Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer

ABSTRACT Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3′ end of the fda, rpsI, or rpmG gene) with the conjugation module of the ICESt3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICESt3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus, and to Enterococcus faecalis was observed. The analysis of the ICE-fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase. IMPORTANCE The ICESt3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of S. salivarius. Closely related ICEs were also detected in silico in other Streptococcus species (S. pneumoniae and S. parasanguinis), thus indicating that diffusion of ICESt3-related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present.
Ethnic identity negotiation among Sami youth living in a majority Sami community in Norway

ABSTRACT Background: This study was part of the international research project “Circumpolar Indigenous Pathways to Adulthood” (CIPA). Objectives: To explore ethnic identity negotiation, an unexplored theme, among indigenous North Sami youth living in a majority Sami community context in Arctic Norway. Methods: A qualitative design was followed using open-ended, in-depth interviews conducted in 2010 with 22 Sami adolescents aged 13–19 years, all reporting Sami self-identification. Grounded theory, narrative analysis, theories of ethnic identity and ecological perspectives on resilience were applied in order to identify the themes. Findings: All 22 youth reported being open about either their Sami background (86%) and/or ethnic pride (55%). Ethnic pride was reported more often among females (68%) than males (27%). However, a minority of youth (14%) with multi-ethnic parentage, poor Sami language skills, not having been born or raised in the community and with a lack of reindeer husbandry affiliation experienced exclusion by community members as not being affirmed as Sami, and therefore reported stressors like anger, resignation, rejection of their Sami origins and poor well-being. Sami language was most often considered as important for communication (73%), but was also associated with the perception of what it meant to be a Sami (32%) and “traditions” (23%). Conclusion: Ethnic pride seemed to be strong among youth in this majority Sami context. Denial of recognition by one’s own ethnic group did not negatively influence ethnic pride or openness about ones’ ethnic background, but was related to youth experience of intra-ethnic discrimination and poorer well-being. As Sami language was found to be a strong ethnic identity marker, effective language programmes for Norwegian-speaking Sami and newcomers should be provided. Language skills and competence would serve as an inclusive factor and improve students’ well-being and health. Raising awareness about the diversity of Sami identity negotiations among adolescents in teacher training and schools in general should be addressed.
Geochemical and Temporal Influences on the Enrichment of Acidophilic Iron-Oxidizing Bacterial Communities

ABSTRACT Two acid mine drainage (AMD) sites in the Appalachian bituminous coal basin were selected to enrich for Fe(II)-oxidizing microbes and measure rates of low-pH Fe(II) oxidation in chemostatic bioreactors. Microbial communities were enriched for 74 to 128 days in fed-batch mode, then switched to flowthrough mode (additional 52 to 138 d) to measure rates of Fe(II) oxidation as a function of pH (2.1 to 4.2) and influent Fe(II) concentration (80 to 2,400 mg/liter). Biofilm samples were collected throughout these operations, and the microbial community structure was analyzed to evaluate impacts of geochemistry and incubation time. Alpha diversity decreased as the pH decreased and as the Fe(II) concentration increased, coincident with conditions that attained the highest rates of Fe(II) oxidation. The distribution of the seven most abundant bacterial genera could be explained by a combination of pH and Fe(II) concentration. Acidithiobacillus, Ferrovum, Gallionella, Leptospirillum, Ferrimicrobium, Acidiphilium, and Acidocella were all found to be restricted within specific bounds of pH and Fe(II) concentration. Temporal distance, defined as the cumulative number of pore volumes from the start of flowthrough mode, appeared to be as important as geochemical conditions in controlling microbial community structure. Both alpha and beta diversities of microbial communities were significantly correlated to temporal distance in the flowthrough experiments. Even after long-term operation under nearly identical geochemical conditions, microbial communities enriched from the different sites remained distinct. While these microbial communities were enriched from sites that displayed markedly different field rates of Fe(II) oxidation, rates of Fe(II) oxidation measured in laboratory bioreactors were essentially the same. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup. IMPORTANCE This study showed that different microbial communities enriched from two sites maintained distinct microbial community traits inherited from their respective seed materials. Long-term operation (up to 128 days of fed-batch enrichment followed by up to 138 days of flowthrough experiments) of these two systems did not lead to the same, or even more similar, microbial communities. However, these bioreactors did oxidize Fe(II) and remove total iron [Fe(T)] at very similar rates. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup. This would be advantageous, because system performance should be well constrained and predictable for many different sites.
Association of ß-hCG Surveillance with Emotional, Reproductive, and Sexual Health in Women Treated for Gestational Trophoblastic Neoplasia.

