Miracle-dz/UniFAR-FTUs huggingface dataset:
Addressing individual behaviours and living conditions: Four Nordic public health policies

Aims: To identify characteristics of the public health policies of four Nordic countries concerning how they present the causes of ill health, the best ways to deal with these causes, and where to place responsibility; additionally, to investigate whether there is a common Nordic policy. Methods: Analyses of recent public health programmes in Denmark, Finland, Norway, and Sweden. Results: Focus is on either, or both, individual behaviour and living conditions as causes of ill health; the remedies are classical liberal as well as social democratic policies. None of the programmes is consistent with either ideological strand; each has its peculiar combination of interpretations and policies. The Danish programme is the most liberal focusing on behaviours and individual’s choices; the Norwegian programme is the most social democratic or social liberal focusing mostly on the social and physical environment and the politicians’ responsibility to improve the population’s health. The Swedish and the Finnish programmes lie between those of Denmark and Norway. The Finnish and Norwegian governments stress their responsibility for the health of the population. Conclusions: No common Nordic political approach to public health exists. All programmes contain contradictory policies and ideological statements with differences regarding the emphasis on individual behaviour versus choice and living conditions and political responsibility. The policies are not entirely predictable from the political stance of the government; national differences seem to play a role.
Associations of high-risk behaviour and HIV status with HIV knowledge among persons in Tallinn, Estonia

Aim: The aim of this study was to determine the associations between the level of HIV knowledge, HIV-related risk behaviours, and HIV status among persons receiving voluntary counselling and testing services in Tallinn, Estonia. Design: A cross-sectional study design was used. Methods: A total of 772 subjects completed a 47-item questionnaire gathering information on demographics, HIV-related risk behaviours, and HIV-related knowledge. Participant’s HIV status was determined by an anonymous rapid test. Only incident HIV cases were included in regression analyses. An analysis of covariance (ANCOVA) modelling evaluated associations between HIV knowledge and high-risk behaviours while multivariable logistic regression assessed association between HIV status and HIV knowledge. Results: The final ANCOVA model indicates that HIV risk behaviours are significantly associated with HIV knowledge (p = 0.01). Compared to participants with no identified high-risk behaviour, the adjusted mean score of HIV knowledge was higher among persons sharing injection equipment (p = 0.05), and persons engaging in unprotected heterosexual intercourse (p = 0.03); there was no statistical difference observed among men engaging in unprotected sex with other men. Women had higher mean scores than men (p = 0.01) and persons of ‘‘other’’ ethnicities had a higher mean knowledge score than ethnic Estonians (p = 0.01) and Russians (p < 0.01). Logistic regression indicated that mean knowledge was higher among participants who tested HIV positive (OR = 1.42; 95% CI = 1.12—1.87). Conclusions: In this sample, higher knowledge scores were not associated with lower infection rates. These results indicate the importance of targeting all high-risk groups in HIV prevention and education programmes.
Engineering Pseudomonas putida S12 for Efficient Utilization of d-Xylose and l-Arabinose

ABSTRACT The solvent-tolerant bacterium Pseudomonas putida S12 was engineered to utilize xylose as a substrate by expressing xylose isomerase (XylA) and xylulokinase (XylB) from Escherichia coli. The initial yield on xylose was low (9% [g CDW g substrate−1], where CDW is cell dry weight), and the growth rate was poor (0.01 h−1). The main cause of the low yield was the oxidation of xylose into the dead-end product xylonate by endogenous glucose dehydrogenase (Gcd). Subjecting the XylAB-expressing P. putida S12 to laboratory evolution yielded a strain that efficiently utilized xylose (yield, 52% [g CDW g xylose−1]) at a considerably improved growth rate (0.35 h−1). The high yield could be attributed in part to Gcd inactivity, whereas the improved growth rate may be connected to alterations in the primary metabolism. Surprisingly, without any further engineering, the evolved d-xylose-utilizing strain metabolized l-arabinose as efficiently as d-xylose. Furthermore, despite the loss of Gcd activity, the ability to utilize glucose was not affected. Thus, a P. putida S12-derived strain was obtained that efficiently utilizes the three main sugars present in lignocellulosic hydrolysate: glucose, xylose, and arabinose. This strain will form the basis for a platform host for the efficient production of biochemicals from renewable feedstock.
Psychotropic drug use among women exposed to intimate partner violence: A population-based study

