Miracle-dz/UniFAR-FTUs huggingface dataset:
Enzymes de dépolymérisation d'exopolysaccharides bactériens marins

Les exopolysaccharides (EPS) sont des biopolymeres pouvant etre synthetises par les Eucaryotes, lesArchees et les Procaryotes. Au niveau bacterien les EPS peuvent etre impliques dans la constitution du biofilm (phenomene de biofouling) lors de la colonisation de nouveaux milieux. Ces biopolymeres ont des proprietes physico-chimiques et biologiques specifiques et innovantes a haut potentiel biotechnologique (agroalimentaire, sante, cosmetique, ingenierie environnementale .). A l'oppose, leurs roles ecologiques lors de l'etablissement de biofilms de souches potentiellement pathogenes peuvent rendre leur eradication compliquee.Les processus de depolymerisation par voie enzymatique sont necessaires pour realiser l'elucidation structurale fine des EPS complexes, pour la production de derives bio-actifs calibres a faible poids moleculaire ou pour empecher la formation de biofilm. La mise en evidence de ces phenomenes enzymatiques sur des microorganismes modeles peut egalement permettre de mieux cerner les flux de matiere au sein de certains compartiments biologiques en particulier en milieu marin. Neanmoins la complexite et grande diversite de structures des EPS rendent la recherche d’enzymes de depolymerisation specifiques difficile.Deux strategies ont ete employees pour trouver des sources d'enzymes.1. La voie bacterienne via l’utilisation de bacteries marines productrices d’EPS.2. La voie virale par la recherche de polysaccharidases de bacteriophages marins. En plus d’EPS marins deja connus, de nouveaux substrats (EPS) originaux ont ete produits et caracterises a partir de bateries marines d’interets biotechnologiques et/ou ecologiques pour les besoins du projet. Un criblage enzymatique sur 11 souches bacteriennes du genre Alteromonas a permis de mettre en evidence que 7 d’entre elles presentaient une activite de depolymerisation endogene vis-a-vis de leur propre EPS. Une bioprospection a ete realisee afin de constituer une virotheque a partir d’hotes bacteriens producteurs d’EPS dans le but de fournir une source de Cazymes virales potentielles. Sur 33 bacteriophages, 10 ont ete selectionnes pour leur capacite a rester infectieux lorsque leurs hotes synthetisent des EPS. Finalement un systeme hote/virus a ete selectionne.Les 5 virus (appeles Carin-1 a 5) infectant Cobetia marina DSMZ 4741 ont ete etudies au niveau de leurs traits de vie. Les capacites de depolymerisation de Carin-1 et Carin-5 sur l'EPS L6 ont ete explores plus en detail. En parallele, la structure chimique de l'EPS L6 a ete integralement elucidee.
Differences in anti-predator behavior and survival rate between hatchery-reared and wild grass carp (Ctenopharyngodon idellus)

Grass carp Ctenopharyngodon idellus , is the primary freshwater species produced in China. Because natural populations have shrunk in the wild, restocking programs using hatchery-reared fish have emerged. Artificial rearing could affect fish anti-predator behavior, thus decreasing their survival in the wild. The impact of artificial rearing on C. idellus 's behavior remains unknown because empirical studies are scarce. In this study, we compared anti-predator behavior and survival rate between hatchery-reared and wild C. idellus . Both hatchery-reared and wild C. idellus displayed clear anti-predator behavior when exposed to visual and odor cues of a predator. However, hatchery-reared C. idellus showed significantly lower aggregation index (reflecting shoaling behavior), inspection rate and spent less time in risky area compared to their wild counterparts. When directly exposed to predators, more hatchery-reared C. idellus were predated. This raises concerns about the efficiency of restocking programs and highlights the need to adjust artificial rearing and stocking conditions of C. idellus to produce fish that are better adapted to natural conditions.
Physical and chemical characteristics of soil from tiger shrimp aquaculture ponds at Malacca, Malaysia

