Empirical Comparison of Graph Embeddings for Trust-Based Collaborative Filtering

In this work, we study the utility of graph embeddings to generate latent user representations for trust-based collaborative filtering. In a cold-start setting, on three publicly available datasets, we evaluate approaches from four method families: (i) factorization-based, (ii) random walk-based, (iii) deep learning-based, and (iv) the Large-scale Information Network Embedding (LINE) approach. We find that across the four families, random-walk-based approaches consistently achieve the best accuracy. Besides, they result in highly novel and diverse recommendations. Furthermore, our results show that the use of graph embeddings in trust-based collaborative filtering significantly improves user coverage.Comment: 10 pages, Accepted as a full paper on the 25th International Symposium on Methodologies for Intelligent Systems (ISMIS'20

Uracil moieties in Plasmodium falciparum genomic DNA

Plasmodium falciparum parasites undergo multiple genome duplication events during their development. Within the intraerythrocytic stages, parasites encounter an oxidative environment and DNA synthesis necessarily proceeds under these circumstances. In addition to these conditions, the extreme AT bias of the P. falciparum genome poses further constraints for DNA synthesis. Taken together, these circumstances may allow appearance of damaged bases in the PlasmodiumDNA. Here, we focus on uracil that may arise in DNA either via oxidative deamination or thymine-replacing incorporation. We determine the level of uracil at the ring, trophozoite, and schizont intraerythrocytic stages and evaluate the base-excision repair potential of P. falciparum to deal with uracil-DNA repair. We find approximately 7–10 uracil per million bases in the different parasite stages. This level is considerably higher than found in other wild-type organisms from bacteria to mammalian species. Based on a systematic assessment of P. falciparum genome and transcriptome databases, we conclude that uracil-DNA repair relies on one single uracil-DNA glycosylase and proceeds through the long-patch base-excision repair route. Although potentially efficient, the repair route still leaves considerable level of uracils in parasite DNA, which may contribute to mutation rates in P. falciparum. © 2018 The Authors. Published by FEBS Press and John Wiley & Sons Ltd

Reliability and validity of a short form household food security scale in a Caribbean community

BACKGROUND: We evaluated the reliability and validity of the short form household food security scale in a different setting from the one in which it was developed. METHODS: The scale was interview administered to 531 subjects from 286 households in north central Trinidad in Trinidad and Tobago, West Indies. We evaluated the six items by fitting item response theory models to estimate item thresholds, estimating agreement among respondents in the same households and estimating the slope index of income-related inequality (SII) after adjusting for age, sex and ethnicity. RESULTS: Item-score correlations ranged from 0.52 to 0.79 and Cronbach's alpha was 0.87. Item responses gave within-household correlation coefficients ranging from 0.70 to 0.78. Estimated item thresholds (standard errors) from the Rasch model ranged from -2.027 (0.063) for the 'balanced meal' item to 2.251 (0.116) for the 'hungry' item. The 'balanced meal' item had the lowest threshold in each ethnic group even though there was evidence of differential functioning for this item by ethnicity. Relative thresholds of other items were generally consistent with US data. Estimation of the SII, comparing those at the bottom with those at the top of the income scale, gave relative odds for an affirmative response of 3.77 (95% confidence interval 1.40 to 10.2) for the lowest severity item, and 20.8 (2.67 to 162.5) for highest severity item. Food insecurity was associated with reduced consumption of green vegetables after additionally adjusting for income and education (0.52, 0.28 to 0.96). CONCLUSIONS: The household food security scale gives reliable and valid responses in this setting. Differing relative item thresholds compared with US data do not require alteration to the cut-points for classification of 'food insecurity without hunger' or 'food insecurity with hunger'. The data provide further evidence that re-evaluation of the 'balanced meal' item is required

A preliminary assessment on use of biochar as a soil additive for reducing the soil-to-plant update of cesium isotopes in radioactively contaminated environments

peer-reviewedA series of Kd tracer batch experiments were conducted to assess the absorptive-desorption properties of Biochar as a potential agent to selectively sequester labile soil Cs or otherwise help reduce the uptake of Cs isotopes into plants. A parallel experiment was conducted for strontium. Fine-grained fractionated Woodlands tree Biochar was found to have a relatively high affinity for Cs ions (Kd > 100) in comparison with untreated coral soil (Kd < 10) collected from the Marshall Islands. The Biochar material also contains an abundance of K (and Mg). These findings support a hypothesis that the addition of Biochar as a soil amendment may provide a simple yet effective method for reducing the soil-to-plant transfer of Cs isotopes in contaminated environments

Aerobic capacity, activity levels and daily energy expenditure in male and female adolescents of the kenyan nandi sub-group

