domains of polarity and spatial analysis. The exploration is performed on the data collected with Europe Media Monitor (EMM), a system which monitors over 2500 online sources and processes 90,000 articles per day. By analyzing the news feeds, we want to find out which topics are important in different countries and what is the general polarity of the articles within these topics. To assess the polarity of a news article, automatic techniques for polarity analysis are employed and the results are represented using Literature Fingerprinting for visualization. In the spatial description of the news feeds, every article can be represented by two geographic attributes, the news origin and the location of the event itself. In order to assess these spatial properties of news articles, we conducted our geo-analysis, which is able to cope with the size and spatial distribution of the data. Within this application framework, we show opportunities how real-time news feed data can be analyzed efficiently.
Open and closed-loop task space trajectory control of redundant robots using learned models

This paper presents a comparison of open-loop and closed-loop control strategies for tracking a task space trajectory, using redundant robots. We do not assume any knowledge of the analytical forward and inverse kinematics, relying instead on learning these models online, while executing a desired task. Specifically, we employ a recent learning algorithm that allows to learn a probabilistic model from which both the forward and inverse solutions can be obtained, as well as the Jacobian of the kinematics map. Such learned model can then be used to implement both types of control. Moreover, the multi-valued solutions provided by the learned model can be applied to redundant systems in which an infinite number of inverse solutions may exist. We present experiments with a simulated version of the iCub, a highly redundant humanoid robot, in which this learned model is employed to execute both open-loop and closed-loop trajectory control. We show the advantages and drawbacks of both control strategies, and we propose a way to combine them to deal with sensor noise and failures, showing the benefits of using a learning algorithm that can simultaneously provide forward and inverse predictions.
X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature

The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L) is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on) state at 1.9 Angstrom resolution and the trans (off) state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA) at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS) at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN) injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form.
Wave packet pseudomodes of variable coefficient differential operators

The pseudospectra of non-selfadjoint linear ordinary differential operators with variable coefficients are considered. It is shown that when a certain winding number or twist condition is satisfied, closely related to Hörmander's commutator condition for partial differential equations, ε-pseudoeigenfunctions of such operators for exponentially small values of ε exist in the form of localized wave packets. In contrast to related results of Davies and of Dencker, Sjöstrand & Zworski, the symbol need not be smooth. Applications in fluid mechanics, non-hermitian quantum mechanics and other areas are presented with the aid of high-accuracy numerical computations.
Executive function outcomes of children with traumatic brain injury sustained before three years

Traumatic brain injury (TBI) is a common cause of disability in childhood. While the outcomes of TBI sustained in school years has been heavily researched, very little is known about the impact of TBI in infants and young children. The aim of this study was to investigate the impact of TBI on executive function (EF) in children who sustained a TBI before 3 years of age. A group of 55 children, 19 with a mild TBI, 16 children with a moderate-severe TBI, and 20 uninjured comparison children participated. The EF of children aged 3 to 6 years were compared using child-based measures of attentional control and information processing. Parents completed questionnaires rating their child's EF. Severity groups differed on the child-based EF measure of attentional control with children with TBI performing below the control group. There were no significant group differences for information processing or parent-rated EF. It appears that children who sustain a TBI before the age of 3 years display impairments in some areas of attentional control 3–4 years postinjury. The findings fit with the existing EF literature for older children.
Fabrication of pillared PLGA microvessel scaffold using femtosecond laser ablation

One of the persistent challenges confronting tissue engineering is the lack of intrinsic microvessels for the transportation of nutrients and metabolites. An artificial microvascular system could be a feasible solution to this problem. In this study, the femtosecond laser ablation technique was implemented for the fabrication of pillared microvessel scaffolds of polylactic-co-glycolic acid (PLGA). This novel scaffold facilitates implementation of the conventional cell seeding process. The progress of cell growth can be observed in vitro by optical microscopy. The problems of becoming milky or completely opaque with the conventional PLGA scaffold after cell seeding can be resolved. In this study, PLGA microvessel scaffolds consisting of 47 μm × 80 μm pillared branches were produced. Results of cell culturing of bovine endothelial cells demonstrate that the cells adhere well and grow to surround each branch of the proposed pillared microvessel networks.
Crystal structure of TiBi2

