Miracle-dz/UniFAR-FTUs huggingface dataset:
BiMat: a MATLAB package to facilitate the analysis of bipartite networks

Bipartite networks are ubiquitous in community ecology, including examples of facilitative interactions, such as plant‐pollinator networks, and antagonistic interactions, such as virus–host infection networks. Statistical network analysis is increasingly used to identify emergent, nonrandom patterns of interaction and the effect of interaction patterns on ecological and evolutionary dynamics. Two recurring patterns are that of modularity and nestedness. Modularity is a feature of networks in which there are densely interacting subgroups. Nestedness is a feature of networks in which the interactions form ordered subsets. Here we describe BiMat, an open‐source MATLAB package for the study of the structure of bipartite ecological networks. Unlike alternative tools, BiMat enables both multiscale analysis of the structure of a bipartite ecological network – spanning global (i.e. entire network) to local (i.e. module‐level) scales – and meta‐analyses of many bipartite networks simultaneously. In common with other tools, BiMat calculates the degree to which a bipartite network is modular and/or nested, the statistical significance of these patterns, and enables visualization of latent structures in the network. BiMat is available as an open‐source MATLAB package, with a quick‐start guide and worked examples at: http://bimat.github. io/.
What does 14C uptake by phytoplankton really measure ? A theoretical modelling approach

The patterns of photosynthetic 14C uptake predicted by four models, each of which incorporates different assumptions about the fate of carbon within a few hours of its fixation by phytoplankton, have been compared with the patterns of net 12C uptake predicted by the same models. According to all models tested, 14C will accumulate in the cells more rapidly (relative to its abundance) than 12C, until an equilibrium is established between the 14C :12C ratio inside the cells and that in the external medium. Since several hours are required for cells to approach this equilibrium, all models predict that measurements of photosynthesis based on 14C uptake overestimate net photosynthesis in incubations of up to 6-12 h, and that this overestimation will be especially severe close to the compensation point, or at depth in a water column. Experiments showed approximately linear uptake of 14C for up to 4-5 h. The only model predicting this pattern indicated that 14C uptake was proportional to gross photosynthesis, and could not be used to estimate either respiration or net photosynthesis. Other physiological and ecological evidence suggests that the conventional assumption that the radiocarbon technique measures net photosynthesis should be re-examined.
Influence of Storage Condition on Seed Oil Content of Maize, Soybean and Sunflower

Summary Th e study was aimed to examine the changes in seed oil content in diff erent genotypes of maize, soybean and sunfl ower from 2002 to 2006, in two types of storage conditions which diff er in air temperature and humidity: 25°C/75% and 12°C/60%, respectively. Aff ected by storage longevity, in average, seed oil content decreased by 0.82% in maize, 2.19% in soybean and 8.53% in sunfl ower. Diff erences in oil content aff ected by storage longevity were signifi cant among tested crops and genotypes within crops. Storage longevity was negatively associated with oil content. At storage conditions at 12°C/60%, decreasing of seed oil content was less by 0.55% (maize), 1.30% (soybean) and 1.75% (sunfl ower) than in storage conditions at 25°C/75%. In summary, the lowest seed quality losses were in maize, then in soybean and the highest losses were in sunfl ower. Decreasing of seed quality losses is possible with suitable storage conditions, particularly for soybean and sunfl ower.
Monoclonal antibodies to plant nuclear matrix reveal intermediate filamentrelated components within the nucleus