ABSTRACT Soil physicochemical properties of the growout ponds of black tiger shrimp (Penaeus monodon) were examined in relation to shrimp yields for one production cycle. The culture ponds were old (>5 years) and new (newly constructed) types. Soil texture was silty clay with low sand content and high proportion of clay for both the pond types with alkaline soil pH (7.87–9.71). Organic matter (OM) concentration was higher (7.48 ± 0.01%) in old ponds and positively related (r = 0.58, P < 0.05) with total nitrogen (TN). The major cations (Ca, Mg, and Na) were higher in the soil of old ponds and did not fluctuate significantly during culture. The majority of trace elements, i.e., Fe (349.22 ± 35.7 ppm), Mn (56.19 ± 30.2 ppm), Zn (88.56 ± 8.09 ppm), Al (454.3 ± 200.6), Pb (1.3 ± 0.96 ppm), Co (3.4 ± 0.2), V (6.56 ± 1.79 ppm), Cr (19.32 ± 0.63 ppm), Ti (82.78 ± 54.3 ppm), As (5.60 ± 0.28 ppm), Ag (0.38 ± 0.5 ppm), and Sb (3.89 ± 0.48 ppm) were found to be higher in new pond soils than the old ponds. Except for soil manganese, no major fluctuations in trace elements were observed during the culture period. Shrimp growth was not significantly different in the two types of ponds, and no distinct correlation between shrimp growth and element content of soils could be drawn. The results indicate that shrimp pond age may not affect production of shrimp if soils are properly managed pre- and postculture. The differences in production in different ponds might be the result of management practice such as quality of shrimp post larvae, pond preparation, water and feed quality, and available live feed in the pond bottom or other environmental factors like water nutrients and physicochemical parameters.
Fruit Quality Analysis in Four New Mandarin Hybrids during Maturation Period

Producing fruits with a desirable degree of maturity and specific organoleptic characteristics has become a necessity in the citrus industry to meet consumer needs. Breeding approaches, with a particular focus on organoleptic quality, may provide the sector with performant varieties and therefore meet its expectations. In this study, four citrus cultivars obtained by hybridization and grafted onto different rootstocks were evaluated for fruit pomological and organoleptic traits, including juice content, organic acids, soluble solids content (SSC). The results obtained for these attributes at different stages of maturity highlighted increasing trends of soluble solids content and maturity index and a decreasing trend of acidity during fruit maturation. In addition, all studied hybrids reached the minimum maturity index (SSC/Acidity = 7.0) by early December. The H8 cultivar was particularly characterized as a late-maturing cultivar since its fruits matured much later than Afourer control. The variation of maturity parameters, which was maintained throughout the harvest period, was influenced by variety and harvest time, while the rootstock factor had little effect.
Agent-based network model predicts strong benefits to youth-centered HIV treatment-as-prevention efforts

We used an agent-based network model to examine the effect of targeting different risk groups with unsuppressed HIV viral load for linkage or re-linkage to HIV-related treatment services in a heterosexual population with annual testing. Our model identifies prevention strategies that can reduce incidence to negligible levels (i.e., less than 0.1 infections per 100 person-years) 20 years after a targeted Treatment-as-Prevention (TasP) campaign. The model assumes that most (default 95%) of the population is reachable (i.e., could, in principle, be linked to effective care) and a modest (default 5% per year) probability of a treated person dropping out of care. Under random allocation or CD4-based targeting, the default version of our model predicts that the TasP campaign would need to suppress viral replication in ~80% of infected people to halt the epidemic. Under age-based strategies, by contrast, this percentage drops to 50% to 60% (for strategies targeting those <30 and <25, respectively). Age-based targeting did not need to be highly exclusive to yield significant benefits; e.g. the scenario that targeted those <25 years old saw ~80% of suppressed individuals fall outside the target group. This advantage to youth-based targeting remained in sensitivity analyses in which key age-related risk factors were eliminated one by one. As testing rates increase in response to UNAIDS 90-90-90 goals, we suggest that efforts to link all young people to effective care could be an effective long-term method for ending the HIV epidemic. Linking greater numbers of young people to effective care will be critical for developing countries in which a demographic “youth bulge” is starting to increase the number of young people at risk for HIV infection.
Non-biological synthetic spike-in controls and the AMPtk software pipeline improve fungal high throughput amplicon sequencing data

High throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize biological communities from environmental samples. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. The fungal internal transcribed spacer (ITS) region is difficult to sequence due to its variability (length and sequence divergence) across the fungal kingdom. To assess the ability of sequencing platforms and data processing pipelines using fungal ITS amplicons, we created two ITS spike-in control mock communities composed of single copy plasmid DNA: a biological mock community (BioMock), consisting of cloned ITS sequences, and a synthetic mock community (SynMock), consisting of non-biological ITS-like sequences. Using these spike-in controls we show that pre-clustering steps for variable length amplicons are critically important and a major source of bias is attributed to initial PCR reactions. These data suggest HTAS read abundances are not representative of starting values. We developed AMPtk (amplicon toolkit), a versatile software solution equipped to deal with variable length amplicons featuring a method to quality filter HTAS data based on spike-in controls. While we describe herein a non-biological (synthetic) mock community for ITS sequences, the concept can be widely applied to any HTAS dataset.
Studying the Market Potential for Specialty Cultivars of Sunflower Cut Flowers

In the United States, there is an increasing demand for fieldor greenhouse-grown, specialty, locally grown cut flowers. However, certain cultivars of cut flowers are not readily available in the market. The purpose of this research was to produce a crop of novelty sunflowers (Helianthus annuus ‘Firecracker’) and study the marketability of the cut flowers to wholesale and retail florists and consumers. The plants were grown in greenhouses. Stems were harvested and shown to local floral wholesalers/retailers who were individually interviewed on their perceptions of the cut flower as a product. Farmers’ market patrons were administered a quantitative survey to determine their perspectives on locally sourced products and willingness to pay (WTP) for the specialty cut flower (SCF). Results indicated half of the local florists interviewed responded positively to locally grown floral products in general, with all florists willing to pay at the least the same amount for the SCF as they are currently paying for their standard commercially grown, imported cut sunflowers. Farmers’ market customers expressed a WTP of $1.34/stem and/or $10.13/bunch of 10 stems for the SCF with participants who expressed a higher concern for sourcing local products often more willing to pay a higher price for the SCF. Furthermore, among demographic comparisons, there were no differences inWTP based on age, income, and education.However, females were more likely to purchase the SCF when compared with males, and African-Americans were less likely to buy the SCF and willing to pay less for 10stem bunches when compared with respondents of other ethnic backgrounds. Although many buyers responded positively to the product, results indicate women and those who prefer to buy local would be a good target demographic market for the product.
Use of a scoring strategy to determine clinical risk of progression and risk group-specific treatment adherence in subjects with latent tuberculosis infection

Background Annual incidence of active tuberculosis (TB) cases has plateaued in the US from 2013-2015. Most cases are from reactivation of latent tuberculosis infection (LTBI). A likely contributor is suboptimal LTBI treatment completion rates in subjects at high risk of developing active TB. It is unknown whether these patients are adequately identified and treated under current standard of care. Methods In this study, we sought to retrospectively assess the utility of an online risk calculator (tstin3d.com) in determining probability of LTBI and defining the characteristics and treatment outcomes of Low: 0-<10%, Intermediate: 10-<50% and High: 50-100% risk groups of asymptomatic subjects with LTBI seen between 2010-2015. Results 51(41%), 46 (37%) and 28 (22%) subjects were in Low, Intermediate and High risk groups respectively. Tstin3d.com was useful in determining the probability of LTBI in tuberculin skin test positive US born subjects. Of 114 subjects with available treatment information, overall completion rate was 61% and rates of completion in Low (60%), Intermediate (63%) and High (57%) risk groups were equivalent. 75% subjects in the 3HP group completed treatment compared to 58% in the INH group. Provider documentation of important clinical risk factors was often incomplete. Logistic regression analysis showed no clear trends of treatment completion being associated with assessment of a risk factor. Conclusion These findings suggest tstin3d.com could be utilized in the US setting for risk stratification of patients with LTBI and select treatment based on risk. Current standard of care practice leads to subjects in all groups finishing treatment at equivalent rates.
Assessment of Endothelial Function in Humans and the Endothelial-protective Effects of 3-hydroxy-3-methylglutaryl coenzyme A Reductase Inhibitors

