Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of five viral nucleic acid extraction kits for the efficient extraction of viral DNA and RNA from cell-free samples

Extraction of viral nucleic acids from serum samples is widely used in diagnostic pathology tests. However, the heterogeneous nature of non-serum samples may contribute to variations in the yields of viral nucleic acids with different extraction methods and specimen types. Five different nucleic acid extraction methods were compared for optimal extraction of viral DNA or RNA from a prepared cell-free specimen. The viruses used were hepatitis B, hepatitis C. The specimen used was DNase and RNase free normal saline spiked with predefined quantities of viral DNA or RNA. The extraction protocol was carried out according to each manufacturer’s recommendations. The extracted nucleic acids from each of the samples were amplified by PCR and compared to the original un-extracted standard control. The RTA kit as well as the Qiagen kit was shown to yield the highest amounts of viral nucleic acid. *Correspondence to: Bandar Ali Suliman, Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia, E-mail: bsuliman@taibahu.edu. sa
Dual functions of the retinal determination gene network member EYES ABSENT as a transcription factor and protein phosphatase

Proper development of cell types and tissues requires the integration of extracellular signals to provide context specific information that ensures appropriate differentiation. The Drosophila eye is an excellent model for the study of this signal integration, as its development is orchestrated by the interactions of common signal transduction pathways in conjunction with organ specific gene expression. Signaling through the NOTCH, DECAPENTAPLEGIC/ TRANSFORMING GROWTH FACTOR-P, WINGLESS, HEDGEHOG, and EPIDERMAL GROWTH FACTOR RECEPTOR pathways sets the stage for appropriate deployment of the Retinal Determination (RD) gene network members to direct formation of the eye and other
DYNAMICS OF PACHYMETRA ROOT ROT SPORE POPULATIONS IN A SUSCEPTIBLE CROP: A COMPARISON OF TWO CONTRASTING ENVIRONMENTS

THIS paper addresses the dynamics of Pachymetra inoculum in soil, as influenced by initial spore density. Two experimental sites were selected, at Miriwinni and Mourilyan in northern Queensland. These sites provided a unique opportunity to assess population dynamics within a growing crop and illustrate how populations are influenced by site. The analyses showed that at a Pachymetra-conducive site, population increases were proportionally greater in plots with lower initial inoculum densities. There appeared to be a plateau in spore populations in all plots after a plant and first ratoon crop. This population was very high at the Miriwinni site (around 600 000 spores/kg), and at a level where very severe yield losses could be expected. Such a plateau is likely to vary according to the fertility of the cropping system. Data from the Mourilyan site illustrate that in some years and locations, populations are greatly limited by the environment. It is not clear from these data whether climatic factors, or soil suppressive factors, are the reason for the very limited increase in inoculum density.
Flatworms (Schmidtea nova) prey upon embryos of the common frog (Rana temporaria) and induce minor developmental acceleration

Amphibians vary in the degree of pre-metamorphic developmental plasticity in response to risk of predation. Changes in hatching time and development rate can increase egg or tadpole survival respectively by shortening the duration of the more vulnerable stages. The intensity of predator induced developmental response and its direction, i.e. delayed, accelerated, or none, varies considerably between amphibian and predator species. We surveyed freshly deposited clutches of the European common frog Rana temporariain a population in Braunschweig, Germany and found that 62% (N = 20) of the clutches contained planarians ( Schmidtea nova), with an average of 3.94 ± 0.79 and a maximum of 13 planarians per clutch. A laboratory predation experiment confirmed that this planaria preys on R. temporariaeggs and early embryos. We further exposed freshly laid egg masses to either free, caged, or no planarians treatments using floating containers within a breeding pond where the two species co-occur. After 10 days exposure, embryos showed developmental stages 14-25 along the Gosner scale with statistically significant positive effects of both predator treatments. The observed effect was rather slight as predator-exposed individuals showed an increase by a single Gosner stage relative to those raised without planarians. The detected trend suggests that direct and indirect cues from flatworms, rarely considered as anuran predators, might induce a developmental response in R. temporariaearly developmental stages.
Coeliac Disease-inducing Gluten: in vitro harmfulness and detoxification by germinating cereal enzymes

