Miracle-dz/UniFAR-FTUs huggingface dataset:
The early embryonic development of the satellite organism Pristionchus pacificus: differences and similarities with Caenorhabditis elegans

As a comparative counterpart for the model organism Caenorhabditis elegans , the nematode Pristionchus pacificus was established as a satellite organism to study developmental processes. However, these studies mainly focused on post-embryonic development and little is known about the early embryonic development. Using 4D microscopy we reconstructed the early embryonic cell lineage of 12 individuals of P. pacificus . By analysing several parameters of early development, including the division sequence, the spatial arrangement of blastomeres, the cell cycle patterns of the AB lineage and cell-cell contacts in different cell stages of the embryo, it was shown that the early embryonic development is nearly identical to C. elegans . Known cell-cell contacts necessary for induction of blastomere fates in C. elegans are also present in P. pacificus . Thus, the spatio-temporal conditions that would allow possible homologous inductions are present. However, at least one model for blastomere specification seems not to apply to P. pacificus since the third division in the AB lineage differs from that of C. elegans . Furthermore, naturally occurring variability of early development was demonstrated, which is clearly permitted since there seems to be no influence on further development into an adult worm.
Isolation and screening of potential fungi and standardization of a process for the production of extracellular lipase

Eighty fungi species were isolated from samples obtained from different areas in and around Delhi. These fungi were screened using tributyrin agar medium. Six of the isolated fungi revealed a clear zone of hydrolysis as compared to others, indicating extracellular lipase activity. These six fungi were selected and identified at the Plant Pathology Division, Indian Agricultural Research Institute, New Delhi under the expert guidance of fungal taxonomist considering morphological and physiological characteristics. These fungi were identified as; Alternaria alternata (A); Penicillium aurantiogriseum (B); Penicillium pinophilus (C); Aspergillus fumigatus (D); Penicillium purpurogenum (E); Penicillium citrinum (F). These fungi were point inoculated on four different production media viz, M1, M2, M3 and M4 to understand the best possible production medium for optimal lipase production. Penicillium aurantiogriseum (isolate B) showed highest lipase activity on M4 as compared to other production medium. The lowest lipase activity was recorded on M2 followed by M1 and M3 media. The most favorable pH and temperature for lipase production by isolate B was 6.8 at 30°C after 96h of incubation period. Besides, enzymatic production increased when the organism was cultured in medium augmented with glucose as a source of C and corn step liquor and til oil as sources of N and fat respectively. The results of this study revealed that lipase activity (1 μM of p-nitro phenol ml -1 min -1 ) increased from 0.065 IU ml -1 min -1 under unstandardized conditions to 16.718 IU ml -1 min -1 under standardized conditions. P. aurantiogriseum could be considered as a potential source of extracellular lipase production under mild acidic environment.
Task scheduling in genetic sequencing tool

This paper proposes a task scheduler to control the demand of sending gaps encountered during the process of genome sequencing processing considering computational resources available. Gaps are spaces without representation in the genome sequencing process. This activity generates many competing tasks that consume a lot of computational resources, mainly memory. The goal of the scheduler is to prevent more required computational resources besides those which can be alive supplied, because in this case, a performance degradation of the system will occur and it may cause a delay in the processing time of the tasks. The motivation for this work is to improve the efficiency of the implementation of the closure of gaps in genome sequencing. For the evaluation of the proposal, a scheduler for gaps with scheduling policies based on monitoring of computing resources has been implemented. Keywords: bioinformatics, scheduling tasks, genetic sequencing.
Refining Synthetic Images with Semantic Layouts by Adversarial Training

