Miracle-dz/UniFAR-FTUs huggingface dataset:
Network analysis of prion disease

P rion diseases are transmissible neuro-degenerative diseases that arises due to conformational change of normal cellular prion protein (PrPc ) to protease-resistant isofrom (rPrPSc ). Deposition of misfolded PrPSc proteins leads to an alteration of many signaling pathways that includes immunological and apoptotic pathways and as a result, culminates in dysfunction and death of neuronal cells. Transcriptional studies have revealed some affected pathways, but it is not clear which is (are) the prime network pathway(s) that change during the disease progression and how the prime pathways are involved in cross talk with each other from the time of incubation to clinical death. To address these issues we performed network analysis on large-scale transcriptional data of differentially expressed genes obtained from whole brain in 6 different mouse prion models. We employed the notion of differential network centrality measurement to identify the potential pathways involved in disease progression. We also used cross-talk ranking method to identify core network elements involved in the cross-talk with different pathways. We identified 148 DEGs (differentially expressed genes) potentially related to the prion disease progression. Functional association of the identified genes implicated strong involvement of immunological pathways. A bow-tie structure was extracted, suggesting that the effects of prion disease on the core elements (PI3Ks and AKT) of the structure leads to potential dysfunction of the biological pathways involved. We also modeled the bow-tie network that can be used to approximate the behavior of this network during prion disease prevalence. In this study we showed using transcriptional data that neuronal dysfunction during prion disease is strongly related to immune response. We conclude that the immunological pathways occupy the network’s influential positions in the protein functional networks related to prion disease and this network-central involvement is prevalent in 5 different mouse strain-prion strain combinations.
Comparative Biochemical Studies on Penicillium albicans (Alkalosensitive) and Verticillium lateritium (Facultative Alkalophile)

High alkalinity inhibited sugar utilization by the alkalosensitive fungus (P. albicans) and increased the polysaccharide content in its fungal mats. The total amino-N content decreased in the culture of P. albicans, whereas its quantity increased in the biomass with progressive alkalinity. Alkalinity inhibited nitrogen uptake and protein synthesis leading to a corresponding decline in growth and hence apparent alkalosensitivity. High alkalinity, caused enhancement of sugar uptake by the facultative alkolophile V. lateritium associated with higher reducing sugar contents and decreased polysaccharide accumulation in mycelial mats. The amino-N content increased in the culture medium of V. lateritium and decreased in the biomass with pH elevation. The utilization of soluble nitrogen increased, accompanied by increased protein synthesis, leading to maximum growth at higher pHs and hence apparent alkalophilicity. The sodium ion content in the medium of the alkalosensitive fungus decreased at high pHs associated with respective increase in the biomasses. Oppositely, in the alkalophilic fungus, the sodium ion content increased in culture and decreased in biomasses with increased alkalinity indicating an important role played by this ion. No clear relation could be obtained between phosphorus content in culture or biomasses of the two tested fungi and alkalophilicity.
Agrifood Research Reports 87

