Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of DNA Extraction Methods from Formalin-Fixed, Paraffin- Embedded Tissue and their Impact on Real-Time PCR-Based Mutation Assays

In this new era of personalized cancer care, molecular testing for somatic mutations plays an increasing role in treatment decisions for many targeted cancer therapeutics. Formalin-fixed paraffin-embedded tissue (FFPET) specimens remain the typical source of nucleic acid for such testing. Because formalin fixation can damage nucleic acids and many tumor specimens are small, obtaining a sufficient quantity of high-quality DNA for mutation testing can be challenging. Given these pre-analytic variables, the availability of a standardized and well-validated method to isolate DNA from such specimen types is critical. We compared two widely available commercial kits for DNA isolation (cobas DNA Sample Preparation Kit from Roche Molecular Systems, and QIAamp DNA FFPE Tissue Kit from Qiagen) using 120 FFPET specimens from a range of tumor types (melanoma, thyroid, colorectal, lung, breast, and ovarian cancer) and examined the effects of the different DNA isolation methods on the subsequent performance of real-time PCR-based assays for BRAF, KRAS and EGFR mutations. Although the two methods gave comparable nucleic acid quantities, the cobas method co-purified significantly less RNA (p<0.001) as determined by comparing DNA yields before and after RNase treatment. The presence of RNA in the extracted DNA was associated with delayed threshold cycle (Ct) in real-time PCR-based mutation tests. The cobas method consistently yielded a sufficient quantity of purified DNA across range of tumor types and specimen sizes for real-time PCR mutation detection tests without requiring an additional step of RNase treatment
EFFECT OF POLYHERBAL FORMULATION ON ETHYLENE GLYCOL INDUCED UROLITHIASIS

The effect of Polyherbal Syrup (Aqueous decoction of Aerva lanata, Astercantha longifolia, Cucumis sativus, Cumimum cyminum, Hemidesmus indicus, Lagenaria siceraria and Tribulus terrestris) against ethylene glycol–induced urolithiasis in male Wistar albino rats was carried out. Urolithiasis was induced in rats by administering 0.75% ethylene glycol in drinking water for 28 days and was manifested by high urinary calcium, phosphorus and low urinary volume, pH, magnesium content and high uric acid, creatinine, urea and BUN in serum. Simultaneous administration of Polyherbal syrup (100 and 200 mg/kg/oral) and standard drug hydrochlorothiazide 150µg/kg orally for 28 days along with ethylene glycol (0.75%) reduced urinary calcium, phosphorus and increased urinary volume, pH and magnesium and reduced uric acid, creatinine, urea and BUN in serum. The histopathological studies confirmed the induction of urolithiasis as microcrystal deposition was observed in sections of kidney from animals treated with ethylene glycol. This was reduced after treatment with the Polyherbal syrup. These observations enable us to conclude that Polyherbal syrup is effective against ethylene glycol–induced urolithiasis.
Detection of Avian Influenza (H5N1) In Some Fish and Shellfish from Different Aquatic Habitats across Some

The global climatic changes impact on air, water and earth could extend scope of Avian Influenza (H5N1) virus to another broad sector of creatures including aquatic animals, especially those with direct relationship to aquatic birds. In the current study, Avian Influenza virus (H5N1) was detected in hemolymph of the Red Swamp crayfish (Procambrus clarkii) from three different provinces across the Nile Delta. Most of the positive cases were from the neighborhood of migratory bird natural stop stations. The virus was also detected in the Mediterranean Cone Shell (Conus mediterraneus) and the Pufferfish Lagocephalus sceleratus (Gmelin, 1789) during its course of invasion to the Mediterranean Sea. Two out of three poultry manure samples collected prior to earthen pond fertilization at three different localities were proved to be positive for the H5N1 virus. Tissue / mucous samples collected from earthen pond raised tilapias were negative for the virus. Catfish (Clarias gariepinus) has presented a striking model for aquatic species carrying the virus in their blood. The current results are suggestive for an important epidemiological role played by aquatic animals in spread of avian influenza (H5N1) virus across the Egyptian aquatic habitat. (A.E. Eissa H.A. Hussein and M.M. Zaki. Detection of Avian Influenza (H5N1) In Some Fish and Shellfish from Different Aquatic Habitats across Some Egyptian Provinces. Life Sci J 2012;9(3):2702-2712) (ISSN:1097-8135). http://www.lifesciencesite. com . 394
Wnt Signaling in Stem Cells and Cancer

