Miracle-dz/UniFAR-FTUs huggingface dataset:
Cladoceran diversity dynamics in lakes from a northern mining region: responses to multiple stressors characterized by alpha and beta diversity

The lakes surrounding the iron ore mining region of Schefferville, Quebec, Canada, sit within a landscape of historical disturbances, two of which have been relatively well documented over time: metal contamination and nutrient loading. Based on the analysis of sediment cores, we used cladoceran zooplankton subfossil assemblages from two lakes located in Schefferville to track both alpha and beta diversity over the last 100+ years. We showed that high metal concentrations were correlated with decreased cladoceran diversity, and that the site that experienced both direct wastewater input and atmospheric metal loading (Lake Dauriat) had the greatest declines in cladoceran richness. In both lakes, turnover in cladoceran assemblages was highest in the mining period. During the period of mine closures and improvement of wastewater treatment, some decreases in metal enrichment in the sediments and increases in cladoceran richness were observed in Lake Dauriat. Overall, a combined use of species richness and bet.
Construction characterization and application of Flavivirus infectious clones

The topics in this thesis revolve around a group of plus-strand RNA viruses that belong to the Flavivirus genus, a general introduction of which is presented in Chapter 1. The experimental chapters in this thesis mainly focus on the construction and characterization of flavivirus infectious clones and the application of these useful tools to address fundamental questions on virus biology or to explore novel vaccine platforms based on the yellow fever virus vaccine strain (YFV-17D). Chapter 2 describes the construction and characterization of recombinant YFV-17D viruses expressing Lassa virus (LASV) glycoprotein coding sequences as bivalent vaccine candidates against wildtype YFV and LASV that circulate in the same region in West Africa. Chapter 3 describes the construction and characterization of an alternative YFV-17D vaccine candidate based on a DNA launched YFV-17D infectious clone, and the study of its immunological characteristics. Chapter 4 describes the construction and characterization of the first NKV (no known vector) flavivirus infectious clone, which was further utilized to study the functional significance of RNA elements present in Modoc virus (MODV) 3’-UTR (untranslated region), as a representative of the NKV flaviviruses. A recently discovered common feature for all flaviviruses is the production of a small flavivirus RNA (sfRNA) in infected cells or animals that results from the incomplete degradation of the viral genome by the host exoribonuclease, XRN-1. XRN-1 was predicted to be stalled by a non-H-type RNA pseudoknot structure that is present is the 3’-UTR of every flavivirus studied thus far. Chapter 5 presents a detailed mutagenesis study of many of the unique sequence and structural characteristics of the XRN-1 stalling site in mosquito-borne flaviviruses using YFV-17D as a model. Chapter 6 describes the establishment of mammalian cell lines that constitutively expressed sfRNA from YFV-17D and WNV. This cell line approach could be valuable to further our understanding of sfRNA function within flavivirus life cycle. Chapter 7 of this thesis is a short epilogue, in which the findings presented in the experimental chapters are summarized and discussed in the context of recently published findings and future research directions are suggested to improve the YFV-17D based vaccine platforms or to address the yet-to-be-solved questions about sfRNA production and function.
Investigating the role of the Hippo pathway member Nf2 in the segregation of trophectoderm and inner cell mass

During mammalian development, the first two lineages to be specified are trophectoderm (TE) and inner cell mass (ICM). Proper segregation of these two cell types requires precise spatial control of the Hippo signaling pathway and its downstream transcriptional activator, Yap. In outside, future TE cells of the embryo, Yap is nuclear-localized and can influence the expression of TE-specifying transcription factors such as Cdx2. In contrast, in inside cells, the Hippo pathway kinases Lats1/2 and the adaptor protein Amot induce phosphorylation and cytoplasmic retention of Yap, preventing this transcriptional influence. The factors acting upstream of Lats1/2, Amot and Yap in this context are not well understood. In this thesis, I have investigated the role of the upstream Hippo pathway member Nf2 in TE/ICM segregation. First, using a dominant negative approach, I show that Nf2 is required in a cell-autonomous manner for the proper localization of Yap in inside cells of the embryo. Second, by generating both zygotic and maternal/zygotic Nf2 mutant embryos, I confirm that Nf2 is required for Hippo signaling and demonstrate that this signaling is broadly required for the segregation of ICM from TE. Finally, using maternal/zygotic mutant embryos as a tool, I provide evidence that Nf2 regulates levels of Amot at the plasma membrane of inside cells during active Hippo signaling. Together, these
Salish Sea Chinook salmon exhibit weaker coherence in early marine survival trends than coastal populations

