Miracle-dz/UniFAR-FTUs huggingface dataset:
A biotelemetry system recording fish activity

A biotelemetry system is described for obtaining, transmitting and recording the electromyograms (EMGs) produced in muscle activity of free-swimming fish as quantitative indicators of overall fish activity. The radiotransmitters used come in the form of cylindrical packages having two sensing electrodes, all fully implantable in the fish body cavity. EMGs are transmitted as radio pulses with the intensity of muscular activity determining the intervals between pulses. The packages also contain temperature sensors and fish temperatures are transmitted with every 32nd pulse. Transmitted EMG pulses are detected, ‘measured’ and stored by a single portable receiver (Model SRX_400, Lotek). Data can be subsequently transferred to a computer (which can also be portable) for storage, processing and statistical analysis. Transmitter battery life can be in excess of 7 months, permitting laboratory or field studies of long duration. Transmitter package implantation surgery requires a mid-ventral incision and internal securing of transmitter and sensing electrodes. Surgical silk, cyanoacrylate tissue adhesives, and polydioxanone (PD), a synthetic absorbable suture, were all tried as means of incision closure. The most effective was PD alone. Trials of the system consisted of forced swims by transmitter-equipped rainbow trout Oncorhynchus mykiss Walbaum. The data obtained provided an inverse linear relation between forced swim speed and EMG pulse interval. Trials were conducted at intervals over periods up to 2 months. Fish showed neither distress, nor difficulty in swimming up to maximum speeds of 60 cm s −1 (fish lengths 41.0, 44.4 cm).
Genetic parameters and genetic trends of reproduction traits in synthetic Pannon rabbits using repeatability and multi-trait animal models

Genetic parameters and genetic trends of total number of born kits (TNB), and number of kits born alive (NBA) were estimated in Pannon White and Pannon Ka rabbits for the first four parities. REML and BLUP procedures were applied using repeatability and multi-trait animal models (PEST and VCE software). Heritability estimates were low for both traits and breeds and ranged between 0.06-0.07 (0.01-0.02) and 0.04-0.06 (0.02-0.02) for TNB and NBA, respectively (standard errors of estimates are given in brackets). The estimated permanent environmental effects showed higher relative importance compared to the additive genetic effects and they ranged between 0.07-0.13 (0.01-0.02) and 0.08-0.14 (0.01-0.02) for TNB and NBA, respectively. High genetic correlation coefficients were found between TNB and NBA (0.97±0.02, 0.96±0.02) for Pannon White and Pannon Ka, respectively. The genetic correlation coefficients estimated between TNB and between NBA of the successive parities (as separate traits) ranged between 0.64-0.97 (0.04-0.11) and 0.56-0.99 (0.03-0.10) for Pannon White and Pannon Ka, respectively. The estimated genetic trends for TNB and NBA were negligible for the Pannon White and small (0.03-0.02 (0.01-0.01)) for Pannon Ka. The mean squared errors (MSE) of the repeatability and multi-trait models were similar but the correlation coefficients of between the observed and predicted values were lower for the multi-trait (0.27-0.61) than for the repeatability models (0.43-0.65).
Using indicators for evaluating, comparing, and communicating the ecological status of exploited marine ecosystems. 2. Setting the scene.

Background is provided to the selection of ecological indicators by the IndiSeas Working Group, and the methodology adopted for analysis and comparison of indicators across exploited marine ecosystems is documented. The selected indicators are presented, how they are calculated is explained, and the philosophy behind the comparative approach is given. The combination of selected indicators is intended to reflect different dynamics, tracking processes that display differential responses to fishing, and is meant to provide a complementary means of assessing marine ecosystem trends and states. IndiSeas relied on inputs and insights provided by the local experts from participating ecosystems, helping to understand state and trend indicators and to disentangle the effect of other potential ecosystem drivers, such as climate variability. This project showed that the use of simple and available indicators under an ecosystem approach can achieve a real, wide-reaching evaluation of marine ecosystem status caused by fishing. This is important because the socio-economics of areas where fishing activities develop differs significantly around the globe, and in many countries, insufficient data are available for complex and exhaustive analyses.
Focus Review Adult mammalian stem cells: the role of Wnt, Lgr5 and R-spondins

