Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic assessment of the subspecies status of Eurasian Magpies (Pica pica) in Norway

Based on phenotypes, two subspecies of EurasianMagpies (Pica pica) are recognized in Norway, with nominate P. p. pica in southern Norway, and P. p. fennorum in northern Norway. In this study, we investigated whether there are genetically distinct groups of Magpies in Norway, which can be considered in the discussion of the subspecies status. We collected DNAfrom 61Magpies from seven locations in Norway, and measured genetic diversity using two types of markers: mitochondrial DNA sequences and microsatellites. Genetic differentiation among the Magpies was extremely low. Most of the variance was within populations, and the population identity and the putative subspecies border did not explain the genetic variance among the samples. Although microsatellite markers indicated genetic differentiation, the pattern was not consistent with the geographic locations of the sampling sites.Mismatch analysis suggested that the Magpie populations in Norway were formed by rapid expansion. Our results suggest that all theMagpies in Norway have originated from the same refugia after the last glaciation, their colonization inNorway happened quickly, and that the subspecies status ofMagpies in Norway needs to be reconsidered.
A measure of agreement across numerous conditions: Reproducibility of co-expression networks across tissues

There is great interest to study how co-expression gene networks change across tissues. However, the reproducibility assessment of these studies is challenged by a lack of fully confirmatory experiments from independent researchers. While an increment in the number of studies with expression data for several tissues is expected, statistical measures are still needed to assess the reproducibility between studies. We identified a gap in the statistical literature concerning the assessment of agreement between studies across numerous conditions. The gap precluded us to test, using standard statistics, the level of agreement between the GTEX (RNAseq) and BRAINEAC (microarray) studies to distinguish the structure of co-expression networks across four brain tissues. We propose a generalization of a classical measure of agreement, Cohen’s κ, derive its distributional characteristics and determine its reliability properties. In the gene expression studies, our generalization of κ showed full agreement for genome-wide networks in BRAINEAC benchmarked against GTEX, and highest agreement for brain specific pathways. Our highly interpretable measure can contribute to anticipated efforts on reproducibility research.
Molecular Docking Studies of Wolbachia Endosymbiont of Brugia Malayi's Carbonic Anhydrase Using Coumarin-chromene Derivatives Towards Designing Anti-filarial Agents

Filariasis causing nematode Brugia malayi is shown to harbor wolbachia bacteria as symbionts. The sequenced genome of the wolbachia endosymbiont from B.malayi ( wBm ) offers an unprecedented opportunity to identify new wolbachia drug targets. Hence the enzyme carbonic anhydrase from wolbachia endosymbiont of Brugia malayi ( wBm ) which is responsible for the reversible interconversion of carbon dioxide and water to bicarbonate and protons (or vice versa) is chosen as the drug target for filariasis. This enzyme is thought to play critical functions in bacteria by involving in various steps of their life cycle which are important for survival, The 3D structure of wBm carbonic anhydrase is predicted by selecting a suitable template using the similarity search tool, BLAST. The BLAST results shows a hexapeptide transferase family protein from Anaplasma phagocytophilum (PDB ID: 3IXC) having 77% similarity and 54% identity with wBm carbonic anhydrase. Hence the above enzyme is chosen as the template and the 3D structure of carbonic anhydrase is predicted by the tool Modeller9v7. Since the three dimensional structure of carbonic anhydrase from wolbachia endosymbiont of Brugia malayi has not yet solved, attempts were made to predict this protein. The predicted structure is validated and also molecular docking studies are carried out with the suitable inhibitors that have been solved experimentally. Induced Fit Docking,
Morphological response of the larvae of Arbacia lixula to near‐future ocean warming and acidification: Towards a Broader Perspective on Ocean Acidification Research Part 2 A special issue of the ICES Journal of Marine Science

