Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing Deadwood Using Harmonized National Forest Inventory Data

Deadwood plays an important role in forest ecological processes and is fundamental for the maintenance of biological diversity. Further, it is a forest carbon pool whose assessment must be reported for international agreements dealing with protection and forest management sustainability. Despite wide agreement on deadwood monitoring by national forest inventories (NFIs), much work is still necessary to clarify definitions so that estimates can be directly compared or aggregated for international reporting. There is an urgent need for an international consensus on definitions and agreement on harmonization methods. The study addresses two main objectives: to analyze the feasibility of harmonization procedures for deadwood estimates and to evaluate the impact of the harmonization process based on different definitions on final deadwood estimates. Results are reported for an experimental harmonization test using NFI deadwood data from 9,208 sample plots measured in nine European countries and the United States. Harmonization methods were investigated for volume by spatial position (lying or standing), decay classes, and woody species accompanied by accuracy assessments. Estimates of mean plot volume based on harmonized definitions with minimum length/height of 1 m and minimum diameter thresholds of 10, 12, and 20 cm were on average 3, 8, and 30% smaller, respectively, than estimates based on national definitions. Volume differences were less when estimated for various deadwood categories. An accuracy assessment demonstrated that, on average, the harmonization procedures did not substantially alter deadwood observations (root mean square error 23.17%). FOR. SCI. 58(3):269–283.
The use of variable fluorescence measurements in aquatic ecosystems: differences between multiple and single turnover measuring protocols and suggested terminology

In this review, we briefly describe the two main techniques used to measure variable fluorescence in the aquatic environment, and show how the parameters derived from this technique can be used to estimate the rate of photosynthesis. The methods estimate the photochemical efficiency of photosystem II from ratios of fluorescence levels. Flashes of light that are transiently saturating for photochemistry (i.e. they are sufficiently bright to close all PSII reaction centres) are used to obtain the maximum fluorescence level. The type of saturating flash differs between methods. In one approach, single turnover (ST) flashes are applied. This allows only one charge separation during the flash and reduces only the primary acceptor of PS II, raising fluorescence to a level Fm(ST) . In a second approach the flashes are multiple turnover (MT), which allow repeated charge separation processes until all electron acceptors of PS II are reduced. A relaxation of quenching is induced by the longer flash, and this raises the maximum fluorescence to a higher level, Fm(MT) Application of the different approaches to an algal sample will result in differing Fm values and, as a result, different values for the photochemical efficiency of PS II, with the MT method giving higher values than ST. Several designs of equipment, based on MT or ST techniques, are available for use with phytoplankton or benthic algae. Both techniques measure variable fluorescence, but there are a number of important differences in the methods used to calculate photosynthetic rates. In our view, this necessitates the use of a different terminology in order to avoid confusion, until the underlying physiological differences are resolved. An example is given showing that combining terminology from the different approaches will result in calculation of erroneous photosynthetic electron transport rates.
A New Species of Polypedates from Sumatra, Indonesia (Amphibia: Anura)

A rhacophorid tree frog from Sumatra that was once identified as Polypedates otilophus (Boulenger, 1893) is sufficiently divergent genetically and morphologically from topotypic specimens from Borneo as to be recognized as a distinct species. It is herein described as P. pseudotilophus sp. nov. The Sumatran frogs can be distinguished easily from the Bornean population by the possession of a much more weakly developed supratympanic bony crest, smoother dorsal skin, and a large, hourglass-shaped dark marking, instead of longitudinal stripes on the dorsum.
Winter frost resistance of leaves of some plants from the three kings Islands, grown outdoors in Dunedin, New Zealand