Volatilization of ammonia (NH3) from animal manure is a major pathway for nitrogen (N) losses that cause eutrophication, acidification, and other environmental hazards. In this study, the effect of alternative techniques of manure treatment (aeration, separation, addition of peat) and application (broadcast spreading, band spreading, injection, incorporation by harrowing) on NH3 emissions in the field and on N uptake by ley or cereals was studied. The effect of a mixture of slurry and peat on soil properties was also investigated. The aim of this study was to find ways to improve the utilization of manure N and reduce its release to the environment. Injection into the soil or incorporation by harrowing clearly reduced NH3 volatilization from slurry more than did the surface application onto a smaller area by band spreading or reduction of the dry matter of slurry by aeration or separation. Surface application showed low NH3 volatilization, when pig slurry was applied to tilled bare clay soil or to spring wheat stands in early growth stages. Apparently, the properties of both slurry and soil enabled the rapid infiltration and absorption of slurry and its ammoniacal N by the soil. On ley, however, surface-applied cattle slurry lost about half of its ammoniacal N. The volatilization of NH3 from surface-applied peat manure was slow, but proceeded over a long period of time. After rain or irrigation, the peat manure layer on the soil surface retarded evaporation. Incorporation was less important for the fertilizer effect of peat manure than for pig slurry, but both manures were more effective when incorporated. Peat manure applications increase soil organic matter content and aggregate stability. Stubble mulch tillage hastens the effect in surface soil compared with ploughing. The apparent recovery of ammoniacal manure N in crop yield was higher with injection and incorporation than with surface applications. This was the case for leys as well as for spring cereals, even though NH3 losses from manures applied to cereals were relatively low with surface applications as well. The ammoniacal N of surface-applied slurry was obviously adsorbed by the very surface soil and remained mostly unavailable to plant roots in the dry soil. Supplementing manures with inorganic fertilizer N, which adds plant-available N to the soil at the start of growth, increased the overall recovery of applied N in crop yields.
Cascading trophic effects on aquatic nitrification: Experimental evidence and potential implications

Experiments, using natural plankton collected from a eutrophic site in Saginaw Bay, Lake Huron (USA) and from a hypereutrophic wetland of southern Lake Erie (USA), were conducted to test the hypothesis that bacterivory can control aquatic nitnfication rates. The dynamics of nitrogen and protists in these experiments revealed a consistent pattern: an increase in concentrations of nitrates due to oxidation of NH,' always followed the collapse of bacterivorous nanoplankton populations. This collapse was, in turn, caused by predation pressure of larger ciliates and metazooplankton. Experiments, using enrichment batch cultures maintained at near-ambient concentrations of NH,', indicated that bacterivorous protists can inhibit nitnfication directly by reducing bacterial numbers and indirectly by promoting bacterial aggregation. The latter experiments also suggest that feeding strategies of microbial grazers, e.g. suspension-feeding Spumella sp. versus surface-feeding Bodo saltans, may determine their grazing impacts on nitrifiers. Finally, ingestion rates of fluorescently labeled nitrifying bacteria (FLNB) by the natural planktonic assemblage from Saginaw Bay demonstrated that nanoflagellates were able to efficiently prey on low concentrations of FLNB. Our study suggests that previously neglected trophic factors may be of potential importance for mediating nitrification rates in the pelagic environment.
A STUDY ON THE EFFECTIVENESS OF METAPHOR AND CULTURAL AWARENESS-RAISING TO THE LEARNING OF IDIOMS IN THE EFL CLASSROOM

Idioms are one of the most fascinating and complex aspects of the language, since they contain a great deal of the TL culture and native speakers' way of perceiving reality. However their figurative nature makes that most EFL students have problems when learning and acquiring them. This situation together with the traditional method employed to teach idioms, which is based on the structural view of language, and that employs drills and repetitive activities in order to memorise idioms, makes that IEs represent a nightmare for students. Taking into account these problems, the objective of this study is to adopt the cognitive view of language to design a methodology to teach idioms in the EFL classroom. The aim of this methodology is to raise students awareness of the metaphors and cultural implications that are behind most idioms in English, in order to facilitate their learning. Moreover, this study also considers students' learning differences, such as level of motivation and learning styles. For that reason, the methodology presented is carried out in two different classrooms in which different levels of motivation and different learning styles are observed. The results of the metaphor and cultural awareness-raising methodology (experimental groups) are compared to those obtained following a traditional methodology (control groups) in order to test the effectivity of the lesson plan presented. Results suggest that the learning differences observed between the two groups are relevant, since they affect the degree of efficiency of the methodology, concluding that the metaphor and cultural awareness-raising methodology is more effective in a group of students with low level of motivation and with preference for a visual learning style.
Aggressive and Peaceful Strategies in Cellular Resource Space