3 TIIVISTELMÄ. 5 CONTENTS. 7 LIST OF ORIGINAL PUBLICATIONS. 9 ABBREVIATIONS . 10 INTRODUCTION. 12 REVIEW OF THE LITERATURE . 14 1. Cereal grains. 14 1.1 The prolamins of the Triticeae cereals . 15 1.2 Germination of grains. 16 2. Coeliac disease . 18 2.1 Clinical characteristics. 19 2.2 Diagnosis . 19 2.3 Genetics . 22 2.4 Pathogenesis. 23 2.4.1 Gluten peptides as a trigger in coeliac disease . 23 2.4.2 Gluten peptides crossing the epithelium . 25 2.4. 3 Activation of immune response . 27 2.5 Treatment . 31 2.5. 1 Current approaches . 31 2.5. 2 Future approaches . 31 3. In vitro models for gluten toxicity . 36 3.1 Epithelial cell culture models. 37 3.2 Patient-derived T-cell lines and clones. 39 3.3 Small-intestinal mucosal biopsies . 40 AIMS OF THE STUDY . 43 4. MATERIALS AND METHODS . 44 4.1 Preparation of gluten prolamines . 44 4.2 Pre-treatment with germinating cereal enzymes. 44
Menachem J. GunzburgNigus D. AmbayeJack T. Hertzog • Mark P. Del BorgoStephanie C. PeroDavid N. KragMatthew C. J. Wilce • Marie-Isabel AguilarPatrick PerlmutterJacqueline A. Wilce

Surface plasmon resonance (SPR) is a useful biosensor technique for the study of biomolecular interac- tions, with the potential for high-throughput screening of ligand interactions with drug targets. The key to its suc- cessful use, however, is in the appropriate design of the experiment, including the mode of immobilization to the biosensor chip. We report an investigation of the use of SPR for measuring the affinity of the G7-18NATE peptide ligand for its Grb7-SH2 domain target involved in the migratory and proliferative potential of cancer cells. Pre- vious studies have shown that the cyclic non-phosphory- lated peptide, G7-18NATE, inhibits Grb7 interactions with upstream binding partners and is able to inhibit both cell migration and proliferation of cancer cells. We report the synthesis of a biotinylated G7-18NATE covalently attached to a linker (G7-18NATE-ASASASK-Biotin) and compare its interaction with the Grb7-SH2 domain by SPR using three different immobilization strategies; immobili- sation of the peptide via streptavidin, immobilization of glutathione S-transferase (GST)-Grb7-SH2 domain via anti-GST antibody, and immobilization of biotinylated Grb7-SH2 domain via streptavidin. This revealed that sensorgrams free from non-specific binding and displaying simple kinetics were most readily achieved by immobilis- ing the protein rather than the peptide, in spite of the lower response associated with this method. KD values of *300 lM were determined for both strategies at pH 7.4. This compared with a KD value of 4.4 lM at pH 6 demonstrating the importance of pH on this interaction. Overall, the im- mobilised protein systems are most suitable for future comparative screening efforts using SPR.
Wat is de invloed van sociale vaardigheden op de keuze voor ondernemerschap

De laatste jaren is de aandacht voor het vakgebied entrepreneurship enorm toegenomen. Dit komt mede gezien het feit dat ondernemerschap en innovatie belangrijke aanjagers zijn voor welvaart en economische groei (Stam, 2008); (Drucker, 1985). Ook in Nederland groeit zelfstandig ondernemerschap nog steeds aan populariteit. In 2016 zijn het aantal ondernemingen met 3% gegroeid ten opzichte van 2015 en het aantal zzp’ers met 4% (Koophandel, 2017). Naast de toename aan ondernemers in Nederland is er een groeiende interesse in ondernemerschap binnen bestaande organisaties, ook wel intrapreneurship genoemd (Sharma & Chrisman, 1999) . Volgens verschillende onderzoeken van onder andere Zahra (1991) en Thornberry (2001) heeft intrapreneurship een positief effect op de financiele resultaten van een organisatie. Volgens Stevenson & Jarillo (1990) kan onderzoek naar ondernemerschap worden opgesplitst in drie stromingen; (1) Hoe handelen ondernemers; (2) Wat zijn de resultaten die voortkomen uit het handelen van ondernemers; (3) Waarom kiezen mensen om ondernemer te worden. Gezien de positieve impact van ondernemerschap, zowel binnen als buiten bestaande organisaties, is er in dit onderzoek gekozen om verder in te gaan op de determinanten van ondernemerschap.
On the computation of poisson probabilities