Abstract The minimum temperature at which plants from the Three Kings Islands escaped damage was determined as -2°C for Elingamita johnsonii, Tecomanthe speciosa, and Meryta sinclairii; -4°C for Pennantia baylisiana, Paratrophis smithii, and Davallia tasmanii; -5°C for Coprosma macrocarpa; and -6°C for Cordyline kaspar. Although the first three species have freezing resistances slightly less than those recorded for any other New Zealand plants, the range of resistance is otherwise similar to that of species of northern and lowland distribution and it appears that low freezing resistance is unlikely to be the major factor preventing the establishment of these species on suitable sites on the mainland.
Influence of gossypol from dietary cottonseed meal on haematology, reproductive steroids and tissue gossypol enantiomer concentrations in male rainbow trout (Oncorhynchus mykiss)

Rainbow trout (Oncorhynchus mykiss) males were fed, during a 9-month period, five experimental diets where fishmeal proteins were gradually replaced with cottonseed meal (CS) proteins (0, 25, 50, 75 and 100%; diets 1–5, respectively). This study was carried out to evaluate the action and tissue concentrations of gossypol. Growth performance of fish was not affected with the increasing levels of CS in the diets. Haemoglobin concentration and haematocrit significantly decreased in fish fed 100% CS compared with other dietary treatments. Gonadosomatic index, plasma sex steroids (testosterone, 11-ketotestosterone and 17,20β-dihydroxy-4-pregnen-3-one) and sperm characteristics (concentration, motility, protein concentration and lactate dehydrogenase activity) were not negatively affected by increasing levels of CS. For the first time, a comprehensive study of gossypol concentrations, total and (+) and (−)-enantiomers, in several tissues (liver, blood plasma, spermatozoa and seminal plasma) was performed. The concentrations of both (+) and (−)-enantiomers significantly increased with increasing levels of CS in the diet. The highest concentrations were found in the liver of fish fed diet 5 (185 ± 18 μg g−1). In blood plasma, the concentrations of total gossypol were 10 times lower than the one found in the liver, but 10 and 100 times higher than the concentrations in the spermatozoa and seminal plasma, respectively. In all tissues studied, the concentration of (+)-enantiomer was higher than the (−)-enantiomer. The ratio (−)-enantiomer/total gossypol did not change significantly with the increasing levels of CS in the diet. The results of the present study indicate that CS can be used over a period of 9 months to replace fishmeal proteins completely without compromising growth and reproduction of rainbow trout males.
Species richness of herbivores on exotic host plants increases with time since introduction of the host

Aim Species richness of insect herbivores feeding on exotic plants increases with abundance as well as range size of the host in the area of introduction. The formation of these herbivore assemblages requires a certain amount of time, and the richness of insect faunas should also increase with the length of time an exotic plant has been present in the introduced range.
Monitoring of the Biological Nutrient Removal Process by an On‐Line NAD(P)H Fluorometer

An on‐line NAD(P)H fluorometer has been used to investigate the fluorescence profile of a simulated anaerobic/anoxic/oxic biological nutrient removal (BNR) process and its dependency on operating parameters, such as the concentrations of organic substrate (acetate) and activated sludge. As expected from the different rates of NAD‐(P)H oxidation at different stages, the order of fluorescence levels was found to be anaerobic > anoxic > oxic. The effects of the acetate and sludge concentrations were observed most clearly at the anoxic stage: an increase in either concentration led to faster recovery of fluorescence from the drop caused by NO3− addition. A higher acetate concentration also resulted in a more significant, continuous rise in fluorescence, corresponding well with the enhanced PO43− release, at the anaerobic stage and a slower initial fluorescence decrease at the oxic stage, indicating the dependency of the decrease on substrate availability. The ratio of the two fluorescence drops caused by NO3− addition and aeration, Δ1/Δ2, obtained with the plant's sludge was found to be 0.7 × 0.1, which is similar to those of pure nitrate‐respiring cultures (e.g., Pseudomonas aeruginosa and Escherichia coli). The dominant majority of nonnitrifiers in the sludge therefore are capable of nitrate respiration, and the nitrifiers either contribute little to the overall fluorescence or perform nitrate respiration as the rest of the sludge population.
Temporal influence of experimental exposure of wistar rats to hexachlorobenzene on the morphology and some enzyme activities of intestinal mucosae

