Miracle-dz/UniFAR-FTUs huggingface dataset:
Problems with using mean germination time to calculate rate of seed germination

Seed scientists and other plant biologists are interested in the measurement of germination because seeds from different individuals, populations, seed lots and treatments can differ in germination percentages, rate (speed) and uniformity. Mean time to germination (MGT) is a measure of the rate and time-spread of germination; however, there is a problem with using this method to calculate germination rate. MGT does not show the time from the start of imbibition to a specific germination percentage. MGT has been used to compare specific pairs or groups of means and to evaluate seed vigour. However, it is not the real time to mean germination but just an index of germination speed. Using MGT is not correct for ANOVA, post-ANOVA or the other comparison tests, because it does not show time to a specific germination percentage. Thus, we recommend that t50 be used instead of MGT. The t50 has all benefits of MGT, but it does not have the problems of MGT in treatment comparisons.
Enhancing the antioxidant activity of immature calamondin by heat treatment

Summary The purpose of this study was to investigate the enhancing effect of heat treatment (110 and 130 °C for 0.5, 1.0, 1.5 and 2.0 h, and 150 °C for 1.5 h) on antioxidant activity and phenolic compounds of immature calamondin (Citrus mitis Blanco). The results indicated that heat treatment could enhance the 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging potency, oxygen radical absorbance capacity (ORAC) and total phenolic content. However, the major flavonoid, 3′,5′-di-C-β-glucopyranosylphloretin (DGPP), decreased drastically after being heated at ≥130 °C over 1.5 h. The increasing ratio of absorbance at UV420 nm coincided with the change of the antioxidant activity. Therefore, it was concluded that the browning products resulted in the increase of the antioxidant activity of immature calamondin heated at ≥130 °C over 1.5 h, while the increase of antioxidant activity at 110 and 130 °C ≤ 1.0 h heating was due to increased phenolic content.
Productive response of broiler chickens to exogenous enzyme combinations added to diets based on corn or triticale

An experiment with Hubbard broiler chickens was carried out to determine the effect of exogenous enzyme additions to diets based either on corn or triticale (D1 and D2) used as different substrates. Two hundred and forty one-day old unsexed broiler chickens were assigned during 28 days to 8 different treatments (T1-T8), each with 3 replicates. Treatments with odd numbers had the corn based diet, while treatments with even numbers had the triticale based diet. T1 and T2 had no enzyme addition; T3 and T4 given cellulase, protease and phytase; T5 and T6 were given b-glucanase and phytase and T7 and T8 were given only phytase. Feed intake, live weight (PV), weight gain (GP) and feed conversion (CA) were recorded. At the end of the trial two chickens of each replicate were sacrificed for weighing their small intestine and liver and for determining the ash content in their left tibias. The highest live weight and weight gain observed in chickens in T6 suggest that the response to the addition of b-glucanase to the diet is positive only in the presence of the specific substrate. T7 also presented positive significant difference for both parameters measured in relation to T1, indicating the effect of phytase on phytate-phosphorus conatined in corn grain. No differences were observed in the the rest of the parameters measured. Finally, the higher cost of diets derived from exogenous enzyme addition did not alter the feed economic efficiency.Se realizo un experimento con pollos broiler de la linea Hubbard para determinar el efecto de la adicion de enzimas exogenas a dietas basadas en maiz o tritricale (D1 y D2). Se asignaron 240 pollos sin sexar, de un dia de edad, durante 28 dias, a 8 tratamientos diferentes (T1-T8) con tres repeticiones cada uno: T1 y T2 sin adicion de enzima; T3 y T4 con adicion de celulasa, proteasa y fitasa; T5 y T6 con adicion de b- glucanasa y fitasa; T7 y T8 con adicion de fitasa solamente. La dieta basada en maiz correspondio a los tratamientos de numero impar y la basada en tritricale a los de numero par. Se registro el consumo de alimento (cons.), el peso vivo (PV), la ganancia de peso (GP) y la conversion de alimento (CA). Al finalizar el experimento se sacrificaron dos pollos de cada repeticion, pesandose el intestino delgado y el higado de cada uno. Ademas se determino el contenido de cenizas de la tibia izquierda de cada ave. El mayor peso vivo y ganancia de peso observado en los pollos en T6 sugiere que la respuesta a la adicion de b-glucanasa a la dieta es positiva solo en presencia del sustrato especifico de la enzima. El tratamiento T7 tambien presento una diferencia positiva significativa para ambos parametros en relacion a T1, indicando la existencia de un posible efecto de la fitasa sobre el fosforofitato presente en el grano de maiz. Los demas parametros medidos no arrojaron diferencias significativas en ningun tratamiento. Finalmente, el aumento en el costo de las dietas debido a la adicion de enzimas exogenas no altero la eficiencia economica de la racion.
Efficacy of diverse capsicum annuum protease inhibitors against the adaptive pasticity of Helicoverpa armigera proteases