Black granular single crystals of monotitanium dibismuth, TiBi2, were synthesized by slow cooling of a mixture of Bi and Ti from 693 K. The title compound is isostructural with CuMg2 (orthorhombic Fddd symmetry). Ti atoms are in the square antiprisms of Bi atoms. The network of one type of Bi atom spirals along the a-axis direction while honeycomb layers of the other type of Bi atom spreading inn the ab plane interlace one another.
Unlocking the Transcriptomes of Two Carcinogenic Parasites, Clonorchis sinensis and Opisthorchis viverrini

The two parasitic trematodes, Clonorchis sinensis and Opisthorchis viverrini, have a major impact on the health of tens of millions of humans throughout Asia. The greatest impact is through the malignant cancer ( = cholangiocarcinoma) that these parasites induce in chronically infected people. Therefore, both C. sinensis and O. viverrini have been classified by the World Health Organization (WHO) as Group 1 carcinogens. Despite their impact, little is known about these parasites and their interplay with the host at the molecular level. Recent advances in genomics and bioinformatics provide unique opportunities to gain improved insights into the biology of parasites as well as their relationships with their hosts at the molecular level. The present study elucidates the transcriptomes of C. sinensis and O. viverrini using a platform based on next-generation (high throughput) sequencing and advanced in silico analyses. From 500,000 sequences, >50,000 sequences were assembled for each species and categorized as biologically relevant based on homology searches, gene ontology and/or pathway mapping. The results of the present study could assist in defining molecules that are essential for the development, reproduction and survival of liver flukes and/or that are linked to the development of cholangiocarcinoma. This study also lays a foundation for future genomic and proteomic research of C. sinensis and O. viverrini and the cancers that they are known to induce, as well as novel intervention strategies.
Randomized, Controlled Intervention Trial of Male Circumcision for Reduction of HIV Infection Risk: The ANRS 1265 Trial

Background Observational studies suggest that male circumcision may provide protection against HIV-1 infection. A randomized, controlled intervention trial was conducted in a general population of South Africa to test this hypothesis. Methods and Findings A total of 3,274 uncircumcised men, aged 18–24 y, were randomized to a control or an intervention group with follow-up visits at months 3, 12, and 21. Male circumcision was offered to the intervention group immediately after randomization and to the control group at the end of the follow-up. The grouped censored data were analyzed in intention-to-treat, univariate and multivariate, analyses, using piecewise exponential, proportional hazards models. Rate ratios (RR) of HIV incidence were determined with 95% CI. Protection against HIV infection was calculated as 1 − RR. The trial was stopped at the interim analysis, and the mean (interquartile range) follow-up was 18.1 mo (13.0–21.0) when the data were analyzed. There were 20 HIV infections (incidence rate = 0.85 per 100 person-years) in the intervention group and 49 (2.1 per 100 person-years) in the control group, corresponding to an RR of 0.40 (95% CI: 0.24%–0.68%; p < 0.001). This RR corresponds to a protection of 60% (95% CI: 32%–76%). When controlling for behavioural factors, including sexual behaviour that increased slightly in the intervention group, condom use, and health-seeking behaviour, the protection was of 61% (95% CI: 34%–77%). Conclusion Male circumcision provides a degree of protection against acquiring HIV infection, equivalent to what a vaccine of high efficacy would have achieved. Male circumcision may provide an important way of reducing the spread of HIV infection in sub-Saharan Africa. (Preliminary and partial results were presented at the International AIDS Society 2005 Conference, on 26 July 2005, in Rio de Janeiro, Brazil.)
Volume Indicators and Left Ventricular Mass during Aggressive Volume Management in Patients on Thrice-Weekly Hemodialysis