markdownabstract__Abstract__ Mammalian development starts from a fertilized egg that initially generates few pluripotent cells which eventually give rise to the embryo proper. Different ‘flavors’ of pluripotency have been captured in vitro which led to the establishment of different pluripotent cell lines. Mouse embryonic stem cells (mESCs) are derived from the preimplantation embryo and have three defining properties: self-renewal, pluripotency, and contribution to chimera formation. By applying specific culture conditions or ectopic expression of the pluripotency factors, similar pluripotent cells can be derived from germ cells or differentiated cells referred to as embryonic germ (EG) and induced pluripotent cells (iPSCs), respectively. When established from post-implantation embryo, the cultured cells are termed epi stem cells (EpiSCs). EpiSCs have limited potential for chimerism and germ line transmission and require different culture conditions when compared to ESCs. Hence, mouse ESCs and EpiSCs represent two different phases of pluripotency usually referred to as the naive and primed states. By employing genetic manipulation or specific culture conditions, the different pluripotent cells can be interconverted which leads to several intermediate states. Unlike their murine counterparts, human ESCs closely resemble the rodent primed EpiSCs and respond to similar signaling pathways. Tumorigenic transformation of primordial germ cells (PGC) and gonocytes can also give rise to pluripotent cells known as embryonal carcinoma cells (hECs), thought to represent the malignant counterpart of hESCs. Among different signaling pathways, Wnt signaling plays a central role in self-renewal and differentiation of pluripotent cells.
Role of the IκB Kinase Complex in Oncogenic Ras- and Raf-Mediated Transformation of Rat Liver Epithelial Cells

ABSTRACT NF-κB/Rel factors have been implicated in the regulation of liver cell death during development, after partial hepatectomy, and in hepatocytes in culture. Rat liver epithelial cells (RLEs) display many biochemical and ultrastructural characteristics of oval cells, which are multipotent cells that can differentiate into mature hepatocytes. While untransformed RLEs undergo growth arrest and apoptosis in response to transforming growth factor β1 (TGF-β1) treatment, oncogenic Ras- or Raf-transformed RLEs are insensitive to TGF-β1-mediated growth arrest. Here we have tested the hypothesis that Ras- or Raf-transformed RLEs have altered NF-κB regulation, leading to this resistance to TGF-β1. We show that classical NF-κB is aberrantly activated in Ras- or Raf-transformed RLEs, due to increased phosphorylation and degradation of IκB-α protein. Inhibition of NF-κB activity with a dominant negative form of IκB-α restored TGF-β1-mediated cell killing of transformed RLEs. IKK activity mediates this hyperphosphorylation of IκB-α protein. As judged by kinase assays and transfection of dominant negative IKK-1 and IKK-2 expression vectors, NF-κB activation by Ras appeared to be mediated by both IKK-1 and IKK-2, while Raf-induced NF-κB activation was mediated by IKK-2. NF-κB activation in the Ras-transformed cells was mediated by both the Raf and phosphatidylinositol 3-kinase pathways, while in the Raf-transformed cells, NF-κB induction was mediated by the mitogen-activated protein kinase cascade. Last, inhibition of either IKK-1 or IKK-2 reduced focus-forming activity in Ras-transformed RLEs. Overall, these studies elucidate a mechanism that contributes to the process of transformation of liver cells by oncogene Ras and Raf through the IκB kinase complex leading to constitutive activation of NF-κB.
Regular Teacher Preparation for Inclusion.