After its discovery as oncogen and morphogen, studies on Wnt focused initially on its role in animal development. With the finding that the colorectal tumour suppressor gene APC is a negative regulator of the Wnt pathway in (colorectal) cancer, attention gradually shifted to the study of the role of Wnt signalling in the adult. The first indication that adult Wnt signalling controls stem cells came from a Tcf4 knockout experiment: mutant mice failed to build crypt stem cell compartments. This observation was followed by similar findings in multiple other tissues. Recent studies have indicated that Wnt agonists of the R-spondin family provide potent growth stimuli for crypts in vivo and in vitro. Independently, Lgr5 was found as an exquisite marker for these crypt stem cells. The story has come full circle with the finding that the stem cell marker Lgr5 constitutes the receptor for R-spondins and occurs in
The effect of rosemary (Rosmarinus officinalis L.) essential oil on digestibility, ruminal fermentation and blood metabolites of Ghezel sheep fed barley-based diets

This study was conducted to evaluate the effects of rosemary essential oil (REO) on feed digestibility, ruminal fermentation and blood metabolites of Ghezel sheep. Four male sheep with average body weight 46 ± 2.0 kg were used in a 4×4 Latin square design. Treatments were control (no REO added), 100 mg d -1 of REO (low), 200 mg d -1 of REO (medium) and 400 mg d -1 of REO (high). Sheep were fed the 4 diets for 4 periods of 21 days (14 days as adaptation and 7 days for sample collection). The results showed that digestibility of dry matter, neutral-detergent fiber, acid-detergent fiber and crude protein were not affected by REO feeding ( p >0.05). The concentration of ammonia-N across sampling times was lower ( p 0.05). Supplementation with REO had no effect on plasma concentrations of glucose, triglyceride, cholesterol, total protein and albumin ( p >0.05). The results of this study indicate that, although a medium dose of REO may have positive effect on rumen fermentation, a low dose of REO may have adverse effects on ruminal fermentation.
WATER QUALITY AND DIVERSITY OF PHYTOPLANKTON IN A HARD-WATER LAKE, THAILAND

A study of water quality and the diversity of phytoplankton in the Rama IX lake, a man-made lake, in Pathumthani province, Thailand. This study was conducted from February 2000 to January 2001. The lake was divided into two parts, identified by the Irrigation North Rungsit as the first and the second sections. The water quality of both sections, as classified by the National Environmental Boards standards of surface water quality, was found to be in the second category and relatively clean for household consumption when properly treated. However, the main problem was the assessment of water quality of the first section which was found to be mesotrophic to eutrophic while the second section was oligotrophic to mesotrophic. Phytoplankton found in the first section showed a total number of 86 different taxa which were divided into 9 taxonomic groups. The taxonomic groups most rich in species were Chlorophyceae with 30, Euglenophyceae with 21, Cyanophyceae with 17, Diatomophyceae with 9, Dinophyceae and Cryptophyceae with 4, Zygnemaphyceae with 3 and Chrysophyceae and Xanthophyceae with 1 taxa. In the second section, phytoplankton were of 59 different taxa, and divided into 8 taxanomic groups. The Chlorophyceae was the most common with 21 species, Cyanophyceae with 12, Euglenophyceae with 11, Diatomophyceae with 9, Cryptophyceae and Dinophyceae with 4, Zygnemaphyceae with 2 and Chrysophyceae with 1. Cylindrospermopsis raciborskii was found to be the dominant species and was the highest phytoplankton biovolume throughout the investigation in the both sections.
Contributions of Oxyrrhis marina to molecular biology, genomics and organelle evolution of dinoflagellates

The ﬂagellate Oxyrrhis marina has been the subject of numerous studies addressing diverse aspects of protist biology including feeding, motility, ecology and cell biology. In spite of the rich body of information that has been built around this organism, the molecular biology of O. marina has remained virtually unstudied until very recently. Studying the molecular biology and genomics of O. marina is not only important due to its role as a model organism and practical accessibility; current evidence shows that it occupies a basal position within the dinoﬂagellate lineage, making it an ideal starting point to reconstruct the evolution of several interesting characters in this diverse group and its sister group Apicomplexa. Among these features, dinoﬂagellates have very divergent mitochondrial genomes, a complex history of plastid evolution and unique features involving the nuclear genome and transcription. Here we review and discuss how recent ﬁndings from O. marina are contributing to shed light on these and other aspects of the evolutionary history of two important eukaryotic lineages, the apicomplexans and dinoﬂagellates.
Molecular Data for the Sea Turtle Population in Brazil