The individual-based approach in the modeling of complex adaptive systems named Artificial Life is considered. Such approach allows to deal with an intrinsic adaptation of the system, with an organism influence on its environment and on other organisms, with altering the whole biosphere and eventually its own possibility to exist, i. e. its own fitness. In the Artificial Life research field of digital ecosystems, such approach provides the ability to trace an a posteriori fitness, which can be treated as emergent features of the system like population size, grouping or stability of exhibited behavior. In the work, we explore the model similar to classic Artificial Life models on spatial lattice and discuss relation between combat and peaceful behavior due to available resource in the system. It is introduced heterogeneous resource landscape in its impact on agent’s behavior, and examine it on the notion of species sustainability. The species sustainability is investigated
Market Integration and Seasonal Price Variation of Pangas Fish in Some Selected Areas of Bangladesh

A study was undertaken to examine the marketing system and price behavior of Pangas fish in selected areas of Mymensingh district of Bangladesh during the month of June-October 2012. The objectives of the study were to estimate costs and margins, seasonal price variation and to test market integration of Pangas fish. Primary and secondary data were used for this study. The higher marketing cost was incurred by aratdars and the lowest by retailer. On the other hand, retailers earned the highest net marketing margins. Analysis of market integration shows that Pangas fish market in Bangladesh was well integrated. The study identified some problems related to economic, technical, marketing, social and natural calamities aspects and suggested some measures for solving these problems. The findings of the study revealed that the marketing of Pangas was a profitable business and some recommendations were provided for the improvement of Pangas marketing in the country.
Impacts of marine instability across the East Antarctic IceSheet on Southern Ocean dynamics

Abstract. Recent observations and modelling studies have demonstrated the potential for rapid and substantial retreat of large sectors of the East Antarctic Ice Sheet (EAIS). This has major implications for ocean circulation and global sea level. Here we examine the effects of increasing meltwater from the Wilkes Basin, one of the major marine-based sectors of the EAIS, on Southern Ocean dynamics. Climate model simulations reveal that the meltwater flux rapidly stratifies surface waters, leading to a dramatic decrease in the rate of Antarctic Bottom Water (AABW) formation. The surface ocean cools but, critically, the Southern Ocean warms by more than 1 °C at depth. This warming is accompanied by a Southern Ocean-wide “domino effect”, whereby the warming signal propagates westward with depth. Our results suggest that melting of one sector of the EAIS could result in accelerated warming across other sectors, including the Weddell Sea sector of the West Antarctic Ice Sheet. Thus, localised melting of the EAIS could potentially destabilise the wider Antarctic Ice Sheet.
In Search of Museum Professional Knowledge Base: Mapping the professional knowledge debate onto museum work

Abstract Museum professionalism remains an unexplored area in museum studies, particularly with regard to what is arguably the core generic question of a sui generis professional knowledge base, and its necessary and sufficient conditions. The need to examine this question becomes all the more important with the increasing expansion of the museum’s roles and functions. This paper starts by mapping out the policy and organizational context within which the roles of museums have expanded in the UK. It then situates the discussion of museum professional knowledge within a cross-disciplinary matrix bearing on the question of what is professional about occupations classified—or classifiable—as professions. Against the backdrop of the current organizational context of the museum as well as theories of professional knowledge, it highlights the ways in which museum work, more specifically museography, poses a distinctive set of questions compared to other ‘professional’ fields; the paper thus homes in on the question of what it is that constitutes the uniqueness of museum professional knowledge in relation to museographic practice and the type of professional knowledge and expertise that can sustain it and enact its creative and educational potentials and affordances.
Comparative Genomics of Domesticated and Wild Sunflower: Complete Chloroplast and Mitochondrial Genomes