Aims: To investigate psychotropic drug use among women ever exposed to intimate partner violence (IPV) in relation to mental distress and sociodemographic, lifestyle and somatic health characteristics, and to assess whether drug use differed for physical and/or sexual violence compared with psychological abuse alone. Methods: Cross-sectional data from women aged 30—60 years were drawn from self-reported questionnaires in the Oslo Health study 2000—2001. Women reporting hypnotic, anxiolytic and/or antidepressant drug use in the previous four weeks were defined as users. Differences in psychotropic drug use by IPV exposure were examined by logistic regression analyses. Results: In total, 880 (14%) of 6,471 included women reported ever experiencing IPV; 494 (8%) reported physical and/or sexual IPV, and 386 (6%) reported psychological IPV alone. Physical and/or sexual IPV was significantly associated with use of all psychotropic drugs: hypnotics (odds ratio (OR) 2.28; 95% confidence interval (95% CI), 1.73—3.00); anxiolytics (OR 3.29; 95% CI, 2.43—4.44); and antidepressants (OR 2.72; 95% CI, 1.97—3.76). The associations remained significant for anxiolytics (OR 1.67; 95% CI, 1.14—2.45) and antidepressants (OR 1.50; 95% CI, 1.02—2.19) after adjusting for mental distress, sociodemographic, lifestyle and somatic health characteristics. Psychological IPV alone was associated with use of anxiolytics (OR 1.81; 95% CI, 1.20—2.75) and antidepressants (OR 2.38; 95% CI, 1.64—3.45). After adjustments the association persisted for use of antidepressants only (OR 1.64; 95% CI, 1.05—2.55). Conclusions: Women exposed to IPV were more likely to report use of psychotropic drugs, even after adjusting for mental distress. The study indicates that exposure to IPV; including psychological abuse should be evaluated as a possible source of distress when psychotropic drug treatment is considered.
Archaeal Diversity and Distribution along Thermal and Geochemical Gradients in Hydrothermal Sediments at the Yonaguni Knoll IV Hydrothermal Field in the Southern Okinawa Trough

ABSTRACT A variety of archaeal lineages have been identified using culture-independent molecular phylogenetic surveys of microbial habitats occurring in deep-sea hydrothermal environments such as chimney structures, sediments, vent emissions, and chemosynthetic macrofauna. With the exception of a few taxa, most of these archaea have not yet been cultivated, and their physiological and metabolic traits remain unclear. In this study, phylogenetic diversity and distribution profiles of the archaeal genes encoding small subunit (SSU) rRNA, methyl coenzyme A (CoA) reductase subunit A, and the ammonia monooxygenase large subunit were characterized in hydrothermally influenced sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa Trough. Sediment cores were collected at distances of 0.5, 2, or 5 m from a vent emission (90°C). A moderate temperature gradient extends both horizontally and vertically (5 to 69°C), indicating the existence of moderate mixing between the hydrothermal fluid and the ambient sediment pore water. The mixing of reductive hot hydrothermal fluid and cold ambient sediment pore water establishes a wide spectrum of physical and chemical conditions in the microbial habitats that were investigated. Under these different physico-chemical conditions, variability in archaeal phylotype composition was observed. The relationship between the physical and chemical parameters and the archaeal phylotype composition provides important insight into the ecophysiological requirements of uncultivated archaeal lineages in deep-sea hydrothermal vent environments, giving clues for approximating culture conditions to be used in future culturing efforts.
Identification of the ATPase Subunit of the Primary Maltose Transporter in the Hyperthermophilic Anaerobe Thermotoga maritima