We report here a dataset comprising nine nuclear markers for the Brazilian population of Cheloniidae turtles: hawksbills (Eretmochelys imbricata), loggerheads (Caretta caretta), olive ridleys (Lepidochelys olivacea), and green turtles (Chelonia mydas). Because hybridization is a common phenomenon between the four Cheloniidae species nesting on the Brazilian coast, we also report molecular markers for the hybrids E. imbricata × C. caretta, C. caretta × L. olivacea, and E. imbricata × L. olivacea and for one hybrid E. imbricata × C. mydas and one between three species C. mydas × E. imbricata × C. caretta. The data was used in previous studies concerning (1) the description of frequent hybrids C. caretta × E. imbricata in Brazil, (2) the report of introgression in some of these hybrids, and (3) population genetics. As a next step for the study of these hybrids and their evolution, genome-wide studies will be performed in the Brazilian population of E. imbricata, C. caretta, and their hybrids.
Current Invasions of Asian Cyclopid Species (Copepoda: Cyclopidae) in Crimea, with Taxonomical and Zoogeographical Remarks on the Hypersaline and Freshwater Fauna

Abstract. The Crimean Peninsula holds a large number of hypersaline water bodies. Our studies focused on these poorly investigated habitats, and included few brackish and freshwater ponds. Seventeen species were identified, of which only 4(5) were collected from hypersaline waters sometimes with extremely high salinities (Acanthocyclops sp. copepodid, 210 ppt; Eucyclops sp. copepodid, 150 ppt; Diacyclops bisetosus and Cyclops furcifer, 140–150 ppt). We also report on the occurrence of three alien thermophilic species (Eucyclops roseus Ishida, 1997, Mesocyclops isabellae Dussart et Fernando, 1988, and Mesocyclops pehpeiensis Hu, 1943) from the brackish and fresh waters of Crimea. Morphological descriptions, illustrations of the diagnostic characters and comments on relevant taxonomic issues are supplemented with discussion of the putative ways of dispersal of the alien copepods to Crimea. We provisionally reinstate Eucyclops roseus, regarded by others as a subspecies of E. agiloides (G. O. Sars, 1909), and retain the name Acanthocyclops trajani Mirabdullayev et Defaye, 2002 which was recently synonymized with A. americanus (Marsh, 1893) here considered a nomen dubium. Species accumulation curves based on our and literature data showed that significantly larger sampling efforts could yield a total of 6–8 species in the hypersaline waters and 47–50 species in all types of continental waters of Crimea.
Tenofovir Diphosphate Is a Poor Substrate and a Weak Inhibitor of Rat DNA Polymerases α, δ, and ε*

ABSTRACT Tenofovir diphosphate (PMPApp) is a weak inhibitor of DNA polymerases (pol) α, δ, and ε*, with values for the Ki for PMPApp (PMPAppKi) relative to the Km for dATP (dATPKm) of 10.2, 10.2, and 15.2, respectively. Its incorporation into DNA was about 1,000-fold less efficient than that of dATP, with PMPAppKm values 350-, 2,155-, and 187-fold higher than dATPKm values for pol α, δ, and ε*, respectively.
The Leaf-Height-Seed plant ecology strategy scheme as applied to species from a Mediterranean old-field succession

A Leaf-Height-Seed (LHS) plant ecology strategy scheme has recently been proposed, whose aim is to capture leading dimensions of variation among species related to major environmental gradients with three simple traits: specific leaf area (SLA), plant height and seed mass. We tested how this scheme applies in species from Mediterranean old fields characteristics of different successional stages. The three traits were measured on 55 species representing a wide range of growthand life form at a field site located in southern France. SLA decreased, while plant height and seed mass increased significantly with the successional status of the species. This was mainly due to the replacement of growthand life forms along the succession in the order: therophytes, hemicryptophytes and geophytes, chamaephytes, deciduous and evergreen phanerophytes. This study shows that the three fundamental traits of the LHS scheme adequately capture the changes in plant specialization along a gradient of secondary succession. However, our data shows that contrary to a major assumption postulated in the initial scheme, the three axes are not independent: plant height and seed mass indeed appeared to be strongly correlated, especially in woody species. This result questions the relevance of using all three traits in broad scale ecological comparisons. Proceedings 10th MEDECOS Conference, April 25 – May 1, 2004, Rhodes, Greece, Arianoutsou & Papanastasis (eds) © 2004 Millpress, Rotterdam, ISBN 90 5966 016 1
Nitrogen losses from the soil/plant system: a review

