Miracle-dz/UniFAR-FTUs huggingface dataset:
Building communities for the exchange of learning objects: theoretical foundations and requirements

In order to reduce overall costs of developing high-quality digital courses (including both the content, and the learning and teaching activities), the exchange of learning objects has been recognized as a promising solution. This article makes an inventory of the issues involved in the exchange of learning objects within a community. It explores some basic theories, models and specifications and provides a theoretical framework containing the functional and non-functional requirements to establish an exchange system in the educational field. Three levels of requirements are discussed. First, the non-functional requirements that deal with the technical conditions to make learning objects interoperable. Second, some basic use cases (activities) are identified that must be facilitated to enable the technical exchange of learning objects, e.g. searching and adapting the objects. Third, some basic use cases are identified that are required to establish the exchange of learning objects in a community, e.g. policy management, information and training. The implications of this framework are then discussed, including recommendations concerning the identification of reward systems, role changes and evaluation instruments. DOI: 10.1080/0968776042000211502
Using next-generation sequencing to determine diversity of horse intestinal worms: identifying the equine ‘nemabiome’

ABSTRACT Next-generation sequencing of DNA from nematode eggs has been utilised to give the first account of the equine ‘nemabiome’. In all equine faecal samples investigated, multiple species of Strongylidae were detected, ranging from 7.5 (SEM 0.79) with 99+% identity to sequences in the NCBI database to 13.3 (SEM 0.80) with 90+% identity. This range is typical of the number of species described previously in morphological studies using large quantities of digesta per animal. However, the current method is non-invasive; relies on DNA analysis, avoiding the need for specialist microscopy identification; and can be carried out with small samples, providing significant advantages over current methods.
Clinical impact of the two ART resistance markers, K13 gene mutations and DPC3 in Vietnam

Background In Vietnam, a rapid decline of P. falciparum malaria cases has been documented in the past years, the number of Plasmodium falciparum malaria cases has rapidly decreased passing from 19.638 in 2012 to 4.073 cases in 2016. Concomitantly, the spread of artemisinin resistance markers is raising concern on the future efficacy of the ACTs. An evaluation of the clinical impact of the artemisinin resistance markers is therefore of interest. Methods The clinical effectiveness of dihydroartemisinin-piperaquine therapy (DHA-PPQ) has been evaluated in three districts characterized by different rates of ART resistance markers: K13(C580Y) mutation and delayed parasite clearance on day 3 (DPC3). Patients were stratified in 3 groups a) no markers, b) one marker (suspected resistance), c) co-presence of both markers (confirmed resistance). In the studied areas, the clinical effectiveness of DHA-PPQ has been estimated as malaria recrudescence within 60 days. Results The rate of K13(C580Y) ranged from 75.8% in Krong Pa to 1.2% in Huong Hoa district. DPC3 prevalence was higher in Krong Pa than in Huong Hoa (86.2% vs 39.3%). In the two districts, the prevalence of confirmed resistance was found in 69.0% and 1.2% of patients, respectively. In Thuan Bac district, we found intermediate prevalence of confirmed resistance. Treatment failure was not evidenced in any district. PPQ resistance was not evidenced. Confirmed resistance was associated to the persistence of parasites on day 28 and to 3.4-fold higher parasite density at diagnosis. The effectiveness of malaria control strategies was very high in the studied districts. Conclusion No treatment failure has been observed in presence of high prevalence of ART resistance and in absence of PPQ resistance. K13(C580Y) was strongly associated to higher parasitemia at admission, on days 3 and 28. Slower parasite clearance was also observed in younger patients.
Morning basal luteinizing hormone, a good screening tool for diagnosing central precocious puberty