Herbivore attack induces defense responses in plants, activating several signaling cascades. As a result, molecules deterrent to the herbivores are produced and accumulated in plants. Expression of defense mechanism/traits requires reorganization of the plant metabolism, redirecting the resources otherwise meant for growth. In the present work, protein profile of Capsicum annuum leaves was examined after herbivore attack/induction. Majority of proteins identified as differentially accumulated, were having roles in redox metabolism and photosynthesis. For example, superoxide dismutase and NADP oxidoreductase were upregulated by 10and 6-fold while carbonic anhydrase and fructose-1,6-bisphosphatase were downregulated by 9and 4-fold, respectively. Also, superoxide dismutase, NADPH quinone oxidoreductase and NADP dependent isocitrate dehydrogenase transcripts showed a higher accumulation in induced leaf tissues at early time points. In general, proteins having role in defense and damage repair were upregulated while those involved in photosynthesis appeared downregulated. Thus metabolic reconfiguration to balance defense and tolerance was evident in the stressinduced leaves.
Growth and behaviour of chicks fed on pellets or mash

Synopsis Newly hatched hybrid and Brown Leghorn chicks were fed on diets in either pellet or mash form and growth and feeding behaviour were studied. The mash was made by re‐grinding the pellets. All chicks fed on pellets were heavier after 40 d, but had eaten no more than those fed on mash. The apparent digestibilities of pellets and mash were about the same in the hybrid chicks but was greater for mash than pellets with the Leghorn birds. All chicks fed on mash spent more time feeding than those fed on pellets, but the times spent on drinking and resting were similar with both food forms. Chicks which were given a choice of food form consistently preferred mash to pellets. It is concluded that pelleted food was converted more efficiently than mash mainly because chicks spent less time feeding on pellets and so expended less energy, and in the case of the Leghorns there may have been improved digestibility when the food was pelleted.
Suppression of Human GD3 Synthase (hST8Sia I) Expression Induced by Retinoic Acid in Human Melanoma SK-MEL-2 Cells

To elucidate the mechanism underlying the suppressive regulation of hST8Sia I expression in retinoic acid (RA)-induced SK-MEL-2 cells, we characterized the promoter region of the hST8Sia I gene. Functional analysis of the 5’-flanking region of the hST8Sia I gene by the transient expression method showed that the -1146 to -646 region, which contains putative binding sites for transcription factors c-Ets-1, CREB, AP-1 and NF-κB, functions as the RA-repressive promoter in SK-MEL-2 cells. Site-directed mutagenesis and ChIP analyses indicated that the NF-κB binding site at -731 to -722 is crucial for the RA-induced repression of hST8Sia I in SK-MEL-2 cells. In addition, the transcriptional activity of hST8Sia I suppressed by RA in SK-MEL-2 cells was strongly inhibited by extracellular signal-regulated protein kinase (ERK) inhibitor U0126 and protein kinase C (PKC) inhibitor GO6976, as determined by RT-PCR and luciferase assay of hST8Sia I promoter containing the -1146 to -646 regions. These results suggest that RA markedly modulates transcriptional regulation of hST8Sia I gene expression through the PKC/ERK signal pathway in SK-MEL-2 cells.
Survival of Campylobacter coli in porcine liver

Abstract Enteropathogenic Campylobacter jejuni, Campylobacter coli and Campylobacter lari are currently the most common causes of acute infectious diarrhoeal illness in the UK and in most developed countries. Many domestic animals, including pigs, act as natural reservoirs of these organisms and infection may occur through the ingestion of contaminated foodstuffs. Therefore, the safety of porcine liver produced in Northern Ireland was assessed in relation toCampylobacter spp. Storage trials showed that Campylobacter spp. were not able to proliferate in liver at 37°C, but could persist at 4°C and 15°C. Survival was better, however, during storage at 4°C than at 15°C. Campylobacter were rapidly killed in raw liver homogenates and distilled water at 37°C, but not at 4°C. An initial inoculum of 8 log10cfu g−1C. coli was undetectable in liver homogenates after 24h storage at 37°C. Campylobacter coli were sensitive to freezing on liver slices at −18°C and were reduced by 5 log10cycles after 7 days storage. Cells survived better on chilled liver slices and in autoclaved liver homogenates than in raw liver homogenates at all temperatures, which indicates the presence of a heat-labile antagonistic agent in raw liver homogenates. Growth and survival of C. coli was not affected by Lactobacillus plantarum, as C. coli was able to reach 8·5 log10cfu ml−1in 7 days and maintain its viability in the presence of 8·0 log10cfu ml−1L. plantarum. Thus, storage of C. coli on porcine liver at 4°C selected for the survival of this pathogen compared to similar storage at 37°C. Such information may be useful in identifying conditions and treatments that could be integrated in HACCP strategies, or be used to design processes that prevent proliferation and/or destroy Campylobacter spp. that may be present in liver.
Mannose-targeted systems for the delivery of therapeutics

