Miracle-dz/UniFAR-FTUs huggingface dataset:
Review of data analysis methods for seed germination

Numerous procedures for data analysis of seed germination responses are scattered throughout the literature. Here an attempt has been made to summarize the existing methods, to compare the information they provide and to examine their strengths and weaknesses. The methods reviewed include the percent germination, germination index, coefficient of velocity, median response time, probit analysis, curve-fitting of cumulative germination, heat sums, survival analysis with life tables, logistic regression, proportional hazards regression and accelerated failure time analysis. Comparisons among these method are discussed and illustrated with data from germination responses in tomato (Lycopersicon eseulentum Mill.). Seed germination involves not only qualitative responses of individuals, but also population responses which are distributed over time. Standard analysis of variance or regression methods are appropriate for a data analysis where germination of all viable seed is observed, but they are inappropriate when some viable seeds fail to germinate. Such missing (censored) data complicates statistical analysis and subsequent interpretation. Germinations tests should be designed to determine the nature of censored responses, which can be subsequently accommodated by several statistical procedures referred to as survival analysis.
Relationship between nitrogen uptake and use efficiency of winter wheat grown in the North China Plain

Wheat (Triticum aestivum L.) cultivars with improved nitrogen-use efficiency (NUE) under low and medium N conditions will help to minimise production costs and nitrate-N contamination. The study was conducted to determine the NUE diversities of winter wheat genotypes, and to evaluate the possible physiological mechanisms contributing to these differences. A set of 12 winter wheat genotypes, including S4185 as control genotype, were grown at high N (applied with 180 kg N/ha as urea) and low N (with no N fertiliser, N-deficient) plots in 2005–06 and 2007–08 growing seasons (i.e. four environments). ANOVA showed significant differences among genotypes for all traits measured. Among genotypes, XJ19-1 had significantly higher NUE and N uptake efficiency (NUpE) than S4185 at the two N levels in the 2 years (P < 0.05). KN9204 had significantly higher NUE in the four environments and higher NUpE in three out of four environments than S4185 (P < 0.05). WR9603 and XJ138-1 had higher NUE and NUpE than S4185 in two or three out of four environments (P < 0.05). XJ19-1, KN9204, WR9603 and XJ138-1 also showed higher grain yield (GY) and aboveground dry matter (DM) than S4185 in at least two environments (P < 0.05). KN9204 were 45.7 and 23.1% higher in root dry weight (RDW) of the top 40-cm soil profile compared with J411 at high N and low N plots, respectively (P < 0.05). In addition, there was a highly positive correlation between RDW and grain N yield (GNY) of KN9204 and J411 (P < 0.01). Closely positive correlation between NUE and GY, DM, GNY and NUpE at both N levels in the 2 years (P < 0.01), and between N utilisation efficiency (NUtE) and NUE only at high N plot (P < 0.05) were found. Our results indicated that NUpE was the important factor of NUE under low N conditions, and both NUpE and NUtE were the most important NUE components under high N conditions.
A pesca demersal de profundidade e os bancos de corais azooxantelados do sul do Brasil

Demersal fishing of important commercial fishes (Lophius gastrophisus, Urophisys brasiliensis and Genipterus brasiliensis) and crustaceans (Chaceon ramosae and Chaceon sp.) along the upper slope off southern Brazil has increased dramatically in the last decade. Compilation of available data on the distribution of azooxanthellate corals between 24° and 35° S, compared with the distribution of bottom-longline, bottom-gillnets, trawl and trap fisheries shows that commercial fishing takes place over coral areas, providing evidence deep-sea reefs are important reservoirs of deep marine biodiversity. Since the initial phase of exploitation by demersal fisheries, onboard observers are describing large captures of corals as "bycatch" suggesting deep-sea communities are being destroyed even before being studied. In order to ensure protection of deep-sea coral ecosystems and economic sustainability of demersal fisheries in southern Brazilian waters, adoption of excluded fishing areas in those locations where azooxanthellate Scleractinia occur is strongly recommended.
Artificial spawning of carp (Cyprinus carpio L.): differences between females of Polish strain 6 and Hungarian strain W treated with carp pituitary homogenate, Ovopel or Dagin