The role of regular teachers is asserted as an integral component in the fruition or otherwise of inclusion in Early Childhood Education (ECE). Consequently, their preparation for inclusion is a cause for concern. An examination of regular teachers’ preparation for inclusion in ECE in Zimbabwe revealed that they had tuition in characteristics, health, attitudes, education, inclusion, assistance, diversity and behavior management of children with disabilities. Regular teachers had also tutelage of social, physical and behavior management environment. They had further grounding in collaboration with peer regular teachers, teacher assistance teams, multidisciplinary teams and parents. Inversely, regular teachers lacked training in instructional environment management, adaptive equipment, environmental adaptations, flexible working with individual children, collaboration with specialist teachers and content, process and assessment
How to strengthen employee engagement among Slovenian criminal investigators

Purpose: In terms of providing security, employee engagement may be defined as an important contribution by individual criminal investigators or their physical, cognitive and emotional dedication to their work. Employee engagement positively correlates with one’s work, as reflected in the dedication, absorption, and psychological state accompanied by personal energy invested in the work. A fundamental question for the criminal investigation police thus arises of how to achieve maximum engagement and commitment in police work, which in turn will contribute to greater security in Slovenia. Design/Methods/Approach: The article is based on empirical research conducted among 160 Slovenian criminal investigators. We used Gallup’s Q12 Employee Engagement Survey to measure employee engagement. Findings: The research encompassing 160 Slovenian criminal investigators shows that most criminal investigators are disengaged. The research also reveals that employee engagement is statistically significantly correlated with self-efficacy, social undermining by one’s supervisor, social support by one’s supervisor and colleagues, as well as cynicism. To raise employee engagement among the Slovenian criminal investigators, we propose several measures affecting the conduct of the police, labour legal matters, operational issues and the leadership. Research Limitations / Implications: The first limitation is social desirability bias. The second limitation is a labour strike that was underway while we were collecting the data from the police officers. Practical Implications: The proposed actions should raise the level of employee engagement of Slovenian criminal investigators, while also enhancing the police service’s reliability. Originality/Value: This is the first paper to research employee engagement among Slovenian criminal investigators.
Effects of thymol, eugenol and malate on in vitro rumen microbial fermentation.

The purpose of this study was to investigate effects of increased levels of eugenol, thymol and malate on pH and the concentrations of VFA, lactate and ammonia-N during in vitro ruminal incubation. One Hanwoo beef steer (741 kg) fitted with a rumen cannula was used and fed 0.5 kg/day rice straw and 10 kg/day corn-based concentrate (ratio of concentrate to rice straw = 95 : 5 on DM basis). Three different doses of thymol, eugenol and malate were used. Treatments of the experiment were as follows: Treatments of thymol were control (1g D-glucose/40ml), T1 (1g D-glucose + 40 mg thymol/40 ml), T2 (1g D-glucose + 50 mg thymol/40 ml) and T3 (1g D-glucose + 60 mg thymol/40 ml). Treatments of eugenol were control (1g D-glucose/40 ml), E1 (1g D-glucose + 55 mg eugenol/40 ml), E2 (1g D-glucose + 65 mg eugenol/40 ml) and E3 (1g D-glucose + 75 mg eugenol/40 ml). Treatments of malate were control (1g D-glucose/40ml), M1 (1g D-glucose + 25 mg malate/40ml), M2 (1g D-glucose + 50 mg malate/40 ml) and M3 (1g D-glucose + 100 mg malate/40 ml). The results of this study showed that eugenol and thymol have improved stability of the ruminal fermentation by decreasing lactic acid concentration and increasing ruminal pH. However, it inhibited the production of total VFA, acetate and propionate. Malate also improved stability of the ruminal fermentation by decreasing lactic acid concentration and increasing ruminal pH, but it had a very little effect on ruminal lactate concentrations and pH. On the other hand, malate did not decrease the concentrations of total VFA, acetate and propionate. Therefore, at the low ruminal pH expected in high-concentrate diets, thymol, eugenol, and malate are potentially useful in Hanwoo finishing diets. Further studies are necessary for determining the effectiveness of these additives on in vivo rumen fermentation and animal performance in Hanwoo finishing steers.
Automatic Story Generation by Learning from Literary Structures