The Poisson distribution is a distribution commonly used in statistics. It also plays a central role in the analysis of the transient behaviour of continuous-time Markov chains. Several methods have been devised for evaluating using floating-point arithmetic the probability mass function (PMF) of the Poisson distribution. Restricting our attention to published methods intended for the computation of a single probability or a few of them, we show that neither of them is completely satisfactory in terms of accuracy. With that motivation, we develop a new method for the evaluation of the PDF of the Poisson distribution. The method is intended for the computation of a single probability or a few of them. Numerical experimentation illustrates that the method can be more accurate and slightly faster than the previous methods. Besides, the method comes with guaranteed approximation relative error.
Long‐term interval burning alters fine root and mycorrhizal dynamics in a ponderosa pine forest

1. Plant roots and their mycorrhizal symbionts are critical components of forest eco- systems, being largely responsible for soil resource acquisition by plants and the main- tenance of soil structure, as well as influencing soil nutrient cycling. Silvicultural treatments should be guided by knowledge of how these below-ground components respond to different forest management practices. 2. We examined the cumulative effects of 20 years of prescribed burning at 2-year inter- vals. We measured fine root length density and fine root and mycorrhizal root biomass in the upper 15 cm of mineral soil in a south-western ponderosa pine forest over a com- plete burn cycle. 3. Repeated burning reduced fine root length, fine root biomass and mycorrhizal root biomass, as well as the amount of nitrogen and phosphorus stored in these below- ground pools. 4. Estimates of fine root production, fine root decomposition and nutrient dynamics were similar in burned and control plots. 5. Synthesis and applications . Although repeated-prescribed fire may be an effective, low-cost approach for reducing fuel loads and lessening the chance of a catastrophic wildfire in ponderosa pine forests, our results suggest that this strategy may negatively affect below-ground biomass pools and nutrient cycling processes in the more » long term. We recommend that mechanical reductions in fuel loads be conducted in these and similar forests that have not experienced fire for decades, before fire is reintroduced as a man- agement tool. « less
METHODOLOGIES FOR INVESTIGATING OCCUPATIONAL ACCIDENTS AND THEIR USE IN OCCUPATIONAL HEALTH AND SAFETY RESEARCH. LITERATURE REVIEW

The objective of this paper is to review the main studies published on occupational accidents to recognize, classify and describe the scientific methodologies used. To achieve the objective set we used a method that has already been implemented and validated, consisting of an extensive review of international scientific literature related to the methodologies for investigating accidents in occupational health and safety. Then, to assess the importance of these methodologies, we analyzed the number of times the selected publications are cited and the impact factor of the journal where it was published. The results of this review show that many different investigation methodologies have been developed over the last few decades. These methodologies cover different areas of application, qualities and limitations, with the understanding that a thorough accident investigation requires a combination of different activities included in these methods. This study describes which methodologies have been used the most in the field of occupational accident investigations. A total of 35 different methodologies were identified. This study reveals that, even to this day, there are not many methodologies available with a single focus on the field of occupational health and safety. On the other hand, in order to develop and advance in the application of occupational accident investigation techniques, it would be advisable to promote studies that verify the proper selection and use of methodologies in real cases of occupational accidents.
PURIFICATION AND CHARACTERIZATION OF THE RECD PROTEIN-HOMOLOGUE FROM DEINOCOCCUS RADIODURANS