We have prepared a nuclear matrix fraction from purified nuclei of carrot ( Daucus carota L.) suspension culture cells, and used this fraction to produce a library of monoclonal antibodies. We report the preliminary characterisation of two antibodies-JIM 62 and JIM 63. The antibodies recognise a polypeptide doublet band at 92xl0 3 M r , which has been partially purified by differential urea extraction. Other intermediate filament antibodies-ME101, which recognises an epitope conserved among many intermediate filament proteins, and AFB, a monoclonal antibody to plant intermediate filament proteins, and an autoimmune serum directed against human lamina A and C (LSI), also label these bands, suggesting they are related to the intermediate filament/lamin family. IFA, another intermediate filament antibody, labels a band at approximately 60x10 3 M r , which is also enriched in the urea extracts of nuclear matrices. Immunofluorescence microscopy with JIM 63, ME 101, AFB and LSI shows network-like staining, often extending around the nucleolus. In many cases the staining reveals structures that appear to be bundles of fibres. JIM 63 also shows a weak staining of the nuclear rim in carrot nuclei, which can be greatly enhanced by treatment of the specimen with cold methanol after fixation. JIM 63 cross-reacts with all the other plant species we have tested. Vibratome sections of pea roots, extracted as for nuclear matrix preparation and stained with JIM 63 show a clear, strong nuclear rim labelling. Furthermore, JIM 63 strongly labels the nuclear lamina in rat liver nuclei. We suggest that the 92x10 3 M r protein(s) are related to intermediate filaments and/or lamins, and are distributed both within the nucleus and at the nuclear periphery.
Evaluation of Seedlings of Three Woody Species under Four Soil Moisture Capacities

Aims: To evaluate the growth performance, their rates of transpiration and water-use efficiencies under different moisture levels. Study Design: A randomised complete design of three tree species, four treatments and three replicates. Place and Duration of Study: Screen house of the University of Buea from January to June 2012. Methodology: 144 uniform seedlings of Markhmia tomentosa , Funtumia africana and Prunus africana were treated to four soil moisture capacities (12.5, 25, 50 and 100%) determined gravimetrically and water supplied to the seedlings three times per week after pre-transplanting. The collar diameter, height and number of leaves were measured nondestructively every fortnight. The seedling biomass, leaf area, mass fractions, number of first order lateral roots, root/shoot ratio, specific leaf area, shoot and root lengths were determined six months after pre-transplanting. The seedlings’ rates of transpiration, evapotranspiration and water-use efficiencies were determined gravimetrically. Results: The growth trends with respect to collar diameter, height and the number of leaves showed significant variations at P = 0.05. The effects of the soil moisture capacities on the growth performances were significantly different at P< 0.001. Markhmia tomentosa seedlings supplied with 25% soil moisture showed maximum leaf number (42) and leaf area (10712.8 cm 2 ) while those with 50% treatment had collar diameter and
Early Screening of Cassava for Resistance to Root-Knot Nematodes

A method was developed for early screening of cassava for resistance to root-knot nematodes. Onenode cassava cuttings were planted in plastic disposable beverage cups filled with sterile 1.1 (by volume) sand-soil mixture. Two weeks after planting, the plantlets were infested with a 10 ml suspension containing approximately 1 000 Meloidogyne spp. eggs. One month after inoculation, the cassava root systems were evaluated for damage and rated for gall index. Densities of Meloidogyne females in the roots were established by differential staining, followed by counting of the female root-knot nematodes under a stereomicroscope. Significant differences in gall index and number of established females, but not in reduction in fresh root weight, were observed among varieties. While some confirmatory field surveys are still required, findings from preliminary surveys carried out in two areas of Uganda suggest that the relative susceptibility of a variety in the field can adequately be predicted
Identifikasi Kontaminasi Telur Nematoda Usus Pada Ayuran Kubis (Brassica Oleracea) Warung Makan Lesehan Wonosari Gunungkidul YOGYAKARTA Tahun 2010