Identifying factors that influence anadromous Pacific salmon (Oncorhynchus spp.) population dynamics is complicated by their diverse life histories and large geographic range. Over the last several decades, Chinook salmon (O. tshawytscha) populations from coastal areas and the Salish Sea have exhibited substantial variability in abundance. In some cases, populations within the Salish Sea have experienced persistent declines that have not rebounded. We analyzed a time series of early marine survival from 36 hatchery Chinook salmon populations spanning ocean entry years 1980–2008 to quantify spatial and temporal coherence in survival. Overall, we observed higher inter-population variability in survival for Salish Sea populations than non-Salish Sea populations. Annual survival patterns of Salish Sea populations covaried over smaller spatial scales and exhibited less synchrony among proximate populations relative to non-Salish Sea populations. These results were supported by multivariate autoregressive state space (MARSS) models which predominantly identified region-scale differences in survival trends between northern coastal, southern coastal, Strait of Georgia, and Puget Sound population groupings. Furthermore, Dynamic Factor Analysis (DFA) of regional survival trends showed that survival of southern coastal populations was associated with the North Pacific Gyre Oscillation, a large-scale ocean circulation pattern, whereas survival of Salish Sea populations was not. In summary, this study demonstrates that survival patterns in Chinook salmon are likely determined by a complex hierarchy of processes operating across a broad range in spatial and temporal scales, presenting challenges to the management of mixed-stock fisheries.
Complete mitochondrial genome of the feather mite Ardeacarus ardeae (Acari, Sarcoptiformes, Pterolichidae)

Abstract In this study, we determined the mitogenome sequence of Ardeacarus ardeae (Canestrini, 1878) in the family Pterolichidae (Acari, Sarcoptiformes), which is the first complete mitogenome sequence in feather mite. The mitogenome of A. ardeae is 14,069 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The phylogenetic tree shows that A. ardeae belong to the supercohort Desmonomatides within the order Sarcoptiformes.
Methicillin-resistant Staphylococcus aureusmenace: A dermatologist′s perspective

Staphylococcus aureus is a facultative anaerobic, Gram-positive coccal bacterium. In contemporary times, one of the major concerns in all fields of medicine is the emerging resistance to S. aureus. There are two types of methicillin-resistant S. aureus (MRSA), that is, hospital acquired (HA) and community acquired (CA). HA-MRSA strains contain staphylococcal cassette chromosome mec (SCCmec) I and II, which are larger and have the capacity for multidrug resistance. High expression of Panton-Valentine leukocidin (PVL), phenol-soluble modulins (PSM), α-toxin, core genome-encoded superantigen SEIX, and teichoic acid contributes to increased virulence in CA-MRSA strains. Methicillin resistance in staphylococci is due to the acquisition of a mobile genetic element (mec) called the SCCmec. All SCCmec types include the mecA gene, which codes for the low-affinity penicillin-binding protein (PBP) 2a. Resistance is due to the fact that β-lactam antibiotics cannot inhibit PBP2a. Biofilms are surface-attached bacterial agglomerations embedded in extracellular matrix. There are various toxins such as PVL, PSMs, surface-anchored S. aureus-binding proteins, and SasX protein. It can cause folliculitis, furunculosis, abscesses, carbuncles, cellulitis, necrotizing pneumonia, urinary tract infection, osteomyelitis, septic arthritis, thrombophlebitis, endocarditis, and toxic shock syndrome. Many diagnostic modalities are available to identify MRSA. The mainstay of treatment is incision and drainage. Systemic antibiotics such as clindamycin, doxycycline, trimethoprim-sulfamethoxazole, linezolid, daptomycin, tigecycline, and tedizolid are the most commonly used antibiotics. The prevalence of CA-MRSA is on the rise, and as a dermatologist, our concern is to prevent the occurrence of recurrent furunculosis and patient dissatisfaction.
Measurement artefacts lead to false positives in the study of birdsong in noise