Recently, progress in learning-by-synthesis has proposed training models on synthetic images, which can effectively reduce the cost of manpower and material resources. However, learning from synthetic images still fails to achieve the desired performance compared to naturalistic images due to the different distribution of synthetic images. In an attempt to address this issue, previous methods were to improve the realism of synthetic images by learning a model. However, the disadvantage of the method is that the distortion has not been improved and the authenticity level is unstable. To solve this problem, we put forward a new structure to improve synthetic images, via the reference to the idea of style transformation, through which we can efficiently reduce the distortion of pictures and minimize the need of real data annotation. We estimate that this enables generation of highly realistic images, which we demonstrate both qualitatively and with a user study. We quantitatively evaluate the generated images by training models for gaze estimation. We show a significant improvement over using synthetic images, and achieve state-of-the-art results on various datasets including MPIIGaze dataset.
Ice algae versus phytoplankton: resource utilization by Arctic deep sea macroinfauna revealed through isotope labelling experiments

We would like to thank the officers and crew of CCGS ‘Amundsen’ and the ArcticNet scientific and technical personnel for support onboard. We would also like to thank C. Grant (ISMER) and G. Kazanidis (University of Aberdeen) for field assistance, ArcticNet 2013 cruise CTD operators and L. Treau de Coeli and L. de Montety (ISMER) for macrofauna identification help. Additional thanks go to V. Johnston (University of Aberdeen) for general lab assistance and K. Chalut (ISMER) for sample preparation help. Work was supported by University of Aberdeen The North theme funding for A.M., Natural Environment Research Council ArcDEEP project grant NE/J023094 awarded to U.W. and ArcticNet and Green Edge funding to P.A.
Molecular phylogeny of the genera Palaemon and Palaemonetes (Decapoda, Caridea, Palaemonidae) from a European perspective

A molecular phylogenetic study by Murphy & Austin (2003) showed that Australian representatives of three shrimp genera of the family Palaemonidae (Palaemon, Palaemonetes, and Macrobrachium) do not cluster according to their generic classification. According to their results, the monophyly of these genera is questioned and the generic classification of the subfamily Palaemoninae is at stake. A large number of representatives of Palaemon and Palaemonetes inhabit European waters, including the type species of each genus. To clarify the phylogeny of these species, and thus the position of the generic names Palaemon and Palaemonetes on a phylogenetic tree, we obtained DNA sequences of the same genetic markers (16S mtDNA) as used by Murphy & Austin (2003) and re-addressed the question of taxonomy and phylogeny of these two genera within the subfamily Palaemoninae. Our results confirm the paraphyly of Palaemon and Palaemonetes. In contrast, the resulting monophyletic clades reflect the geographic distribution of the species according to their respective continents: Africa-Europe, Asia, Australia, and America. With the exception of Palaemon elegans the Afro-European species cluster in a way that would support monophyly of the two genera, if representatives from other continents are excluded. Possible taxonomic solutions are discussed.
Production of FAME from freshwater microalgae and profiling of fatty acids for biodiesel feedstock

Due to diminishing fossil fuel reserves, it is necessary to shift for an alternative fuel source that could be sustainable and eco-friendly. Microalgae produce different ratios of lipids, proteins and carbohydrates. The lipid composition of microalgae is similar to vegetable oil which has already been used as biodiesel so that it can potentially be employed for biodiesel production. In present study has demonstrated the total lipid content, fatty acid profile and biodiesel production from a naturally isolated fresh water strain of Chlorella sp. and the total lipid content was found to be 8% under normal nutrient conditions. Gas Chromatography of FAME was analyzed, it was found to be the major fatty acids were palmitic acid, stearic acid, oleic acid, linoleic acid and alpha linolenic acid and pH of the biodiesel was found to be 8.1.
Testing Statistical Significance of the Area under a Receiving Operating Characteristics Curve for Repeated Measures Design with Bootstrapping