The intestinal reactivity to the oral administration to rats of 16 mg of Hexachlorobenzene (HCB) kg−1 b.w. (1.6% of LD50) for 30 days was explored in the beginning and at the end of the rest light phase of animals to check whether the presence of food in the intestine could lessen the impact of this pesticide. The treatment caused a mucosa layer hypertrophy and consequently a severe reduction of the intestinal lumen. The morphometric measurements presented a positive correlation with the values of the mucosa weight. The specific activities of alkaline phosphatase, gamma glutamyl transferase, sucrase, maltase and lactase were measured and used to estimate the functional state of the organ. The observed effects could reflect an inflammatory process without significant impact on the absorptive function of the organ. And, the influence of the HCB-dosing time on the reactivity of the intestine was not confirmed and appeared not to be related to the level of filling of the intestinal lumen with alimentary bolus.
Biodegradation of polycyclic aromatic hydrocarbons by soil fungi

Thirteen deuteromycete ligninolytic fungal strains were grown in media containing polycyclic aromatic hydrocarbons (PAHs), for 6 and 10 days. The PAHs were added directly with the inocula or on the third day of cultivation. A selection of the best strains was carried out based on the levels of degradation of the PAHs and also on the ligninolytic activities produced by the fungi. The selected strains were cultivated for 3, 6, 9, 12 and 15 days in the PAHs-containing media. Degradation of PAHs, as measured by reversed-phase HPLC on a C18 column, varied with each strain as did the ligninolytic enzymes present in the culture supernatants. Highest degradation of naphthalene (69%) was produced by the strain 984, having Mn-peroxidase activity, followed by strain 870 (17%) showing lignin peroxidase and laccase activities. The greatest degradation of phenanthrene (12%) was observed with strain 870 containing Mn-peroxidase and laccase activities. When anthracene was used, the strain 710 produced a good level of degradation (65%).
Desiccation tolerance in fully developed embryos of two cicadas, Cryptotympana facialis and Graptopsaltria nigrofuscata

In two Japanese cicadas, Cryptotympana facialis and Graptopsaltria nigrofuscata, with different habitat distributions, fully developed embryos hatch in response to high humidity due to rainfall. Despite the advantage of hatching on rainy days, this trait burdens embryos with an extra period of desiccation until the unpredictable advent of rain. We compared the ability of the fully developed embryos of these cicadas to endure periods of low humidity. Eggs were exposed to a combination of different humidities (43% and 75% relative humidity, RH) and durations (0–15 days), and then transferred to an environment with 100% RH to stimulate hatching. In both species, total hatching rates decreased as duration increased, although there was no significant effect of humidity. In C. facialis, a considerable proportion of the eggs hatched during the desiccation period, and the hatching rate was higher at 75% RH than at 43% RH. After transfer to 100% RH, most hatching occurred within a day regardless of the desiccation level. In G. nigrofuscata, no nymphs hatched during the desiccation periods. However, more eggs required more than a day after transfer to 100% RH to hatch after desiccation at 43% RH than at 75% RH. Consequently, the overall proportion of timely hatching of eggs (eggs hatching within a day of moisture supply) was higher after desiccation at 43% RH in C. facialis, but it was higher after desiccation at 75% RH in G. nigrofuscata. These different physiological responses of the two species may reflect adaptation to habitat dryness.
Habitat selection by red lechwe (Kobus leche leche Gray, 1850)

