Miracle-dz/UniFAR-FTUs huggingface dataset:
Discard Estimates from Self-Reported Catch Data: an Example from the U.S. Northeast Shelf

AbstractDiscarded catch can account for a significant amount of fishing mortality and can be a major source of uncertainty when calculating total removals for stock assessments and management. Observers provide estimates on the types and quantity of fish that are caught, but observer coverage of a fleet can often vary directly with funding. On the Northeast U.S. shelf, the Northeast Fisheries Observer Program (NEFOP) has collected data on catch and discards for assessment and management purposes since 1989. The Cooperative Research Study Fleet (hereafter “Study Fleet”), working with the Northeast Fisheries Science Center, collects self-reported catch and discards from commercial vessels; however, the Study Fleet program was not developed as an observer program, and these data are not used for management. The number of vessels reporting data in the Study Fleet program is much smaller than the total number of vessels recorded through the observer program (NEFOP plus the At-Sea Monitoring Program), and unlik.
Invited Commentary: Fifty Years of Raptor Research

Abstract This review examines the main developments that have occurred over the past 50 years in our understanding of three aspects of raptor biology: (1) natural factors that limit breeding densities; (2) influences of toxic chemicals; and (3) movements and migrations. Early evidence indicated that raptor breeding densities were limited naturally by the availability of either prey or nest sites, whichever was in shortest supply in the area concerned. More recent evidence has shown that predation can have additional influence, with larger raptors and owls limiting the numbers of smaller ones to below what food or nest sites would permit. In addition, it has become apparent that some migratory raptors, like other migratory birds, can be limited in their migration and wintering areas to levels below those that conditions in breeding areas would permit. As many raptor populations have recovered from the effects of organochlorine pesticides, attention has switched to other limiting agents, including lead (from ammunition), which is currently preventing California Condors (Gymnogyps californianus) from establishing self-sustaining populations in the wild, and anti-inflammatory veterinary drugs, which have caused massive declines in Asia vultures (Gyps spp.). The development of radio-tracking enabled studies of the local movements of individual raptors, providing new information on territories and ranging behavior, while satellite-based tracking has revealed the migration routes, wintering areas, and behavior of hundreds of individual birds.
Antioxidant response to cold stress in two oil plants of the genus Jatropha

Spano C. , Bottega S. , Ruffini Castiglione M. , Pedranzani H.E. (2017): Antioxidant response to cold stress in two oil plants of the genus Jatropha. Plant Soil Environ. , 63: 271–276. Jatropha curcas and J. macrocarpa, suitable for production of biodiesel oil from their seeds, are able to live in arid and semi-arid regions, where most crops cannot survive. J. curcas is characterized by higher oil quality and seed yield, but it is not a good candidate for oil production in arid areas with freezing temperatures, due to its sensitivity to chilling in comparison to J. macrocarpa. In this work, for the first time, the effects of cold stress and different mechanisms activated in these conditions have been studied in the two species. Seedlings were treated with low non-freezing temperatures with or without a previous acclimation period. Water status, pigment content, oxidative stress and antioxidant response were studied in acclimated and non-acclimated plants. The key features that differentiate J. macrocarpa from J. curcas were the ability to accumulate, at low temperatures, high concentrations of pigments and glutathione and significantly higher activities of ascorbate peroxidase. These data could explain the greater resistance to low temperatures of J. macrocarpa. A period of acclimation was not able to improve cold tolerance of J. curcas and this confirms its limited adaptability to arid areas with freezing temperatures.
Uji Daya Antihelmintik Dekok Daun Pepaya (Carica papaya L.) terhadap Ascaris suum secara In Vitro

Askariasis merupakan salah satu infeksi cacing terbanyak yang disebabkan oleh cacing Ascaris lumbricoides yang merupakan nematoda patogen pada usus halus yang dapat menyebabkan malnutrisi, gangguan pertumbuhan, gangguan kognitif, dan obstruksi saluran pencernaan. Cacing Ascaris suum berasal dari genus yang sama seperti Ascaris lumbricoides serta memungkinkan dilakukannya model terhadap Ascaris lumbricoides penelitian dengan cara in vitro . Adanya efek samping dan harga yang mahal pada obat anthelmintik konvensional, maka perlu dilakukannya evaluasi terhadap tanaman obat sebagai alternatif obat antihelmintik. Tujuan dari penelitian ini adalah untuk mengetahui daya antihelmintik dari dekok daun papaya ( Carica papaya L .) terhadap cacing Ascaris suum secara in vitro dan untuk mengetahui lethal time (LT100) dan lethal concentration (LC100) dari dekok daun pepaya. Penelitian ini merupakan penelitian eksperimental laboratorium dengan rancangan penelitian post test only control group design . Subjek dari penelitian ini adalah cacing Ascaris suum yang didapat dari Rumah Potong Hewan Gadang. Penelitian ini menggunakan 5 kelompok perlakuan yaitu NaCl 0,9 % sebagai kontrol negatif dan pirantel pamoat 1 % sebagai kontrol positif serta dekok daun papaya dengan konsentrasi 25 %, 50 %, dan 75 %. Data yang diperoleh diuji secara statistik dengan analisis probit untuk mengetahui Lethal concentration (LC100) dan Lethal time 100 (LT100) dari dekok daun papaya. Hasil uji normalitas menunjukkan distribusi normal (p > 0,05). Hasil analisis probit menunjukkan lethal concentration 100 (LC100) dekok daun papaya adalah 72,68 % sedangkan lethal time 100 (LT100) pada konsentrasi 75 % adalah 14.17 jam. Dari penelitian ini dapat disimpulkan bahwa dekok daun papaya memiliki daya antihelmintik terhadap Ascaris suum secara in vitro . Kata Kunci : Antihelmintik , Ascaris suum , Carica papaya L, Dekok.
Systems and techniques used in the culture of soft-shell swimming crabs