Are mind and machine capable of solving the same tasks? Creativity is one of the arguments that some philosophers and psychologists use as a proof of what computers cannot achieve; however, these arguments might be based on a misconception of what both intelligence and creativity mean. This book provides arguments supporting that creativity, as storytelling, can be emulated through computer programs. The assumption of creativity presents a major problem: Complexity. Even if we consider creativity just as a product of novel ways of achieving a goal, the number of combinations found when dealing with the ‘real world’ is astronomically huge. We can recall The Library of Babel (Borges, 1944), a library that contains any possible book that could be written in the history of humanity. This metaphor reveals the combinatory problem that emerges if a brute force algorithm is designed to generate texts. According to our hypothesis, our proposal is a heuristic that uses simple syntactic and semantic properties found in a text corpus in order to generate novel and coherent fiction texts based on what has been already written.
Significance and transmission of maize streak virus disease in Africa and options for management: A review

The distribution of leafhopper vector populations and the viral diseases they vector are inherently influenced by agro-ecological factors. This review discusses the distribution and classification of MSV strains, their vectors and how agro-ecological factors mediate the prevalence of MSV disease. Important strains of MSV have been characterised on the African continent using molecular techniques, however, evidence on the characterisation of geographically separate populations of Cicadulina spp. and the viral strains they vector is inadequate. The potential of applying knowledge on the influence of soil nutrients, altitude and temperature on the biology of maize streak virus (MSV) / vector populations is discussed. This review has considered the potential of using soil nutrients in determining nutritive status of maize host plants and its effects on population dynamics of Cicadulina mbila Naude (Homoptera: Cicadelidae), an important vector of MSV disease and the expression of MSV disease. Future research options that can provide information on the influence of soil fertilization on the behaviour of characterised vector populations, MSV disease transmission, virulence and disease expression are proposed.
Costs and benefits of mycorrhizal infection in a spring ephemeral, Erythronium americanum

SUMMARY Spring ephemerals have evolved specific growth strategies that take advantage of the high photon Huence rates of early spring. These strategies involve a sequential growth of different organs. Erythronium americanum (KerGawl), a common spring ephemeral of northern maple forests, produces its roots in the autumn, although stems and leaves develop in the spring. Mycorrhizal infection of the root system occurs very rapidly and intensively. The fungi thus depend on carbohydrate reserves accumulated in the eorm (underground reserve organ) for their growth and development through the winter. We found that the presence of mycorrhizas drastically decreases root growth during the cold period and is more costly of carbohydrate reserves than root growth alone. However, during the spring, the presence of mycorrhizas fully benefits the plant: we measured an annual growth rate of mycorrhizal plants twice that of fungicide-treated plants which were non-mycorrhizal. We suspect that E. americanum is highly susceptible to water stress during the growing season and might rely on its mycorrhizas for water supply to a greater extent than for nutrient supply. Nutrient uptake might occur mainly in the autumn when arbuscules are at their most abundant.
Phylogeny and Biogeography of the Ormocarpum Group (Fabaceae): a New Genus Zygocarpum from the Horn of Africa Region

Abstract The genus Zygocarpum is described with six species formerly of Ormocarpum. This genus is endemic to the Horn of Africa, the southern end of the Arabian Peninsula, and the island of Socotra. Analysis of combined nuclear ribosomal ITS/5.8S and morphological data reveals that Zygocarpum is strongly supported as monophyletic and the basal-most lineage of a mainly African-Madagascan clade comprising also Ormocarpum, Ormocarpopsis, and Peltiera. A second analysis involving a combination of nuclear ribosomal ITS/5.8S, chloroplast trnL intron, and morphological data reveals some well supported relationships among the species of Zygocarpum. Zygocarpum dhofarense and Z. yemenese, endemic to the Arabian Peninsula, form a sister clade to the central Somalian Z. gillettii. The precise relationships among the other two Somalian species, Zygocarpum rectangulare and Z. somalense, as well as the endemic Socotran Zygocarpum coeruleum, are less certain. The distribution of Zygocarpum, which spans the Gulf of Aden, is considered to be due to a Late Tertiary vicariant event involving the separation of the Arabian Peninsula from continental Africa. Communicating Editor: Aaron Liston
A segmentation algorithm for the automatic recognition of tomato at harvest