Investigations of the effects of controlled reproduction were conducted on carp females of Polish strain 6 and Hungarian strain W after ovulation stimulation with carp pituitary homogenate (CPH) (0.3 mg+2.7 mg kg(-1) body weight), Ovopel (1/5+1 pellet kg(-1) body weight) or Dagin (1 dose kg(-1) body weight). In both strains, the highest percentage of spawning females was found after the Ovopel treatment. After treatments with CPH and Dagin this percentage did not differ in strain 6; however, after Dagin, it was higher in fish of strain W. After CPH or Ovopel stimulation the females of line 6 yielded eggs of higher weight compared with line W. After the Dagin treatment the weight of eggs obtained from females, both strains was similar but much lower than after the two remaining agents. The quality of eggs expressed both by the percentage of fertilization and that of living embryos after 24 and 36 h incubation was similar in the two strains only in the group treated with Ovopel. After CPH application eggs of better quality were obtained from strain 6 compared with strain W; however, after the treatment with Ovopel, eggs of much better quality were noted in strain W. In general, the best effects of reproduction were recorded in the case of Ovopel and the poorest in that of Dagin. Females of strain 6 yielded eggs of a higher weight but the percentages of spawning females were higher in strain W after each of the applied spawning agents. A new approach to this problem consisted in investigating the interaction between ovulation stimulators and origin of females of fish treated with Dagin.
EFFECT OF NITROGEN AND CARBON SOURCES ON THE INORGANIC PHOSPHATE SOLUBILIZATION BY DIFFERENT ASPERGILLUS NIGER STRAINS

The Mineral phosphate solubilization (MPS) was studied in ten Aspergillus niger strains. MPS activity was measured in solid (Pikovskaya's medium) as well as liquid media using different phosphate sources (tricalcium, dicalcium, ferric and aluminium phosphates, and bone meal), carbon sources (glucose, mannitol, fructose, sucrose, xylose, and sorbitol), and nitrogen sources (ammonium sulfate, ammonium chloride, ammonium nitrate, sodium nitrate, potassium nitrate, and urea). All the strains showed a zone of clearance of tricalcium phosphate in Pikovskaya's medium in plates and solubilized dicalcium and tricalcium phosphates in broth efficiently. Solubilization was lower in ferric and aluminium phosphates. The activity was very poor in bone meal medium. Among the carbon sources the fungi preferred mannitol for higher P solubilization. Nitrogen in the form of nitrate was very effective in solubilizing inorganic phosphates. Xylose and urea were the poorest sources of carbon and nitrogen for all the strains of Aspergillus. Phosphate release was associated with reduction in pH.
A new species of Acynodon (Crocodylia) from the upper cretaceous (Santonian–Campanian) of Villaggio del Pescatore, Italy

Abstract: The new species Acynodon adriaticus is described on the basis of remains from the Santonian–Campanian of Villaggio del Pescatore (Trieste, NE Italy). This species differs in several cranial features from Acynodon iberoccitanus, the only other Acynodon species whose cranial osteology is known in detail. The absence of maxillary and dentary caniniform teeth coupled with the presence of enlarged molariform teeth suggests that Acynodon probably fed on slowly moving hard‐shelled prey. Moreover, the new materials reveal for the first time the morphology of some postcranial elements of Acynodon: in particular, medial‐most paravertebral osteoderms that are characterized by two keels. A new cladistic phylogenetic analysis resolves the previously reported polytomy among the basal Globidonta: Acynodon is recognized as the most primitive globidontan. This genus may represent the geologically oldest known globidontan. The fact that Acynodon has been found only in Europe and that the outgroup of Globidonta, the Diplocynodontinae, is mainly known from Europe, suggests that globidontans may have originated in Europe and not in North America as previously supposed.
Manure and nitrogen fertilizer effects on corn productivity and soil fertility under drip and furrow irrigation