The academic interest in the production of soft-shell swimming crabs has increased in direct proportion to the increasing demand worldwide for this gastronomic delicacy. The techniques of obtaining this product are essentially based on the maintenance of swimming crabs at premoult stage in open, semi-closed or closed farming systems, until the moment of moulting. These different types of systems reflect the biological e environmental control method evolution. To achieve industrial scale production of soft swimming crabs, the option of using closed systems has increased in recent years. This type of system offers several advantages, such as greater control over environmental variables, greater ease of installation, higher storage densities, greater ease of monitoring ecdysis occurrence and, especially, the possibility of incorporating several forms of automation. In this review, the main production systems currently used, as well as the main techniques for obtaining the animals, their management under controlled conditions, harvesting and slaughter, are presented and discussed, focusing on future perspectives for the world production of soft-shell swimming crabs.
Decreasing population trend in coastal bottlenose dolphin (Tursiops truncatus) from the Gulf of Guayaquil, Ecuador

The population status of the coastal bottlenose dolphin (Tursiops truncatus) inhabiting the inner estuary of the Gulf of Guayaquil, Ecuador (3°S, 81°W) was assessed. Evaluated aspects included social organization, abundance and spatial distribution. Surveys focused on the western part of the estuary (Posorja and Estero Salado) but other areas in the central and eastern inner estuary were also surveyed. Effort included 68 trips, 5001 km of survey and 288.8 h at sea. Between 735 and 793 dolphins in 92 groups were recorded during the study. Dolphins are not evenly distributed but concentrated their activities in the mouths of large channels. A cluster analyses indicated that dolphins organize in partially discrete subunits referred to as communities. Abundance estimations were obtained using mark–recapture modelling for two communities: Posorja and Estero Salado (43 dolphins, 95% CI 37–49 and 65 dolphins, 95% CI 52–82 respectively). Four demographic parameters: average size of communities, average group size, average encounter rate and average density were compared with information obtained during the 1990s. In all cases the current values were between 39 and 54% lower; in the last three cases the difference was statistically significant. Possible causes of this apparent decline include bycatch, ship strikes, pollution and habitat degradation; however, none of these have been assessed in depth. Most probably, different stressors are affecting dolphin communities to different extents. A comprehensive assessment of the whole population inside the gulf is needed. Identifying major threats is a priority to define concrete actions to prevent further population decline.
Origins and diversity of exotic silverleaf nightshade (Solanum elaeagnifolium Cav.) present in Australia as determined by sequence analysis of a chloroplast DNA intergenic spacer region

Solanum elaeagnifolium Cav. (silverleaf nightshade) is a native perennial of the Americas present in Australia as a Weed of National Significance. Knowledge of the genetic diversity and origins of silverleaf nightshade in Australia may inform future programs that propose using geographic source specific biocontrols to mitigate the weed. Here we sequenced the trnS-trnG intergenic spacer in chloroplast DNA (cpDNA) from native and introduced populations of silverleaf nightshade to identify haplotypes representative of cpDNA lineages in the species distribution. We used network analysis to infer a genealogy among identified haplotypes and compared the array of haplotypes detected in Australia to those found elsewhere. Eleven silverleaf nightshade haplotypes were identified and parsimoniously arranged as a shallow star-like genealogy. Two of five haplotypes in Australia were also in the United States of America, Mexico and South Africa. A third haplotype prevalent in Australia and South Africa was absent elsewhere but previously reported from Paraguay. Presence of two haplotypes unique to Australia indicated our sample was insufficient to identify all cpDNA diversity in the native distribution. Haplotype diversity in Australia was similar to that elsewhere and showed no signs of diminished genetic diversity expected if foundered by few colonisers. We argue silverleaf nightshade in Australia originated from genetically diverse populations in North and South America. Silverleaf nightshade in Australia is likely at a late successional stage of colonisation, containing a variety of genetic backgrounds that may respond differently to various biocontrols. Our future work will explore additional genealogies to pinpoint geographic origins of silverleaf nightshade in Australia.
Role of pycnidia in twig and blossom blight and stem dieback of highbush blueberry caused by Phomopsis vaccinii in British Columbia