BACKGROUND To assess the emotional, reproductive, sexual health, and relationship concerns of women treated for gestational trophoblastic neoplasia (GTN) and examine associations with ß-hCG surveillance. METHODS This institutional review board approved study surveyed GTN survivors (n = 51) who received treatment from 1996 to 2008. Fifty-one women, including those actively followed or formerly treated, were surveyed. The survey consisted of background/medical information, the Reproductive Concerns Scale, the Female Sexual Function Index, an item from the Abbreviated Dyadic Adjustment Scale, the Center for Epidemiologic Studies-Depression scale, the Menopausal Symptom Checklist, the Impact of Life Events Scale, and exploratory items. RESULTS Mean age at diagnosis was 37.1 years; 41.6 years at study enrollment. Twenty-seven patients (56%) expressed worry about treatment harm and 30 (60%) about recurrence. Twenty percent reported significant depressive symptomatology. Mild cancer-related distress, reproductive concerns, sexual dysfunction, and bothersome menopausal symptoms were noted. Nineteen patients (40%) rated their ß-hCG surveillance worry as "high. " Among patients who attempted conception after treatment, 3 of 12 (25%) succeeded in the ß-hCG high-worry group versus 13 of 19 (68%) in the ß-hCG low-worry group. Survivors with high ß-hCG worry had greater reproductive concerns than those with low worry (p = 0.002) and reported less sexual desire (p = 0.025). There was no difference in the number of low-worry versus high-worry participants in active surveillance (p = 0.09). CONCLUSION Our study suggests that cancer-specific distress, sexual health, and reproductive concerns continue to impact women years after treatment. High worry about ß-hCG surveillance is negatively associated with the emotional well-being of GTN survivors and possibly influences reproductive attempts and success.
Mixed aortic valve disease: midterm outcome and predictors of adverse events.

AIMS The aim of this article is to determine freedom from adverse events (AE) defined as symptoms, aortic valve replacement (AVR), or death in the mixed aortic valve disease (MAVD) population. METHODS AND RESULTS We reviewed patients with moderate/severe MAVD followed at Mayo Clinic from 1994-2013. Only asymptomatic patients with normal ejection fraction and trileaflet aortic valve were included. Cox proportional-hazard models and Kaplan-Meier method were used. We identified 213 patients with moderate/severe MAVD; mean age was 69 years (±11) and 67% were males. An AE endpoint was reached in 172 patients, and 69% of these AEs occurred in moderate MAVD (peak velocity of 3-3.9 m/s). Mean follow-up was 10.1 ± 3 years, and mean time to AE was 2.9 ± 2.1 years. A mechanical prosthesis was implanted in 71/151 (47%), and 54/151 (36%) had concomitant coronary artery bypass grafting and/or aorta replacement during AVR. Early surgical mortality was 0.7%. Freedom from AE endpoint was 42% [confidence interval (CI) 39-45%] and 30% (CI 27-33%) at 3 and 5 years, respectively. Predictors of AE were peak aortic velocity [hazard ratio (HR) 2.73; CI 1.97-2.84, P < 0.0001] for every 1 m/s difference and having severe stenosis or severe regurgitation at presentation (HR 2.58; CI 2.01-4.44, P = 0.001). CONCLUSION Moderate MAVD had high rate of AEs comparable to severe isolated aortic stenosis and should be followed as such. Patients with severe MAVD should be evaluated at least every 6 months because half of them will become symptomatic and require AVR within 1 year.
Recommendation and Configuration of Value-Added Services for Repurposing Electric Vehicle Batteries: A Vertical Software Prototype

Due to degradation effects, electric vehicle batteries (EVBs) have a lifetime of approximately ten years in electric vehicles (EVs). Recycling EVBs is inefficient and ecologically undesirable if the batteries can be repurposed to second life scenarios. Decision support systems (DSSs) can be implemented to identify the best second life scenario for which to repurpose individual batteries. However, the properties of EVBs as used products can cause information asymmetries that challenge or even disrupt the market for used EVBs. Providing value-added services with used EVBs is one strategy to mitigate the information asymmetry. Guided by seven design principles, we develop and demonstrate a vertical software prototype for configuring energy storage solutions (ESSs), consisting of used EVBs and value-added services. Core of the system is an item-based collaborative filtering recommender system. The prototype can serve as a blueprint for a class of information systems to repurpose other used goods as customer solutions.
Sustained safety and performance of the second-generation drug-eluting absorbable metal scaffold in patients with de novo coronary lesions: 12-month clinical results and angiographic findings of the BIOSOLVE-II first-in-man trial

