Miracle-dz/UniFAR-FTUs huggingface dataset:
Inorganic elements in the livers of Eurasian otters, Lutra lutra, from England and Wales in 2007 & 2008: a Predatory Bird Monitoring Scheme (PBMS) report

This is a report on the initial findings of a collaborative study between the Predatory Bird Monitoring Scheme (PBMS) and the Cardiff University Otter Project (CUOP). The study analysed the concentrations of 16 metals and semi-metals in the livers of 107 Eurasian otters (Lutra lutra) that had been found dead in 2007 and 2008 and collected by the CUOP. This aim of this work was to determine the current concentrations of inorganic elements accumulated by otters and whether exposure to heavy metals (lead, mercury, cadmium) in particular is likely to be associated with adverse effects. This is the first study of inorganic elements in otter livers from Europe for nearly 10 years. The otters that were analysed were from England and Wales and included adult and subadult males and females. Liver tissue was analysed using Inductively Coupled Plasma mass spectrometry (ICP-MS) techniques. The concentrations of inorganic elements measured in the present study were within the range previously reported for Eurasian otters in Britain and elsewhere in Europe. Concentrations varied with age and/or sex for some elements. For the heavy metals mercury and cadmium, liver concentrations generally increased with age whereas for lead, juveniles generally had higher liver lead concentrations than adults although for lead these difference were not statistically significant. Aluminium and chromium were the only elements that varied significantly in concentrations between years. It is unclear whether the inter-year variation in aluminium and chromium represent significant inter-year changes in exposure and/or accumulation or may simply reflect local-scale variation in the provenance of otters and their associated exposure. The liver concentrations of heavy metals (mercury, cadmium and lead) in all the otters analysed were below those associated with toxic effects in mammals, although liver lead concentrations in a small number of otters were close to the level of concern.
REARING OF FRY TO FINGERLING OF SAUL (Channa Striatus) ON ARTIFICIAL DIETS

Three diets (F1, F2 and F3) containing protein levels of 38.60 to 38.98 % crude protein were used to assess the growth performances of Channa striatus fry (weight 0.52±0.0 to 0.53±0.02 g) in a completely randomized experiment design in five replicate set for 12 weeks. The fry were reared in 15 FRP tanks at a stocking density of 100 fry m3 and fed ad libitum. The diets F1 and F3 showed significantly (P<0.05) low survival levels of 74±1.2% and 76±4.4% in comparison to diets F2 (82±3.1%) 84th day of rearing. The net biomass gain %, length gain %, SGR, PER and per day weight gain were found significantly (P<0.05) higher and FCR low with diet F2 in comparison to diets F1 and F3. The proximate analysis of carcass showed that the fishes fed diets F2 had significantly (P<0.5) higher deposition of crude protein and lipids in the tissue. The study revealed that the growth performance of C. striatus fry is better in feed F2 and the fry could be reared to fingerling size on formulated diets.
Coding characters from different life stages for phylogenetic reconstruction: a case study on dragonfly adults and larvae, including a description of the larval head anatomy of Epiophlebia superstes (Odonata: Epiophlebiidae)

The exclusive use of characters coding for specific life stages may bias tree reconstruction. If characters from several life stages are coded, the type of coding becomes important. Here, we simulate the influence on tree reconstruction of morphological characters of Odonata larvae incorporated into a data matrix based on the adult body under different coding schemes. For testing purposes, our analysis is focused on a well-supported hypothesis: the relationships of the suborders Zygoptera, ‘Anisozygoptera’, and Anisoptera. We studied the cephalic morphology of Epiophlebia, a key taxon among Odonata, and compared it with representatives of Zygoptera and Anisoptera in order to complement the data matrix. Odonate larvae are characterized by a peculiar morphology, such as the specific head form, mouthpart configuration, ridge configuration, cephalic musculature, and leg and gill morphology. Four coding strategies were used to incorporate the larval data: artificial coding (AC), treating larvae as independent terminal taxa; non-multistate coding (NMC), preferring the adult life stage; multistate coding (MC); and coding larval and adult characters separately (SC) within the same taxon. As expected, larvae are ‘monophyletic’ in the AC strategy, but with anisopteran and zygopteran larvae as sister groups. Excluding larvae in the NMC approach leads to strong support for both monophyletic Odonata and Epiprocta, whereas MC erodes phylogenetic signal completely. This is an obvious result of the larval morphology leading to many multistate characters. SC results in the strongest support for Odonata, and Epiprocta receives the same support as with NMC. Our results show the deleterious effects of larval morphology on tree reconstruction when multistate coding is applied. Coding larval characters separately is still the best approach in a phylogenetic framework. © 2015 The Linnean Society of London
Effect of indigenous arbuscular - mycorrhiza (Glomus spp) on apple (Malus domestica) seedlings grown in replant disease soil