ABSTRACT Thermotoga maritima is a hyperthermophilic anaerobic bacterium that produces molecular hydrogen (H2) by fermentation. It catabolizes a broad range of carbohydrates through the action of diverse ABC transporters. However, in T. maritima and related species, highly similar genes with ambiguous annotation obscure a precise understanding of genome function. In T. maritima, three putative malK genes, all annotated as ATPase subunits, exhibited high identity to each other. To distinguish between these genes, malK disruption mutants were constructed by gene replacement, and the resulting mutant cell lines were characterized. Only a disruption of malK3 produced a defect in maltose catabolism. To verify that the mutant phenotype arose specifically from malK3 inactivation, the malK3 mutation was repaired by recombination, and maltose catabolism was restored. This study demonstrates the importance of a maltose ABC-type transporter and its relationship to sugar metabolism in T. maritima. IMPORTANCE The application and further development of a genetic system was used here to investigate gene paralogs in the hyperthermophile Thermotoga maritima. The occurrence of three ABC transporter ATPase subunits all annotated as malK was evaluated using a combination of genetic and bioinformatic approaches. The results clarify the role of only one malK gene in maltose catabolism in a nonmodel organism noted for fermentative hydrogen production.
Attached Bacterial Populations Shared by Four Species of Aquatic Angiosperms

ABSTRACT Symbiotic relationships between microbes and plants are common and well studied in terrestrial ecosystems, but little is known about such relationships in aquatic environments. We compared the phylogenetic diversities of leaf- and root-attached bacteria from four species of aquatic angiosperms using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of PCR-amplified 16S rRNA genes. Plants were collected from three beds in Chesapeake Bay at sites characterized as freshwater (Vallisneria americana), brackish (Potomogeton perfoliatus and Stuckenia pectinata), and marine (Zostera marina). DGGE analyses showed that bacterial communities were very similar for replicate samples of leaves from canopy-forming plants S. pectinata and P. perfoliatus and less similar for replicate samples of leaves from meadow-forming plants Z. marina and V. americana and of roots of all species. In contrast, bacterial communities differed greatly among plant species and between leaves and roots. DNA sequencing identified 154 bacterial phylotypes, most of which were restricted to single plant species. However, 12 phylotypes were found on more than one plant species, and several of these phylotypes were abundant in clone libraries and represented the darkest bands in DGGE banding patterns. Root-attached phylotypes included relatives of sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Deltaproteobacteria. Leaf-attached phylotypes included relatives of polymer-degrading Bacteroidetes and phototrophic Alphaproteobacteria. Also, leaves and roots of three plant species hosted relatives of methylotrophic Betaproteobacteria belonging to the family Methylophilaceae. These results suggest that aquatic angiosperms host specialized communities of bacteria on their surfaces, including several broadly distributed and potentially mutualistic bacterial populations.
Pyrosequencing of the Genital Microbiotas of HIV-Seropositive and -Seronegative Women Reveals Lactobacillus iners as the Predominant Lactobacillus Species

ABSTRACT The species of vaginal lactobacilli in HIV-seropositive and -seronegative women were determined by 16S gene pyrosequencing. Lactobacillus iners sequences were the predominant lactobacillus sequences in 66% of HIV+ women and 90% of HIV− women. This has implications for resistance of HIV+ and HIV− women to genital colonization by pathogenic organisms.
Increased Lysine Content Is the Main Characteristic of the Soluble Form of the Polyamide Cyanophycin Synthesized by Recombinant Escherichia coli

Cyanophycin, a polyamide of cyanobacterial or noncyanobacterial origin consisting of aspartate, arginine, and lysine, was synthesized in different recombinant strains of Escherichia coli expressing cphA from Synechocystis sp. strain PCC 6308 or PCC 6803, Anabaena sp. strain PCC 7120, or Acinetobacter calcoaceticus ADP1. The molar aspartate/arginine/lysine ratio of the water-soluble form isolated from a recombinant strain expressing CphA6308 was 1:0.5:0.5, with a lysine content higher than any ever described before. The water-insoluble form consisted instead of mainly aspartate and arginine residues and had a lower proportion of lysine, amounting to a maximum of only 5 mol%. It could be confirmed that the synthesis of soluble cyanobacterial granule polypeptide (CGP) is independent of the origin of cphA. Soluble CGP isolated from all recombinant strains contained a least 17 mol% lysine. The total CGP portion of cell dry matter synthesized by CphA6308 from recombinant E. coli was about 30% (wt/wt), including 23% (wt/wt) soluble CGP, by using terrific broth complex medium for cultivation at 30ï¿½C for 72 h. Enhanced production of soluble CGP instead of its insoluble form is interesting for further application and makes recombinant E. coli more attractive as a suitable source for the production of polyaspartic acid or dipeptides. In addition, a new low-cost, time-saving, effective, and common isolation procedure for mainly soluble CGP, suitable for large-scale application, was established in this study.
Test–retest reliability of a knee joint position sense measurement method in sitting and prone position