Numerous studies over the past decade have reported correlations between elevated levels of anthropogenic noise and a rise in the minimum frequency of acoustic signals of animals living in noisy habitats. This pattern appears to be occurring globally, and higher pitched signals have been hypothesized to be adaptive changes that reduce masking by low‐frequency traffic noise. However, the sound analysis methods most often used in these studies are prone to measurement errors that can result in false positives. In addition, the commonly used method of measuring frequencies visually from spectrograms might also lead to observer‐expectancy biases that could exacerbate measurement errors. We conducted an experiment to (i) quantify the size and type of errors that result from ‘eye‐balling’ frequency measurements with cursors placed manually on spectrograms of signals recorded in noise and no‐noise conditions, and (ii) to test whether observer expectations lead to significant errors in frequency measurements. We asked 54 volunteers, blind to the true intention of our study, to visually measure the minimum frequency of a variety of natural and synthesized bird sounds, recorded either in noise, or no‐noise conditions. Test subjects were either informed or uninformed about the hypothesized results of the measurements. Our results demonstrate that inappropriate methodology in acoustic analysis can yield false positives with effect sizes as large, or even larger, than those reported in published studies. In addition to these measurement artefacts, psychological observer biases also led to false positives – when observers expected signals to have higher minimum frequencies in noise, they measured significantly higher minimum frequencies than uninformed observers, who had not been primed with any expectation. The use of improper analysis methods in bioacoustics can lead to the publication of spurious results. We discuss alternative methods that yield unbiased frequency measures and we caution that it is imperative for researchers to familiarize themselves both with the functions and limitations of their sound analysis programmes. In addition, observer‐expectancy biases are a potential source of error not only in the field of bioacoustics, but in any situation where measurements can be influenced by human subjectivity.
Diversity and conservation status of small mammals in Kelantan, Malaysia

There is little information and research on the diversity of the small mammals in Kelantan. Thus, a series of wildlife surveys were done at five localities in Kelantan to further elucidate the diversity of small mammals in this state. There were 39 species of small mammals recorded, 13 of these are new records for Kelantan. This significantly increased the known diversity of small mammals from 71 to 84 species. However, the diversity of small mammals in Kelantan is still underrepresented and further surveys are needed to add more information to the current knowledge.
Discriminatory pre-hoarding handling and hoarding behaviour towards germinated acorns by Niviventer confucianus

Germination is an important stage in the seed life cycle, but it decreases seed nutrients and increases secondary compounds, which is disadvantageous to seed hoarders or consumers. Therefore, seed hoarders often use pre-hoarding handling behaviour (PHB) to prevent the further deterioration of germinated seeds. Although PHB is an important component of seed dispersal ecology, few studies have described or estimated the effectiveness of PHB. In this study, we investigated the PHB and hoarding strategies of Niviventer confucianus Milne-Edwards towards germinated and ungerminated acorns (Quercus variabilis Bl.). We observed that N. confucianus (1) displayed radicle-excision behaviour towards germinated acorns; (2) often removed the pericarps of the germinated acorns more than those of ungerminated acorns before hoarding; and (3) tended to larder-hoard ungerminated acorns but scatter-hoard germinated acorns. Our results indicate that (1) PHB towards germinated seeds exists in this species as well as in members of the family Sciuridae; (2) N. confucianus consumed and hoarded acorns in different condition discriminately, and adopted a flexible strategy when hoarding perishable seeds. These pre-hoarding handling and hoarding behaviours are possibly evolutionary adaptations in rodents to manage and hoard easily germinated acorns and inevitably impacts on seed dispersal, seed fate, seed germination, and sapling recruitment.
Micro-aerobic, Anaerobic and Two-stage Condition for Ethanol Production by enterobacter aerogenes from Biodiesel-derived Crude Glycerol