Receiver operating characteristic (ROC) curve is an effective and widely used method for evaluating the discriminating power of a diagnostic test or statistical model. As a useful statistical method, a wealth of literature about its theories and computation methods has been established. The research on ROC curves, however, has focused mainly on cross-sectional design. Very little research on estimating ROC curves and their summary statistics, especially significance testing, has been conducted for repeated measures design. Due to the complexity of estimating the standard error of a ROC curve, there is no currently established statistical method for testing the significance of ROC curves under a repeated measures design. In this paper, we estimate the area of a ROC curve under a repeated measures design through generalized linear mixed model (GLMM) using the predicted probability of a disease or positivity of a condition and propose a bootstrap method to estimate the standard error of the area under a ROC curve for such designs. Statistical significance testing of the area under a ROC curve is then conducted using the bootstrapped standard error. The validity of bootstrap approach and the statistical testing of the area under the ROC curve was validated through simulation analyses. A special statistical software written in SAS/IML/MACRO v8 was also created for implementing the bootstrapping algorithm, conducting the calculations and statistical testing.
When Strategic Plans Fail to Lead. A Complexity Acknowledging Perspective on Decision-Making in Urban Development Projects—The Case of Kortrijk (Belgium)

Nowadays, cities formulate long-term strategies to address the challenges and opportunities they face. Numerous strategic plans or planning instruments are developed for this purpose. In this article, we would like to examine the role, impact and relevance of these types of plans in decision-making processes concerning urban development projects (UDPs) in the Flemish Region of Belgium. To what extent do strategic plans succeed in capturing and steering the complexity of spatial interventions in contemporary urban contexts? We argue that a complexity-acknowledging perspective provides a more realistic and adequate view here by seeing strategic plans as only one among many elements in the set of tangled inter- and intrastrategic processes which together determine UDPs. A comparative and qualitative case study was carried out in the city of Kortrijk. The decision-making of three UDPs was studied thoroughly. Interviewing key actors and analysing policy documents helped us to (re)construct the complex decision-making processes and to stipulate the meaning of all involved formal plans and planning tools.
Phytochemical, anti-oxidant, anti-microbial, anti- inflammatory and anti-ulcer properties of Helianthemum lippii

The medicinal plants have been considered a healthy source of life for all people and the therapeutical properties of the medical plants are very useful in curing range of diseases. The aims of the study are to evaluate the anti-oxidant, antimicrobial, anti-inflammatory and anti-ulcer properties of Helianthemum lippii (MHL) methanolic extracts. MHL samples were collected in the mountain region of Libya. The antioxidant properties of MHL were evaluated using free radical scavenging assay. Stomach ulcers were induced in rats by ethanol. Pretreatment with ranitidine and MHL samples were performed before the ulcer induction. Gastric mucosal histological changes in rat stomach tissue were evaluated. Antimicrobial efficacy of MHL was also studied against gram-positive bacteria S. aureus, gram-negative bacteria E. coli , and fungal strain C. albicans. The phytochemical screening of MHL showed presence of flavonoids, tannins, saponine and simple phenolic compounds. MHL exhibited a powerful anti-oxidant activity, where 31.17 ± 1.40 µg/ml of extract caused 50% inhibition on 2,2, Diphenyl-1-picryhydrazyl (DPPH) scavenging activity in comparison to standard ascorbic acid (15.35 ± 3.2 µg/ml). MHL also showed substantial anti-microbial activity against a strain of gram-positive bacteria, S. aureu, with zone of inhibition (21 mm) and MIC (12.25 mg/ml) and a fungal strain, C. albicans, with zone of inhibition (20 mm) and MIC (6.25 mg/ml) compared to ciprofloxacin or amphotericin B. MHL at doses of 250 and 500 mg/kg produced statistical significant anti-inflammatory activity (23.6%, 50%) in comparison to aspirin (60%). It further showed significant anti-ulcer activity in doses of 250mg/kg and 500mg/kg with percentage of gastric lesions inhibitions of 48.78% and 76.82%, respectively, in comparison to standard anti-ulcer ranitidine (50 mg/kg), which showed 69.78%. MHL has clearly a protective effect against ethanol-induced gastric mucosal lesion, and this effect, at least in part, depends on the increase of anti-oxidant activity. In conclusion, the MHL extract showed anti-oxidant, anti-ulcer, anti-microbial activities against tested microbes, antioxidant and anti-inflammatory; mightily due to combined mechanisms of MHL’s constituents. Keyword: gastric ulcer, Helianthemum lippii, Cistaceae, anti-oxidant, anti-microbial, anti-inflammatory, anti-ulcer. Abbreviations: DPPH: 2,2, Diphenyl-1-picryhydrazyl; MEHL: methanolic extract of H. lippii; MHL: Helianthemum lippii; MIC: Minimum inhibitory concentration
Borrower Characteristics and Mortgage Choices ∗