There are many indications of defects in motor control being part of the aetiopathogenesis of degenerative joint diseases. Measurement of proprioceptive functions may increase our understanding of these diseases. Furthermore, reproducible tests will enable researchers to demonstrate the results of targeted physiotherapy. The purpose of this study was to determine the test–retest reliability of a method to measure knee joint position sense (JPS). Thirty-nine healthy volunteers (17 women, 18–50 years old) participated. The JPS was measured as the participant's ability to reproduce the same position in the right knee (target vs. estimated angle). The result was expressed as the difference between target and estimated angle. Measurements were repeated three times with three different target angles (prone position: 40°, 70°, 100° flexion; sitting position: 30°, 50°, 70° flexion), and for single leg and both legs. Three test sessions were performed with 1-h and 1-week interval. The outcome measure was the difference between the target and the estimated position (absolute error, AE). The degree of reliability was evaluated by using the intraclass correlation coefficient (ICC). The mean AE summarized for all measurements was 4.16° in sitting position and 5.06° in prone position. The ICCs ranged from 0.31 to 0.82 in sitting position and from 0.17 to 0.75 in prone position. Based upon the fair to good reliability of the applied method for measuring JPS over the knee, we suggest the following procedures for determination of JPS over the knee: (i) the JPS should be calculated as the AE between target and estimate position; (ii) sitting should be preferred to prone; (iii) ipsilateral should be preferred to counter-lateral; (iv) test angle should be in the middle (suggested from 40° to 80° flexion) of the knee joint's range of motion. With these precautions, the test seems to be a reliable measure of JPS in healthy controls.
Daily steps among Finnish adults: Variation by age, sex, and socioeconomic position

Aims: The aim of this study was to provide descriptive population-based pedometer data from adults aged 30-45 years in Finland, and to compare daily step counts with evidence-based indices. Methods: The data was collected from 1853 participants in 7 consecutive days in winter 2007—08 in part of 27-year follow up of the Cardiovascular Risk in Young Finns study. Results: The participants took (mean±standard deviation) 7499 ± 2908 steps/day. Step counts included 1925 ± 2052 aerobic steps/day gathered in bouts of at least 10 min continuous ambulatory activity. Women had more total steps than men ((7824 ± 2925 vs. 7089 ± 2774; p < 0.001). Although participants had higher mean total steps on weekdays than on weekend days, they took more aerobic steps on weekend days than weekdays (p < 0.001). High-level non-manual work, and unemployment were associated with having fewer total steps, but high-level non-manual workers had more aerobic steps than other occupation groups. According to pedometer thresholds proposed by Tudor-Locke and Basset, 26% of men and 16% of women could be classified as inactive (<5000 steps/day) and 20% of women and 15% of men would be classified as active (>10,000 steps/day). Conclusions: We conclude that about one-quarter of men and one-fifth of women are considered as inactive, based on the number of daily total steps. Our results suggest that total steps may provide a very different picture of activity from aerobic steps; important differences are evident by socioeconomic position and day of the week.
Interrelationships between education, occupational social class, and income as determinants of disability retirement