The entire chloroplast and mitochondrial genomes of domesticated and wild type sunflower were sequenced. The comparative analysis of chloroplast genomes revealed 43 variant sites, including 21 polymorphic SSR loci and 22 SNPs. About 14 variant sites were found by collation of mitochondrial DNA (mtDNA), among them 4 SSRs, 8 SNPs and 2 deletions. About 9 SNPs were located in coding region of chloroplast DNA (cpDNA) and single SNP was mapped in mitochondrial gene. Only three SNPs caused amino acid changes: Two SNPs in cpDNA and one mtDNA SNP. Despite the fact that sunflower mitochondrial genome sequence is twice as long as chloroplast genome sequence, mtDNA has one third as much variant sites than cpDNA.
The IRAM-30m line survey of the Horsehead PDR I. CF + as a tracer of C + and as a measure of the fluorine abundance

C+ is a key species in the interstellar medium, but its 158 μm fine structure line cannot be observed from ground-based telescopes. Current models of fluorine chemistry predict that CF+ is the second-most important fluorine reservoir in regions where C+ is abundant. We detected the J = 1-0 and J = 2-1 rotational lines of CF+ with high signal-to-noise ratio toward the photo-dissociation region and dense core positions in the Horsehead. Using a rotational diagram analysis, we derive a column density of N(CF+) = (1.5-2.0) × 1012 cm-2. Because of the simple fluorine chemistry, the CF+ column density is proportional to the fluorine abundance. We thus infer the fluorine gas-phase abundance to be F/H = (0.6-1.5) × 10-8. Photochemical models indicate that CF+ is found in the layers where C+ is abundant. The emission arises in the UV-illuminated skin of the nebula, tracing the outermost cloud layers. Indeed, CF+ and C+ are the only species observed to date in the Horsehead with a double-peaked line profile caused by kinematics. We therefore propose that CF+, which is detectable from the ground, can be used as a proxy of the C+ layers.
EFFICIENT SEMI-AUTOMATIC SEGMENTATION OF LIVER-TUMORS FROM CT-SCANS WITH INTERACTIVE REFINEMENT

This article presents a fast and efficient method for segmentation of liver tumors. The main focus of attention was set to comply with limitations in terms of runtime, hardware requirements and intuitive usability by the surgeon. Therefore a simple Region-Growing approach was considered which is satisfactory for liver-metastases, a frequent disease pattern. In order to achieve a high level of reliability, automated and optimized user correction possibilities were implemented.
Optical and Electrical Effects of p-type μc-SiOx:H in Thin-Film Silicon Solar Cells on Various Front Textures

p-type hydrogenated microcrystalline silicon oxide (µc-Si:H) was developed and implemented as a contact layer in hydrogenated amorphous silicon (a-Si:H) single junction solar cells. Higher transparency, sufficient electrical conductivity, low ohmic contact to sputtered ZnO:Al, and tunable refractive index make p-type µc-Si:H a promising alternative to the commonly used p-type hydrogenated microcrystalline silicon (µc-Si:H) contact layers. In this work, p-type µc-Si:H layers were fabricated with a conductivity of up to 10−2 S/cm and a Raman crystallinity of above 60%. Furthermore, we present p-type µc-Si:H films with a broad range of optical properties (2.1 eV < band gap eV and 1.6 < refractive index ). These properties can be tuned by adapting deposition parameters, for example, the CO2/SiH4 deposition gas ratio. A conversion efficiency improvement of a-Si:H solar cells is achieved by applying p-type µc-Si:H contact layer compared to the standard p-type µc-Si:H contact layer. As another aspect, the influence of the front side texture on a-Si:H p-i-n solar cells with different p-type contact layers, µc-Si:H and µc-Si:H, is investigated. Furthermore, we discuss the correlation between the decrease of and the cell surface area derived from AFM measurements.
A case study of observations of volcanic ash from the Eyjafjallajökull eruption: 2. Airborne and satellite radiative measurements