Purpose The standard method used to diagnose central precocious puberty (CPP) is the gonadotropin releasing hormone stimulation test (GnRHST). However, this test is inconvenient for children because it is time-consuming and requires multiple samples. This study aimed to determine the reliability of morning unstimulated luteinizing hormone (mLH) level when screening for CPP, with an emphasis on the influence of diurnal variation. Methods This study included 160 girls with signs of early puberty (SMR 2) under 8 years of age. They were classified as CPP or non-CPP based on their standard GnRHST. The auxological, biochemical, and hormonal characteristics of subjects were retrospectively evaluated. The prognostic value of single morning unstimulated gonadotropin level was examined for use in CPP screening. Results Of 160 patients, 121 (75.6%) presented with CPP, and 39 (24.4%) were determined to be prepubertal. The mLH/mFSH (morning unstimulated follicular stimulating hormone) ratio showed significant differences between the 2 groups (P<0.001). The mLH was correlated with GnRHST variables (r=0.532, P<0.001). The mLH cutoff point when screening for CPP was 0.22 IU/L, which had sensitivity and specificity of 69.4% and 82.1%, respectively. In regression analysis, bone age (BA) (odds ratio [OR], 1.018; 95% confidence interval [CI], 0.967–1.071; P=0.506) and body mass index (BMI) (OR, 0.874; 95% CI, 0.583–1.310; P=0.515) were not significant predictors. The mLH≥0.22 IU/L group (OR, 9.596; 95% CI, 3.853–23.900; P<0.001) was highly suggestive of CPP. Conclusions In this study, single morning unstimulated luteinizing hormone had clinical efficacy for CPP screening, but BA advanced over chronological age and BMI was not useful for CPP screening.
On Development of Continuous Time Monte Carlo Methods for Problems of Boltzmann Equation with External Forces

Abstract We consider continuous time Monte Carlo (CTMC) methods [Khisamutdinov, A. I. (1988) Simulation statistical modeling of the kinetic equation of rarefied gases. Dokl. Akad. Nauk SSSR 302:75–79], based on some special Markov jump processes, and inhomogeneous smoothed Boltzmann equation with external forces. In the first place, the corresponding changes are brought into definitions of these methods to correct their applications to the problems with external forces. Secondly, we revise and refine a “generalized fictitious collisions” technique and a “rejection” one for simulation of scatterings. Third, a non‐stationary problem on plane Poiseuille flow is solved by employing one of the modified methods.
An examination of differential repetition priming effects for natural and man-made objects

Abstract It has been theorized that differential cognitive resources may be involved in the processing of information pertaining to natural and man-made categories, commonly referred to as category specificity. The present study used four experiments to assess whether a natural priming advantage exists and, if so, whether color, texture, color diagnosticity, object complexity, and familiarity could account for the categorical difference. To do so, a repetition priming paradigm was used in which masked primes were briefly presented, and targets were categorized as natural or man-made. Across four experiments, a greater degree of priming was observed for natural as opposed to man-made stimuli. Examination of stimulus characteristics that could account for the differences revealed that the natural priming advantage was in part driven by color diagnosticity and familiarity. Results of this study support the notion that different cognitive resources represent and/or are involved in the processing of natural and man-made categories.
Antioxidant Activity In Vitro of N-(1-deoxy-α-d-xylulos-1-yl)-Phenylalanine: Comparison Among Maillard Reaction Intermediate, End-Products and Xylose-Phenylalanine.

The Maillard reaction end-products (MRPs) and intermediate (MRI, N-(1-deoxy-α-D-xylulos-1-yl)-phenylalanine) derived from xylose (Xyl) and phenylalanine (Phe) model system were synthesized in an aqueous medium, and their antioxidant activity was evaluated. Both the MRPs and N-(1-deoxy-α-d-xylulos-1-yl)-phenylalanine exhibited the Fe2+ chelating activity at their addition concentration of 2 to 12 mg/mL. While their reducing power, free radical scavenging activity, and inhibition effect on lipid peroxidation were observed at a lower addition concentration of only 0.2 to 1.2 mg/mL. The free radical scavenging activity was improved with the increase in their concentration, and a time-dependent scavenging effect of the MRI was also shown in the results. However, a weak chelating activity of Xyl-Phe on Fe2+ in a concentration-dependent manner was observed, but no significant free radical scavenging activity or reducing power of Xyl-Phe was found. Based on these results, possible free radical scavenging pathway of the MRI was proposed. As the MRI showed lower antioxidant activity than MRPs, the application of the MRI in combination with MRPs as an antioxidant was proposed in cooked or semi-processed foods to avoid the deterioration induced by oxidation. PRACTICAL APPLICATION: The Maillard reaction intermediates (MRIs) showed antioxidant activity and could be applied in foods as both antioxidants and flavor enhancer. The MRIs will probably extend the shelf-life of lipid rich foods and could be the substitute of artificial antioxidants.
Severe Illnesses Associated With Outbreaks of Respiratory Syncytial Virus and Influenza in Adults