Aims: The association between a low socioeconomic position and disability retirement is established in the literature, but the interrelationships between various subdomains of socioeconomic position are poorly understood. We examined the independent and interdependent effects of education, social class, and income on disability retirement. Methods: Using nationally representative register data we followed up over 260,000 Finns aged 30–63 at the end of 1995 for disability retirement from 1996 to 2004. Cox regression analysis was used to calculate hazard ratios (HR) and relative indices of inequality (RII). Results: Each socioeconomic indicator had a linear negative association with disability retirement. The socioeconomic gradients were stronger in the younger age groups. The effect of education was largely mediated through succeeding social class. Social class was largely explained by preceding education, but was only moderately mediated through income. Income was largely explained by education, and even further by social class. The independent effects of education, social class, and income on disability retirement as measured by the RII were 1.74 (95% CI 1.60–1.90), 1.95 (1.78–2.15), and 1.35 (1.25–1.47) for men and 1.76 (1.61–1.92), 2.14 (1.95–2.34), and 1.14 (1.05–1.24) for women. Conclusions: The effects of socioeconomic position on disability retirement may not be fully captured if the pathways between the various subdomains are disregarded. Our results suggest that efforts to delay and prevent disability retirement should focus on lifestyle and cognitive factors associated with education, as well as on factors associated with social class such as working conditions and power resources.
Plant-Pathogenic Oomycetes, Escherichia coli Strains, and Salmonella spp. Frequently Found in Surface Water Used for Irrigation of Fruit and Vegetable Crops in New York State

ABSTRACT In the United States, surface water is commonly used to irrigate a variety of produce crops and can harbor pathogens responsible for food-borne illnesses and plant diseases. Understanding when pathogens infest water sources is valuable information for produce growers to improve the food safety and production of these crops. In this study, prevalence data along with regression tree analyses were used to correlate water quality parameters (pH, temperature, turbidity), irrigation site properties (source, the presence of livestock or fowl nearby), and precipitation data to the presence and concentrations of Escherichia coli, Salmonella spp. , and hymexazol-insensitive (HIS) oomycetes (Phytophthora and Pythium spp.) in New York State surface waters. A total of 123 samples from 18 sites across New York State were tested for E. coli and Salmonella spp. , of which 33% and 43% were positive, respectively. Additionally, 210 samples from 38 sites were tested for HIS oomycetes, and 88% were found to be positive, with 10 species of Phytophthora and 11 species of Pythium being identified from the samples. Regression analysis found no strong correlations between water quality parameters, site factors, or precipitation to the presence or concentration of E. coli in irrigation sources. For Salmonella, precipitation (≤0.64 cm) 3 days before sampling was correlated to both presence and the highest counts. Analyses for oomycetes found creeks to have higher average counts than ponds, and higher turbidity levels were associated with higher oomycete counts. Overall, information gathered from this study can be used to better understand the food safety and plant pathogen risks of using surface water for irrigation.
SVD free matrix completion with online bias correction for Recommender systems

In this work we address the problem of design of an efficient Recommender system based on collaborative filtering framework which achieves improved accuracy with reduced computational complexity and shorter run times. This work is based on representing the low rank constraint as the Ky-Fan norm instead of the commonly employed nuclear norm term. Our formulation uses majorization minimization approach to cast the problem as simple least squares. The enhanced efficiency of our algorithm in terms of higher accuracy of recovery and shorter execution times is demonstrated by comparison to existing techniques for matrix completion.
Mobilization of a Tn402-Like Class 1 Integron with a Novel Cassette Array via Flanking Miniature Inverted-Repeat Transposable Element-Like Structures

ABSTRACT A Tn402-like class 1 integron was recovered from a prawn-associated bacterium. One of its cassettes included methionine sulfoxide reductase genes, the first example of such genes being captured by an integron. The integron was flanked by direct repeats that resemble miniature inverted-repeat transposable element sequences. Excision of the integron by homologous recombination through these sequences was demonstrated.
Alterações hematológicas em pacientes com dengue

Dengue is a neglected disease with high morbidity and mortality among children and adults that occurs mainly in tropical and subtropical regions. The objective of this study was to evaluate hematological changes in patients with clinical manifestations of dengue. Medical records relating to 543 cases of dengue virus 3 that occurred during the 2007 epidemic in Campo Grande, Mato Grosso do Sul, were studied. Cases of classic dengue predominated (90.2%), with mild clinical manifestations lacking complications. The main hematological findings were leukopenia (68.3%), thrombocytopenia (66.5%), lymphocytopenia (67.2%) and atypical lymphocytes (67%). In dengue hemorrhagic fever, thrombocytopenia was more prolonged and the number of atypical lymphocytes was higher, while the other hematological abnormalities presented daily evolution similar to those in classic dengue. The hematological changes observed in dengue present according to the clinical course of the disease and its severity.