A field experiment was conducted at the Arkansas Valley Research Center in 2005 through 2007 to study the effects of manure and nitrogen fertilizer on corn yield, nutrient uptake, N and P soil tests, and soil salinity under furrow and drip irrigation. Manure or inorganic N was applied in 2005 and 2006 only. There were no significant differences in corn yield between drip and furrow irrigation even though, on average, 42% less water was applied with drip irrigation. Inorganic N or manure application generally increased grain yield, kernel weight, grain and stover N uptake, and grain P uptake. Nitrogen rates above 67 kg ha−1 did not increase grain yield significantly in 2005 or 2006, nor did manure rates in excess of 22 Mg ha−1. High manure rates increased soil salinity early in the season, depressing corn yields in 2005 and 2006, particularly with drip irrigation. Salts tended to accumulate in the lower half of the root zone under drip irrigation. Residual nitrate nitrogen from manure and inorganic N application sustained corn yields above 12.0 Mg ha−1 in 2007. More research is needed to develop best manure and drip irrigation management for corn production in the Arkansas Valley.
MicroReview Cascades of sigma factors revisited

Programmed gene expression during the process of endospore formation in Bacillus subtilis is governed by the successive appearance of five developmental sigma factors. These sigma factors are encoded by genes in which mutations arrest sporulation at a defined stage. These genes are turned on sequentially and depend for their own transcription on the activity of a previously synthesized sigma factor. Superimposed on the regulation of synthesis of the sigma factors are post‐transcriptional control mechanisms that couple the activation of the developmental sigma factors to the course of sporulation. Here we review evidence indicating that these developmental transcription factors comprise a regulatory cascade in the order σH→σF→σE→σG→σK in which the activity of each sigma factor depends on the action of the preceding sigma factor in the cascade.
The effects of plant litter on vegetation: a meta‐analysis

1 We used data from 35 independently published studies world‐wide to analyse the effects of plant litter on the germination, establishment, species richness and above‐ground biomass of plants. Overall, the short‐term effects of litter on vegetation were mostly negative, although their magnitude varied with vegetation variable, study method, experimental duration, latitude, habitat, type and quantity of litter and target species.
The stimulatory effect of a muscle protein hydrolysate from Atlantic cod,Gadus morhuaL., on Atlantic salmon,Salmo salarL., head kidney leucocytes

Abstract This study shows the stimulatory capacity of a cod muscle protein hydrolysate on Atlantic salmon head kidney leucocytes both in vivo and in vitro . Increased respiratory burst activities were demonstrated in leucocytes after stimulation with a peptide fraction in the molecular weight range 500–3000 Da. The respiratory burst activity was quantified using reduction of nitroblue tetrazolium (NBT) as a measure of superoxide anion production following stimulation with phorbol myristate acetate (PMA) as the trigger. In vitro dose-response studies demonstrated an increased stimulation with increasing concentrations of the peptide fraction (30–1000 μg ml −1 ). Intraperitoneal injection of the peptide fraction in Atlantic salmon (100 mg kg −1 ) resulted in enhanced levels of superoxide anion production in head kidney leucocytes 2 and 4 days post-injection when assayed immediately after isolation. Culturing the cells for 18 or 41 h abolished the stimulatory capacity of the peptides. Also, increased levels of the lysosomal enzyme acid phosphatase were measured in the isolated head kidney leucocytes after intraperitoneal injection. Microscopic examination of tissue slices two days after i.p. administration revealed accumulation of FITC-labelled muscle hydrolysate (500–3000 Da) mainly in macrophages and endothelial cells of the kidney.
SUPPLEMENTS TO THE ATLAS OF BUTTERFLIES (LEPIDOPTERA: RHOPALOCERA) OF SLOVENIA