Title of Dissertation: PURIFICATION AND CHARACTERIZATION OF THE RECD PROTEIN-HOMOLOGUE FROM DEINOCOCCUS RADIODURANS Jianlei Wang, Doctor of Philosophy, 2004 Dissertation directed by: Professor Douglas A. Julin Department of Chemistry and Biochemistry In many gram-negative bacteria, RecBCD enzyme is found to be responsible for double strand DNA break repair through homologous recombination. The AddAB enzyme, a RecBCD analog, is found in some gram-positive bacteria and functions in a similar way as RecBCD. A few bacteria appear to lack both RecBCD and AddAB enzymes entirely. One such organism is the bacterium Deinococcus radiodurans. This remarkable organism is able to survive in the presence of very high levels of radiation or DNA-damaging chemicals, levels that would overwhelm the DNA repair capacity of most other organisms. Interestingly, the D. radiodurans genome does have an open reading frame that would encode a protein that is homologous to the E. coli RecD protein. The amino acid sequence of this D. radiodurans RecD-like protein suggests that it is a helicase and therefore could function in some aspect of DNA repair, as does its E. coli homologue. However, the RecD protein of D. radiodurans must serve a different and novel function compared to the E. coli RecD protein. The D. radiodurans RecD protein can be expressed at high levels in E. coli and is readily purified by chromatography on a nickel column followed by single-stranded DNA-cellulose. The purified protein exhibits DNA-dependent ATPase and DNA helicase activities. The helicase activity requires at least a 10 nucleotide single strand overhang at the 5’-end of the double strand DNA substrate to start unwinding. The helicase assay shows that D. radiodurans RecD-like protein unwinds dsDNA substrates catalytically, but with low processivity, even with the help of single strand binding proteins (SSB) from either E. coli or D. radiodurans. These results show that D. radiodurans RecD-like protein is a DNA helicase that moves with 5’-3’ polarity on single-stranded DNA. The E. coli RecD protein was shown recently to unwind dsDNA with the same 5’-3’ polarity. The low processivity of the D. radiodurans RecD-like protein suggests that it may function in a complex with other proteins. The identity of these proteins is not known. We have also generated insertion mutations that are likely to disrupt all of the recD gene copies in the D. radiodurans genome after multiple generations growing in media with antibiotics. The in vivo effects of the insertion mutation, such as the growth curve and the sensitivity to UV radiation and DNA damaging chemicals, were studied. PURIFICATION AND CHARACTERIZATION OF THE RECD PROTEIN-HOMOLOGUE FROM DEINOCOCCUS RADIODURANS
Models of Vascular Pattern Formation in Leaves.

The vegetative hormone Auxin is involved in vascular tissues formation throughout the plant. Trans-membrane carrier proteins transporting auxin from cell to cell and distributed asymmetrically around each cell give to auxin a polarized movement in tissues, creating streams of auxin that presume future vascular bundles. According to the canalization hypothesis, auxin transport ability of cells is thought to increase with auxin flux, resulting in the self-enhancement of this flux along auxin paths. In this study we evaluate a series of models based on canalization hypothesis using carrier proteins, under different assumptions concerning auxin flux formation and carrier protein dynamics. Simulations are run on a hexagonal lattice with uniform auxin production. A single cell located in the margin of the lattice indicates the petiole, and acts as an auxin sink. The main results are: (1) We obtain branching auxin distribution patterns. (2) The type of self-enhancement described by the functional form of the carrier proteins regulation responding to the auxin flux intensity in different parts of a cell, has a strong effect on the possibility of generating the branching patterns. For response functions with acceleration in the increase of carrier protein numbers compared to the auxin flux, branching patterns are likely to be generated. For linear or decelerating response functions, no branching patterns are formed. (3) When branching patterns are formed, auxin distribution greatly differs between the case in which the number of carrier proteins in different parts of a cell are regulated independently, and the case in which different parts of a cell compete for a limited number of carrier proteins. In the former case, the auxin level is lower in veins than in the surrounding tissue, while in the latter, the auxin is present in greater abundance in veins. These results suggest that canalization is a good candidate for describing plant vein pattern formation. ****** Formation of the vascular system in plant leaves can be explained by the canalization hypothesis which states that veins are formed in an initially homogeneous field by a self-organizing process between the plant hormone auxin and auxin carrier proteins. Previous models of canalization can generate vein patterns with branching but fail to generate vein patterns with closed loops. However, closed vein loops are commonly observed in plant leaves and are important in making them robust to herbivore attacks and physical damage. Here we propose a new model which generates a vein system with closed loops. We postulate that the ‘‘flux bifurcator'' level is enhanced in cells with a high auxin flux and that it causes reallocation of auxin carriers toward neighbouring cells also having a high bifurcator level. This causes the auxin flux to bifurcate, allowing vein tips to attach to other veins creating vein loops. We explore several alternative functional forms for the flux bifurcator affecting the reallocation of efflux carriers and examine parameter dependence of the resulting vein pattern.
Effects of Substitution of Maize with Dried Orange Pulp on Performance and Blood Metabolites of Male Calves