aerogenes from biodiesel-derived crude glycerol DTU Orbit (25/05/2019) Micro-aerobic, anaerobic and two-stage condition for ethanol production by Enterobacter aerogenes from biodieselderived crude glycerol The microbial production of ethanol from biodiesel-derived crude glycerol by Enterobacter aerogenes TISTR1468, under micro-aerobic and anaerobic conditions, was investigated. The experimental results showed that micro-aerobic conditions were more favorable for cellular growth (4.0 g/L DCW), ethanol production (20.7 g/L) as well as the ethanol yield (0.47 g/g glycerol) than anaerobic conditions (1.2 g/L DCW, 6.3 g/L ethanol and 0.72 g/g glycerol, respectively). Crude glycerol (100 g/L) was consumed completely with the rate of 1.80 g/L/h. Two-stage fermentation (combination of micro-aerobic and anaerobic condition) exhibited higher ethanol production (24.5 g/L) than using one-stage fermentation (either microaerobic or anaerobic condition. The two-stage configuration, exhibited slightly higher crude glycerol consumption rate (1.81 g/L/h), as well as ethanol yield (0.56 g/g) than the one-stage configuration. Therefore, two-stage process was selected for ethanol production from E. aerogenes TISTR1468 in scale-up studies.
MORPHOLOGICAL IDENTIFICATION AND TAXONOMIC RELATIONSHIP OF FARMED FISH OF THE GENUS CHRYSICHTHYS

Variation of Chrysichthys nigrodigitatus, C. maurus and C. auratus from the fish farm of Jacqueville were studied using morphometric and meristic analyses. The morphological analysis included thirty nine morphometric measurements and eight meristic counts. The Principal Component Analysis and the Discriminant function Analysis were used in order to determine morphological difference and relationship between the species of Chrysichthys. Average of coefficient of variation of morphometric was lower (CV< 30 %) for all variables within groups, except NBL and MBlL2, showing that most of the morphometric characters were not variable among three species of Chrysichthys. The specimens of C. nigrodigitatus were significantly differentiated from those of C. maurus and C. auratus. These last two species were morphologically similar. C. nigrodigitatus were distinguished from the other species by a large occipital process, a long nasal barbell. In this species, the mandible barbells and the nostrils were well separated. In addition, this species is defined by the higher number of branched anal fin rays, the number of gill raker on the epibranchial of the first gill arch and the number of gill raker on the cerato and hypo-branchial of the first gill arch. The utility of morphometric measurements for discriminating Chrysichthys species has been demonstrated but the result must be corroborated by genetic analysis.
Can model-free reinforcement learning operate over information stored in working-memory?

Model-free learning creates stimulus-response associations. But what constitutes a stimulus? Are there limits to types of stimuli a model-free or habitual system can operate over? Most experiments on reward learning in humans and animals have used discrete sensory stimuli, but there is no algorithmic reason that model-free learning should be restricted to external stimuli, and recent theories have suggested that model-free processes may operate over highly abstract concepts and goals. Our study aimed to determine whether model-free learning processes can operate over environmental states defined by information held in working memory. Specifically, we tested whether or not humans can learn explicit temporal patterns of individually uninformative cues in a model-free manner. We compared the data from human participants in a reward learning paradigm using (1) a simultaneous symbol presentation condition or (2) a sequential symbol presentation condition, wherein the same visual stimuli were presented simultaneously or as a temporal sequence that required working memory. We found a significant effect of reward on human behavior in the sequential presentation condition, indicating that model-free learning can operate on information stored in working memory. Further analyses, however, revealed that the behavior of the participants contradicts the basic assumptions of our hypotheses, and it is possible that the observed effect of reward was generated by model-based rather than model-free learning. Thus it is not possible to draw any conclusions from out study regarding model-free learning of temporal sequences held in working memory. We conclude instead that careful thought should be given about how to best explain two-stage tasks to participants.
The Evolution and Dissemination of Methicillin Resistance Determinant in Staphylococcus aureus