Background: The specific targeting of nanomedicines to mannose receptors, highly expressed in cells of the immune system, performs a useful strategy for improving the efficacy of vaccines and chemotherapy. Objective: This review discusses the potential of mannose-targeted drug/antigen delivery systems for vaccination and treatment of diseases localized in macrophages and other antigen-presenting cells. Methods: The first part of the review describes the characteristics, localization and functions of mannose receptors. The following sections are devoted to the description of different methods used to deliver therapeutic agents, including mannose conjugates and mannosylated carriers or particulates (i.e., liposomes, nanoparticles and niosomes). Results/conclusions: A general overview of published reports confirms the effectiveness of mannosylation strategies, although the optimization and full exploitation of mannose-targeted drug delivery systems would require a deeper understanding of the structure–activity relationship. In the near future, these nanomedicines have the potential to treat a number of diseases (including cancer) and improve the quality of life of patients.
The Strategic View of Biological Agents

What is a strategy? The term strategy has been used by many disciplines in a variety of contexts ranging, for example, from the game of chess and the Cuban missile crisis to markets, computer networks, political systems, cooperation, mating, parasitism, intragenomic conflict, and growth patterns. Despite this wide use of the term, only one discipline—game theory— has carefully examined the concept. In game theory, a pure strategy is a complete plan for a player’s choices in the game under consideration. A chess player’s pure strategy would thus have to specify all moves in all the situations that might arise on the chessboard during a match. Whereas in chess the pieces on the board are visible to both players, in many games players have only limited information about the objective state of affairs. In a number of card games, for example, a player’s one hand is not known to the other. Thus, players’ strategies must make use of the subjective state of affairs. This state is often referred to as the information situation or information set. Strategies can therefore be viewed as a map of information states to actions (adding the term “conditional” to “strategy” is thus redundant). For agents with memory, the information situation often includes knowledge about the course of play. This is of great importance to many applications and it demonstrates the richness of the strategy concept. A lot can be gained from widening the concept’s scope beyond that of pure strategies. What game theorists call a behavior strategy is a plan that assigns to each situation a probability distribution over the choices in that situation. This distribution may or may not place all weight on one choice. In a behavior strategy, the choices for different situations are stochastically independent. Another concept is that of a mixed strategy which differs from that of a behavior strategy as follows. In a mixed strategy, the player chooses among a number of pure strategies according to a probability distribution over these pure strategies—as opposed to choices during the game. To illustrate the difference, let us compare a behavior strategy with a cooking recipe. The recipe may at some stage contain the instruction to flip a coin in order to decide about mild or hot spicing. In contrast, a mixed strategy would flip a coin to decide between Italian and Mexican recipes. The concept of a mixed strategy can be extended to mixtures of behavior strategies.
Greedy vs. L1 Convex Optimization in Sparse Coding: Comparative Study in Abnormal Event Detection

Sparse representation has been applied successfully in many image analysis applications, including abnormal event detection, in which a baseline is to learn a dictionary from the training data and detect anomalies from its sparse codes. During this procedure, sparse codes which can be achieved through finding the L0-norm solution of the problem: min ‖Y −Dα‖2 +‖α‖0, is crucial. Note that D refers to the dictionary and α refers to the sparse codes. This L0-norm solution, however, is known as a NP-hard problem. Despite of the research achievements in some classification fields, such as face and action recognition, a comparative study of codes in abnormal event detection is less studied and hence no conclusion is gained on the effect of codes in detecting abnormalities. We constrict our comparison in two types of the above L0-norm solutions: greedy algorithms and convex L1-norm solutions. Considering the property of abnormal event detection, i.e., only normal videos are used as training data due to practical reasons, effective codes in classification application may not perform well in abnormality detection. Therefore, we compare the sparse codes and comprehensively evaluate their performance from various aspects to better understand their applicability, including computation time, reconstruction error, sparsity, detection Proceedings of the 31 st International Conference on Machine Learning, Lille, France, 2015. JMLR: W&CP volume 37. Copyright 2015 by the author(s). accuracy on the UCSD Anomaly Dataset. Experiments show that greedy algorithms, especially MP and StOMP algorithm could achieve better abnormality detection with relatively less computations.
Arthropod diversity in pure oak forests of coppice origin in northern Thrace (Turkey)