Objective: We examined the relationship between various volume indicators, i.e. multifrequency bioelectric impedance analysis (BIA), predialysis serum N-terminus-pro-brain natriuretic peptide (NT[-]pro[-]BNP) levels, and inferior vena cava diameter, and left ventricular mass index (LVMI) at baseline and with rigorous volume management on thrice-weekly hemodialysis. Methods: Twenty-two patients on chronic thrice-weekly hemodialysis were followed for 52 weeks. Left ventricular hypertrophy was present in 100% of the cohort at baseline. Results: There were no significant correlations among volume indicators except for a correlation between extracellular-volume-to-body-mass ratio and collapsibility index (r = 0.476; p = 0.039) at 6 months. There were no correlations between blood pressure and volume indicators. Baseline (but not follow-up) collapsibility index correlated with LVMI (r = 0.506; p = 0.038). In ‘lag-time’ analyses, there were no correlations between volume indicators at baseline or 6 months and LVMI at subsequent time points. LVMI decreased from 243.6 ± 83.3 g/m2 at baseline to 210.6 ± 62.9 g/m2 at 6 months (p = 0.104) and further to 203.2 ± 49.0 g/m2 at 12 months (p = 0.035). Conclusions: (1) Left ventricular hypertrophy was prevalent in hemodialysis patients; (2) BIA, inferior vena cava ultrasound and serum NT-pro-BNP levels yield discordant results for fluid volumes; (3) regression of LVMI could occur with rigorous fluid management, even with thrice-weekly dialysis.
Less is More: Using a single knowledge representation in dialogue systems

The approach to knowledge representation taken in a multi-modal multi-domain dialogue system - SMARTKOM - is presented. We focus on the ontological and representational issues and choices helping to construct an ontology, which is shared by multiple components of the system, can be re-used in different projects and applied to various tasks. Finally, examples highlighting the usefulness of our approach are given.
Identifying Personal Information in Internet Traffic

Users today access a multitude of online services---among the most popular of which are online social networks (OSNs)---via both web sites and dedicated mobile applications (apps), using a range of devices (traditional PCs, tablets, and smartphones) that are connected via a variety of networks. The resulting infrastructure makes these services conveniently available anytime and anywhere, enabling them to become an integral part of daily life. As a consequence, users explicitly and implicitly provide a wealth of Personal Information (PI) that reflects several aspects of their life. Service providers monetize this information by selling to third parties (e.g., advertisers). Unfortunately, today, it remains difficult for end users to fully understand the amount and nature of the collected data. Our goal in this paper is to bring visibility into PI collected when accessing online services such as online social networks. This is a major challenge because PI is transferred in a proprietary way by each service. We develop a novel method that can automatically discover various types of PI carried within protocol fields of network traffic; the method includes techniques to filter out potential "containers" that do not actually carry PI and extend the set of containers initially found with additional ones. We evaluate the false positive/negative rates of our proposed method and show examples of interesting findings, including what kind of web sites or apps are more likely to transmit PI and which types of PI are most commonly collected.
CLEC5A Regulates Japanese Encephalitis Virus-Induced Neuroinflammation and Lethality