&NA; The distribution of the sea urchin Arbacia lixula, a warm affinity species, has been expanding in the Mediterranean Sea. To address questions on potential for future success of this species in the region, the thermotolerance of larval development was investigated in context of regional warming. The larvae were reared in present day spawning period (20 °C) and warming conditions (+4 = 24 and +6 = 26 °C). As the calcifying larvae of sea urchins are vulnerable to stunted growth caused by ocean acidification, the impact of lower pH (−0.3 pH units) on larval development was also investigated in combination with warming. Morphological traits of the larvae, post‐oral length arms, overall length of larvae and body length, were affected by increased temperature across pH treatments, indicating that for the larvae of southern Mediterranean population here, 24 °C appears to approximate the optimal temperature for development. A slightly negative effect of pH was evident. Increased temperature ameliorated the stunting effect of acidification on growth. The thermal tolerance of A. lixula development overlaps with projections for warming in the region by 2100 and also indicates that this species has acclimatized or adapted its reproductive biology to the broad environmental conditions of the Mediterranean Sea. Due to the broad thermal range (˜10 °C) of development of A. lixula across its distribution, this species is likely to be a winner in the climate change stakes. The broad thermal tolerance of the larvae is likely to assure population connectivity between Mediterranean sub‐basins populations. The continued success of A. lixula can have a strong consequences for the ecological structure of Mediterranean rocky habitat.
Effectiveness of different mechanical bacterial plaque removal methods in patients with fixed orthodontic appliance: a systematic review/meta-analysis = Eficácia de diferentes métodos de remoção mecânica de placa bacteriana em pacientes com aparelho ortodontico fixo: revisão sistemática / meta-análi

the presence of a fixed orthodontic appliance and its accessories tends to affect bacterial plaque removal, resulting in inadequate cleaning being performed by the patient. Thus, the aim of this systematic review and meta-analysis was to answer the following focal question: are the mechanical methods of oral cleaning effective for the reduction of bacterial dental plaque in patients with a fixed orthodontic appliance? A systematic search of the literature was conducted in the following databases: Scopus, PubMed, Cochrane, Web of Science, Embase, and Medline, in addition to Controlled Trials and Grey Literature, without limitations of language and year of publication. Furthermore, searches were also conducted in the reference lists of the articles selected. Included in the present review were clinical studies with patients undergoing therapy with fixed orthodontic appliances, which would, by means of comparison, evaluate the effectiveness of different mechanical bacterial plaque removal methods. The methodological quality of the articles included was evaluated in accordance with the checklist prepared as methodological evaluation protocol, and was classified as high, moderate or low. In order to perform the meta-analysis, articles with high methodological quality were included. Analysis of sub-groups was performed according to the type of intervention. The plaque index was defined as the continuous outcome variable, using the fixed effect when there was homogeneity among the articles, and the random effect in cases of heterogeneity. 1815 articles were found, of which only 23 fulfilled the eligibility criteria, with 17 being of high methodological quality and 6 of moderate quality. Of these, 18 included an analysis of the effectiveness of the conventional manual brush, 4 of the manual orthodontic brush,15 of electric brushes, 3 of interdental brushes, 1 of dental floss and 4 or oral irrigation devices, and 1 of Siwak. In the qualitative evaluation of the studies, the use of these mechanical control methods was shown to be effective, with exception of the use of Siwak, which presented an increase in bacterial plaque. Moreover, the results of the meta-analysis indicated a significant reduction of -0.98 (IC 95%) in the plaque index for the use of conventional manual brushes in the period of one month (p<0.001). There is a body of evidence that proves the effectiveness of mechanical bacterial plaque removal in patients using orthodontic appliances and accessories. The findings of the meta-analysis proved the effectiveness of the conventional manual brush. Further studies with better standardization of samples are required to strengthen the evidences.
Fermentación ruminal: un análisis de las poblaciones microbianas y los parámetros fermentativos en sistemas in vitro = Ruminal fermentation: an analysis of microbial populations and fermentation parameters in in vitro systems

En esta Tesis Doctoral se realizaron varios experimentos para analizar diferentes factores que afectan a la fermentacion ruminal in vitro y a los microorganismos ruminales que se desarrollan en cultivos no renovados de microorganismos ruminales y en fermentadores RUSITEC. El objetivo del primer estudio fue evaluar los efectos de dosis crecientes [0 (control: CON), 20, 60, 180 y 540 mg/L de medio de incubacion] de aceite de ajo (GO) y cinamaldehido (CIN) sobre la fermentacion ruminal in vitro de dos dietas. Los cultivos no renovados de microorganismos ruminales fueron inoculados con fluido ruminal procedente de cuatro ovejas alimentadas con una dieta con el 50% de concentrado (MC; 50 : 50 heno de alfalfa : concentrado) o de cuatro ovejas alimentadas con dieta alta en concentrado (AC; 15 : 85 paja de cebada : concentrado)
Algal DNA Repair Kinetics Support Culture-Based Enumeration for Validation of Ultraviolet Disinfection Ballast Water Treatment Systems