Summary Lechwe habitat use was studied intensively for 2.5 years and monitored for a further 7.5 years in the Linyanti Swamp, northern Botswana. It was found to be highly selective with respect to both resting and feeding sites. The selection of resting sites was probably a function of predator avoidance behaviour, while the selection of feeding sites was probably a function of pasture quality. The results of the study were consistent with the argument of IIlius & Gordon (1987) that sexual segregation of feeding sites is due to allometry of food intake and with the contention of Jarman (1974) that social factors may also affect habitat use. Resume On a etudie intensement depuis 2.5 ans, et surveille depuis 7.5 ans supplementaires, la facon dont les Iechwe utilisent l'habitat dans les marais de Linyanti, au nord du Botswana. On a trouve qu'ils etaient tres selectifs, tant pour les endroits de repos que pour ceux ou ils se nourrissent. La selection des endroits de repos etait liee au comportement visant aeviter les predateurs, tandis que le choix des sites de nourrissage etait probablement fonction de la qualite du fourrage. Les resultats de cette etude concordent avec la discussion de Illius & Gordon (1987) sur le fait que la segregation sexuelle des sites de nourrissage est due a l'allometrie de la ration alimentaire, et avec l'affirmation de Jarman (1974), que des facteurs sociaux aussi peuvent affecter l'utilisation de l'habitat.
Changes in Algal Species Composition Affect Juvenile Sockeye Salmon Production at Woss Lake, British Columbia: A Lake Fertilization and Food Web Analysis

Abstract In recent decades, the abundance of sockeye salmon Oncorhynchus nerka in the Nimpkish River watershed (Vancouver Island) has declined by more than 80%. To improve sockeye salmon abundance, one of three Nimpkish nursery lakes (Woss Lake, 13.6 km2) was fertilized; a second (Vernon Lake, 8.4 km2) was maintained as an unmanipulated reference. For 3 years (2000–2002), we assessed changes in phytoplankton, zooplankton, and juvenile sockeye salmon and then used food web analysis to model the fate of fertilizer phosphorus (FP) as it moved up the food web to juvenile sockeye salmon. As the experiment progressed, we found two distinctly different results. During the first 2 years (2000 and 2001), fertilization was associated with higher concentrations of P, chlorophyll, and phytoplankton. However, because most of the algae were inedible diatoms (principally Rhizosolenia eriensis), only 8% of the algal standing stock was available to zooplankton and less than 0.1% of the FP was incorporated into sockeye sal.
Lipopolysaccharide-induced Tumor Necrosis Factor-α Promoter Activity Is Inhibitor of Nuclear Factor-κB Kinase-dependent*

The adverse effects of lipopolysaccharide (LPS) are primarily mediated by tumor necrosis factor-α (TNF-α). TNF-α production by LPS-stimulated macrophages is regulated both transcriptionally and post-transcriptionally. Transcriptional regulation of the TNF-α gene is dependent on nuclear factor-κB (NF-κB). We examined the signaling pathways involved in the regulation of NF-κB that lead to TNF-α promoter activity. We determined a role for one or both of the recently identified inhibitor of NF-κB kinases, IκB kinase-1 and IκB kinase-2, in LPS induction of an NF-κB reporter and of TNF-α promoter activity. IκB kinase activation is one of the earliest signaling events known to be induced by LPS. Furthermore, our results suggest roles for the IκB kinases NF-κB-inducing kinase and mitogen-activated protein kinase/extracellular signal-regulated kinase kinase kinase 1 in the regulation of IκB kinase-2, as well as in LPS-induced TNF-α transcription.
The Paradox of the Plankton: An Equilibrium Hypothesis

A model of nutrient-limited phytoplankton growth, based on Michaelis-Menten uptake kinetics, is offered as an explanation of the so-called paradox of the plankton. The model suggests that an assemblage of coexisting phytoplankton may be limited by several nutrients, each species principally limited by the availability of a different nutrient. The principal requirement of the model is that each species be less effective at obtaining at low concentration the nutrient of which it requires larger amounts for continued growth. The model offers an explanation for the continued coexistence of associated phytoplankters in a stable equilibrium. It also offers a possible explanation for the decreased diversity commonly observed in eutrophic lakes and is consistent with observations that a larger number of different nutrients are in short supply in oligotrophic waters.
Chloroplast thylakoid protein changes induced by low growth temperature in maize revealed by immunocytology