Background : Vegetables can be eaten by fully or in portion on fresh condition (lalapan) or in be cooked. Fresh vegetables (lalapan) useful for the healthy of our bodies caused have good nutrition that relative high in vitamine and mineral shape, and one kind of thats vegetables is cabbage or kol. Cabbage which have been cleaned may still find the germs agent for example is the intestinal nematode. In Indonesia, intestinal nematode remain caused the serious public health problem, are Ascaris lumbricoides, hook worm and Trichuris trichiura. Soil, vegetables and water are the important one of the transmission way of the eggs of intestinal nematode, if there found many eggs of intestinal nematodes on the contamination sources (like vegetables, soil and the others) automatically will followed with the increasing of endemic degree. Method : This was descriptive qualitative research using laboratory enclosed. The cabbage that are used for examination materials, cabbage that usually use on food court especially pedestrian food court (warung makan lesehan) which sold on the midle of the city Wonosari Gunungkidul Yogyakarta. To make sediment of the eggs of intestinal nematode is used NaOH 0,2% solution as detergent solution. The practice of this exam use sedimentation technique and than be checked the diagnosting on microscope. The result of data that shown on therefore any contamination or yet the eggs of intestinal nematode, the kind of species of intestinal nematode and infective stage of those species. Data will be analyzed in descriptive qualitative statistic and been shown on table and chart. Result: The result of this research showed that there any contamination of the eggs of intestinal nematode from the cabbage (Brassica oleracea) that was been analyzed (38,89%), for the species of the eggs of intestinal nematode that shown positive samples are found Ascaris lumbricoides (50%), hook worm (12,5%) and Trichuris trichiura (37,5%). The infective stage that known is only one kind of infective stage that is an infective stage from Ascaris lumbricoides egg. Conclution: There was any contamination of the eggs of intestinal nematode on the cabbage (Brassica oleracea) that used for fresh vegetable menu (lalapan) on pedestrian food court in the midle of the city Wonosari Gunungkidul Yogyakarta. Keyword : Contamination, Cabbage (Brassica oleracea), The eggs of intestinal nematode
Fossorial morphotype does not make a species in water voles

Abstract Phenetic and ecological plasticity in Arvicola has caused a long-standing dispute over the number of species within the genus, which is currently thought to consist of two aquatic (sapidus, amphibius) and one fossorial species (scherman). We used mitochondrial cytochrome b (cytb) gene sequences to reconstruct phylogenetic relationships between the fossorial and the aquatic water voles from the various regions of their European and Asiatic range. These two types differed morphologically and exhibited allopatric ranges. Our study provided 50 new haplotypes, generating a total dataset of 70 different water vole cytb haplotypes. Phylogenetic reconstructions retrieved two major lineages that were in a sister position to A. sapidus: a fossorial Swiss lineage and a widespread cluster, which contained aquatic and fossorial water voles from Europe and western Siberia. The phylogeographic architecture in water voles is explained by Quaternary climatic dynamics. Our results show that A. scherman in its present scope is not a monophyletic taxon.
Disarticulation patterns of some modern East African mammals

The sequences of skeletal disarticulation in a broad range of African mammals in a tropical savanna environment suggest that in general the process is very consistent. There is some variation among species, but this cannot yet be convincingly related to higher taxonomic categories or to body size. Disarticulation begins shortly after death, proceeds more or less continuously, and is almost complete after 5 yr. Because of the overall predictability of disarticulation, the stage of disarticulation reached by comparable fossil skeletons provides useful information about their taphonomic history prior to burial.
Anti-obesity effect of EGCG and glucosamine-6-phosphate through decreased expression of genes related to adipogenesis and cell cycle arrest in 3T3-L1 adipocytes

Purpose: Several studies have proven that EGCG, the primary green tea catechin, and glucosamine-6-phosphate (PGlc) reduce triglyceride contents in 3T3-L1 adipocytes. The objective of this study is to evaluate the combination effect of EGCG and PGlc on decline of accumulated fat in differentiated 3T3-L1 adipocytes. Methods: EGCG and PGlc were administered for 6 day for differentiation of 3T3-L1 adipocytes. Cell viability was measured using the CCK assay kit. In addition, TG accumulation in culture 3T3-L1 adipocytes was investigated by Oil Red O staining. We examined the expression level of several genes and proteins associated with adipogenesis and lipolysis using real-time RT-PCR and Western blot analysis. A flow cytometer Calibar was used to assess the effect of EGCG and PGluco on cell-cycle progression of differentiating 3T3-L1 cells. Results: Intracelluar lipid accumulation was significantly decreased by combination treatment with EGCG 60 μM and PGlc 200 μg/m compared with control and EGCG treatment alone. In addition, use of combination treatment resulted in directly decreased expression of PPARγ, C/EBPα, and SREBP1. In addition, it inhibited adipocyte differentiation and adipogenesis through downstream regulation of adipogenic target genes such as FAS, ACSL1, and LPL, and the inhibitory action of EGCG and PGlc was found to inhibit the mitotic clonal expansion (MCE) process as evidenced by impaired cell cycle entry into S phase and the S to G2/M phase transition of confluent cells and levels of cell cycle regulating proteins such as cyclin A and CDK2. Conclusion: Combination treatment of EGCG and PGlc inhibited adipocyte differentiation through decreased expression of genes related to adipogenesis and adipogenic and cell cycle arrest in early stage of adipocyte differentiation.
Population genetics and genotyping for mark-recapture studies of Northern Goshawks (Accipiter gentilis) on the Kaibab Plateau, Arizona