The endothelium plays an essential role in the regulation of vascular homeostasis and a state of endothelial dysfunction, which develops in the presence of cardiovascular risk factors, may contribute to the development and progression of cardiovascular disease. As such, the measurement of endothelial function, beyond being an experimental tool, may serve as an important tool to complement current risk assessment algorithms in the identification of high-risk patients. Flow-mediated dilation (FMD) is a non-invasive measure of peripheral conduit artery endothelial function that holds great promise. Presently, FMD suffers from methodological heterogeneity and a poor understanding of the various biological components involved in eliciting the dilatory response to a given shear stimulus. We compared both traditional and alternative methods of arterial diameter characterization with regards to their repeatability, nitric oxide-dependency, and their sensitivity in distinguishing between normal and dysfunctional endothelial responses. Our findings emphasize the importance of continuous arterial diameter measurement and suggest that the time to peak FMD is not a useful adjunctive measure of the
Status of inflammatory markers and growth factor in gastric ulcer protective effects of Punica granatum L. peel extract in rat

Background: Inflammatory markers, namely, myeloperoxidase (MPO), cytokines (tumor necrosis factor-alpha [TNF-α], and interleukin-1 beta [IL-1β]) and vascular endothelial growth factor (VEGF) have been reported to play an important role in ulcerogenesis and healing. Recently, we reported that the gastric ulcer (GU) protective and healing effects of 50% ethanol (EtOH) extract of Punica granatum peel (PGE) in rats were predominantly due to strengthening of mucosal defense and antioxidants status. Aims and Objectives: The present study incorporates the effects of PGE on rat gastric mucosal inflammatory markers (MPO, TNF-α, and IL-1β) and angiogenic factor (VEGF) in GU induced by cold-restraint stress (CRS) and EtOH in rats. Materials and Methods: PGE (100 mg/kg) was administered orally once daily to rats for 7 days before induction of CRS and EtOH GU. Ulcer index (UI), gastric mucosal MPO, TNF-α, and IL-1β, and VEGF were estimated. Results: CRS rats showed increase in UI and MPO (419.5, P < 0.001) compared with unstressed rats while PGE caused decrease in UI (46.1%, P < 0.05) and MPO (51.1%, P < 0.001) compared with CRS rats. EtOH rats showed increase in UI, TNF-α (936.5%, P < 0.001), IL-1β (37.2%, P < 0.05), and VEGF (13.0%, P < 0.05) compared with control normal saline-treated rats. PGE-treated EtOH rats showed decrease in UI (68.9%, P < 0.05), TNF-α (77.9%, P < 0.01), and IL-1β (24.8%, P < 0.05) but tended to decrease VEGF (7.3%, P < 0.2) compared with EtOH rats. Conclusion: Both the inflammatory markers and VEGF were found to increase in GU rats while PGE EtOH extract decreased the status of inflammatory markers with little change in VEGF level with concomitant decrease in ulceration indicating their role in ulcer healing and repair.
Neural control of lipid metabolism and inflammation : implications for atherosclerosis

The brain is increasingly recognized as the regulator of body homeostasis and as possible treatment target for cardiovascular disease. This thesis further reveals the role of the autonomic nervous system (ANS) in the control of lipid metabolism and inflammation, and identified pathological consequences of disturbed regulation. Part I focuses on regulation of lipid metabolism by the ANS, with special attention for brown adipose tissue (BAT) as an emerging pharmacological target for therapy. We describe novel targets that modulate BAT, both directly (e.g. CB1R) and via the brain (e.g. MC4R, GLP-1R) to show that BAT activation improves dyslipidemia, glucose tolerance and T2D and even atherosclerosis. In addition, we identified the biological clock as an important regulator of BAT function and showed the consequences of disturbed circadian rhythmicity for lipid metabolism. Part II of this thesis describes studies on the regulation of inflammation by the ANS, with focus on the anti-inflammatory reflex. During this reflex, binding of acetylcholine to α7nAChR and subsequent intracellular signaling results in transcriptional repression of pro-inflammatory genes. We investigated the effects of hematopoietic α7nAChR deficiency and the consequences of selective parasympathetic and sympathetic denervation of the spleen for this reflex, and for inflammation and atherosclerotic plaque development.
Adaptive Governance of Cape Mountain Zebra, Can It Work?

