Miracle-dz/UniFAR-FTUs huggingface dataset:
Interbacterial Adhesion Networks within Early Oral Biofilms of Single Human Hosts

ABSTRACT Specific interbacterial adhesion, termed coaggregation, is well established for three early colonizers of the plaque biofilm: streptococci, actinomyces, and veillonellae. However, little is known about interactions of other early colonizers and about the extent of interactions within the bacterial community from a single host. To address these gaps, subject-specific culture collections from two individuals were established using an intraoral biofilm retrieval device. Molecular taxonomy (Human Oral Microbe Identification Microarray [HOMIM]) analysis of biofilm samples confirmed the integrity and completeness of the collections. HOMIM analysis verified the isolation of Streptococcus gordonii and S. anginosus from only one subject, as well as isolation of a previously uncultivated streptococcal phylotype from the other subject. Strains representative of clonal diversity within each collection were further characterized. Greater than 70% of these streptococcal strains from each subject coaggregated with at least one other coisolate. One-third of the strains carry a known coaggregation mediator: receptor polysaccharide (RPS). Almost all nonstreptococcal isolates coaggregated with other coisolates. Importantly, certain Rothia strains demonstrated more coaggregations with their coisolated bacteria than did any Streptococcus or Actinomyces strain, and certain Haemophilus isolates participated in twice as many. Confocal microscopy of undisturbed biofilms showed that Rothia and Haemophilus each occur in small multispecies microcolonies. However, in confluent high-biomass regions, Rothia occurred in islands whereas Haemophilus was distributed throughout. Together, the data demonstrate that coaggregation networks within an individual's oral microflora are extensive and that Rothia and Haemophilus can be important initiators of cell-cell interactions in the early biofilm. IMPORTANCE Extensive involvement of specific interbacterial adhesion in dental plaque biofilm formation has been postulated based on in vitro coaggregation between oral bacteria from culture collections that are not subject specific. In the present study, subject-specific culture collections were obtained from early plaque biofilm of two volunteers, and coaggregations within each culture collection were assayed. Coaggregations, several of which involved a coaggregation-mediating cell surface molecule known from well-studied streptococci, were widespread. Unexpectedly, the little-studied organisms Haemophilus and Rothia participated in the greatest numbers of interactions with community members; these two organisms showed different distributions within the undisturbed biofilm. The data show that coaggregation networks encompass most organisms within the biofilm community of each individual, and they indicate prominent participation of organisms such as Haemophilus and Rothia in early plaque biofilm formation.
Decreased expression of miR-490-3p in osteosarcoma and its clinical significance.

OBJECTIVE Increasing evidence has revealed that miRNAs play a key role in the development and progression of tumor and are being explored as a prognostic biomarker. The aim of this study was to investigate the clinical significance of miR-490-3p expression in osteosarcoma. PATIENTS AND METHODS Quantitative real-time PCR (qRT-PCR) was used to evaluate miR-490-3p level in osteosarcoma tissues. We also analyzed the correlations between the expression level of miR-490-3p and the clinical characteristics in cases of osteosarcoma. Also, Kaplan-Meier curve and the log-rank test were conducted to detect the prognostic value of miR-490-3p. Finally, univariable and multivariable Cox regression analyses were used to evaluate independent prognostic factors. RESULTS MiR-490-3p expression level was significantly downregulated in osteosarcoma tissues in comparison with noncancerous bone tissues. Moreover, low miR-490-3p expression was significantly associated with distant metastasis, advanced clinical stage and poor overall survival and relapse-free survival. Univariate and multivariate analysis results indicated that miR-490-3p was an independent prognostic factor in osteosarcoma. CONCLUSIONS Our results showed that miR-490-3p plays critical roles in osteosarcoma progression and serves as a novel prognostic indicator and a potential therapeutic target for osteosarcoma.
Embryophyte stress signaling evolved in the algal progenitors of land plants