Advances in molecular techniques have facilitated use of genetic data in demographic wildlife studies. An important first step in genetic mark-recapture is selecting markers that uniquely ‘‘mark’’ and reliably ‘‘recapture’’ individuals. Markers should be tested on reliable DNA from known individuals (blood) before being used on non-invasively sampled DNA (hair, scat, or molted feathers). To evaluate whether Northern Goshawks (Accipiter gentilis) can be uniquely identified by genotyping, 113 known (banded, sexed) goshawks from the Kaibab Plateau, Arizona, were genotyped using DNA from blood and five microsatellite markers and a sex-linked gene. We used mean relatedness to test whether adults in the population were related and probability of identity (P(ID) = probability that two random individuals from the population have the same genotype) to test the ability of multi-locus genotyping for uniquely identifying goshawks. We used genetic data to assess inbreeding and demographic data to estimate the effective population size. Sixty-nine adult goshawks were sexed correctly and genotyped. Expected heterozygosity was high (HE = 0.81), and relatedness among adults was low (r = -0.017). All individuals sampled (69 adults, 44 nestlings) had unique five-locus genotypes, the overall probability of identity was low (P(ID) unbiased = 7.03 x 10-7), and the observed P(ID) was e = 37 individuals), goshawks on the Kaibab Plateau functioned as a large breeding population with no inbreeding (FIS = -0.001). We hypothesized that genetic diversity is maintained by gene flow via immigration of individuals from distant forests.
Micropropagation of carob, Ceratonia siliqua L., by apex culture

Abstract The great variability of Ceratonia siliqua, its sexual polymorphism and its long stage of juvenility imply the use of conventional and in vitro culture techniques. The high phenotypic variation between carob cultivars has important implications for selection, cultivation practices and establishment of new plantations to improve productivity of this crop. The present work was undertaken to develop a simple protocol for micropropagation of carob through meristem culture on half-strength Murashige and Skoog medium. The best results were obtained by introducing the meristem culture when buds were starting to swell. Meristem sprouting was stimulated on Murashige and Skoog medium supplemented with 2,4-dichlorophenoxyacetic acid. The highest number of well-developed shoots from meristems was obtained with 2 mg l–1 6-benzylaminopurine and 2 mg l–1 2,4-dichlorophenoxyacetic acid. Higher rooting ability and root quality were obtained with 4 mg l–1 naphthalene acetic acid.
Induced systemic resistance in radish is not associated with accumulation of pathogenesis-related proteins

The non-pathogenic Pseudomonas fluorescens strain WCS417r has been shown to induce systemic resistance in radish against Fusarium oxysporum f.sp. raphani. In this paper we investigate the involvement of pathogenesis-related (PR) proteins in this Pseudomonas-induced resistance. For comparison, salicylic acid (SA) and isonicotinic acid (INA) were used as inducers. It appeared that in our rock wool artificial soil system both strain WCS417r and SA could induce resistance, whereas strain WCS417r-B4, a lipopolysaccharide-mutant, and INA could not. The induced resistance was expressed as a reduction in the percentage of diseased plants, but not in the disease severity. Western blot analyses revealed that in the control plants PR-2 is constitutively present in the intercellular fluid of leaves and PR-3 in the roots. Treatment with either of the inducing agents, with or without pathogen-inoculation, induced no further accumulation of cross-reacting homologues of PR-1-5. We concluded that in our system induction of systemic resistance by strain WCS417r and SA is not associated with accumulation of PRs proteins. This demonstrates that accumulation of PR proteins is not a prerequisite for the expression of induced systemic resistance.
Dynamics of p53 tetramers in live single cells