Abstract Aims Metal absorbable scaffolds constitute a conceptually attractive alternative to polymeric scaffolds. Promising 6-month outcomes of a second-generation drug-eluting absorbable metal scaffold (DREAMS 2G), consisting of an absorbable magnesium scaffold backbone, have been reported. We assessed the 12-month safety and performance of this novel device. Methods and results The prospective, international, multi-centre, first-in-man BIOSOLVE-II trial enrolled 123 patients with up to two de novo lesions with a reference diameter between 2.2 and 3.7 mm. All patients were scheduled for angiographic follow-up at 6 months, and—if subjects consented—at 12 months. Dual antiplatelet therapy was recommended for 6 months. Quantitative coronary angiography (QCA) parameters remained stable from 6 to 12 months [paired data of 42 patients: in-segment late lumen loss 0.20 ± 0.21 mm vs. 0.25 ± 0.22 mm, P = 0.117, Δ 0.05 ± 0.21 mm (95% CI: −0.01;0.12); in-scaffold late lumen loss 0.37 ± 0.25 mm vs. 0.39 ± 0.27 mm, P = 0.446, Δ 0.03 ± 0.22 (95% CI: −0.04;0.10), respectively]. Intravascular ultrasound and optical coherence tomography findings corroborated the QCA results. Target lesion failure occurred in four patients (3.4%), consisting of one death of unknown cause, one target-vessel myocardial infarction, and two clinically driven target lesion revascularization. No additional event occurred beyond the 6-month follow-up. During the entire follow-up of 12 months, none of the patients experienced a definite or probable scaffold thrombosis. Conclusion The novel drug-eluting metal absorbable scaffold DREAMS 2G showed a continuous favourable safety profile up to 12 months and stable angiographic parameters between 6 and 12 months. ClinicalTrials.gov identifier NCT01960504.
Action Recognition With Spatio–Temporal Visual Attention on Skeleton Image Sequences

Action recognition with 3D skeleton sequences became popular due to its speed and robustness. The recently proposed convolutional neural networks (CNNs)-based methods show a good performance in learning spatio–temporal representations for skeleton sequences. Despite the good recognition accuracy achieved by previous CNN-based methods, there existed two problems that potentially limit the performance. First, previous skeleton representations were generated by chaining joints with a fixed order. The corresponding semantic meaning was unclear and the structural information among the joints was lost. Second, previous models did not have an ability to focus on informative joints. The attention mechanism was important for skeleton-based action recognition because different joints contributed unequally toward the correct recognition. To solve these two problems, we proposed a novel CNN-based method for skeleton-based action recognition. We first redesigned the skeleton representations with a depth-first tree traversal order, which enhanced the semantic meaning of skeleton images and better preserved the associated structural information. We then proposed the general two-branch attention architecture that automatically focused on spatio–temporal key stages and filtered out unreliable joint predictions. Based on the proposed general architecture, we designed a global long-sequence attention network with refined branch structures. Furthermore, in order to adjust the kernel’s spatio–temporal aspect ratios and better capture long-term dependencies, we proposed a sub-sequence attention network (SSAN) that took sub-image sequences as inputs. We showed that the two-branch attention architecture could be combined with the SSAN to further improve the performance. Our experiment results on the NTU RGB+D data set and the SBU kinetic interaction data set outperformed the state of the art. The model was further validated on noisy estimated poses from the subsets of the UCF101 data set and the kinetics data set.
THE EFFECT OF THE MUSHY-ZONE CONSTANT ON SIMULATED PHASE CHANGE HEAT TRANSFER

Solid-liquid phase change heat transfer is of the t ype of problem known as “moving boundary” problems. With very few solutions known analytical ly, the fast majority of those problems are solved numerically; either through the use of defor mable mesh/grid, or the more common use of enthalpy or modified specific heat methods. Those methods account for the additional latent heat of fusion required for physical energy conservation du ring phase change. It has also been shown through numerous experimenta l work that natural convection in the liquid phase during melting plays a dominating role. This t erefore requires the addition of buoyancy forces to model natural convection during overall p hase change processes of various phase change materials. Since most methods used to simulate pha se change heat transfer cannot handle a constant temperature phase change process, they must simulat e ph se change over a given temperature interval, which results in the addition of a mushy region where the phase change materials is in a state between fully solid and fully liquid. The tr eatment of possible fluid flow from natural convection in this mushy zone has been the subject of numerous discussions at heat transfer conferences in the last few years. Typically, an e quation of this form is used to account for the change in viscosity, from liquid to nearly infinite in the solid, and to force trivial solutions of th e Navier-Stokes equations in the solid: with ε being a small constant to avoid division by zero, B(T) is a function changing from 0 to 1 over the mushy region and C is the mushy-zone constant that is debated here. Various commercial software guidelines and various researchers using d ifferent values ranging from 10 3 to nearly 1010, a variation of 7 orders of magnitude. This paper presents a study of the impact of this m u hy-zone constant C value on overall melting simulation results. A simple rectangular geometry is employed for which experimental results are published; the impact of the value of C on the physicality of the results can therefore be assessed. Simulation are also performed using two different s of ware: ANSYS Fluent which has a predefined phase change physics where the constant C is an input and COMSOL Multiphysics where the enti re set of physical equations needed to account for nat ural convection and phase change material movement must be added by the user, again with cons tant C playing a definite role.
Validation of a contextualized assessment of smoking behaviour in students

