Miracle-dz/UniFAR-FTUs huggingface dataset:
CHARACTERIZATION OF VARIOUS VIRULENCE PROPERTIES OF DRUG-RESISTANT KLEBSIELLA ISOLATES: AN IN VITRO STUDY AMONG â€œSUPERBUGSâ€

Objective: The objective of this study was to evaluate the various virulence factors among all extended-spectrum beta-lactamase (ESBL)-producing Klebsiella isolates. Methods: Klebsiella species (n=201) isolated from various non-repeated clinical samples from October 2016 to May 2017 were collected and identified by biochemical method and confirmed by BD Phoenix. Antibiotic susceptibility test was performed by Kirby-Bauer disc diffusion method, and ESBL detection was done by combined disc diffusion method. Capsule detection was done by nigrosin dye staining, hypermucoviscosity was done by string test, biofilm was performed by microtiter plate assay, and hemagglutination was performed with human erythrocytes treated with tannic acid. Results: Among 201 ESBL-producing Klebsiell a isolates, 63.2 % were multidrug resistance and 24.4% were extensively drug-resistant. Among these isolates, Klebsiella infection is more in older patients. All isolates were (100%) positive for capsule and siderophores production. Of all 201 isolates, 14 (7%) were strong, 61 (30.3%) were moderate, and 104 (51.8%) were weak biofilm producers. Among these isolates, 36 (17.9%) were type 1 fimbriae, 140 (69.7%) were type 3 fimbriae, and only 17 (8.5%) were positive for hypermucoviscosity. Conclusion: Several virulence factors were studied, in which biofilm with fimbriae is the main cause for the resistance of antibiotics. Bacterial resistance profile found to be high with ESBL production and multiple drug resistance in the majority of the Klebsiella i solates, which is a result of improper antibiogram schedule and their virulence property.
Improvement of Antioxidant Activity of Grass Carp (Ctenopharyngodon idella) Protein Hydrolysate by Washing and Membrane Removal Pretreatments and Ultrasonic Treatment

ABSTRACT To improve the antioxidant activity of grass carp hydrolysate, washing and membrane removal pretreatments and ultrasonic treatment were applied in this study. Various pretreatment methods (washing methods and membrane removal methods) for removing the prooxidants and phospholipid in minced fish were evaluated. The effects of ultrasonic treatment prior to enzyme hydrolysis on the antioxidant activities of minced carp hydrolysate were investigated. The minced carp subjected to washing with 0.4% NaCl solution and subsequent membrane removal with CaCl2 and citric acid solution had the lowest content of prooxidants and phospholipid remaining in the minced fish. The hydrolysate produced from washing/membrane removal pretreated carp with ultrasonic treatment for 20 min had the highest ferric reducing antioxidant power and scavenging activities against 1,1-diphenyl-2-picrylhydrazyl and 2,2ʹ-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) radicals. This suggested that the combination approach of washing/membrane removal pretreatment and ultrasonic treatment could improve the antioxidant activity of carp hydrolysate, and this hydrolysate could be a potential antioxidant ingredient for functional foods.
The impact of geographic range, sampling, ecology, and time on extinction risk in the volatile clade Graptoloida

Abstract. Although extinction risk has been found to have a consistent negative relationship with geographic range across wide temporal and taxonomic scales, the effect has been difficult to disentangle from factors such as sampling, ecological niche, or clade. In addition, studies of extinction risk have focused on benthic invertebrates with less work on planktic taxa. We employed a global set of 1114 planktic graptolite species from the Ordovician to lower Devonian to analyze the predictive power of species' traits and abiotic factors on extinction risk, combining general linear models (GLMs), partial least-squares regression (PLSR), and permutation tests. Factors included measures of geographic range, sampling, and graptolite-specific factors such as clade, biofacies affiliation, shallow water tolerance, and age cohorts split at the base of the Katian and Rhuddanian stages. The percent variance in durations explained varied substantially between taxon subsets from 12% to 45%. Overall commonness, the correlated effects of geographic range and sampling, was the strongest, most consistent factor (12–30% variance explained), with clade and age cohort adding up to 18% and other factors <10%. Surprisingly, geographic range alone contributed little explanatory power (<5%). It is likely that this is a consequence of a nonlinear relationship between geographic range and extinction risk, wherein the largest reductions in extinction risk are gained from moderate expansion of small geographic ranges. Thus, even large differences in range size between graptolite species did not lead to a proportionate difference in extinction risk because of the large average ranges of these species. Finally, we emphasize that the common practice of determining the geographic range of taxa from the union of all occurrences over their duration poses a substantial risk of overestimating the geographic scope of the realized ecological niche and, thus, of further conflating sampling effects on observed duration with the biological effects of range size on extinction risk.
De Novo Sequence Assembly of Viral Quasispecies