To mitigate the potential spread of invasive species and pathogens, the International Maritime Organization and U.S. Coast Guard (USCG) adopted discharge performance standards for ballast water management that will take full effect in 2017. The USCG requires staining methods for enumerating ballast water treatment system (BWTS) efficacy. These stains do not detect DNA damage, the primary mechanism for ultraviolet (UV) disinfection, and neglect potential DNA repair after discharge. These factors necessitate investigation of enumeration methods for accurate validation and approval of UV-based BWTSs. To molecularly assess DNA damage and repair kinetics, UV-induced DNA lesions were quantified by an enzyme-linked immunosorbent assay in Tetraselmis suecica control and UV-treated samples that were cultured and tested over time. Most DNA repair occurred within 6 h, was essentially complete within 24 h, and was insensitive to light or nutrient conditions during incubation. Asymptotic repair kinetics indicated a ma.
Neuroprotection of Dopaminergic Neurons and their Subcellular Structures from Parkinson's Disease-like Treatment

WIEMERSLGE, LYLE N. , Ph.D., MAY 2014, Biological Sciences Neuroprotection of Dopaminergic Neurons and their Subcellular Structures from Parkinson’s Disease-like Treatment Director of Dissertation: Daewoo, Lee In this dissertation, I explore the molecular mechanisms involved in the neuroprotection of dopaminergic (DA) neurons from Parkinson’s disease (PD)-like treatment. PD is movement disorder characterized by the slow, gradual death of DA neurons in the substantia nigra pars compacta. Neuroprotection is the idea that these cells could be rescued or protected from pathology. I establish a Drosophila primary culture system to study PD-like neurodegeneration and screen potential neuroprotective therapies. DA neurons, as well as their subcellular structures, are quantified and compared between treatment groups. I show that1-methyl-4-phenylpyridinium (MPP), the active metabolite of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), selectively damages DA neurons and their mitochondrial morphology. I also show that the dopamine type 2 (D2) receptor agonist quinpirole can prevent, but not reverse, MPPinduced degeneration. Furthermore, I show that D2 autoreceptors (presynaptic receptors which respond to autologous DA release) are required for the rescue by quinpirole. However, even in DA neurons lacking D2 autoreceptors, MPP-induced degeneration was prevented by reducing cellular excitability: either with the Na-channel blocker tetrodotoxin (TTX) or by Ca chelation. Moreover, DA neurons with mutated Ca channels were inherently protected from MPP treatment. Lastly, I describe the time4 course of MPP-induced degeneration within this model system. DA neurons are nearcompletely post-mitotic by 3 days in vitro (DIV), which is the time point when cultures are treated with drugs. I find that damage to mitochondria precedes the death of DA neurons, and that rescue therapy must be given almost concomitantly with PD-inducing treatment to be effective.
Estimating stand density, biomass and tree species from very high resolution stereo-imagery- towards an all-in-one sensor for forestry applications?

