Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic Response of Escherichia coli O157:H7 to Oxidative Stress

ABSTRACT Chlorinated water is commonly used in industrial operations to wash and sanitize fresh-cut, minimally processed produce. Here we compared 42 human outbreak strains that represented nine distinct Escherichia coli O157:H7 genetic lineages (or clades) for their relative resistance to chlorine treatment. A quantitative measurement of resistance was made by comparing the extension of the lag phase during growth of each strain under exposure to sublethal concentrations of sodium hypochlorite in Luria-Bertani or brain heart infusion broth. Strains in clade 8 showed significantly (P < 0.05) higher resistance to chlorine than strains from other clades of E. coli O157:H7. To further explore how E. coli O157:H7 responds to oxidative stress at transcriptional levels, we analyzed the global gene expression profiles of two strains, TW14359 (clade 8; associated with the 2006 spinach outbreak) and Sakai (clade 1; associated with the 1996 radish sprout outbreak), under sodium hypochlorite or hydrogen peroxide treatment. We found over 380 genes were differentially expressed (more than twofold; P < 0.05) after exposure to low levels of chlorine or hydrogen peroxide. Significantly upregulated genes included several regulatory genes responsive to oxidative stress, genes encoding putative oxidoreductases, and genes associated with cysteine biosynthesis, iron-sulfur cluster assembly, and antibiotic resistance. Identification of E. coli O157:H7 strains with enhanced resistance to chlorine decontamination and analysis of their transcriptomic response to oxidative stress may improve our basic understanding of the survival strategy of this human enteric pathogen on fresh produce during minimal processing.
Aquacultured Rainbow Trout (Oncorhynchus mykiss) Possess a Large Core Intestinal Microbiota That Is Resistant to Variation in Diet and Rearing Density

ABSTRACT As global aquaculture fish production continues to expand, an improved understanding of how environmental factors interact in fish health and production is needed. Significant advances have been made toward economical alternatives to costly fishmeal-based diets, such as grain-based formulations, and toward defining the effect of rearing density on fish health and production. Little research, however, has examined the effects of fishmeal- and grain-based diets in combination with alterations in rearing density. Moreover, it is unknown whether interactions between rearing density and diet impact the composition of the fish intestinal microbiota, which might in turn impact fish health and production. We fed aquacultured adult rainbow trout (Oncorhynchus mykiss) fishmeal- or grain-based diets, reared them under high- or low-density conditions for 10 months in a single aquaculture facility, and evaluated individual fish growth, production, fin indices, and intestinal microbiota composition using 16S rRNA gene sequencing. We found that the intestinal microbiotas were dominated by a shared core microbiota consisting of 52 bacterial lineages observed across all individuals, diets, and rearing densities. Variations in diet and rearing density resulted in only minor changes in intestinal microbiota composition despite significant effects of these variables on fish growth, performance, fillet quality, and welfare. Significant interactions between diet and rearing density were observed only in evaluations of fin indices and the relative abundance of the bacterial genus Staphylococcus. These results demonstrate that aquacultured rainbow trout can achieve remarkable consistency in intestinal microbiota composition and suggest the possibility of developing novel aquaculture strategies without overtly altering intestinal microbiota composition.
Anesthetic concerns in patients with hyper-reactive airways

Hyperreactive airway disease occurs due to acute viral or bacterial infections in children, and due to chronic bronchitis, Asthma or Emphysema in adults. Smoking and exposure to allergens may worsen the disease. Anaesthesia in these patients is associated with higher incidence of perioperative bronchospasm, postoperative laryngospam, breath holding, and hypoxia due to maldistribution of Ventilation and Perfusion. Smoking and exposure to allergens may worsen the outcome. Severe bronchospasm is a life threatening emergency. Selective β2 agonists form the main drug of choice for bronchospasm. Corticosteroids should be given early to reduce inflammation and mucosal oedema. For anaesthesia, Propofol, Vecuronium or Rocuronium, Halothane or Sevoflurane and Fentanyl are drugs of choice. Histamine releasing drugs like morphine and atracurium should be avoided. If ventilator support is required, Non invasive Pressure Support ventilation should be used first. However, Intubation and mechanical ventilation may become necessary, which however, may be associated with difficult weaning.
Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration

ABSTRACT Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities. IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages.
Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon

Strains of Bifidobacterium animalis subsp. lactis are extensively exploited by the food industry as health-promoting bacteria, although the genetic variability of members belonging to this taxon has so far not received much scientific attention. In this article, we describe the complete genetic makeup of the B. animalis subsp. lactis Bl12 genome and discuss the genetic relatedness of this strain with other sequenced strains belonging to this taxon. Moreover, a detailed comparative genomic analysis of B. animalis subsp. lactis genomes was performed, which revealed a closely related and isogenic nature of all currently available B. animalis subsp. lactis strains, thus strongly suggesting a closed pan-genome structure of this bacterial group.
Health, sleep, and professional career in female white-collar workers back to work after long-term sick-listing due to minor mental disorders

Aims: This study is a 3-year follow up of female white-collar workers, who were on long-term sick leave in 2004 due to stress-related and minor mental disorders. The aim is to show what promotes return-to-work (RTW) and the impact of a long period of sickness absence on professional career. Methods: The study includes a cohort of 233 women who were currently on medically certified sick leave lasting ≥90 days in 2004. A postal questionnaire was sent out after 34 months, regarding self-rated health, quality of sleep, sick-listing status, occupational status, etc. Results: After 34 months, 69% of the women had fully returned to working life. One of the most salient findings is that almost half of those had changed jobs and more than a third were in a new profession. Those who were back in working life rated less negative consequences of the long-term sick-listing on their professional career and their quality of sleep was better (OR 2.90, 95% CI 1.50–5.60 “sleeping all night”). Self-rated health did not show significant association with RTW (OR 2.83, 95% CI 0.91–8.77). Those who had returned to working life reported more control over their lives (OR 1.98, 95% CI 1.01–3.88). Conclusions: The findings imply that, in work health promotion and rehabilitation and efforts to prevent sickness absence due to stress-related disorders, important factors to be considered are job mobility, changes in present work, improved sleep, and control over one's own life.
Placement and Permanency Outcomes for Children in Out-of-Home Care by Prior Inpatient Mental Health Treatment

Objective: This longitudinal study followed 5,978 children in out-of-home care to examine whether placement and permanency outcomes differ between children with and without a history of inpatient mental health treatment. Method: Data were drawn from child welfare and Medicaid records from the state of Illinois. Logistic regression and survival analysis were applied. Results: A history of inpatient mental health treatment preceding out-of-home placement was associated with an increased risk for placement instability for White children and a decreased likelihood of achieving permanency for African American children. Conclusions: Children with an inpatient mental health treatment episode may benefit from assessment of service needs upon their entry into out-of-home care and continued follow-ups for reducing placement disruptions and facilitating timely permanence.
Does the school food environment influence the dietary behaviours of Norwegian 11-year-olds? The HEIA study

Aims: The aim of the study is to investigate the influence of the school food environment on the dietary behaviours of 11-year-old Norwegian children in elementary schools. Methods: Baseline data from a school-based intervention study: the Health In Adolescents study was used. A total of 1425 11-year-old children from 35 schools from the eastern part of Norway were included. School administrators provided information on the physical, political, and sociocultural school food environment and students reported their intake of fruits, vegetables, sugar-sweetened beverages (SSB), and snacks. Multilevel modelling was used to assess the school-level variance in dietary behaviours and to investigate the association of school food environmental factors with these dietary behaviours. Results: After adjustment for student characteristics, the school level accounted for a small proportion (1.1%–3.0%) of the variance in the dietary behaviours investigated. None of the investigated school food environmental factors were found to be related to the children’s reported intake of fruits, vegetables, snacks or SSB. Conclusions: Most of the variance in the dietary behaviours investigated was at the personal level. Thus in this sample, the investigated school-level factors do not appear to exert a strong influence on the dietary behaviours of children. Longitudinal studies using validated measures of the school food environment are needed.
Transfer Efficiency of Bacteria and Viruses from Porous and Nonporous Fomites to Fingers under Different Relative Humidity Conditions