Adaptive governance and network governance theory provide a useful conceptual framework to guide the conservation of threatened species in complex multi-actor, multijurisdictional social ecological systems. We use principles from this theory to assess strengths and weaknesses in (1) national legislation, and (2) the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) Regulations applicable to the conservation of the Cape mountain zebra (Equus zebra zebra) (CMZ) in South Africa. A legislated conservation tool, Biodiversity Management Plans for Species (BMP-S), establishes a collaborative network of role players and facilitates the important principles of collaborative learning and adaptation. Effective governance of this network is critical to success, but challenging because of a mandate gap and limited capacity in government to provide essential network-level competencies. National regulations governing human use of CMZ (Threatened or Protected Species (TOPS) Regulations) accords with the principles of (1) being developed in consultation with stakeholders and (2) open to revision and adaptation. CITES Regulations also provide adequately for adaptation. Poor alignment of regulations between different regulatory authorities in South Africa and limited capacity for implementation of regulations seriously constrain learning and adaptation.
WERF Phase 1: Factors affecting conditioning during dewatering: Sludge and Polymer Characteristics

A study was performed to investigate the factors which impact polymer demand during conditioning such as biocolloid concentration, polymer characteristics and shear. The central hypothesis of the research was that biocolloids were directly related to polymer demand, and factors affecting biocolloid concentration and their charge neutralization would impact polymer demand. This is the first paper in the two-paper series which examines the role of biocolloids and polymer characteristics on polymer demand. Biocolloids are defined as small particles that are detached from the larger flocs, and are primarily protein and polysaccharide produced by microbes. In addition the role of polymer characteristics was investigated. The results showed a very good linear correlation (r2=0.83) between biocolloid concentration and the optimum polymer dose (OPD) measured for a number of different sludge types. The thermophilic sample had the greatest polymer demand, followed by mesophilic anaerobic, aerobically digested, and activated sludges. The polymer charge density and molecular weight also impacted the OPD. The greater charge density of the polymer resulted in increased polymer demand when the polymer demand is expressed on an equivalent charge basis, while higher molecular weight polymers had lower polymer demand. The results can be applied by practitioners to understand the factors which will affect polymer dosages and ultimately polymer costs.
Spatial variability of chemical and agronomic attributes of soil in wheat seed production field.

The need to rationalize the use of fertilizers and other chemicals, and financial resources has generated, increasingly, research in order to describe the spatial variability of soil properties in crops. This study aimed to study the spatial organization of soil properties in a wheat seed production field in an area of 11 ha in Lavras do Sul, RS, Brazil. Collecting soil four subsamples for chemical analysis and 10 for compression using a 100m X 100m grid by sampling was performed. Descriptive analysis and geostatistical was performed to characterize the samples and identify the spatial dependence of the studied attributes. From the results obtained maps were drawn by "Agricultural System CR-Campeiro 7" software. The greater variability checked by coefficient of variation was observed for the phosphorus content, the other had medium and low variability. All attributes have moderate spatial dependence and range equal to or above the maximum search radius.
Efficacy of plant oils against insect pests of cowpea in farmscapes

The relative efficacy of plant oils of neem Azadirachta indica and karanj Pongamia pinnata (3%) as aqueous sprays was evaluated under field conditions against insect pests of cowpea cultivated under farmscape treatments (sole cowpea, cowpea + niger, cowpea + marigold, cowpea + maize bordered with marigold and cowpea + maize bordered with niger) during kharif 2012 and 2013. Their efficacy in terms of population reduction revealed significantly maximum effect with cowpea + marigold (2:1); the respective pest population reduction pooled values for two years after 1 and 3 days of spray were 73.50 and 80.96 (aphids), 83.10 and 77.84 (jassids), 85.05 and 80.41 (whitefly), 85.42 and 81.59 (thrips), 77.62 and 72.76 (blister beetles), 78.341 and 73.80 (coreid bug), and 77.82 and 73.83 (green stink bug). Significant minimum population reduction was observed in the sole crop of cowpea for all the pests.