Significance The evolution of land plants from algae is an age-old question in biology. The entire terrestrial flora stems from a grade of algae, the streptophyte algae. Recent phylogenomic studies have pinpointed the Zygnematophyceae as the modern-day streptophyte algal lineage that is most closely related to the algal land plant ancestor. Here, we provide insight into the biology of this ancestor that might have aided in its conquest of land. Specifically, we uncover the existence of stress-signaling pathways and the potential for intimate plastid-nucleus communication. Plastids act as environmental sensors in land plants; our data suggest that this feature was present in a common ancestor they shared with streptophyte algae. Streptophytes are unique among photosynthetic eukaryotes in having conquered land. As the ancestors of land plants, streptophyte algae are hypothesized to have possessed exaptations to the environmental stressors encountered during the transition to terrestrial life. Many of these stressors, including high irradiance and drought, are linked to plastid biology. We have investigated global gene expression patterns across all six major streptophyte algal lineages, analyzing a total of around 46,000 genes assembled from a little more than 1.64 billion sequence reads from six organisms under three growth conditions. Our results show that streptophyte algae respond to cold and high light stress via expression of hallmark genes used by land plants (embryophytes) during stress–response signaling and downstream responses. Among the strongest differentially regulated genes were those associated with plastid biology. We observed that among streptophyte algae, those most closely related to land plants, especially Zygnema, invest the largest fraction of their transcriptional budget in plastid-targeted proteins and possess an array of land plant-type plastid-nucleus communication genes. Streptophyte algae more closely related to land plants also appear most similar to land plants in their capacity to respond to plastid stressors. Support for this notion comes from the detection of a canonical abscisic acid receptor of the PYRABACTIN RESISTANCE (PYR/PYL/RCAR) family in Zygnema, the first found outside the land plant lineage. We conclude that a fine-tuned response toward terrestrial plastid stressors was among the exaptations that allowed streptophytes to colonize the terrestrial habitat on a global scale.
ICDAR2017 Competition on Recognition of Documents with Complex Layouts - RDCL2017

This paper presents an objective comparative evaluation of page segmentation and region classification methods for documents with complex layouts. It describes the competition (modus operandi, dataset and evaluation methodology) held in the context of ICDAR2017, presenting the results of the evaluation of seven methods – five submitted, two state-of-the-art systems (commercial and open-source). Three scenarios are reported in this paper, one evaluating the ability of methods to accurately segment regions and two evaluating both segmentation and region classification (one focusing only on text regions). For the first time, nested region content (table cells, chart labels etc.) are evaluated in addition to the top-level page content. Text recognition was a bonus challenge and was not taken up by all participants. The results indicate that an innovative approach has a clear advantage but there is still a considerable need to develop robust methods that deal with layout challenges, especially with the non-textual content.
The Contribution of Social Media to Body Dissatisfaction, Eating Disorder Symptoms, and Anabolic Steroid Use Among Sexual Minority Men

Abstract Social media has been associated with body dissatisfaction and eating disorder symptoms among young women and adolescent girls. However, despite notable evidence of susceptibility to body image pressures, it remains unknown whether these associations generalize to sexual minority men. A nationwide sample of 2,733 sexual minority men completed an online survey advertised to Australian and New Zealand users of a popular dating app. Participants answered questions about how frequently they used 11 different social media platforms in addition to questions about their dating app use, body image, eating disorder symptoms, and anabolic steroids. Facebook, Youtube, Instagram, and Snapchat were the most frequently used social media platforms. A pattern of small-sized and positive associations emerged between social media use and body dissatisfaction, eating disorder symptoms, and thoughts about using anabolic steroids. Facebook, Instagram, and Snapchat evidenced the strongest associations. The associations of social media use with both muscularity dissatisfaction and eating disorder symptoms were stronger for image-centric social media platforms (e.g., Instagram) than nonimage-centric platforms (e.g., Wordpress); no differences were observed for body fat dissatisfaction, height dissatisfaction, or thoughts about using anabolic steroids. Previously documented associations of social media use with body dissatisfaction and related variables among women and girls appear to generalize to sexual minority men. Social media platforms that more centrally involve imagery may be of greater concern than nonimage-centric platforms. Additional research with sexual minority men is needed to elucidate the distinctions between adaptive and maladaptive social media use in the context of body dissatisfaction, eating disorders, and anabolic steroid use.
Patients in Haemodialysis Experienced Uraemic Pruritus as a Dual Phenomenon

BACKGROUND Uraemic pruritus (UP) is one of the most frequent symptoms for patients in haemodialysis. Studies show that UP decreases quality of life including sleep. Patients find it difficult to describe the symptoms of UP to healthcare professionals. OBJECTIVES To explore how patients in haemodialysis experience the phenomenon of UP. METHODS A qualitative phenomenological-hermeneutic framework was used. Fifteen semi-structured interviews were undertaken at a Danish university hospital in November 2015. The interviews were transcribed and analysed using Malterud's principles of systematic text condensation. RESULTS Patients gave conflicting descriptions of the phenomenon. Patients experienced UP as a dual phenomenon described as 'the itch' and 'itching'. 'The itch' will never disappear and is unmanageable, and 'itching' appears intermittently and is possible to prevent and alleviate. CONCLUSION/APPLICATION TO PRACTICE It is impossible for patients to manage UP on their own but it may be possible to manage it as a dual phenomenon. This knowledge can give both patients and healthcare professionals a new perspective on UP and its symptoms.
Retrospective Correction of Physiological Noise: Impact on Sensitivity, Specificity, and Reproducibility of Resting-State Functional Connectivity in a Reading Network Model