Protein homo-oligomerization is the process through which identical peptides bind together to form higher order complexes. Self-interactions in many cases are constitutive and stable, used as building blocks for biological structures, such as rings, filaments and membranes. Further, homo-oligomerization can also be a regulatory process that influences the proteins’ function such as change in transcriptional activities for transcription factors. Innovative methods to measure oligomerization in live cells are needed in order to understand regulation and function of homooligomerization in the native cellular context. This thesis examines the case of the tumor suppressor p53, whose homo-tetramerization greatly influences its activity as a transcription factor. We develop methods to quantify p53’s self-interaction in individual living cells and follow it in time after DNA damage. The two methods we developed have complementary qualities and different applications. We first use fluorescent correlation spectroscopy to study the molecular events occurring in the first three hours of the p53 in response to double strand breaks. We find that in the absence of stress p53 is present in a mixture of, monomers, dimers and tetramers. When damage is sensed, oligomerization is rapidly induced and nearly all p53 is found bound in tetramers. We combine our data with a mathematical framework to propose the existence of a dedicated mechanism triggering p53 oligomerization independently of protein stabilization. Next, we use bimolecular fluorescent complementation to probe for tetramerization in the longer
Plug formation and peroxidase accumulation in two orders of siphonous green algae (Caulerpales and Dasycladales) in relation to fertilization and injury

Abstract A cytochemical survey of fourteen green algal species of the siphonous orders Caulerpales and Dasycladales has shown that plug formation during separation of reproductive organs and sterile side branches from the vegetative main axis is a common morphological characteristic in these algae. Additionally, in all these species peroxidase is accumulated almost exclusively in the plugs. Plugs in the siphonous green algae may play a role in protection of the cell interior against the external medium, either during normal development or after mechanical injury. Peroxidase may support this function by its possible antimicrobial activity.
The Effects of Baker's Yeast (Saccharomyces cerevisiae) in Dairy Cow Diets on Milk Yield, Some Rumen Fluid Parameters and Blood Metabolites of Dairy Cow Diets

The objective of this study was to investigate the effects of baker's yeast as a protein source instead of soybean meal in dairy cow diets. Four dairy cows were utilized in a 4 x 4 Latin Square experiment. Diets included 0.0% (Control Diet), 6.6% (Diet 1), 13.2% (Diet 2), and 19.8% (Diet 3) baker's yeast containing 3.56 x 108 CFU/g. Forty percent of the dry matter intake of dairy cows was supplied from concentrate, and forage was offered ad libitum. The dry matter intake, milk yield, and composition of milk were similar. While the rumen NH3-N level was significantly low (p < 0.05) 3 h post-feeding, acetic acid concentration was significantly high (p < 0.05) 12 h post-feeding in cows that consumed diets containing yeast. Propionic acid concentrations were lower (p < 0.01) 3 h post-feeding in cows that consumed Diets 2 and 3 compared with those that consumed the other diets. While serum triglyceride levels were significantly higher (p < 0.05) in cows that consumed diets containing baker's yeast than in those that consumed the control diet, serum protein, urea, glucose, calcium, phosphorus, gamma glutamyl transferase and aspartate aminotransferase were similar in cows that consumed different diets. It was concluded from this study that there were some positive effects, such as low rumen NH3-N level and high acetic acid concentration, in cows that consumed diets containing yeast, and thus, baker's yeast can be utilized in dairy cow diets as a protein source.
Condition-dependent spermatophore size is correlated with male's age in a bushcricket (Orthoptera: Phaneropteridae)

During mating, male bushcrickets transfer a spermatophore that consists of a sperm-containing ampulla and a product of the accessory glands, the spermatophylax, which females directly ingest. In the present study, we demonstrate male spermatophore allocation in the bushcricket Poecilimon zimmeri. Males of this species show condition-dependent spermatophore investment. This investment depended upon the age at first mating of males, with older individuals transferring larger spermatophores than younger ones of the same body mass. Independently of age, heavier males transfer larger spermatophores, but the size of males (as measured by femur length) was not a good predictor. Heavier males allocate a lower proportion of their mass to spermatophores and reach their maximal investment point earlier than less heavy males. Spermatophylax production levelled off to a species specific maximum earlier than that of sperm investment (measured as ampulla mass), suggesting that males face high levels of sperm competition. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 354–360.