ABSTRACT Fomites can serve as routes of transmission for both enteric and respiratory pathogens. The present study examined the effect of low and high relative humidity on fomite-to-finger transfer efficiency of five model organisms from several common inanimate surfaces (fomites). Nine fomites representing porous and nonporous surfaces of different compositions were studied. Escherichia coli, Staphylococcus aureus, Bacillus thuringiensis, MS2 coliphage, and poliovirus 1 were placed on fomites in 10-μl drops and allowed to dry for 30 min under low (15% to 32%) or high (40% to 65%) relative humidity. Fomite-to-finger transfers were performed using 1.0 kg/cm2 of pressure for 10 s. Transfer efficiencies were greater under high relative humidity for both porous and nonporous surfaces. Most organisms on average had greater transfer efficiencies under high relative humidity than under low relative humidity. Nonporous surfaces had a greater transfer efficiency (up to 57%) than porous surfaces (<6.8%) under low relative humidity, as well as under high relative humidity (nonporous, up to 79.5%; porous, <13.4%). Transfer efficiency also varied with fomite material and organism type. The data generated can be used in quantitative microbial risk assessment models to assess the risk of infection from fomite-transmitted human pathogens and the relative levels of exposure to different types of fomites and microorganisms.
Improved delaunay graph based video summarization with semantic features and canonical correlation

Key frame based video summarization, which enables an user to access any video in a friendly and meaningful way, has emerged as an important area of research for the multimedia community. Various pattern clustering techniques are applied for the extraction of key frames from a video to form a storyboard. In this work, we improve existing Delaunay graph based video summarization framework with i) semantic features represented by visual bag of words and ii) an improved feature fusion strategy with canonical correlation. Performance of the present method is compared with previous Delaunay graph based key frame extraction algorithms using Fidelity, Shot Reconstruction Degree and Compression Ratio. Experiments on standard video datasets clearly indicate the supremacy of the proposed approach.
Selection of Amine-Oxidizing Dairy Lactic Acid Bacteria and Identification of the Enzyme and Gene Involved in the Decrease of Biogenic Amines

ABSTRACT Accumulation of biogenic amines (BAs) in cheese and other foods is a matter of public health concern. The aim of this study was to identify the enzyme activities responsible for BA degradation in lactic acid bacteria which were previously isolated from traditional Sicilian and Apulian cheeses. The selected strains would control the concentration of BAs during cheese manufacture. First, 431 isolates not showing genes encoding the decarboxylases responsible for BA formation were selected using PCR-based methods. Ninety-four out of the 431 isolates degraded BAs (2-phenylethylamine, cadaverine, histamine, putrescine, spermine, spermidine, tyramine, or tryptamine) during cultivation on chemically defined medium. As shown by random amplification of polymorphic DNA-PCR and partial sequencing of the 16S rRNA gene, 78 of the 94 strains were Lactobacillus species (Lactobacillus casei, Lb. fermentum, Lb. parabuchneri, Lb. paracasei, Lb. paraplantarum, and Lb. rhamnosus), Leuconostoc species (Leuconostoc lactis and Ln. mesenteroides), Pediococcus pentosaceus, Lactococcus lactis, Streptococcus species (Streptococcus gallolyticus and S. thermophilus), Enterococcus lactis, and Weissella paramesenteroides. A multicopper oxidase-hydrolyzing BA was purified from the most active strain, Lb. paracasei subsp. paracasei CB9CT. The gene encoding the multicopper oxidase was sequenced and was also detected in other amine-degrading strains of Lb. fermentum, Lb. paraplantarum, and P. pentosaceus. Lb. paracasei subsp. paracasei CB9CT and another strain (CACIO6CT) of the same species that was able to degrade all the BAs were singly used as adjunct starters for decreasing the concentration of histamine and tyramine in industrial Caciocavallo cheese. The results of this study disclose a feasible strategy for increasing the safety of traditional cheeses while maintaining their typical sensorial traits. IMPORTANCE Because high concentrations of the potentially toxic biogenic amines may be found in traditional/typical cheeses, the safety of these food items should be improved. Lactic acid bacteria selected for the ability to degrade biogenic amines may be used during cheese making to control the concentrations of biogenic amines.
Feature correspondence finding with vertical cylinder and epipolar geometry for indoor environments