The rapid replication and high mutation rates of viruses like HIV lead to the formation of a community of highly similar genomes, referred to as a viral quasispecies, in an infected individual. Next-generation sequencing technologies enable researchers to sequence a complete quasispecies community with reduced expense and effort compared to traditional sequencing methods. However, typical sequence assembly software is designed to reconstruct a single genome from sequencing reads rather than a community of highly similar genomes. We describe and implement a de novo assembly method for reconstructing variants from a quasispecies community using de Bruijn graphs and a novel, heuristic pathconstruction method designed to identify corresponding variations at long distances across the genome. We predict the relative abundance of reconstructed variants using an approach inspired from Markov chains.
Mitochondrial genomes of the South American electric knifefishes Eigenmannia humboldtii (Steindachner 1878), Eigenmannia limbata (Schreiner and Miranda Ribeiro 1903), Sternopygus aequilabiatus (Humboldt 1805) and Sternopygus macrurus (Bloch and Schneider 1801), (Gymnotiformes, Sternopygidae)

Abstract We report four mitochondrial genomes of South American electric knifefishes, derived from target capture and Illumina sequencing (HiSeq 2500 PE100). Two trans-Andean species Eigenmannia humboldtii (mitochondrial consensus genome of 25 individuals) and Sternopygus aequilabiatus (mitochondrial consensus genome of 30 individuals) from Colombia and two cis-Andean species Eigenmannia limbata from Suriname and Sternopygus macrurus from Argentina. Regarding Eigenmannia humboldtii, Eigenmannia limbata, and Sternopygus macrurus mitochondrial genomes have 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs, 22 transfer RNAs, and are 13,394 bp, 10,921 bp, and 13,013 bp in length respectively, for Sternopygus aequilabiatus mitochondrial genomes have 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and is 14,270 bp in length.
Diet specialization does not explain occupancy or abundance in a test of the resource breadth hypothesis in a small mammal community

The abundance-occupancy relationship (AOR) is a recurrent pattern in ecology and biogeography, in which species with expansive distributions are locally common while those with restricted distributions are locally rare. Despite occurring across a wide variety of taxa and spatial scales, the mechanisms underlying AORs are not well understood. I tested two such mechanisms regarding dietary generalism in a guild of 8 small, herbivorous African mammals: (1) the degree to which diet was explained by food availability, and (2) population-level diet breadth. I expected that food availability would better predict diet for abundant, widespread species than rare, restricted species. Additionally, I predicted that species that use a diversity of C3 and C4 plants and arthropod resources (dietary generalists) both would occupy more sites and, given occupancy, be more abundant than rare, restricted species (i.e., purported dietary specialists). For two species, diet was related to food availability, albeit weakly; food availability was a poor predictor of diet for the remaining six species. I detected no relationship between population-level diet breadth and abundance, nor between
INFLUENCE OF EXTRUSION ON THE NUTRITIVE VALUE OF PEAS: IN VITRO ASSAY

Pengaruh ekstrusi terhadap nilai nutrisi pea: analisa in vitro. Sampel Pea dianalisis baik dalam bentuk yang tidak diekstrusi maupun yang diekstrusi dengan menggunakan kombinasi dua kondisi kadar air (19 and 22%) dan tiga perbedaan suhu (120, 140 dan 170 o C). Â Hasil penelitian menunjukkan bahwa ekstrusi secara signifikan (P 0,05) kandungan lemak dan abu. Secara umum, kandungan polisakarida bukan pati yang larut dan TI dari hampir semua sampel pea yang diekstrusi lebih tinggi (P 0,05) dari suhu barrel pada kandungan kadar air pakan yang rendah (19%), tetapi pada kandungan kadar air yang tinggi (22%), kandungan protein kasar dari pea yang diekstrusi meningkat (P<0,05) seiring dengan meningkatnya suhu barrel. Ekstrusi meningkatkan (P<0,05) daya cerna pati secara in vitro dari pea, tetapi menurunkan (P<0,05) daya cerna protein in vitro. Kesimpulannya, ekstrusi merubah secara signifikan kandungan kimia kacang pea, meningkatkan daya cerna pati, tetapi menurunkan daya cerna protein. Penelitian lanjutan diperlukan untuk mengevaluasi pengaruh ekstrusi terhadap ketersediaan nutrisi dari pea. Keyword : ekstrusi,suhu, kadar air, in vitro, nutrisi, pea.
Experimental increases in glucocorticoids alter function of the neuroendocrine stress axis in wild red squirrels without negatively impacting survival and reproduction