Abstract The Atlas of butterflies (Lepidoptera: Rhopalocera) of Slovenia (Verovnik et al. 2012) treats 179 butterfly species whose occurrence in Slovenia is confirmed, and 24 species for which only unconfirmed data exist. By the end of 2011, 212.936 distribution records by 167 contributing authors were collected for the Atlas. The Digital database of butterflies of the Jovan Hadži Institute of Biology of the Scientific Research Centre of the Slovenian Academy of Sciences and Arts was not considered in the process of collecting the data for the Atlas. This database contains 30.630 distribution records for butterfly species found in Slovenia from research projects undertaken by the Institute from 1995 to date. Given that this rich data source was not included in the Atlas, I here provide a supplement to the existing Atlas, reporting 1529 new records for 140 butterfly species. These updates provide new areas or range limits for 14 species, the presence of 71 species in areas the Atlas designated as “white spots”, new information on 3 species with very limited distribution in Slovenia, and additional corroboration for distribution of 27 species that the Atlas covered. Izvleček Atlas dnevnih metuljev (Lepidoptera: Rhopalocera) Slovenije (Verovnik et al. 2012) obravnava 179 vrst, katerih prisotnost v Sloveniji je potrjena, in 24 vrst, za katere obstajajo le nepotrjene navedbe o najdbah na ozemlju Slovenije. Do konca leta 2011 je bilo za Atlas zbranih 212.936 podatkov, ki jih je prispevalo 167 avtorjev. Pri zbiranju podatkov za Atlas ni bila upoštevana Digitalna podatkovna zbirka dnevnih metuljev Biološkega inštituta Jovana Hadžija Znanstvenoraziskovalnega centra Slovenske akademije znanosti in umetnosti. Zbirka obsega 30.630 podatkov o vrstah dnevnih metuljev najdenih na ozemlju Slovenije, pridobljenih večinoma pri raziskovalnih projektih Biološkega inštituta J. H. ZRC SAZU, ki so potekali od leta 1995 naprej. S primerjavo med podatki v Atlasu in v inštitutski podatkovni zbirki sem ugotovila, da je smiselno objaviti dopolnitve k obstoječemu Atlasu. Dopolnitve obsegajo 1529 podatkov za 140 vrst. Med njimi je 14 vrst za katere so opredeljena nova območja in meje razširjenosti v Sloveniji, in 71 vrst najdenih v območjih, ki so v Atlasu opredeljena kot “bele lise”. Dopolnitve vključujejo tudi nove informacije o nahajališčih 3 vrst z zelo omejeno razširjenostjo v Sloveniji in o pojavljanju 27 vrst na že znanih nahajališčih.
On the Question of an Arboreal Ancestry of the Marsupialia, and the Interrelationships of the Mammalian Subclasses

RECENT researches have seemed to indicate that the theory, proposed by Huxley, of a genetic succession of the former representatives of the Monotremata, Marsupialia, and Placentalia, is untenable, and have thus reopened the most fundamental question of mammalian zoology, as to the interrelationships of the primary subclasses and the possibility of a dior polyphyletic origin. The recent publication by Dollo ('99) of the results of his studies on the foot structure of the Marsupialia, which he interprets as confirming the growing idea of a placental origin of the group, renders this an opportune time to review and comment upon certain features of the evidence which has lately been produced in opposition to Huxley's theory.
Volatile fatty acids in stored animal slurry

Volatile fatty acids (VFAs) were measured in slurry stored in farm and laboratory conditions. All slurries from farm sources contained VFAs; acetic acid was predominant, followed by propionic, n-butyric, iso-butyric, iso-valeric and n-valeric. On average, pig slurry contained more total VFAs than did cow slurry. VFAs persisted in anaerobic conditions but decomposed rapidly when air was passed through slurry in laboratory experiments; decomposition was slower when air was passed over the slurry surface. Very little VFA formed when anaerobic conditions were re-imposed on aerated slurry unless glucose or protein hydrolysate was added. The pH of slurry was increased by passing air or nitrogen through it and decreased by adding glucose.
Purification, crystallization and preliminary X-ray analysis of a hexameric β-glucosidase from wheat

The wheat β-glucosidase TaGlu1b, which is only active in a hexameric form, was tagged with 6×His at the N-terminus, overexpressed in Escherichia coli and purified in two steps. The protein complexed with a substrate aglycone was crystallized at 293 K from a solution containing 10 mM HEPES pH 7.2, 1 M LiSO4 and 150 mM NaCl using the hanging-drop vapour-diffusion method. Diffraction data were collected to 1.7 A at the Photon Factory. The crystal belongs to space group P4132, with unit-cell parameters a = b = c = 194.65 A, α = β = γ = 90°. The asymmetric unit was confirmed by molecular-replacement solution to contain one monomer, giving a solvent content of 72.1%.
Ptiotosynthetic activity and chloroplast membrane polypeptides in euploid cells of Ricinus