Poor growth and short life of newly planted apple trees at old apple site is known as apple (Malus domestica Borkh)replant problem. It is very difficult to be managed due to its complex etiology. To find out a sustainable management of this problem, effect of indigenous arbuscular-mycorrhizal fungi (AMF) was observed on growth of apple seedlings grown in apple replant diseased (ARD) soil. Out of five AMF isolates collected from apple orchards in Himachal Pradesh, one isolate AMFS-2 (Glomus fasciculatum) was selected on the basis of its colonization and growth promotion in inoculated apple seedlings. This AMF isolate was then used to see its effect on growth of apple seedlings grown in ARD soil collected from replant affected apple orchards. The AMF inoculation resulted significant increase in growth parameters, viz. plant height, stem diameter, internodal length, leaf area, shoot/ root fresh and dry weight of inoculated seedlings as compared to uninoculated seedlings grown in ARD soil in pot cultures. The effect of AMF inoculation on seedling growth was more when these were grown in ARD or virgin soil fumigated with formaldehyde. The phosphorus content of AMF inoculated seedlings were significantly more than uninoculated ones. The population of fungi, bacteria and actinomycetes was also less in the rhizosphere of mycorrhizal inoculated apple seedlings grown in ARD soil.
Opsin4, Opsin5, and Pax6 significantly increase their expression in recently settled juveniles of the sea urchin Strongylocentrotus intermedius (Echinodermata: Echinoidea)

Detection of light is essential for the interaction of sea urchins with a complex marine environment because it strongly affects various behavioral and physiological responses. Gene expression patterns of related genes of photoreceptor cells during larva development and metamorphosis in sea urchins remain unknown. We investigated the expression patterns of two representative opsin genes (Opsin4 and Opsin5) and Pax6 during larva development and after metamorphosis in the sea urchin Strongylocentrotus intermedius. Gene expression patterns of SIPax6, SIOpsin4, and SIOpsin5 were significantly different during the experimental period (p < 0.001). Expression of SIPax6 generally increased from the blastula stage to the eight-arm larva. However, SIOpsin5 and SIOpsin4 kept a relatively low expression during the whole experimental period except for a significant increase at the stage of early post-metamorphosis (23 days after fertilization) (p < 0.001). Like the expression pattern of SIOpsin4 and SIOpsin5, SIPax6 significantly increased its expression from the eight-arm larva stage to the juvenile (p < 0.001). After the high expression in early settled juveniles, however, the expression of all the three genes significantly decreased to a level similar to that in eight-arm larvae (p < 0.05).
Total polyphenol content, antioxidant activity and lipid peroxidation inhibition efficacy of branded tea (Camellia sinensis) available in India.