Losses of nitrogen from the soil/plant system not only reduce soil fertility and plant yield but can also create adverse impacts on the environment. Ammonia emissions into the atmosphere contribute to acid rain and represent an indirect source of nitrous oxide greenhouse gas emissions. Nitrate leaching losses into rivers and lakes can cause eutrophication resulting in excessive growth of aquatic weeds and algae, which can reduce fish populations and the recreational value of the water. Nitrate contamination of drinking water supplies can cause health risks. Legislation that is designed to limit nitrate leaching losses from land has become a constraint on agricultural land use in many countries. Nitrous oxide emissions into the atmosphere contribute to the depletion of the ozone layer and also make a significant contribution to climate change. This review describes the nitrogen cycle in temperate soil/plant systems, the processes involved in each of the individual nitrogen loss pathways, the factors affecting the amounts of losses and the methods that are available to reduce these losses. The review has shown that careful management of temperate soil/plant systems using best management practices and newly developed technologies can increase the sustainability of agriculture and reduce its impact on the environment.
The influence of ecology on sociality in the killer whale (Orcinus orca)

The persistence and size of social groups can be plastic and governed by ecological selection or be under greater genetic control and constrained by phylogenetic inertia. Comparing sociality of phylogenetically divergent populations under the same ecological conditions or between groups within a population under different ecological conditions can identify the relative influence of ecological selection on group formation. Here, we compare the size and persistence of social groups within a community of Atlantic killer whales, comparing between data collected from an area around Scotland where the whales have mainly been seen to hunt seals and data collected from an area around Iceland where the whales have mainly been seen to hunt herring. Additionally, we compare the observed social structure with that of previously studied Pacific ecotypes. Atlantic killer whale groups in both locations had a stable long-term primary social tier (association index level > 0.8) similar to that of Pacific killer whales. However, associations between these groups were much lower when hunting for seals than for fish in both the Atlantic and the Pacific. The occurrence of these differences in sociality between Atlantic groups, which are linked in a single social network, suggests that ecological selection partially determines sociality in this species. Furthermore, if sociality was constrained by phylogenetic inertia, then the Atlantic killer whales would all be expected to be more similar to the Pacific fish-eating ecotype than the more phylogenetically distant Pacific mammal-eating ecotype. Our study suggests that sociality in killer whales is to some extent plastic and can be adapted to the local ecological conditions.
Identification of Human Macrophage Inflammatory Proteins 1α and 1β as a Native Secreted Heterodimer*

Chemokines are secreted proteins that function as chemoattractants for leukocytes. The chemokines macrophage inflammatory protein 1α and 1β (MIP-1α and MIP-1β) now have been shown to be secreted from activated human monocytes and peripheral blood lymphocytes (PBLs) as a heterodimer. Immunoprecipitation and immunoblot analysis revealed that antibodies to either MIP-1α or MIP-1β precipitated a protein complex containing both MIP-1α and MIP-1β under normal conditions from culture supernatants and lysates of these cells. Mass spectrometry of the complexes, precipitated from the culture supernatants of monocytes and PBLs, revealed the presence of NH2-terminal truncated MIP-1α (residues 5–70) together with either intact MIP-1β or NH2-terminal truncated MIP-1β (residues 3–69), respectively. The secreted MIP-1α/β heterodimers were dissociated into their component monomers under acidic conditions. Exposure of monocytes or PBLs to monensin induced the accumulation of heterodimers composed of NH2-terminal truncated MIP-1α and full-length MIP-1β in the Golgi complex. The mixing of recombinant chemokines in vitro demonstrated that heterodimerization of MIP-1α and MIP-1β is specific and that it occurs at physiological conditions, pH 7.4, and in the range of nanomolar concentrations. The data presented here provide the first biochemical evidence for the existence of chemokine heterodimers under natural conditions. Formation of heterodimers of MIP-1α/β may have an impact on intracellular signaling events that contribute to CCR5 and possibly to other chemokine receptor functions.
Growth responses to thinning and pruning in Eucalyptus globulus, Eucalyptus nitens, and Eucalyptus grandis plantations in southeastern Australia