The aim of the study was to assess the effect of substitution of maize with dried orange pulp on performance and some blood parameters of young Holstein male calves. Twenty Holstein male calves (3 days old and average body weight 42.3±3.6 kg were assigned to two treatment groups. The orange pulp was dried at 80°C with hot air application in the band dryer system. The first group was fed calf starter including 10% dried orange pulp (DOP) and the second treatment group was fed calf starter without dried orange pulp (Control=CNT) during the treatment. Calf starters were formulated to contain average 21% crude protein, 3.4% crude fat and 2600 kcal/kg metabolic energy (DM basis). Calves were weaned after 8 weeks then all calves were fed a total mixed diet containing 50% alfalfa hay and 50% calf starter for another three weeks. Feed intake and body weight gain were recorded weekly and individual blood samples were collected once in two weeks. The results showed that there was no significant difference (P>0.05) between the groups in terms of feed consumption, body weight gain and metabolites as glucose, cholesterol, none esterified fatty acids, β-hydroxybutyric acid and IGF-1 levels in serum. However, there was a significant difference between the groups in terms of IGF-1 (P<0.05). Those results showed that maize could be substituted with dried orange pulp in calf starters.
Unravelling the algae: the past, present, and future of algal systematics

INTRODUCTION AND OPINIONS Introduction, J. Brodie and J. Lewis Algae in the warp and weave of life: bound by plastids, C.F. Delwiche Evolution and relationships of algae: major branches of the tree of life, T. Cavalier-Smith Classification and diatom systematics: the past, the present and the future, D.M. Williams SYSTEMATICS OF THE ALGAE The taxonomy of cyanobacteria: molecular insights into a difficult problem, P.K. Hayes, N.A. El Semary, and P. Sanchez-Baracaldo Molecular systematics of red algae: building future structures on firm foundations, C.A. Maggs, H. Verbruggen, and O. De Clerck Systematics of the green algae: conflict of classic and modern approaches, T. Proschold and F. Leliaert In the shadow of giants: systematics of the charophyte green algae, J.D. Hall and C.F. Delwiche The chlorarachniophytes: evolution and classification, K. Ishida, A. Yabuki, and S. Ota Molecular systematics of Haptophyta, B. Edvardsen and L.K. Medlin Decrypting cryptomonads: a challenge for molecular taxonomy, F. Cerino and A. Zingone On dinoflagellate phylogeny and classification, O. Moestrup and N. Daugbjerg Molecular genetics and the neglected art of diatomics, D.G. Mann and K.M. Evans Classification of the Phaeophyceae from past to present and current challenges, B. de Reviers, F. Rousseau, and S.G. A. Draisma Molecular systematics of the Chrysophyceae and Synurophyceae, R.A. Andersen A decade of euglenoid molecular phylogenetics, R.E. Triemer and M.A. Farmer THE FUTURE The contribution of genomics to the understanding of algal evolution, C. Bowler and A.E. Allen Algal molecular systematics: A review of the past and prospects for the future, L.K. Medlin, K. Metfies, U. John, and J.L. Olsen Glossary