Natural phenols and polyphenols are compounds found naturally in plants. A group of natural polyphenols called "flavonoids" are of most popular interest because researchers have found them to be of health-contributing potential. One of the natural sources of polyphenols is tea and the polyphenol contents of various teas from China and Japan are well documented. Such documentation on Indian tea from Assam and Darjeeling is not reported extensively. In the present study the total polyphenol content, antioxidant activities and lipid peroxidation inhibition efficacy of five most popular branded tea samples from Darjeeling and Assam (BGT-1, BBT-1, BBT-2, BBT-3, and BBT-4) available in India are estimated and compared with reports on tea from other parts of the world. Antioxidant activity (IC 50 values) of these tested samples measured the highest for BGT-1 and the lowest for BBT-4. The total polyphenol content of the samples ranged from 20.7 mg GAE/g to 36 mg GAE/g, the highest being recorded for green tea followed by leafy Darjeeling tea. Similarly, the highest reducing power of tea antioxidants was recorded for green tea (0.95 ABU) and the lowest (0.48 ABU) for Assam CTC tea. Lipid peroxidation could be inhibited up to 29.8% by the tested green tea sample. Inhibition of lipid peroxidation showed positive correlation (r 2 = 0.9479) with hydroxyl radical scavenging activity which ranged from 20.91% to 81.16%. The antioxidant activity and the total polyphenol content were observed to be positively and highly correlated (r 2 = 0.9958). This study has made it possible to understand the functional properties of Indian tea with respect to teas from other parts of the world.
Polyphenolic composition of Lantana camara and Lippia chevalieri, and their Antioxidant and Antimicrobial Activities

In the present study, the antioxidant and antibacterial activities of methanolic extracts of two Verbenaceae ( Lantana camara L. and Lippia chevalieri Moldenke: aerial part) were investigated. Their polyphenolic composition in the ethyl acetate and aqueous fractions were characterized by HPLC-DAD. The antioxidant capability of the methanolic extracts was assessed by the Ferric Reducing Antioxidant Power (FRAP) and the scavenging activity of the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH). The Minimum Inhibitory Concentrations (MIC) of the methanolic extracts (25 µg mL -1 ), and the minimum bactericidal concentrations (MBC) (12.5 µg mL -1 ) against 13 pathogenic bacteria and four serotyped bacteria from the American Type Culture Collection (ATCC) were also determined by the agar-well diffusion method. The results indicated that the L. chevalieri extracts are rich in phenolic compounds (among the 27 polyphenolic compounds detected, 20 belong to L. chevalieri ) and showed the highest antioxidant activities, simultaneously on iron (III) to iron (II)-reducing activity and the radical scavenging activity. However, L. camara displayed the best and the broadest antimicrobial spectrum, especially on Shigella flexneri and Pantoea sp. (two Gram-negative strains of bacteria). The nature of polyphenolics compounds detected (phenol acid and flavone) in the L. camara can justify this activity. Key words : Verbenaceae, HPLC-DAD, antioxidant activity, antimicrobial activity, polyphenolic compounds
Effects of the proportion and spatial arrangement of un‐cropped land on breeding bird abundance in arable rotations

Summary 1. The response of bird abundance to the proportional availability of un-cropped land (i.e. land that could be cultivated, such as fallows, grass–flower or wild bird areas) is under-studied but of considerable significance for managing declining populations on farmland in western Europe. 2. In this study, bird abundance was examined at a scale consistent with many national monitoring schemes. Birds were counted on 28 farm sites of c. 100 ha, representing cereal-based and organic rotations. Sites were surveyed in summer, from 2007 to 2010, to assess the effect of the percentage cover and spatial arrangement of un-cropped land on bird abundance, with data analysed at the whole-farm (not patch) scale. 3. Un-cropped land area had significant effects on the abundance of key species (those with a high dependency on farmland) when controlling for effects of semi-natural habitats and management. On farms with 10% area of un-cropped land. 4. Positive, significant effects of the percentage area of un-cropped land were detected for lapwing, skylark, linnet and yellowhammer and for all highly farmland-dependent species combined. The relationship between un-cropped land and bird abundance was stronger on conventional compared with organic farms, suggesting a greater importance of un-cropped land on conventional farms. 5. Un-cropped land patch arrangement was significant for skylark and linnet abundance but generally weak amongst species compared with the availability of un-cropped land. Skylarks were positively associated with a larger relative edge effect amongst patches, whereas linnets were more associated with larger blocks of contiguous habitat. 6. Synthesis and applications. This study provides important evidence for a proportionate effect of habitat provision on farmland bird abundance. The relative area of un-cropped land had the strongest effect on bird abundance. Sites with <3% (and, to a lesser extent, <5%) un-cropped land were highly under-populated. A two-fold increase in the area of un-cropped land was associated with an average 16–53% increase in the relative abundance of key species, which has implications for the contribution of un-cropped areas towards population stabilization amongst farmland birds in Europe.
Genetic and mechanistic determinants of prostate cancer progression and metastasis