AIMS The aim of this study was to validate an audio simulation of culture-specific social contexts associated with smoking to provide a medium for researchers to investigate social-contextual influences on tobacco use in the laboratory. METHODS Eighty-one students (34.6% men; n = 28) listened to five audio simulations of peer social contexts where offers to smoke tobacco were made [Smoking Simulated Intoxication Digital Elicitation (S-SIDE)]. For each social scenario, participants answered questions about their willingness to accept the offer to smoke and completed measures of smoking cognitions and tobacco use. Thirty days later, participants completed online assessments of smoking behaviour. RESULTS Willingness to accept smoking offers in the S-SIDE procedure was related to smoking at both time-points (T1: r(81) = 0.37, P < 0.001;T2: r(81) = 0.36, P = 0.001). Performance on the simulation improved prediction of smoking at 1 month follow-up over and above smoking expectancies, F(2,74) = 4.27, P = 0.02; R2 = 0.21; ΔR2 = 0.09, as well as other indices of smoking willingness, F(2,75) = 4.22, P = 0.02; R2 = 0.22: ΔR2 = 0.09, while neither expectancies nor willingness was related to smoking above and beyond the simulation. CONCLUSIONS Social context plays an important role in smoking-related decision-making and simulated social contexts have potential for the study of context-related decision-making in addiction.
The Impact of Massage Therapy on Function in Pain Populations—A Systematic Review and Meta-Analysis of Randomized Controlled Trials: Part I, Patients Experiencing Pain in the General Population

Abstract Purpose Pain is multi-dimensional and may be better addressed through a holistic, biopsychosocial approach. Massage therapy is commonly practiced among patients seeking pain management; however, its efficacy is unclear. This systematic review and meta-analysis is the first to rigorously assess the quality of massage therapy research and evidence for its efficacy in treating pain, function-related and health-related quality of life outcomes across all pain populations. Methods Key databases were searched from inception through February 2014. Eligible randomized controlled trials were assessed for methodological quality using SIGN 50 Checklist. Meta-analysis was applied at the outcome level. A diverse steering committee interpreted the results to develop recommendations. Results Sixty high quality and seven low quality studies were included in the review. Results demonstrate massage therapy effectively treats pain compared to sham [standardized mean difference (SMD) = −. 44], no treatment (SMD = −1.14), and active (SMD = −0.26) comparators. Compared to active comparators, massage therapy was also beneficial for treating anxiety (SMD = −0.57) and health-related quality of life (SMD = 0.14). Conclusion Based on the evidence, massage therapy, compared to no treatment, should be strongly recommended as a pain management option. Massage therapy is weakly recommended for reducing pain, compared to other sham or active comparators, and improving mood and health-related quality of life, compared to other active comparators. Massage therapy safety, research challenges, how to address identified research gaps, and necessary next steps for implementing massage therapy as a viable pain management option are discussed.
Identification of IL2RG and CYBB mutations in two Chinese primary immunodeficiency patients by whole-exome sequencing

ABSTRACT Background Primary immunodeficiency diseases are a group of genetic disorders that lead to increased propensity to a variety of infections, sometimes with fatal outcomes. Method In this study, whole-exome sequencing (WES) was used to identify mutations in two patients suspected of having primary immunodeficiency. Sanger sequencing was used to confirm the results in the patients and their family. Result One patient was diagnosed as X-linked severe combined immunodeficiency (X-SCID) and another patient as X-linked chronic granulomatous disease (X-CGD) by WES. Sequencing analysis of IL2RG gene revealed a novel mutation (c.794T>A, p.I265N) and CYBB gene revealed a missense mutation (c.935T>A, p.M312K). Discussion and conclusion This study identifies one novel mutation in the IL2RG gene and another, previously described mutation in the CYBB genes. It is the first report establishing a diagnosis of X-SCID and X-CGD using WES in Chinese patients.