The estimation of various forest inventory attributes from high spatial resolution airborne remote sensing data has been widely examined and proved to be successful at the experimental level. Nevertheless, the operational use of these data in automated procedures to support forest inventories and forest management is still limited to a small number of cases. The reasons for this are high data costs, limited availability of remote sensing data over large areas and resistance from practitioners. In this review the main aim is to stimulate debate about spaceborne very high resolution stereo-imagery (VHRSI) as an alternative to airborne remote sensing data by presenting: (1) a case study on the retrieval of stand density, aboveground biomass and tree species using a set of easy-to-calculate variables obtained from VHRSI data combined with image processing and nonparametric classification and modelling approaches; and (2) the results of an expert opinion survey on the potential of VHRSI as compared with Light Detection and Ranging (LiDAR), hyperspectral and airborne digital imagery to derive a range of forest inventory attributes. In the case study, stand density was estimated with r² = 0.71 and RMSE = 156 trees (rel./norm. RMSE = 24.9 per cent/12.4 per cent), biomass with r² = 0.64 and RMSE of 36.7 t/ha (rel./norm. RMSE = 20.0 per cent/12.8 per cent) while tree species classifications with five species reached overall accuracies of 84.2 per cent (kappa = 0.81). These results were comparable to earlier studies in the same test site, obtained with more expensive airborne acquisitions. Expert opinions were more diverse for VHRSI and aerial photographs (Shannon index values of 0.94 and 0.97) than for LiDAR and hyperspectral data (Shannon index values 0.69 and 0.88). In our opinion, this reflects the current state-of-the-art in the application of VHRSI for automatically retrieving forest inventory attributes. The number of studies using these data is still limited, and the full potential of these datasets is not yet completely explored. Compared with LiDAR and hyperspectral data, which both mostly received high scores for forest inventory products matching the sensor systems’ strengths, VHRSI and aerial photographs received more homogeneous scores indicating their potential as multi-purpose instruments to collect forest inventory information. In summary, considering the simpler acquisition, reasonable price and the comparably easy data format and handling of VHRSI compared with other sensor types, we recommend further research on the application of these data for supporting operational forest inventories.
The role of circadian clock genes in the photoperiodic timer of the linden bug Pyrrhocoris apterus during the nymphal stage

Many insects survive seasonal adversities during diapause, a form of programmed developmental and metabolic arrest. Photoperiodically regulated entry into diapause allows multivoltine insect species to optimize the number of generations. The molecular mechanism of the photoperiodic timer is unknown in insects. In the present study, we take advantage of the robust reproductive diapause response in the linden bug Pyrrhocoris apterus and explore the fifth‐instar nymphal stage, which is the most photoperiod‐sensitive stage. The nymphs display daily changes in locomotor activity during short days; this differs from the activity observed during long days. We find evidence of cyclical expression of the circadian clock genes, per and cyc, in nymphal heads; in addition, per expression is also photoperiod‐dependent. The RNA interference‐mediated knockdown of the two circadian clock genes, Clk and cyc, during the nymphal stage results in reproductive arrest in adult females. Furthermore, Clk and cyc knockdown induces the expression of the storage protein hexamerin in the fat body, whereas the expression of vitellogenin diminishes. Taken together, these data support the involvement of circadian clock genes in photoperiodic timer and/or diapause induction.
Isolation, characterization and antibiogram of pathogenic Escherichia coli recovered from broiler chicken, Riyadh, Saudi Arabia.

Present study was conducted on 200 fecal samples of broilers chickens suffering from colisepticemia from poultry farms in Riyadh, Saudi Arabia. Escherichia coli strains were isolated from 88 (44%) samples. Out of E. coli strains, 79 (89.77%) belonged to O126: K71, O158: K-, O114: K90, O111: K58, O78: K80 and O119: K69. Whereas, O126: K71, O158: Kand O114: K90 were the most prevalent. The antibiotic sensitivity pattern showed that all isolates were totally resistant to ampicillin. chloramphenicol and streptomycin (100%). Resistance against erythromycin and naldixic acid reached 81.01 % and was recorded in 20 strains O126: K71, 17 strains O158: K-, 15 strains O114: K90, 12 strains O111: K58, and decrease to 78.48% against ciprofloxacin in O126: K71, O114: K90, O111: K58, O78: K80 and O119: K69 strains. It should note that the recovered isolates were 84.81% intermediate to cephalexin and 53.16% sensitive gentamycin. This study highlights the high resistance of E. coli to antibiotics constitutes a threat to poultry industry in Saudi Arabia and the need for continuous surveillance of antibiotic sensitivity pattern of E. coli with a view to selecting appropriate therapy.
Spatial and Spatiotemporal Modeling of Epidemiological Data