We introduce an improved approach, called FCVC, that finds accurate matches from two related images of indoor environments by matching corresponding vertical cylinders of features, then retrieves more matches by epipolar geometry. Feature matching is a critical technique for many vision-based applications. However, since the preliminary matching results obtained by SIFT sometimes are not accurate enough, and therefore, post processing methods, like RANSAC, have been proposed to increase the correctness of feature mappings. As RANSAC iteratively selects partial matches from preliminary matches and recovers the epipolar geometry to find correct matches, our method first finds accurate matches in vertical cylinders, based on three consistency properties which are common while two images are taken on a flat floor: (1) altitudinal order, (2) composition of features for each vertical cylinder, and (3) horizontal order of all vertical cylinders. Once some accurate matches are acquired, the epipolar geometry is recovered to retrieve matches that are not grouped into any vertical cylinder previously. Experiments in different indoor environments reveal that the proposed FCVC in general spends at most 6% of the time required by RANSAC, has at least 71% of the number of matches obtained by RANSAC, and yet with accuracy rate similar to that of RANSAC.
Internalization of Salmonella enterica in Leaves Is Induced by Light and Involves Chemotaxis and Penetration through Open Stomata

ABSTRACT Outbreaks of salmonellosis related to consumption of fresh produce have raised interest in Salmonella-plant interactions leading to plant colonization. Incubation of gfp-tagged Salmonella enterica with iceberg lettuce leaves in the light resulted in aggregation of bacteria near open stomata and invasion into the inner leaf tissue. In contrast, incubation in the dark resulted in a scattered attachment pattern and very poor stomatal internalization. Forcing stomatal opening in the dark by fusicoccin had no significant effect on Salmonella internalization. These results imply that the pathogen is attracted to nutrients produced de novo by photosynthetically active cells. Indeed, mutations affecting Salmonella motility and chemotaxis significantly inhibited bacterial internalization. These findings suggest a mechanistic account for entry of Salmonella into the plant's apoplast and imply that either Salmonella antigens are not well recognized by the stoma-based innate immunity or that this pathogen has evolved means to evade it. Internalization of leaves may provide a partial explanation for the failure of sanitizers to efficiently eradicate food-borne pathogens in leafy greens.
Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park

ABSTRACT Thermoproteales (phylum Crenarchaeota) populations are abundant in high-temperature (>70°C) environments of Yellowstone National Park (YNP) and are important in mediating the biogeochemical cycles of sulfur, arsenic, and carbon. The objectives of this study were to determine the specific physiological attributes of the isolate Pyrobaculum yellowstonensis strain WP30, which was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS], 80°C, pH 6.1, 135 μM As) and relate this organism to geochemical processes occurring in situ. Strain WP30 is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, 58% G+C content), revealing numerous metabolic pathways for the degradation of carbohydrates, amino acids, and lipids. Multiple dimethyl sulfoxide-molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for the de novo synthesis of nearly all required cofactors and metabolites were identified. The comparative genomics of P. yellowstonensis and the assembled metagenome sequence from JCHS showed that this organism is highly related (∼95% average nucleotide sequence identity) to in situ populations. The physiological attributes and metabolic capabilities of P. yellowstonensis provide an important foundation for developing an understanding of the distribution and function of these populations in YNP.
Breastfeeding and Obesity

The American Pediatric Association (APA) recommends breast milk as the sole source of nutrition for infants aged 6 months and younger. This recommendation is a result of numerous studies demonstrating the benefits of breast milk in relation to decreased infection rates, improved digestion, and decreased complications of prematurity in infants hospitalized in the neonatal intensive care unit. Emerging studies now suggest a protective link for mother and baby against obesity and related sequelae when infants are breast-fed. As obesity rates in women and children continue to rise, breast milk is becoming recognized as a key intervention to keep both mother and baby healthy.