Staphylococcus aureus is an opportunistic pathogen and is frequently associated with the antimicrobial resistance. There has been horizontal gene transfer of Staphylococcus chromosome cassette mec (SCC mec ) among the staphylococcal species that colonize a similar colonization niche, which eventually results in emergence of new variant with enhanced survival ability in terms of antimicrobial resistance and virulence level in S. aureus . Evolution and dissemination of SCC mec structure resulted in the emergence of methicillin-resistant S. aureus (MRSA) clones around the world covering hospital, community, and livestock settings. MRSA also has the ability to resist different antibiotic profiles known as multidrug-resistant S. aureus (MDR S. aureus ).
A Pilot Proteomic Analysis: The Study of P19 Cells in Cardiac Differentiation

This study utilized a proteomics-based approach for the purpose of better understanding cardiomyocyte differentiation. In particular, the study concentrated on those proteins involved in differentiation of P19 cells into cardiomyocytes. This type of research is vital to the medical field where there is an immense need for novel therapies that involve the use of an individual’s own stem cells for generating new cardiomyocytes. The P19 cell line was used as a model for gaining more insight into those proteins possibly involved in differentiation of human adult stem cells into new cardiomyocytes. To accomplish this task, P19 cells were cultured in a 1% DMSO medium to induce differentiation and harvested at specific time points. The harvested samples were then subjected to a Modified Bradford Assay, which determined protein concentration. After determination of each samples’ protein concentration, the samples were subjected to twodimensional gel electrophoresis (2DGE) which produced a protein profile for each sample. To visualize these protein “maps”, gels were initially stained with Coomassie Brilliant Blue stain. Upon obtaining preliminary data, 2DGE was carried out again, this time using the highly sensitive SYPRO Ruby protein gel stain to visualize proteins. The SYPRO stained gels were subjected to analysis using PDQuest software for in-depth comparison of the protein profiles on each gel. Resultant data suggested a change in the protein profiles at specific time points during differentiation. This change in proteins expressed by the P19 cells signifies a change in gene expression and thus a change in cell function. Future work includes excising those differentially protein spots and subjecting them to mass spectrometry for exact identification of those proteins possibly involved in cardiomyocyte differentiation.
Targeting Multiple Signaling Pathways, a Potential Explanation to the Therapeutic Actions of Traditional Chinese Medicine in Cancer?

Traditional herbal therapies such as Traditional Chinese Medicine (TCM) are increasingly used in the treatment of diseases including cancer. These medicines are either a single herb based or frequently made of multiple herbs, based on the combinational benefits of the herbal medicine. The formulations are supported by traditional sometimes ancient theories, others based on practical experience. This has frequently made the understanding of how the medicine(s) works (or potential mechanism) a challenge. However, some of the herbal medicine(s) that have demonstrable and reproducible clinical benefits attracted attention to explore mechanism(s) of action, attempt to separate the active ingredient(s) from the herbs. Artemisinin perhaps serves a good example. The compound is extracted and purified from an anti-malaria Chinese herb QingHao in nineteen seventies and found to be a highly effective anti-malaria medicine. It is now used throughout the world since nineteen nineties as one of the first line treatment for malaria [1]. Another example is the discovery of Taxol from Western Yew barks in the nineties, which (including its derivatives) is now one of the popular frontline drugs for cancer treatment.