Growth responses to pruning or thinning are well documented but their interactions are not, even though they are sometimes performed simultaneously. Growth responses to thinning and pruning were examined in nine plantation silvicultural experiments at five sites in southeastern mainland Australia. The species studied were Eucalyptus globulus Labill. , Eucalyptus nitens (Deane and Maiden) Maiden, and Eucalyptus grandis Hill ex Maiden. Thinning from about 1100–1300 trees·ha–1 to about 300 or 500 trees·ha–1 at either age 3–4 years or 7–10 years increased the volume of sawlog crop trees in all species. Multiple lift pruning to 6.5 m height on the sawlog crop trees that retained at least 70% of the live crown length at any lift significantly reduced tree growth at only one of the six site–species combinations where both thinning and pruning were studied. And here, thinning interacted with pruning such that the pruning effects were not significant in unthinned stands because only shaded and inefficient foliage w.
Making the most of alarm signals: the adaptive value of individual discrimination in an alarm context

The value of individual discrimination is straightforward for many signal contexts, such as with contact or isolation calls, territorial marks, or status announcements. In contrast, the value of individual discrimination is less straightforward for alarm signals, and it is not yet known how or under what circumstances individual discrimination would be beneficial in an alarm context. One proposed mechanism is that receivers may discriminate individual signalers and respond differently based on the signaler's reliability, and that this may allow the receivers to optimize their antipredator behavior. To evaluate this mechanism, I constructed a dynamic model to test the fitness outcomes of 5 receiver response strategies under varying environmental, life history, and social conditions. The individual discrimination strategy yielded the highest fitness under the widest range of conditions, and the difference was substantial except in cases of very low predation pressure and high signaler accuracy. The adaptive value of individual discrimination of alarm signals may thus be a general phenomenon in nature and may provide evolutionary pressure for animals to increase their discrimination abilities. For species that use alarm signals nepotistically, the value of individual discrimination could provide selective pressure for the evolution of individual signatures in alarms and may help explain why the alarm signals of many species are so individualistic. Copyright 2011, Oxford University Press.
Rumen microbial degradation of allyl cyanide as a possible explanation for the tolerance of sheep to brassica-derived glucosinolates

Previous studies have shown that sheep are relatively tolerant to the prop-2-enyl glucosinolate breakdown product, allyl cyanide (ACN). In order to examine the extent to which this is due to degradation of the toxin in the rumen, the in-vitro stability of ACN in sheep rumen fluid was determined. Gas chromatography of the volatiles in rumen fluid sequentially sampled following addition of ACN revealed a steady reduction in ACN concentration in the rumen fluid of cabbage-fed sheep (1.0 μmol ml−1 to 0.36 μmol ml−1 in 100 min) but not in that from sheep fed dried grass (1.0 μmol ml−1 unchanged after 160 min). In a further experiment the time taken to develop an adapted rumen microbial population was determined by switching sheep abruptly from a grass to a cabbage diet and measuring the ‘ACN-degrading potential’ of rumen fluid over 29 days. Adaptation was rapid (< 6 days) and could confer tolerance to the effects of ACN to sheep consuming forage brassica crops.
Regulation of Ketone Body and Coenzyme A Metabolism in Liver

xvii CHAPTER 1: KETONE BODY METABOLISM 1.1 Overview 1 1.1.1 General introduction of ketone bodies 1 1.1.2 Ketogenesis is stimulated by fasting, stress and diabetes 1 1.1.3 Ketone body utilization in peripheral tissues 2 1.2 Adipose tissue lipolysis and regulation 3 1.2. 1 General introduction of lipolysis 3 1.2. 2 Lipolysis is regulated by dietary, hormonal and neurological factors 3 1.2. 3 Enzymes involved in lipolysis 4 1.2. 4 Mechanism of lipolysis 5 1.2. 5 Measurement of lipolysis 7 1.2. 6 Adipocyte lipolysis provides substrates for ketogenesis 8 1.3 Fatty acid β-oxidation and its regulation 9 1.3. 1 Formation of acyl-CoA and its regulation 9 1.3. 2 CPT system and its regulation by malonylCoA, dietary and