Abstract Background Recent reports have described the contribution of adult respiratory syncytial virus (RSV) infections to the use of advanced healthcare resources and death. Methods Data regarding patients aged ≥18 years admitted to any of Maryland’s 50 acute-care hospitals were evaluated over 12 consecutive years (2001–2013). We examined RSV and influenza (flu) surveillance data from the US National Respiratory and Enteric Virus Surveillance System and the Centers for Disease Control and Prevention and used this information to define RSV and flu outbreak periods in the Maryland area. Outbreak periods consisted of consecutive individual weeks during which at least 10% of RSV and/or flu diagnostic tests were positive. We examined relationships of RSV and flu outbreaks to occurrence of 4 advanced medical outcomes (hospitalization, intensive care unit admission, intubated mechanical ventilation, and death) due to medically attended acute respiratory illness (MAARI). Results Occurrences of all 4 MAARI-related hospital advanced medical outcomes were consistently greater for all adult ages during RSV, flu, and combined RSV–flu outbreak periods compared to nonoutbreak periods and tended to be greatest in adults aged ≥65 years during combined RSV–flu outbreak periods. Rate ratios for all 4 MAARI-related advanced medical outcomes ranged from 1.04 to 1.38 during the RSV, flu, or combined RSV–flu outbreaks compared to the nonoutbreak periods, with all 95% lower confidence limits >1. Conclusions Both RSV and flu outbreaks were associated with surges in MAARI-related advanced medical outcomes (hospitalization, intensive care unit admission, intubated mechanical ventilation, and death) for adults of all ages.
Amplifying the Range of News Stories with Creativity: Methods and their Evaluation, in Portuguese

Headlines are key for attracting people to a story, but writing appealing headlines requires time and talent. This work aims to automate the production of creative short texts (e.g., news headlines) for an input context (e.g., existing headlines), thus amplifying its range. Well-known expressions (e.g., proverbs, movie titles), which typically include word-play and resort to figurative language, are used as a starting point. Given an input text, they can be recommended by exploiting Semantic Textual Similarity (STS) techniques, or adapted towards higher relatedness. For the latter, three methods that exploit static word embeddings are proposed. Experimentation in Portuguese lead to some conclusions, based on human opinions: STS methods that look exclusively at the surface text, recommend more related expressions; resulting expressions are somewhat related to the input, but adaptation leads to higher relatedness and novelty; humour can be an indirect consequence, but most outputs are not funny.
GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies

Abstract Since proteins evolve by divergent evolution, proteins with distant homology to each other may or may not bear similar functions. Improved computational approaches are required to recognize distant homologues that are functionally similar. One of the methods of assigning function to sequences is to use profiles derived from sequences of known structure. We describe an update of the Genomic Distribution of protein structural domain Superfamilies (GenDiS) database, namely GenDiS+, which provides a projection of SCOP superfamily members on the sequence space (NR database, NCBI). The sequences are validated using structure-based sequence alignment profiles and domain and full-length sequence alignments. GenDiS+ is a `tour de force’ for detecting homologues within around 160 000 taxonomic identifiers, starting from nearly 11 000 domains of known structure. Features, like full-sequence alignment and phylogeny, domain sequence alignment and phylogeny, list of associated structural and sequence domains with strength of interactions, links to databases like Pfam, UniProt and ModBase and list of sequences with a PDB structure, are provided.
Different Pathophysiology and Outcomes of Heart Failure With Preserved Ejection Fraction Stratified by K-Means Clustering