Hormones including glucocorticoids (stress hormones) are well known for their effects on animal behavior and life history traits, and this understanding has come through both correlative and manipulative studies. While the latter offers a higher level of control (and ability to assign causality), there are important methodological concerns that are often not considered when manipulating hormones, including glucocorticoids, in wild animals. In this study, we examined how experimental elevations of cortisol concentrations in wild North American red squirrels (Tamiasciuгus hudsonicus)affected their hypothalamic-pituitary-adrenal (HPA) axis reactivity, and life history traits including body mass, litter survival, and adult survival. The effects of exogenous cortisol on plasma cortisol concentrations depended on the time between treatment consumption and blood sampling. In the first nine hours after consumption of exogenous cortisol, individuals had significantly higher true baseline plasma cortisol concentrations, but adrenal gland function was impaired. Approximately 24 hours after consumption of exogenous cortisol, individuals had much lower plasma cortisol concentrations than controls, but adrenal function was restored. Corticosteroid binding globulin (CBG) concentrations were also significantly reduced in squirrels treated with cortisol. Despite these profound shifts in the functionality of the neuroendocrine stress axis, fitness proxies including squirrel body mass, offspring survival, and adult survival were unaffected by experimental increases in cortisol concentrations. Our results highlight that even short-term experimental increases in glucocorticoids can affect adrenal gland functioning and CBG concentrations, but may have no side-effects on proxies of fitness.
Régulation de la stabilité de la protéine anti-apoptotique BCL2A1

L’apoptose ou mort cellulaire programmee joue un role preponderant dans l’homeostasie cellulaire. Ce processus est tres finement regule par les proteines de la famille BCL-2 qui controlent la permeabilite de membrane mitochondriale externe et la liberation du cytochrome c, deux evenements majeurs precedant la mort cellulaire. Les proteines anti-apoptotiques de la famille BCL-2 contribuent a la tumorigenese et sont impliquees dans la resistance des cancers aux molecules chimiotherapeutiques ; a ce titre, elles representent des cibles importantes pour le developpement de nouvelles therapies. BCL2A1 est un membre anti-apoptotique de la famille BCL-2 implique dans la chimioresistance de nombreuses tumeurs. La proteine BCL2A1 a pour caracteristique d’avoir une demi-vie courte due a sa degradation constitutive par le systeme ubiquitine-proteasome. Ceci regule la stabilite et la fonction anti-apoptotique de BCL2A1 et represente un mecanisme suppresseur de tumeur majeur. Cependant, les enzymes qui controlent les modifications post-traductionnelles impliquees dans l’ubiquitination et la degradation de BCL2A1 demeurent, a ce jour, inconnues. Dans la presente these, nous donnons un apercu des acteurs et des mecanismes impliques dans la regulation de l’ubiquitination de BCL2A1. Nous presentons des preuves que TRIM28 est une E3 ubiquitine-ligase pour BCL2A1. En effet, les proteines TRIM28 et BCL2A1 endogenes interagissent ensemble au niveau des mitochondries et la depletion de TRIM28 diminue l’ubiquitination de BCL2A1. Nous montrons aussi que TRIM17 stabilise BCL2A1 en empechant son interaction avec TRIM28 et son ubiquitination mediee par TRIM28, et que l’activite de GSK3 est impliquee dans l’inhibition de la degradation de BCL2A1. Ainsi, BCL2A1 et son proche homologue MCL-1 sont regules par des facteurs communs mais de facon oppose. Finalement, la surexpression de TRIM28 ou l’inactivation de TRIM17 diminue le niveau proteique de BCL2A1 et restaure la sensibilite des cellules de melanomes aux therapies utilisant des inhibiteurs de la kinase BRAF. Globalement, nos resultats decrivent un rheostat moleculaire au sein duquel deux proteines de la famille TRIM regulent de facon antagoniste la stabilite de BCL2A1 et modulent ainsi la mort cellulaire.
The complete mitochondrial genome of Sanghuangporus sanghuang (Hymenochaetaceae, Basidiomycota)