CLEC5A/MDL-1, a member of the myeloid C-type lectin family expressed on macrophages and neutrophils, is critical for dengue virus (DV)-induced hemorrhagic fever and shock syndrome in Stat1 −/− mice and ConA-treated wild type mice. However, whether CLEC5A is involved in the pathogenesis of viral encephalitis has not yet been investigated. To investigate the role of CLEC5A to regulate JEV-induced neuroinflammation, antagonistic anti-CLEC5A mAb and CLEC5A-deficient mice were generated. We find that Japanese encephalitis virus (JEV) directly interacts with CLEC5A and induces DAP12 phosphorylation in macrophages. In addition, JEV activates macrophages to secrete proinflammatory cytokines and chemokines, which are dramatically reduced in JEV-infected Clec5a−/− macrophages. Although blockade of CLEC5A cannot inhibit JEV infection of neurons and astrocytes, anti-CLEC5A mAb inhibits JEV-induced proinflammatory cytokine release from microglia and prevents bystander damage to neuronal cells. Moreover, JEV causes blood-brain barrier (BBB) disintegrity and lethality in STAT1-deficient (Stat1 −/−) mice, whereas peripheral administration of anti-CLEC5A mAb reduces infiltration of virus-harboring leukocytes into the central nervous system (CNS), restores BBB integrity, attenuates neuroinflammation, and protects mice from JEV-induced lethality. Moreover, all surviving mice develop protective humoral and cellular immunity against JEV infection. These observations demonstrate the critical role of CLEC5A in the pathogenesis of Japanese encephalitis, and identify CLEC5A as a target for the development of new treatments to reduce virus-induced brain damage.
Expression of EBV Latent Antigens, Mammalian Target of Rapamycin, and Tumor Suppression Genes in EBV-Positive Smooth Muscle Tumors: Clinical and Therapeutic Implications

Purpose: EBV-positive smooth muscle tumor (EBV+SMT) is a rare disease with no established therapy. We describe the largest single institution analysis in renal transplant recipients. It aims to define its clinical features and determine the expression of EBV latent genes as well as key molecular pathways. Experimental Design: Patients with EBV+SMT were identified from the Singapore General Hospital Renal Transplant Registry database. These tumors were investigated for expression of EBV latent genes with Southern blots, EBV latent antigens, mammalian target of rapamycin (mTOR), Akt, p70 S6 kinase, and vascular endothelial growth factor using immunohistochemistry, as well as methylation status of cancer-related genes using methylation-specific PCR. Results: Eight were found to be EBV+SMT in 1,123 transplant patients. All displayed indolent clinical courses and were unresponsive to immunosuppression reduction. Complete tumor regression was seen in one patient following administration of sirolimus. These tumors display the full range of known EBV latent genes. Immunohistochemistry with total and phosphorylated mTOR and Akt were positive for all patients, and vascular endothelial growth factor was positive in 25% of patients, suggesting activation of the mTOR/Akt pathway. Methylation of RASSF1A was found in all tissue samples, whereas promoter hypermethylation of RARβ, GSTP1, DAPK, and p14 was observed in some samples. Conclusions: Our results suggest that these tumors display a EBV type III latency pattern. The mTOR pathway is also activated. EBV may play a role in silencing RASSF1A. EBV-specific immunotherapy, mTOR inhibitors, and demethylating agents are possible therapeutic options in this disease. (Clin Cancer Res 2009;15(17):5350–8)
eduComponents: a component-based e-learning environment

We present the eduComponents, a component-based approach to e-learning system architecture. In contrast to typical "integrated" platforms, the eduComponents are implemented as extension modules for a general-purpose content management system (CMS). The components can be used individually, together, and in combination with other modules. The use of a general-purpose (i.e., note-learning-specific) CMS means that a single platform can be used for e-learning and other Web content, providing the advantages of a uniform user interface, reduced system administration overhead, and extensive code reuse.
Congenital facial deformity : experiences of mothers of twins

The topic of cleft lip and/or palate is widely researched in literature. However no research to date has focused on mothers’ experiences raising twins when one twin is born with a cleft lip and/or palate. This qualitative study aims to explore the unique experiences of these mothers. The epistemological foundations of this study are postmodern, social constructionist and systemic. In accordance with a qualitative methodology data was collected in the form of the participants’ personal written stories. This was done from a post-modern paradigm, from a systemic perspective. Themes that were extracted from the stories according to thematic content analysis, not only reflect the experiences of mothers raising twins when one twin is born with a cleft lip and/or palate, they also provide an in-depth understanding of these mothers’ experiences and unique situations. Recommendations for future research are offered. Key terms: Congenital facial deformity, cleft lip and/or palate, twins, mothers, family systems, post modernism, support systems thematic content analysis and qualitative research.