The relative importance of genetic and socio-cultural influences contributing to the success of east Africans in endurance athletics remains unknown in part because the pre-training phenotype of this population remains incompletely assessed. Here cardiopulmonary fitness, physical activity levels, distance travelled to school and daily energy expenditure in 15 habitually active male (13.9±1.6 years) and 15 habitually active female (13.9±1.2) adolescents from a rural Nandi primary school are assessed. Aerobic capacity ([Formula: see text]) was evaluated during two maximal discontinuous incremental exercise tests; physical activity using accelerometry combined with a global positioning system; and energy expenditure using the doubly labelled water method. The [Formula: see text] of the male and female adolescents were 73.9±5.7 ml(.) kg(-1.) min(-1) and 61.5±6.3 ml(.) kg(-1.) min(-1), respectively. Total time spent in sedentary, light, moderate and vigorous physical activities per day was 406±63 min (50% of total monitored time), 244±56 min (30%), 75±18 min (9%) and 82±30 min (10%). Average total daily distance travelled to and from school was 7.5±3.0 km (0.8-13.4 km). Mean daily energy expenditure, activity-induced energy expenditure and physical activity level was 12.2±3.4 MJ(.) day(-1), 5.4±3.0 MJ(.) day(-1) and 2.2±0.6. 70.6% of the variation in [Formula: see text] was explained by sex (partial R(2) = 54.7%) and body mass index (partial R(2) = 15.9%). Energy expenditure and physical activity variables did not predict variation in [Formula: see text] once sex had been accounted for. The highly active and energy-demanding lifestyle of rural Kenyan adolescents may account for their exceptional aerobic fitness and collectively prime them for later training and athletic success

The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities

We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by a spread rather than a series of seeding events from the community into LTCFs. The sequencing of samples taken consecutively from the same individuals at the same facilities showed the persistence of the same genome sequence, indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics allowed probable transmission sources to be better characterised. The transmission between LTCFs was detected in multiple studies. The mortality rate among residents was high in all facilities, regardless of the lineage. Bioinformatics methods were inadequate in a third of the studies reviewed, and reproducing the analyses was difficult because sequencing data were not available in many facilities

A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes

The clinical global impression scale and the influence of patient or staff perspective on outcome

<p>Abstract</p> <p>Background</p> <p>Since its first publication, the Clinical Global Impression Scale (CGI) has become one of the most widely used assessment instruments in psychiatry. Although some conflicting data has been presented, studies investigating the CGI's validity have only rarely been conducted so far. It is unclear whether the improvement index CGI-I or a difference score of the severity index CGI-S_difis more valid in depicting clinical change. The current study examined the validity of these two measures and investigated whether therapists' CGI ratings correspond to the view the patients themselves have on their condition.</p> <p>Methods</p> <p>Thirty-one inpatients of a German psychotherapeutic hospital suffering from a major depressive disorder (age M = 45.3, SD = 17.2; 58.1% women) participated. Patients filled in the Beck Depression Inventory (BDI). CGI-S and CGI-I were rated from three perspectives: the treating therapist (THER), the team of therapists involved in the patient's treatment (TEAM), and the patient (PAT). BDI and CGI-S were filled in at admission and discharge, CGI-I at discharge only. Data was analysed using effect sizes, Spearman's <it>ρ </it>and intra-class correlations (ICC).</p> <p>Results</p> <p>Effect sizes between CGI-I and CGI-S _difratings were large for all three perspectives with substantially higher change scores on CGI-I than on CGI-S _dif. BDI_difcorrelated moderately with PAT ratings, but did not correlate significantly with TEAM or THER ratings. Congruence between CGI-ratings from the three perspectives was low for CGI-S _dif(ICC = .37; Confidence Interval [CI] .15 to .59; <it>F</it>_30,60= 2.77, <it>p </it>< .001; mean <it>ρ </it>= 0.36) and moderate for CGI-I (ICC = .65 (CI .47 to .80; <it>F</it>_30,60= 6.61, <it>p </it>< .001; mean <it>ρ </it>= 0.59).</p> <p>Conclusions</p> <p>Results do not suggest a definite recommendation for whether CGI-I or CGI-S _difshould be used since no strong evidence for the validity of neither of them could be found. As congruence between CGI ratings from patients' and staff's perspective was not convincing it cannot be assumed that CGI THER or TEAM ratings fully represent the view of the patient on the severity of his impairment. Thus, we advocate for the incorporation of multiple self- and clinician-reported scales into the design of clinical trials in addition to CGI in order to gain further insight into CGI's relation to the patients' perspective.</p

Preparation and optical properties of novel bioactive photonic crystals obtained from core-shell poly(styrene/α-tert-butoxy-ω-vinylbenzyl-polyglycidol) microspheres

Optical properties of polymer microspheres with polystyrene cores and polyglycidol-enriched shells poly(styrene/α-tert-butoxy-ω-vinylbenzyl-polyglycidol) (P(S/PGL) particles with number average diameters Dn determined by scanning electron microscopy equal 237 and 271 nm), were studied before and after immobilization of ovalbumin. The particles were synthesized by emulsifier-free emulsion copolymerization of styrene and polyglycidol macromonomer (poly(styrene/α-tert-butoxy-ω-vinylbenzyl-polyglycidol)) initiated with potassium persulfate. Molar fraction of polyglycidol units in the interfacial layer of the microspheres determined by XPS was equal 42.6 and 34.0%, for the particles with Dn equal 137 and 271 nm, respectively. Colloidal crystals from the aforementioned particles were prepared by deposition of particle suspensions on the glass slides and subsequent evaporation of water. It was found that optical properties of colloidal crystals from the P(S/PGL) microspheres strongly depend on modification of their interfacial layer by covalent immobilization of ovalbumin. The coating of particles with ovalbumin resulted in decreasing their refractive index from 1.58 to 1.52