The possible effects of altered nuclear complement size on the poiypeptide composition and photochemical activity of chloroplasts in haploid, diploid, and tetraploid cells, of Ricinus communis L. have been evaluated. The electron transport capacity in isolated chloroplasts decreases with the increase in nuclear genome size. Both Photosystem II (DCPIP reduction) and Photosystem 1 oxygen uptake (TMPD to methyl viologen) activities were lower in plastid preparations from tetraploid individuals than in diploid and haploid cell preparations. Photosynthetic O2-evolution and CO2-fixation rates in leaf tissue from euploid individuals were also found to decrease with the increase in size of the nuclear genome. Specific activity levels of RuBP-carboxylase were observed to increase with ploidy. Electrophoretic examination of the poiypeptide composition of thylakoid membranes from haploid, diploid, and tetraploid celis revealed no difference in the relative proportions of the constituent polypeptides of these membranes. The regulation of chloroplast development and the basis for altered plastid function in the presence of altered nuclear genome size are discussed.
Tannic Acid and Iron Alum with Safranin and Orange G in Studies of the Shoot Apex

A schedule is given for staining the cell walls of young plant tissues in tannic acid and iron alum after the protoplasts have been stained in safranin and orange G. Sections are placed for one minute in 2% aqueous ZnCl2, and are then stained in a 1/25,000 aqueous solution of safranin O. From this they are placed for five minutes in a bath consisting of orange G (2 g.), tannic acid (5 g.). water (up to 100 cc.) and HC1 (4 drops). This is followed by five minutes in 5% aqueous tannic acid and two minutes in a 1% solution of iron alum. A brief rinse in tap water is given between each stage; the slides are raised and lowered about a dozen times at each change to ensure that the new solution reaches the material quickly. The method was originated for shoot apices but it also works excellently on more mature tissues and on adult material. It has the advantage of allowing extremely easy detection of protophloem in the strands even at the very onset of vascular differentiation.
Systematic and phylogenetic value of wood anatomy in Heteromorpheae (Apiaceae, Apioideae)

The wood anatomy of all four woody genera of the tribe Heteromorpheae (Apiaceae, subfamily Apioideae) has been described and compared, based on 40 wood samples (representing nine species of Anginon, one species of Glia, three species of Heteromorpha and two species of Polemannia). The four genera were found to be relatively similar in their wood anatomy. Helical thickenings on the vessel walls occur in all species investigated and appear to represent an ancestral character state and a symplesiomorphy for the tribes Bupleurieae and Heteromorpheae. Each of four genera has a diagnostically different combination of character states relating to the diameter of vessels, size of intervessel pits, length of fibres, presence and arrangement of banded axial parenchyma, size of rays and ray cells, and presence of septate fibres and crystals in the ray cells. The occurrence of marginal axial parenchyma in Anginon and Glia may be an additional synapomorphy for these taxa. Variation in the wood anatomy of 31 samples from nine species of Anginon is not correlated with habitat (Fynbos or Succulent Karoo Biomes), but instead appears to reflect adaptations to seasonal aridity found in both ecosystems. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 569–583.
Independent Inheritance of Erucic Acid Content and Flower Colour in the C‐Genome of Brassica napus L.

The synthetic Brassica napus L. line No7076 was obtained from a cross between yellow-flowered and zero-erucic turnip rape (B. campestris) Sv85-38301 and white-flowered and high-erucic (41.4%) B. oleracea ssp. alboglabra No6510. This synthetic B. napus is pale-flowered and has an average erucic acid content of 25.8 %. It was crossed with the yellow-flowered and zero-erucic B. napus line SvS4-2S053 and segregation of the erucic acid content and flower colour was studied in F1 and F2 generations. The high erucic acid content was controlled by a single gene in the C-genome and was additively inherited. Strong evidence was obtained in support of independent segregation of the erucic-arid content and the flower colour characters controlled by the C-genome of B. napus.