Background: Stratified medicine may enable the development of effective treatments for particular groups of patients with heart failure with preserved ejection fraction (HFpEF); however, the heterogeneity of this syndrome makes it difficult to group patients together by common disease features. The aim of the present study was to find new subgroups of HFpEF using machine learning. Methods: K-means clustering was used to stratify patients with HFpEF. We retrospectively enrolled 350 outpatients with HFpEF. Their clinical characteristics, blood sample test results and hemodynamic parameters assessed by echocardiography, electrocardiography and jugular venous pulse, and clinical outcomes were applied to k-means clustering. The optimal k was detected using Hartigan's rule. Results: HFpEF was stratified into four groups. The characteristic feature in group 1 was left ventricular relaxation abnormality. Compared with group 1, patients in groups 2, 3, and 4 had a high mean mitral E/e′ ratio. The estimated glomerular filtration rate was lower in group 2 than in group 3 (median 51 ml/min/1.73 m2 vs. 63 ml/min/1.73 m2 p < 0.05). The prevalence of less-distensible right ventricle and atrial fibrillation was higher, and the deceleration time of mitral inflow was shorter in group 3 than in group 2 (93 vs. 22% p < 0.05, 95 vs. 1% p < 0.05, and median 167 vs. 223 ms p < 0.05, respectively). Group 4 was characterized by older age (median 85 years) and had a high systolic pulmonary arterial pressure (median 37 mmHg), less-distensible right ventricle (89%) and renal dysfunction (median 54 ml/min/1.73 m2). Compared with group 1, group 4 exhibited the highest risk of the cardiac events (hazard ratio [HR]: 19; 95% confidence interval [CI] 8.9–41); group 2 and 3 demonstrated similar rates of cardiac events (group 2 HR: 5.1; 95% CI 2.2–12; group 3 HR: 3.7; 95%CI, 1.3–10). The event-free rates were the lowest in group 4 (p for trend < 0.001). Conclusions: K-means clustering divided HFpEF into 4 groups. Older patients with HFpEF may suffer from complication of RV afterload mismatch and renal dysfunction. Our study may be useful for stratified medicine for HFpEF.
Epifaunal Habitat Associations on Mixed and Hard Bottom Substrates in Coastal Waters of Northern Norway

Hard and mixed seafloor substrates are an important benthic habitat in coastal northern Norway and they are known to be colonized by relatively diverse communities of sessile epifauna. These assemblages are highly susceptible to physical damage and stresses imposed by organic material from industrial and municipal sources. However, despite increasing prevalence of stressors, the diversity and distribution of benthic substrates and biological communities in coastal Arctic and sub-Arctic regions remain poorly documented. In response, this study has characterized the composition of mixed and hard bottom substrates and associated sessile epifauna in fjords in Finnmark, northern Norway, using remote sensing and an innovation low-cost towed camera method. The study fjords supported a dense covering (0.1 to 0.68 individuals m–2) of sponge taxa common to deep-water ostur sponge habitats (Geodia sp., Mycale lingua, Polymastia sp., Phakellia ventilabrum, and Axinella infundibuliformis). In addition, aggregations of the soft coral (Duva florida), the tunicate (Ascidia sp.), the seastar (Ceramaster granularis) and anemone (Hormathia digitata) were prominent fauna. The small-scale spatial patterns of the epifaunal communities in this study were primarily influenced by the local hydrodynamic regime, depth, the topographical slope and the presence of hard bedrock substrates. This description of the composition, distribution and the identification of environmental drivers of epibenthic communities is valuable for the development of predictive habitat models to manage the benthic impact of multiple stressor on these ecological valuable and vulnerable Arctic habitats.
Genetic Mutations Associated with Hormone-Positive Breast Cancer in Ethiopian Women