Empirical evidence on the role of borrower characteristics in mortgage product choice is mixed. Using uniquely detailed data on over 600,000 mortgage applications we show that borrower characteristics play a significant role in choosing between adjustable rate mortgages and more complex products. Whilst this indicates that mortgage markets are incomplete, the results are consistent with product choice which reduces household exposure to income, wealth and mobility risk. As the sample covers the period 2003-2009 we exploit the change in supply conditions arising from the global financial crisis to examine the effect of the increased cost to the bank of holding risky loans on their balance sheet. The observed changes in the effects of borrower characteristics on household mortgage product choice are consistent with the bank responding by changing the terms of the mortgage or transferring income and mobility risk to the mortgage applicant. JEL Categories: G21, G01
BACKCASTING AND FORECASTING BIOLOGICAL INVASIONS OF INLAND LAKES

Human introduction of nonindigenous species constitutes a serious threat to many ecosystems, particularly lakes. Recent attempts to predict invasions have focused on the supply of propagules of nonindigenous species to recipient ecosystems from source populations. Here we develop a spatially explicit ''gravity'' model to test this concept for Bythotrephes longimanus, a crustacean waterflea from Eurasia that is rapidly invading lakes in Ontario, Canada. The gravity model predicted spread of Bythotrephes based upon seven identified risk factors (e.g., use of contaminated fishing or boat anchor line) that may allow dispersal of either live individuals or their resting eggs from invaded to noninvaded lakes, as well as based on the spatial arrangement of invaded and noninvaded lakes in Ontario. Discriminant analysis of lake gravity scores successfully identified invasion status for 74% of 170 inland lakes. A retrospective analysis of 31 invaded lakes revealed that the order in which lakes were invaded was directly related to the magnitude of vector inflows from invaded sources. Analysis of the dominant vector inflow to each invaded lake revealed a ''stepping stone'' pattern in which at least five lakes were sequentially invaded from the source population in Lake Huron. One invaded lake (Muskoka) apparently served as an invasion ''hub,'' resulting in up to 18 additional direct and 17 indirect invasions. Species spread occurred via a combination of dominant, local diffusion (median distance 12.5 km) and rare, long-distance ( .100 km) dispersal. Eleven of 131 lakes that were not invaded in 2000 were reported invaded in 2001. Gravity scores of these lakes were significantly higher than those of other noninvaded systems, indicating that susceptibility to invasion can be related to the magnitude of vector inflows. A GIS model based on gravity scores indicated that distribution of Bythotrephes is expected to expand to eastern and northwestern Ontario, although most new invasions are expected to occur in the central region of the province. Our results indicate that quantitative analysis of human dispersal vectors provides a robust starting point with which to assess vulnerability of discrete ecosystems to invasion. Man- agement efforts focused on reducing the number and magnitude of human-mediated dis-
Intravenous immunoglobulin is a treatment option for refractory dermatomyositis in adult patients

A critical appraisal and clinical application of Dalakas MC, Illa I, Dambrosia JM, et al. A controlled trial of high-dose intravenous immune globulin infusions as treatment for dermatomyositis. N Engl J Med. 1993;329:1993-2000. doi: 10.1056/nejm199312303292704.
Méthode d'assemblage de maillages recouvrants autour de géométries complexes pour des simulations en aérodynamique compressible