It is well accepted that physiological noise (PN) obscures the detection of neural fluctuations in resting-state functional connectivity (rsFC) magnetic resonance imaging. However, a clear consensus for an optimal PN correction (PNC) methodology and how it can impact the rsFC signal characteristics is still lacking. In this study, we probe the impact of three PNC methods: RETROICOR: (Glover et al., 2000 ), ANATICOR: (Jo et al., 2010 ), and RVTMBPM: (Bianciardi et al., 2009 ). Using a reading network model, we systematically explore the effects of PNC optimization on sensitivity, specificity, and reproducibility of rsFC signals. In terms of specificity, ANATICOR was found to be effective in removing local white matter (WM) fluctuations and also resulted in aggressive removal of expected cortical-to-subcortical functional connections. The ability of RETROICOR to remove PN was equivalent to removal of simulated random PN such that it artificially inflated the connection strength, thereby decreasing sensitivity. RVTMBPM maintained specificity and sensitivity by balanced removal of vasodilatory PN and local WM nuisance edges. Another aspect of this work was exploring the effects of PNC on identifying reading group differences. Most PNC methods accounted for between-subject PN variability resulting in reduced intersession reproducibility. This effect facilitated the detection of the most consistent group differences. RVTMBPM was most effective in detecting significant group differences due to its inherent sensitivity to removing spatially structured and temporally repeating PN arising from dense vasculature. Finally, results suggest that combining all three PNC resulted in "overcorrection" by removing signal along with noise.
Effects of heating rate, quartz particle size, viscosity, and form of glass additives on high‐level waste melter feed volume expansion

Nuclear waste can be vitrified by mixing it with glass-forming and -modifying additives. The resulting feed is charged into an electric glass melter. To comprehend melting behavior of a high-alumina melter feed, we monitored the volume expansion of pellets in response to heating at different heating rates. The feeds were prepared with different particle sizes of quartz (the major additive component) and with varied silica-to-fluxes ratio to investigate the glass melt viscosity effects. Also, we used additional melter feeds with additives premelted into glass frit. The volume of pellets was nearly constant at temperatures <600°C. After a short period of volume shrinkage at ~600°C–700°C, foam generation produced massive volume expansion. The low heat conductivity of foam hinders the transfer of heat from molten glass to the reacting feed. The extent of foaming increased with faster heating and higher melt viscosity, and decreased with increasing size of quartz particles and fritting of the additives. Volume expansion data are needed for the mathematical modeling of the cold cap.
The “glymphatic” mechanism for solute clearance in Alzheimer's disease: game changer or unproven speculation?

How solutes and macromolecules are removed from brain tissue is of central importance in normal brain physiology and in how toxic protein aggregates are cleared in neurodegenerative conditions, including Alzheimer's disease (AD). Conventionally, solute transport in the narrow and tortuous extracellular space in brain parenchyma has been thought to be primarily diffusive and nondirectional. The recently proposed “glymphatic” (glial‐lymphatic) hypothesis posits that solute clearance is convective and driven by active fluid transport from para‐arterial to paravenous spaces though aquaporin‐4 water channels in astrocyte endfeet. Glymphatic, convective solute clearance has received much attention because of its broad implications for AD and other brain pathologies and even the function of sleep. However, the theoretical plausibility of glymphatic transport has been questioned, and recent data have challenged its experimental underpinnings. A substantiated mechanism of solute clearance in the brain is of considerable importance because of its implications for pathogenic mechanisms of neurologic diseases and delivery of therapeutics. —Smith, A. J., Verkman, A. S. The “glymphatic” mechanism for solute clearance in Alzheimer's disease: game changer or unproven speculation? FASEB J. 32, 543–551 (2018). www.fasebj. org
The Campylobacter jejuni Ferric Uptake Regulator Promotes Acid Survival and Cross-Protection against Oxidative Stress

ABSTRACT Campylobacter jejuni is a prevalent cause of bacterial gastroenteritis in humans worldwide. The mechanisms by which C. jejuni survives stomach acidity remain undefined. In the present study, we demonstrated that the C. jejuni ferric uptake regulator (Fur) plays an important role in C. jejuni acid survival and acid-induced cross-protection against oxidative stress. A C. jejuni Δfur mutant was more sensitive to acid than the wild-type strain. Profiling of the acid stimulon of the C. jejuni Δfur mutant allowed us to uncover Fur-regulated genes under acidic conditions. In particular, Fur was found to upregulate genes involved in flagellar and cell envelope biogenesis upon acid stress, and mutants with deletions of these genes were found to be defective in surviving acid stress. Interestingly, prior acid exposure of C. jejuni cross-protected against oxidative stress in a catalase (KatA)- and Fur-dependent manner. Western blotting and reverse transcription-quantitative PCR revealed increased expression of KatA upon acid stress. Electrophoretic mobility shift assays (EMSAs) demonstrated that the binding affinity between Fur and the katA promoter is reduced in vitro under conditions of low pH, rationalizing the higher levels of expression of katA under acidic conditions. Strikingly, the Δfur mutant exhibited reduced virulence in both human epithelial cells and the Galleria mellonella infection model. Altogether, this is the first study showing that, in addition to its role in iron metabolism, Fur is an important regulator of C. jejuni acid responses and this function cross-protects against oxidative stress. Moreover, our results clearly demonstrate Fur's important role in C. jejuni pathogenesis.
UvA-DARE (Digital Academic Repository) Neural vector spaces for unsupervised information retrieval