In Ethiopia, a breast cancer diagnosis is associated with a prognosis significantly worse than that of Europe and the US. Further, patients presenting with breast cancer in Ethiopia are far younger, on average, and patients are typically diagnosed at very late stages, relative to breast cancer patients of European descent. Emerging data suggest that a large proportion of Ethiopian patients have hormone-positive (ER+) breast cancer. This is surprising given 1) the aggressive nature of the disease, 2) that African Americans with breast cancer frequently have triple negative breast cancer (TNBC), and 3) these patients typically receive chemotherapy, not hormone-targeting drugs. To further examine the similarity of Ethiopian breast tumors to those of African Americans or of those of European descent, we sequenced matched normal and tumor tissue from Ethiopian patients from a small pilot collection. We identified mutations in 615 genes across all three patients, unique to the tumor tissue. Across this analysis, we found far more mutations shared between Ethiopian patient tissue and White patients (103) than we did comparing to African Americans (3). Several mutations were found in extracellular matrix encoding genes with known roles in tumor cell growth and metastasis. We suggest future mechanistic studies on this disease focus on these genes first, toward finding new treatment strategies for breast cancer patients in Ethiopia.
Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data

Next-generation sequencing (NGS) technologies have provided great opportunities to analyze pathogenic microbes with high-resolution data. The main goal is to accurately detect microbial composition and abundances in a sample. However, high similarity among sequences from different species and the existence of sequencing errors pose various challenges. Numerous methods have been developed for quantifying microbial composition and abundance, but they are not versatile enough for the analysis of samples with mixtures of noise. In this paper, we propose a new computational method, PGMicroD, for the detection of pathogenic microbial composition in a sample using NGS data. The method first filters the potentially mistakenly mapped reads and extracts multiple species-related features from the sequencing reads of 16S rRNA. Then it trains an Support Vector Machine classifier to predict the microbial composition. Finally, it groups all multiple-mapped sequencing reads into the references of the predicted species to estimate the abundance for each kind of species. The performance of PGMicroD is evaluated based on both simulation and real sequencing data and is compared with several existing methods. The results demonstrate that our proposed method achieves superior performance. The software package of PGMicroD is available at https://github.com/BDanalysis/PGMicroD.
Diagnostic Accuracy of Stool Xpert MTB/RIF for Detection of Pulmonary Tuberculosis in Children: a Systematic Review and Meta-analysis

Invasive collection methods are often required to obtain samples for the microbiological evaluation of children with presumptive pulmonary tuberculosis (PTB). Nucleic acid amplification testing of easier-to-collect stool samples could be a noninvasive method of diagnosing PTB. ABSTRACT Invasive collection methods are often required to obtain samples for the microbiological evaluation of children with presumptive pulmonary tuberculosis (PTB). Nucleic acid amplification testing of easier-to-collect stool samples could be a noninvasive method of diagnosing PTB. We conducted a systematic review and meta-analysis to evaluate the diagnostic accuracy of testing stool with the Xpert MTB/RIF assay (“stool Xpert”) for childhood PTB. Four databases were searched for publications from January 2008 to June 2018. Studies assessing the diagnostic accuracy among children of stool Xpert compared to a microbiological reference standard of conventional specimens tested by mycobacterial culture or Xpert were eligible. Bivariate random-effects meta-analyses were performed to calculate pooled sensitivity and specificity of stool Xpert against the reference standard. From 1,589 citations, 9 studies (n = 1,681) were included. Median participant ages ranged from 1.3 to 10.6 years. Protocols for stool processing and testing varied substantially, with differences in reagents and methods of homogenization and filtering. Against the microbiological reference standard, the pooled sensitivity and specificity of stool Xpert were 67% (95% confidence interval [CI], 52 to 79%) and 99% (95% CI, 98 to 99%), respectively. Sensitivity was higher among children with HIV (79% [95% CI, 68 to 87%] versus 60% [95% CI, 44 to 74%] among HIV-uninfected children). Heterogeneity was high. Data were insufficient for subgroup analyses among children under the age of 5 years, the most relevant target population. Stool Xpert could be a noninvasive method of ruling in PTB in children, particularly those with HIV. However, studies focused on children under 5 years of age are needed, and generalizability of the evidence is limited by the lack of standardized stool preparation and testing protocols.