La simulation numerique des ecoulements (CFD) est largement utilisee aujourd'hui dans l'industrie aeronautique, de l'avant-projet a la conception des appareils. En parallele, la puissance des calculateurs s'est accrue, permettant d'effectuer des simulations resolvant les equations de Navier-Stokes moyennees (RANS) dans un delai de restitution acceptable du point de vue industriel. Cependant, les configurations simulees sont de plus en plus complexes geometriquement, rendant la realisation du maillage tres couteuse en temps humain. Notre objectif est de proposer une methode permettant de simplifier la generation de maillages autour de geometries complexes, en exploitant les avantages de la methode Chimere, tout en levant les difficultes principales rencontrees par cette methode dans le calcul des connectivites. Dans notre approche, le domaine de calcul est decoupe en regions proches et en regions eloignees des corps. Des grilles curvilignes de faible extension decrivent les regions autour des corps. Le maillage de fond est defini par un ensemble de grilles cartesiennes superposees aux grilles de corps, qui sont engendrees et adaptees automatiquement selon les caracteristiques de l'ecoulement. Afin de traiter des maillages recouvrants autour de geometries complexes sans surcout humain, les differentes grilles sont regroupees par composant Chimere. Des relations d'assemblage sont alors definies entre composants, en s'inspirant de la Geometrie de Construction des Solides (CSG), ou un solide peut etre construit par operations booleennes successives entre solides primitifs. Le calcul des connectivites Chimere est alors realise de maniere simplifiee. Des simulations RANS sont effectuees autour d'un fuselage d'helicoptere avec mât de soufflerie et autour d'une aile NACA0015 en incidence, afin de mettre en oeuvre la methode.
Image Enhancement Technique using Adaptive Multiscale Retinex for Face Recognition Systems

Various illumination effects in an image are one of the states of difficulty that should be solved in order to get a satisfactory result in face recognition task. The inhomogeneous intensities of the image has led to many plans and algorithms to devastate the cause and next to eliminate the illumination. The focus of this paper is to enhance the image by reducing illumination effects; employing a preprocessing step i.e. adaptive multiscale retinex as the illumination correction method before accomplishing the recognition task. The performance of this method is evaluated using the Yale database and has lower equal error rate compared with single scale retinex and conventional multiscale retinex.
Single Langmuir probe characteristic in a magnetized plasma at the text tokamak

A single Langmuir probe tip was used at TEXT-Upgrade to obtain I-V characteristics in a magnetized plasma. Noisy data were reduced by a boxcar-averaging routine. Unexpected effects, namely nonsaturation of ion current, hysterises in the characteristics and I(V)-data were observed, which are in disagreement to the common single probe model. A double probe model allows parameterization of the I(V) curves and to determine the plasma properties in the scrape-off layer. It is shown in this model that a Langmuir probe does perturb the local space potential in the plasma. Comparisons were made with the triple probe technique of measuring temperatures. The nonsaturation of ion current leads to an error in the triple probe technique of order 20%.
Lexical Networks in !Xung

We investigate the lexical network properties of the large phoneme inventory Southern African language Mangetti Dune ! Xung as it compares to English and other commonly-studied languages. Lexical networks are graphs in which nodes (words) are linked to their minimal pairs; global properties of these networks are believed to mediate lexical access in the minds of speakers. We show that the network properties of ! Xung are within the range found in previously-studied languages. By simulating data (”pseudolexicons”) with varying levels of phonotactic structure, we find that the lexical network properties of ! Xung diverge from previously-studied languages when fewer phonotactic constraints are retained. We conclude that lexical network properties are representative of an underlying cognitive structure which is necessary for efficient word retrieval and that the phonotactics of ! Xung may be shaped by a selective pressure which preserves network properties within this cognitively useful range.
Short communication cAMP Signaling Affects Irreversible Attachment During Biofilm Formation by Pseudomonas aeruginosa PAO1

Pseudomonas aeruginosa responds to environmental changes and regulates its life cycle from planktonic to biofilm modes of growth. The control of cell attachment to surfaces is one of the critical processes that determine this transition. Environmental signals are typically relayed to the cytoplasm by second messenger systems. We here demonstrated that the second messenger, cAMP, regulated the attachment of cells. Our results suggest cAMP inhibited the transition from reversible to irreversible attachment. Further analyses revealed that cell surface hydrophobicity, one of the key factors in cell attachment, was altered by cAMP.