Tissue-specific effects of low growth temperature on maize chloroplast thylakoid protein accumulation were analysed using immunocytology. Sections of leaves from plants grown at 25 and 14°C were probed with antibodies to specific chloroplast thylakoid proteins from the four major protein multisubunit complexes of the thylakoid membrane followed by fluorescein-conjugated goat anti-rabbit antibodies. At a normal growth temperature of 25°C, the 32 kDa D1 protein of the photosystem II reaction centre and the 33 kDa protein of the extrinsic oxygen-evolving complex of photosystem II are both accumulated to a greater degree in the mesophyll than in the bundle sheath chloroplasts. In contrast, subunit II of photosystem I, cytochrome f and the α- and β-subunits of ATP synthetase are predominant in the bundle sheath thylakoids at 25°C. A striking difference between the 25°C-grown and the 14°C-grown leaf tissue was the presence in the latter of (20–30%) cells whose chloroplasts apparently completely lack several of the thylakoid proteins. In plants grown at 14°C, the accumulation of the 33 kDa protein of the extrinsic oxygen-evolving complex of photosystem II was apparently unchanged, but other thylakoid proteins showed a significant reduction. The uneven distribution of proteins between the bundle sheath and mesophyll chloroplasts observed at 25°C was also maintained at 14°C. Reduction in the fluorescence at 14°C was manifested either as an overall reduction in the diffuse fluorescence across the chloroplast profiles or less frequently as a reduction to small discrete bodies of intense fluorescence. The significance of these results to low-temperature-induced reduction in the photosynthetic productivity of maize is discussed.
Refinement of Knowledge Sharing Platforms to Promote Effective Use: A Use Case

This work focuses on the improvement of a line of corporate knowledge management systems, knowledge repositories. For the implementation of such systems, companies can deploy important means for small gains. Indeed, management services often notice very limited use compared to what they actually expect. We present a use case of a five-step re-designing user-centered approach that combines a top-down content architecture, integration with other corporate information systems and adapted interfaces and interactions design to increase the use of these artifacts. Our implementation is done on the knowledge repository used by operators from Société du Canal de Provence (SCP),a French water management company. Their system was taken into production but very occasionally used. We describe the reasons for this limited use and we propose a design methodology adapted to the context. Promoting the effective use of the system, our approach has been experimented and evaluated with a panel of users working at SCP. Results of our semi-structured questionnaire reveal that more than half of the participant are satisfied and present a positive attitude towards the re-designed system.
Identification of Potential Substrates of N-acteylglucosamine Kinase by a Proteomic Approach

Post-translational O-GlcNAc modification (O-GlcNAcylation) of serine or threonine is a new protein modulation mechanism. In contrast to the classical glycosylation, O-GlcNAcylation occurs in a onestep transfer of O-GlcNAc on both nuclear and cytoplasmic proteins. In contrast to the general consensus that O-GlcNAc is a final modification, a recent paper (J Proteome Res. 2011 10:2725? 2733) showed the presence of O-GlcNAc-P on a synaptic assembly protein AP180. This finding raises a fundamental question about its prevalence. To address this question, we used proteomics to identify those proteins that were phospho-signal enriched by GlcNAc kinase (NAGK). Comparison of pDsRed2-NAGK WT -transfected HEK293T cell extract with pDsRed2-NAGK D107A -transfected control culture revealed 15 phospho-signal increased spots. Excluding those spots that had no detectable amount of protein expression yielded 7 spots, which were selected for ID determination. Among these, two duplicate spots (two HSP90β and two ENO1 spots) were shown to be O-GlcNAcylated, two (dUTP nucleotidohydrolase mitochondrial isoform 2, glutathione S-transferase P) were not known to be involved in OGlcNAcylation, and one (heat shock protein gp96 precursor or grp94) was a glycoprotein. The increase in the phospho-levels of O-GlcNAc by NAGK strongly indicates that these proteins are phosphorylated on O-GlcNAc. Our present data support the idea that O-GlcNAc is not a terminal modification.