We propose the Neural Vector Space Model (NVSM), a method that learns representations of documents in an unsupervised manner for news article retrieval. In the NVSM paradigm, we learn low-dimensional representations of words and documents from scratch using gradient descent and rank documents according to their similarity with query representations that are composed from word representations. We show that NVSM performs better at document ranking than existing latent semantic vector space methods. The addition of NVSM to a mixture of lexical language models and a state-of-the-art baseline vector space model yields a statistically significant increase in retrieval effectiveness. Consequently, NVSM adds a complementary relevance signal. Next to semantic matching, we find that NVSM performs well in cases where lexical matching is needed. NVSM learns a notion of term specificity directly from the document collection without feature engineering. We also show that NVSM learns regularities related to Luhn significance. Finally, we give advice on how to deploy NVSM in situations where model selection (e.g., cross-validation) is infeasible. We find that an unsupervised ensemble of multiple models trained with different hyperparameter values performs better than a single cross-validated model. Therefore, NVSM can safely be used for ranking documents without supervised relevance judgments.
Approximation and Online Algorithms for NFV-Enabled Multicasting in SDNs

Multicasting is a fundamental functionality of networks for many applications including online conferencing, event monitoring, video streaming, and system monitoring in data centers. To ensure multicasting reliable, secure and scalable, a service chain consisting of network functions (e.g., firewalls, Intrusion Detection Systems (IDSs), and transcoders) usually is associated with each multicast request. Such a multicast request is referred to as an NFV-enabled multicast request. In this paper we study NFV-enabled multicasting in a Software-Defined Network (SDN) with the aims to minimize the implementation cost of each NFV-enabled multicast request or maximize the network throughput for a sequence of NFV-enabled requests, subject to network resource capacity constraints. We first formulate novel NFV-enabled multicasting and online NFV-enabled multicasting problems. We then devise the very first approximation algorithm with an approximation ratio of 2K for the NFV-enabled multicasting problem if the number of servers for implementing the network functions of each request is no more than a constant K (1). We also study dynamic admissions of NFV-enabled multicast requests without the knowledge of future request arrivals with the objective to maximize the network throughput, for which we propose an online algorithm with a competitive ratio of O(log n) when K = 1, where n is the number of nodes in the network. We finally evaluate the performance of the proposed algorithms through experimental simulations. Experimental results demonstrate that the proposed algorithms outperform other existing heuristics.
Study on Silica Infused Recycled Aggregate Concrete Using Design of Experiments

Recycled Aggregate (RA) generated from the construction industry is used as a material for sustainable construction. The old mortar attached to these aggregates makes it porous and are generally used for low-grade applications. However, by infusing with silica fumes, the properties of recycled aggregate concrete (RAC) can be improved, as the silica fumes get infused into the pores of old mortar attached to it. In this study, the optimum percentage of recycled aggregate that can be used in fresh concrete for higher grade applications was found out. Design of experiments (DoE) was used to optimize percentage of silica fumes and recycled aggregate to achieve optimum properties of concrete. Equations to predict the properties of concrete were also modelled using regression analysis.
Likelihood-based methods for evaluating principal surrogacy in augmented vaccine trials

There is growing interest in assessing immune biomarkers, which are quick to measure and potentially predictive of long-term efficacy, as surrogate endpoints in randomized, placebo-controlled vaccine trials. This can be done under a principal stratification approach, with principal strata defined using a subject’s potential immune responses to vaccine and placebo (the latter may be assumed to be zero). In this context, principal surrogacy refers to the extent to which vaccine efficacy varies across principal strata. Because a placebo recipient’s potential immune response to vaccine is unobserved in a standard vaccine trial, augmented vaccine trials have been proposed to produce the information needed to evaluate principal surrogacy. This article reviews existing methods based on an estimated likelihood and a pseudo-score (PS) and proposes two new methods based on a semiparametric likelihood (SL) and a pseudo-likelihood (PL), for analyzing augmented vaccine trials. Unlike the PS method, the SL method does not require a model for missingness, which can be advantageous when immune response data are missing by happenstance. The SL method is shown to be asymptotically efficient, and it performs similarly to the PS and PL methods in simulation experiments. The PL method appears to have a computational advantage over the PS and SL methods.