Abstract Sanghuang is a polypore mushroom, which has been widely used in oriental medicine. Since recent molecular phylogenetic studies elucidated its species delimitation, Sanghaungporus sanghuang became the official name of this fungus. In this study, the complete sequence of the mitochondrial DNA of S. sanghuang was determined. The whole genome was 112,060 bp containing 14 proteins, 2 ribosomal RNA subunits, and 45 transfer RNAs. The overall GC content of the genome was 23.21%. A neighbour-joining tree based on atp6 sequence data showed its close relationship with the species of Ganoderma and Trametes.
The Effects of Code-Mixing on Second Language Development

Second language development is an important topic of discussion in an increasingly multilingual world. This study aims to examine and detail research on the effects of code-mixing (CM) on second language development, answering how CM facilitates or constrains second language acquisition. Peer-reviewed articles on the topic published between 2013 and 2018 were examined and synthesized. Language learners/ multilinguals answered questionnaires about their views on CM and second language acquisition, and a language teacher was interviewed regarding use of L1 in the language classroom and CM as a pedagogical tool. This study found that CM can be a beneficial tool for language learning and instruction at the beginning stages of a learner’s acquisition, but use of L1 becomes less necessary and less beneficial as a language learner moves closer to fluency. However, CM is not necessarily a sign of low language competence and is used by multilinguals for a number of reasons.
Intraspecific Behavioural Diversity in a Freshwater Zooplankton: A study of the fitness consequences of vertical migration behaviour for distinct morphs of Daphnia pulicaria

ii Acknowledgements . iv List of Tables . vii List of Figures . viii List of Abbreviations . ix Chapter 1 General Introduction and Literature Review. 1 1.1 Intraspecific Behavioural Diversity in Disparate Literatures . 2 1.2 Towards a General Explanation of Individual Behavioural Strategies. 7 1.3 Scope of Thesis . 14 Chapter 2 Behavioural Diversity between Hemoglobin Morphs of Daphnia pulicaria: Are distinct migration behaviours maintained as a conditional strategy? 16 2.
Alternative super-enhancers result in similar gene expression in different tissues

Super-enhancers (SEs) are clusters of highly active enhancers, regulating cell type-specific and disease-related genes, including oncogenes1–3. The individual regulatory regions within SEs might be simultaneously bound by different transcription factors (TFs) and co-regulators such as P300, BRD4 and Mediator, which together establish a chromatin environment conducting to effective gene induction4–6. While cells with distinct TF profiles can have different functions, an unanswered question is how different cells control overlapping genetic programmes. Here, we show that the construction of oestrogen receptor alpha (ERα)-driven SEs is tissue specific, and both the collaborating TFs and the active SE components are largely differing between human breast cancer-derived MCF-7 and endometrial cancer-derived Ishikawa cells; nonetheless, SEs common to both cell types have similar transcriptional outputs. In the MCF-7 cell line, ERα-dominated SEs are also driven by the well-known FoxA1 and AP2γ TFs, as described previously7, whereas in Ishikawa cells, FoxM1, TCF12 and TEAD4 are as important as ERα for SE formation. Our results show that SEs can be constructed in several ways, but the overall activity of common SEs is the same between cells with a common master regulator. These findings may reshape our current understanding of how these regulatory units can fine-tune cell functions. From a broader perspective, we show that systems assembled from different components can perform similar tasks if a common functional trigger drives their assembly.
Androgen Receptor-Induced Integrin α6β1 and Adhesion to Laminin Promotes Survival and Drug Resistance in Castration-Resistant Prostate Cancer through BNIP3