In order to study a complex biological phenomenon such as tumor cell metastasis, one must focus on examining discrete aspects of the process which are amenable to experimentation. In this thesis, I made use of xenograft and spontaneous in vivo mouse models of prostate cancer to approach this problem from two perspectives. First, I sought to identify genes which were involved with metastasis. Second, I focused on the mechanistic elements involved with tumor cell intravasation into lymphatics. The results from this work have shown that loss of Protein 4.1B, a 4.1/ezrin/radixin/moesin (FERM) domaincontaining cytoskeletal protein, is a frequent event in prostate cancer. The significance of this finding was confirmed by experimental ablation of 4.1B, which enhanced tumor progression and metastasis, at least in part, by protecting cells against apoptosis. This thesis has also shown that metastatic dissemination to lymph nodes is mediated primarily by peritumoral lymphatic vessels, which surround the tumor at the invasive margins. In contrast, inhibition of intratumoral lymphatics did not affect metastatic spread, indicating that these vessels were unnecessary for tumor cell dissemination. The genetic and mechanistic findings from this thesis were consistent across both model systems examined, and are also in concordance with observations made in human clinical prostate cancer. Thus, the results of this work have contributed small pieces of knowledge to our overall understanding of how tumors initiate, and frequently complete, the elaborate and often lethal process of spreading throughout the body. Thesis Supervisor: Richard Hynes Title: Professor of Biology
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ∞ AND METABOLIC DISEASE

■ Abstract The nuclear peroxisome proliferator‐activated receptor∞ (PPAR∞ )i s a transcription factor that is activated by polyunsaturated fatty acids and their metabolites and is essential for fat cell formation. Although obesity is a strong risk factor for type 2 diabetes mellitus and other metabolic diseases, potent PPAR∞ activators such as the glitazone drugs lower glucose and lipid levels in patients with type 2 diabetes and also have antiatherosclerotic and antihypertensive effects. We review recent studies providing insight into the paradoxical relationship between PPAR∞ and metabolic disease. We also review recent advances in understanding the structural basis for PPAR∞ activation by ligands. The unusual ligand-binding properties of PPAR∞ suggest that it will be possible to discover new chemical classes of receptor “modulators” with distinct pharmacological activities for the treatment of type 2 diabetes and other metabolic diseases.
GENETIC VARIABILITY AND CORRELATION STUDY IN SEGREGATING GENERATION OF TWO CROSSES IN SCENTED RICE

Genetic parameters, heritability and correlation were estimated for seven quantitative characters in two crosses Gourav × Ratna and Kasturi × Ratna. The population showed highly significant difference for most of the characters. Moderate to high genetic variability and high genetic advance were observed for all the characters studied in both the crosses. Single plant yield was positively and significantly correlated with plant height, ear bearing tiller and panicle length in both the crosses. From the study it was found that plant height, ear bearing tiller, panicle length were best characters in selection of yield in these two crosses.
A study of the proteinase, cathepsin L, in the context of tumour invasion.