[1] An extensive set of airborne and satellite observations of volcanic ash from the Eyjafjallajokull Icelandic eruption are analyzed for a case study on 17 May 2010. Data collected from particle scattering probes and backscatter lidar on the Facility for Airborne Atmospheric Measurements (FAAM) BAe 146 aircraft allow estimates of ash concentration to be derived. Using radiative transfer simulations we show that airborne and satellite infrared radiances can be accurately modeled based on the in situ measured size distribution and a mineral dust refractive index. Furthermore, airborne irradiance measurements in the 0.3–1.7 μm range are well modeled with these properties. Retrievals of ash mass column loading using Infrared Atmospheric Sounding Interferometer (IASI) observations are shown to be in accord with lidar-derived mass estimates, giving for the first time an independent verification of a hyperspectral ash variational retrieval method. The agreement of the observed and modeled solar and terrestrial irradiances suggests a reasonable degree of radiative closure implying that the physical and optical properties of volcanic ash can be relatively well constrained using data from state-of-the-science airborne platforms such as the FAAM BAe 146 aircraft. Comparisons with IASI measurements during recent Grimsvotn and Puyehue volcanic eruptions demonstrate the importance of accurately specifying the refractive index when modeling the observed spectra.
Effect of information displays on cage-free and organic egg sales: Evidence from two field experiments

This research determines the effect of point-of-purchase informational displays on the difference in quantity and type of eggs purchased. Informative displays were introduced in two supermarkets and consumer purchasing behavior before, during, and after the introduction of the signage was analyzed. A random utility model was fit to the data, which described consumer choice as a function of price, egg type, day-of-the-week, promotional deals, and informative displays. Results indicate informative displays did not cause a large shift toward organic or cage-free eggs. The signs, however, did increase the total amount of eggs purchased, thus indicating the signs served as an overall demand enhancement mechanism.
The Pennsylvania State University The Graduate School The College of Health and Human Development EFFECTS OF A DAIRY-RICH DIET ON MODULATING BIOMARKERS OF INFLAMMATION IN WEIGHT-STABLE OVERWEIGHT AND OBESE ADULTS

Inflammation and oxidative stress are exacerbated in the overweight and obese conditions and may contribute to the progression of obesity comorbidities. Dairy consumption has been associated with more favorable inflammatory status and reduced oxidative stress. A systematic search of the literature was conducted to identify experimental and observational studies in overweight and obese adults, some of whom had metabolic syndrome (MetS) that assessed the effects of dairy intake on modulating biomarkers of inflammation and oxidative stress. Eight randomized controlled trials (RCTs) and 1 cross-sectional study were found and reviewed. Among habitual low-dairy consumers, clinical trials in overweight and obese adults suggest a modest reduction in inflammation with an adequate dairy diet. Participants with MetS did not respond consistently to an increase in dairy consumption. The cross-sectional study supported the notion that adequate dairy intake is associated with lower concentrations of inflammatory 6 biomarkers. In the context of excess adiposity, increasing dairy intake to the recommended 3 servings/d may modify inflammation and oxidative stress. Methodological consistency and manipulations using various dairy foods will enable a better, more mechanistic understanding of how dairy affects inflammation and oxidative stress.
Impact of Emulsifiers Addition on the Retrogradation of Rice Gels during Low-Temperature Storage

Rice and its products are widely consumed in Asian countries; however, starch retrogradation decreases the quality and shortens the shelf-life of rice foods particularly at low temperature. In this study sucrose ester (SE), glycerol monostearate (GMS), and sodium stearoyl lactylate (SSL) were added to rice flour and corresponding rice gels. Then, gelatinization properties, retrogradation characteristics, texture, and water content of these rice gels were investigated at 4°C and −20°C storage, respectively. The results demonstrated that the rice gels with 0.2% GMS had the lowest retrogradation index (/) (11.84%) and hardness (1359 g) at 4°C for a 10 d period, which was significantly lower in comparison to control and the other two emulsifiers (). Adhesiveness and water content were increased compared to the other samples. Furthermore, the retrogradation of rice gels stored at 4°C was comparatively rapid compared to gels stored at −20°C. Gel samples stored at −20°C were still acceptable for more than 15 days. Thus it was revealed that GMS has the potential to retard starch retrogradation and produce high-quality rice products in preservation.