Although castration-resistant prostate cancers no longer respond to anti-androgen therapies, the androgen receptor (AR) is still required to promote tumor survival. However, the signaling pathways downstream of AR that promote this survival are not well known. We recently identified an AR-dependent survival pathway whereby AR induction of integrin α6β1 and adhesion to laminin activates NF-kB/RelA signaling and Bcl-xL. This pathway acts in parallel with the PI3K/Akt pathway in Pten-null tumor cells such that combined inhibition of both PI3K and integrin α6β1 is required to kill tumor cells adherent to laminin. However, PTEN-null castration-resistant tumors were not effectively inhibited by this combination. We discovered that BNIP3, a hypoxia-induced BH3-only, pro-mitophagic Bcl2 family member, is induced by androgen in castration-resistant cells through integrin α6β1 signaling to HIF1α. Furthermore, castration-resistant cells adherent to laminin were much more efficient at inducing autophagy in response to androgen. Androgen blocked the ability of the PI3K inhibitor PX-866 to kill castration-resistant tumors, but this was reversed by loss of BNIP3. Although BNIP3 was dispensable for androgen-induced autophagy, its mitophagy function was required for BNIP3 to promote resistance to PI3K inhibition. Thus, adhesion to laminin triggers signaling through AR/α6β1/HIF1α in castration-resistant cells to drive the expression of BNIP3 and cooperates with AR/α6β1-mediated autophagy, both of which contribute to PI3K resistance through induction of mitophagy.
A new method for restoring ditches in peatlands: ditch filling with fiber bales

Ditching is a common practice to dewater wetlands, including peatlands, and ditch blocking is a common method for restoring wetlands because substrate is often unavailable for filling the ditches. However, filling has many advantages compared to blocking ditches. Our goal was to test whether ditches could be filled in a Colorado sloping fen (Chattanooga Fen) using bales created from shredded aspen (Populus tremuloides) tree‐fiber. We monitored water table levels before and after we filled two ditches (combined length of approximately 165 m × 3 m wide) as well as an undisturbed reference portion of Chattanooga fen. The reference site had stable water tables that rarely dropped more than 20 cm below the soil surface. The ditches had been dewatering large areas of the fen for at least 100 years. Filling the ditches with fiber bales resulted in a water table increase between 2 and 22 cm in an area up to 150 m below the ditch. Native sedges now cover the area where we filled the ditches, with no erosion or compression/settling of the ground observed and no water backing up behind the filled ditches. Filling the ditches with shredded fiber bales is a good option for restoration in wilderness areas, or areas lacking peat or mineral soil fill because it is a natural material that is easily transported and placed in the ditches.
Instructions for optimal any-aged forestry

In this study, any-aged forestry (AAF) refers to forest management in which no explicit choice is made between even- and uneven-aged management, or between rotation forest management and continuous cover forestry. Optimal AAF is more profitable than optimal even- or uneven-aged management because AAF has fewer constraints. This study developed management instructions for optimal AAF. The instructions consist of four models, the first indicating the probability that an immediate cutting in the stand is the optimal decision. In case of cutting, the second model gives the probability that partial cutting (thinning) is optimal. If thinning is selected, the remaining two models indicate how many trees should be removed from different diameter classes. The models for optimal management were based on optimized cutting schedules of 2095 stands, located in different parts of Finland. The use of the model requires that discount rate is specified, and site fertility and temperature sum of the stand are known. The required growing stock characteristics are stand basal area, mean tree diameter and the basal area of pulpwood-sized trees (dbh 8–18 cm). High stand basal area and large mean tree size increase the probability that cutting is the optimal decision. High basal area of pulpwood-sized trees increases the probability that partial cutting is optimal. Thinning from above is the optimal type of cutting in most cases. The models were tested by comparing the model-driven stand management schedules with stand-level optimizations. Schedules based on the models resulted in equally good net present values as schedules based on optimizations. When the discount rate was 3 per cent or more, the models led to similar profitability as stand-level optimization.
Seamount attractiveness to top predators in the southern Tyrrhenian Sea (central Mediterranean)

Seamounts are expected to attract pelagic top predators due to the higher abundance of possible prey aggregating around these structures. The importance of seamounts on benthic fauna and bottom fish is vastly documented, while little is known about their role as possible hotspots of pelagic biodiversity. This aspect is poorly investigated in the Mediterranean Sea, a basin considered a hotspot of endemism and biodiversity where, in addition, seamounts are widely present, with 227 structures. Our study focuses on the determination of the attraction effect of seamounts on some pelagic species in a Mediterranean sub-basin: the Tyrrhenian Sea. Here, seamounts are thought to be attraction structures for pelagic top predators. Cetaceans and sea turtles were found to be the most attracted taxa among the top predators taken into consideration with peak of presence around 5–10 miles from the seamounts.