The proteinase, cathepsin L, has been strongly implicated in the processes of tumour invasion and metastasis . A new purification method, three-phase partitioning, characterised in terms of the parameters which affected its fractionation of proteins, was found to simplify the purification of cathepsin L from sheep liver. This 11'"tethod, together wi th a novel cationexchange step on S-Sepharose and molecular exclusion chrol1latography, enabled the enzyme to be purified to homogeneity, in a single-chain form. A further enzyme fraction was isolated as a proteolytically active complex with the endogenous inhibitor of cysteine proteinases, cystatin. Studies on the proteolytically active complex revealed that approximately 60% of it was covalently bound and proteolytically active, while the other 40% was non-covalently bound and proteolytically inactive, in the manner normally found for the binding of cysta tin to cysteine proteinases. A cystatin fraction from sheep liver containing variants of cystatin ~, was shown to be able to form complexes with free cathepsin L in vitro in a pH-dependent, rapid process, which was mildly stimulated by a reducing agent. Cathepsin L was also isolated from human spleen, but only as a protcolytically inactive complex, presumably also with cystatin(s). The complexed and free cathepsin L from sheep liver were analysed for their pH-dependent characteristics, and it "vas found that both forms of the enzyme were more active and stable at, or near, neutral pH, than would have been expected from published values. Specific polyclonal antibodies to pure sheep cathepsin L were raised in rabbi ts and chickens. The chicken egg yolk antibodies were of a much higher titre and were immunoinhibitory towards the enzyme, which the rabbit antibodies were not. Anti-peptide antibodies, raised in rabbits against a peptide sequence selected from the active site of human cathepsin L, were highly specific for cathepsin Land immunoinhibitory towards the enzyme. Together with the polyclonal anti-cathepsin L antibodies, they show promise for immunoinhibitory and immunocytochemical studies on the enzyme, and as potential anti-tumour
Impact of cutting frequency on the vigour of Rumex obtusifolius

The control of Rumex obtusifolius, even with the use of herbicides, is difficult in permanent grasslands where R. obtusifolius reduces both productivity and nutritive value of herbage. It is important to find alternative approaches to managing R. obtusifolius. Two greenhouse experiments were conducted to compare the impact of different cutting frequencies, which simulated grazing (three cuts), silage making (two cuts) and hay making (one cut) on shoot and root measurements of the vigour of R. obtusifolius. In both experiments the same cutting frequencies were imposed but in Experiment 1 the treatments were imposed for 2 years and in Experiment 2 for 1 year. Compared to the silage-making and hay-making treatments, there was a reduction in the vigour of the aerial parts of R. obtusifolius on the grazing treatment, associated with a reduction in the number of leaves (Experiment 1), in the size of the largest leaf (Experiment 1) and in the herbage mass of dry matter (Experiments 1 and 2). Roots had higher concentrations of total soluble sugar and lower concentrations of starch in the grazing treatment than in the other treatments. These results showed that a reduction in the vigour of R. obtusifolius in permanent grasslands is possible only if the plants are submitted to a high frequency of defoliation under cutting or grazing.
Conservación de la biodiversidad en Costa Rica: análisis de la correspondencia entre áreas identificadas clave por su biodiversidad (Araceae, Arecaceae, Bromeliaceae y Scarabaeinae) y zonas de vida prioritarias para la conservación

El presente estudio analiza la distribucion de areas de alta riqueza especifica y endemismos basado en plantas (Araceae, Arecaceae, y Bromeliaceae) y escarabajos del estiercol (Scarabaeinae), que habitan las diferentes Zonas de Vida de Holdridge en Costa Rica. Mediante el uso de un sistema de informacion geografica (SIG) analizamos provincias biogeograficas, en relacion a la representatividad de las areas de muestreo, las zonas de vida y las areas protegidas. Los mapas de alta riqueza especifica y endemismo sirvieron de base para realizar un analisis de vacios (gaps) y definir 6 niveles distintos de alta prioridad de areas de conservacion. Tambien se investigo que porcentaje de estas areas prioritarias se encontraba bajo algun esquema de proteccion o conservacion, y cuales de estas areas son susceptibles de ser ampliadas. Se indica igualmente el grado de factibilidad para que estas areas crezcan. Incluimos una lista de todas las especies registradas para las familias antes mencionadas en Costa Rica, e indicamos su presencia en las diferentes Zonas de Vida de Holdridge, asi como su condicion de endemismo. Se identificaron 4 areas de maxima riqueza especifica y 3 areas nuevas de alto endemismo. Las areas prioritarias para la conservacion identificadas fueron: (1), el bosque humedo tropical de las tierras bajas del noreste; (2), la region de la peninsula de Osa, y (3), el bosque humedo premontano, a lo largo de las vertientes de las cordilleras de Guanacaste, Tilaran y Central. Este estudio demostro claramente la necesidad de incluir y comparar a diferentes grupos de organismos en estudios sobre patrones espaciales de biodiversidad-endemismo, con lo cual es posible obtener resultados mas robustos y mas detallados.