Abstract: Oak (Quercus spp.) forests are among the most important forest types in Turkey. In the past, oak forests were managed through coppice clear-cutting, but in recent decades they have mostly been converted to high forest. This study was aimed at explaining how arthropod diversity is affected during conversion from coppice to high oak forest and during the early stages of coppice succession. We tested the hypothesis that arthropod richness, abundance and diversity in coppice oak sites varied according to stand age and a number of other forest characteristics. Arthropod communities were sampled in 50 plots using four different methods: pitfall traps, sweep nets, sticky cards and cloth shaking. A total of 13 084 individuals were collected and classified into 193 Recognizable Taxonomic Units (RTUs), with the most RTUs and the greatest number of specimens captured by sweep netting. We identified 17 taxa within RTU’s with more than 1% of the captured arthropods, which constituted 75% of the total specimens. The number of RTUs varied significantly according to trap type. Arthropod richness and Shannon-Wiener biodiversity index (H′) increased with elevation and precipitation. In young (1-40 yrs-old) and middle-aged (41-80 yrs) stands, arthropod biodiversity was not significantly affected by stand type, but slightly increased with diameter at breast height and tree height. Forest characteristics, such as the litter layer, understory and crown diameter, weakly influenced arthropod richness and abundance. Cluster analysis revealed that stand types and trap types differed taxonomically. Principal component analysis showed that stand types were clearly separated by the stand parameters measured. Insect families (Formicidae, Thripidae, Lygaeidae, Dolichopodidae, Luaxanidae, Cicadellidae and Ichneumonidae) could potentially be used as indicators of coppice oak conditions. As the coppice oak changes to mature forest, further studies are needed to better assess the relation between arthropods, forest types and structural characteristics of stands.
Analysis of Antioxidant Compounds and Hydroxymethylfurfural in Processing Tomato Cultivars

-1 79.7 to 155.0 mg·kg -1 79.7 to 155.0 mg·kg fresh weight. There was a signifi cant difference between the lycopene concentrations of fruit harvested at two different dates. The values were higher at the second harvest, probably due to the cooler weather conditions preceding that harvest. Total polyphenols correlated strongly with TAS but the other antioxidants did not have any relationship to TAS. GDD were strongly and positively correlated with hydroxymethylfurfural content in fresh tomatoes.
Perspectives of improved tolerance of drought in crops

Summary The mechanisms are discussed tluough which crops suffer yield reductions when water shortage occurs. Cultivars differ in their tolerance of drought but how tolerance is detem1ined, how changes in crop characteristics reduce yields, how crop modeling can be used to explore the potential improvement en whether increased tolerance is associated with negative effects is discussed in this review.
naima: a Python package for inference of relativistic particle energy distributions from observed nonthermal spectra

The ultimate goal of the observation of nonthermal emission from astrophysical sources is to understand the underlying particle acceleration and evolution processes, and few tools are publicly available to infer the particle distribution properties from the observed photon spectra from X-ray to VHE gamma rays. Here I present naima, an open source Python package that provides models for nonthermal radiative emission from homogeneous distribution of relativistic electrons and protons. Contributions from synchrotron, inverse Compton, nonthermal bremsstrahlung, and neutral-pion decay can be computed for a series of functional shapes of the particle energy distributions, with the possibility of using user-defined particle distribution functions. In addition, naima provides a set of functions that allow to use these models to fit observed nonthermal spectra through an MCMC procedure, obtaining probability distribution functions for the particle distribution parameters. Here I present the models and methods available in naima and an example of their application to the understanding of a galactic nonthermal source. naima's documentation, including how to install the package, is available at this http URL
Transfer of a β-Glucuronidase Marker Gene to Triticale (xTriticosecale Wittmack) via Particle Bombardment (Biolistic) Method*

Abstract This study was carried out to investigte the biotechnology laboratory of Department of Field Crops, Ankara University with the aim of investigating the optimum parameters of gene transfer to mature embryo and leaf segment explants of Triticale (x Triticosecale Wittmack) via particle bombardment (Biolistic) method. Mature embryo and leaf segment explants obtained from Triticale (x Triticosecale Wittmack) were bombardment with accelerated gold or tungsten particles coated with the plasmid pBI221.23 containing the b -glucuronidase (GUS: u idA ) marker gene. Different bombardment distances from the stopping plate (6, 9, 12, cm) and different rupture disk pressures (900, 1100, 1550 psi ) were used as physical parameters. Blue cells expressing the b -glucuronidase gene were detected by using a histochemical assay. The variation in the number of blue spots in bombarded explants was used to determine the gene transfer efficiency. The mature embryos of triticale were found to be more amenable for the direct delivery of foreign DNA by the particle bombardment technique than the leaf segments. Also the gold particles were more suitable than tungsten particles in the gene transfer efficiency. The highest gene transfer results were obtained in mature embryos when 6 cm bombardment distance and 1100 psi rupture disk pressure were used.