SPATIAL AND SPATIOTEMPORAL MODELING OF EPIDEMIOLOGICAL DATA LAXMAN KARKI 2017 This dissertation focuses on modeling approach for spatial and spatiotemporal data with epidemiological applications. Chapter one gives the general overview of spatial and spatiotemporal data and challenges in the statistical analysis of spatial and spatiotemporal data, and motivation and objectives of the study. Chapter two describes the regression models commonly used in spatial data analysis. Various types of regression methods such as OLS, GWR and MGWR were used to study the association between diabetes prevalence and socioeconomic and lifestyle factors on county level data of Midwestern United States. A new analysis workflow is purposed for regression analysis of spatial data. Chapter three describes recently developed INLA as an alternative of traditionally used MCMC in Bayesian hierarchical models. INLA method was used to identify the best regression model for the spatiotemporal regression analysis of Lyme disease count data with climatic covariates in county-level data in Minnesota. Chapter four gives the contribution of this dissertation and discusses the direction for the future research.
Anticancer activity of aqueous myrrh extract alone and in combination with cisplatin in HeLa cells

Purpose: To study the impact of an aqueous myrrh extract on the proliferation of cervical cancer cells in vitro . Methods: First, 100 g of ground myrrh resin was boiled in 1000 mL of distilled water for 30 min. Different components of the decoction were identified using gas chromatography–mass spectrometry and high-performance liquid chromatography. The effects of high (20 μg/mL) and low (10 μg/mL) concentrations of cisplatin, serial concentrations of myrrh (20, 40, 60, and 80 μg/mL), and a combination of both were evaluated using cell proliferation assay, DNA fragmentation, and electron microscopy. Results: All four myrrh concentrations decreased the viability of HeLa cells (16.25 % p < 0.01). A significant further decrease occurred when myrrh was combined with 10 μg/mL cisplatin (11.42 % p < 0.01). This was confirmed by quantifying DNA fragmentation. Ultrastructurally, HeLa cells showed typical apoptosis after treatment with 10 μg/mL cisplatin or a high dose of myrrh. The use of 20 μg/mL cisplatin or the combined therapy resulted in cell necrosis with ruptured cell membranes and autophagosomes. The effect of combined therapy was more lethal than the effect of either of them alone. Conclusion: Myrrh induces apoptosis and autophagy and enhances the activity of cisplatin in vitro . It is potentially a basis for further studies of other types of cancer cell. The clinical use of myrrh in the palliative therapy of human cervical carcinoma might be justified. Keywords: Cervical cancer, Cell viability, Chemotherapy, DNA fragmentation, Myrrh, Cisplatin, Cell ultrastructure, HeLa cells
L'espace kurde entre unité et diversité

Le contexte regional d’avant 2010 se caracterisait par une double radicalisation de l’espace kurde, d’abord dans chacune de ses parties en Turquie, en Iran, en Irak et en Syrie par rapport aux Etats, puis dans sa dimension transfrontaliere, impliquant de nombreuses interactions entre divers acteurs politiques. Mais, depuis juin-juillet 2012, la situation regionale a bascule dans un etat de violence. Au cœur de l’espace kurde, terme qu’on pourrait preferer a celui de Kurdistan pour mieux apprehender toutes les ramifications et toute la complexite de la question kurde a l’echelle moyen-orientale, il y a desormais le Kurdistan d’Irak qui dispose du statut d’entite federee et qui pourrait, potentiellement du moins, constituer le noyau d’un futur Etat kurde. Il est evident que l’existence de cette entite suscite autant d’espoir chez les Kurdes que d’inquietude dans les Etats ou ils se trouvent ; elle sert en tout cas de repere symbolique fort expliquant la radicalisation de l’espace kurde dans sa totalite.
A new fern species for Queensland: Diplazium squamuligerum (Rosenst.) Parris (Woodsiaceae)

The taxonomic status of an unknown fern species from the Atherton Tableland, north-east Queensland, hitherto attributed to Asplenium L. , was investigated. Phylogenetic analysis of trnL-F and rbcL chloroplast DNA sequences supported classification in Diplazium Sw. , a finding supported by closer examination of scale features. Inspection of Diplazium type material determined that the Australian material belongs to Diplazium squamuligerum (Rosenst.) Parris, a species previously described from Papua New Guinea. A thorough description of this species and an amended key to the Diplazium species of Australia are provided. This study highlights the value of molecular study and close inspection of scale features for fern identification. Taxonomic revision in Diplazium is also discussed in light of the findings presented.