Tomato is one of the most important products in the world, thus, tendency to grow tomato in greenhouse is increasing. On the other hand, automatic control methods in agricultural and greenhouse operations in order to increase efficiency and reduce labor costs are increasing, too. Since tomato is a plant which fruits do not ripe simultaneously, it is necessary to find a system for machines to distinguish the ripe tomato from unripe. In this study an algorithm was developed for recognizing ripe tomato and keeping unripe tomato for later. For this purpose, the 200 color images of tomato were acquired under natural light condition of greenhouse. Then the color data of ripe and unripe tomato and background were extracted and considered. Finally, observed color spectrum of unripe and ripe tomato were very close to each other and color of ripe tomato was not uniform. To overcome the problems, different color models like RGB, HIS and YIQ were used. Recognition of ripe tomato was performed in two steps, first removing background and second extracting ripe tomato. For removing background, the RGB color space was used. Extracting of ripe tomato was done in three steps: at the beginning, yellow parts of ripe and unripe tomato were extracted by using of the YIQ and HIS color spaces. In the second step, the RGB color space was used to extract red and orange parts of tomato. At the final steps, for recognizing of ripe tomato, two conditional relations in the YIQ color space were defined. Composite of above three steps gave the best results. The algorithm was able to identify the area of a ripe tomato in the image to the extent of 96%. It is very important to extract the full area of ripe tomato, because catching the tomato by robot will be easy. The harvest arm of robot can be opened as the size of tomato.
Comparative metabolomic analyses of Dendrobium officinale Kimura et Migo responding to UV-B radiation reveal variations in the metabolisms associated with its bioactive ingredients

Background Dendrobium officinale Kimura et Migo, a member of the genus Dendrobium, is a traditional Chinese medicine with high commercial value. The positive roles of UV-B radiation on active ingredient metabolism in various medicinal plants have been studied. However, the metabolic responses of D. officinale stems to UV-B treatment is largely unknown. Methods An untargeted metabolomics method was used to investigate the metabolic variations in D. officinale stems between the control and UV-B treatments. Results In total, 3,655 annotated metabolites, including 640 up- and 783 down-regulated metabolites, were identified and grouped into various primary metabolic categories. Then, a number of metabolites involved in the polysaccharide, alkaloid and flavonoid biosynthesis pathways were identified. For polysaccharide biosynthesis, several intermediate products, such as pyruvate, secologanate, tryptophan and secologanin, were significantly up-regulated by the UV-B treatment. For polysaccharide biosynthesis, many key fundamental building blocks, from the glycolysis, starch and sucrose metabolism, and fructose and mannose metabolism pathways, were induced by the UV-B treatment. For flavonoid metabolism, accumulations of several intermediate products of chalcone synthase, chalcone isomerase and flavanone 3-hydroxylase were affected by the UV-B treatment, indicating an involvement of UV-B in flavonoid biosynthesis. The UV-B induced accumulation of polysaccharides, alkaloids and flavonoids was confirmed by HPLC analysis. Our study will help to understand the effects of UV-B on the accumulation of active ingredients in D. officinale.
Systematic review of motor control and somatosensation assessment tests for the ankle

Background/Aim Ankle sprains are frequent musculoskeletal injuries that can lead to sensorimotor deficits provoking long-term instability at the ankle joint. A broad variety of clinical tests currently exist to assess sensorimotor processing, and are commonly clinically referred to as proprioceptive tests. However, there is a discrepancy in the use of the term proprioception when looking at the main outcome of these tests. As identifying specific deficits is important for motor recovery, it is critical for clinicians to select the most appropriate tests. Methods A systematic review of four databases was performed to provide an up-to-date review of the psychometric properties of available tests referred to as proprioceptive tests. Seventy-nine articles on eight ankle proprioceptive tests were included and critically appraised. Data on validity, reliability and responsiveness were extracted from the included articles and synthesised. The tests reviewed were then divided into two categories based on their main outcome: motor control or somatosensation. Results Strong evidence showed that the Star Excursion Balance Test, a motor control test, is capable of differentiating between stable and unstable ankles. Moderate evidence suggests that somatosensation tests, such as Joint Position Sense, are also valid and reliable, but their responsiveness has yet to be evaluated. Conclusions Together, these findings indicate that the Star Excursion Balance Test can be used in the clinic to assess motor control based on its excellent psychometric properties. However, as ankle stability control involves complex sensorimotor interactions, care has to be taken regarding the use of this test as a specific tool for proprioception assessment.