Abstract Twig and blossom blight, and stem dieback, has become an impediment to highbush blueberry (Vaccinium corymbosum L.) production in British Columbia. Periodic assessment of disease symptoms and pathogenicity test confirmed Phomopsis vaccinii to be the major causal agent of the disease. Symptomatic tissues sampled at 7- to 10-day intervals in the 2014 and 2015 growing seasons were examined for presence of pycnidia, their developmental stages, and conidial presence in relation to phenological status of blueberry. Based on histological analysis, pycnidia were grouped into a series of developmental stages, referred to as pre-conidial, early-conidial, conidial, conidial-release and post-conidial stages. These different stages of development coincided with the phenological stages of blueberry plants during the growing season. Pycnidia at the conidial and conidial-release stages were predominantly found on symptomatic tissues sampled from bud-break to bloom; these pycnidia had high conidial contents of 1.0–2.0 × 104 conidia pycnidium−1. Pycnidia at the post-conidial stage were mostly found on symptomatic tissues sampled from green-fruit to post-harvest, under warm and dry weather conditions. Pycnidia at the pre-conidial stage were predominantly observed on symptomatic tissues sampled during latter parts of the growing season, from bud-set to leaf-fall. Mycelial growth of P. vaccinii isolates on potato dextrose agar was measured in response to temperatures from 4 to 32°C; the optimum growth occurred between 20 and 28°C. The number of pycnidia produced on quarter-strength potato dextrose agar at different incubation conditions varied amongst P. vaccinii isolates, and the optimum production was recorded at 16°C with a photoperiod of 14 h light/10 h dark or 14 h UV-A/10 h. Percentage germination of conidia of P. vaccinii isolate 11 BB 14 on water agar was higher at 16, 20 or 24°C than at 8 or 12°C. Conidia at 16°C reached 50% germination at ≥56 h incubation, whereas conidia at 20 and 24°C reached 50% germination at ≥72 h. Percentage germination of conidia at 8 and 12°C remained <50% during 104 h incubation. These findings provide an improved understanding of the role of pycnidia in the epidemiology of twig and blossom blight and stem dieback caused by P. vaccinii on highbush blueberry.
Pathological and Ultra-structural Changes in Testis of Rats due to Doxorubicin Toxicity and its Amelioration with Quercetin

Anthracyclins are currently the most effective group of antineoplastic drugs used in clinical practice, among them Doxorubicin (DOX), is a key chemotherapeutic agent in cancer treatment, isolated from the soil fungus Streptomyces peucetiuscaesius. Doxorubicin, known as topoisomerase II (TOP2) poison, blocks the synthesis of DNA by intercalating into the DNA strand. Although doxorubicin is considered a very potent and efficient chemotherapeutic drug, it also kills healthy cells, especially those under rapid and constant proliferation. Therefore, DNA of rapidly dividing cells such as the testicular germ cells can be the preferential target of doxorubicin resulting in reproductive toxicity. DOX-induced organopathy involves the generation of free radicals which result in membrane and macromolecule damage by lipid peroxidation, DNA fragmentation and protein oxidation (Granados-Principal et al., 2010). Because of high concentration of polyunsaturated fatty acids and low antioxidant capacity the mammalian International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 7 (2017) pp. 2295-2306 Journal homepage: http://www.ijcmas. com
Localizing Islam in the West : Mazrui's Journey from the Study of African Politics to Global Cultures

Ali Mazrui attempted to correct many misunderstandings of Islam in the West and demonstrate its closeness to and impact upon western civilization in several ways. For example, Islam is a fellow monotheistic religion, has preserved and added to the Greco-Roman legacy, preceded mercantilism and capitalism in hailing free trade and hard work, and modeled the western view of a tripartite world in the second half of the twentieth century. Mazrui's interest in studying Islam was originally part of his general exploration of postcolonial Africa. Although trained in mainstream political science, which emphasizes materialism, he quickly realized that culture is a powerful key to understanding politics. From this cultural optic, Mazrui began to interpretatively revive Islam as a powerful factor in African politics and highlight its values as capable of improving African conditions. His most celebrated work, namely, the 1986 television series "Africa: The Triple Heritage," was in part a call to reconsider Islam as a major foundation of African societies. His cultural studies helped him gain new constituencies among the larger Muslim community and then go global. His global studies upheld Islam against both Marxism and racism, which helped him escape the narrowness of Afro-centrism and broaden his concept of pan-Africanism to include not only sub-Saharan Africans and their Arab neighbors to the north, but also the Arab neighbors to the east and diasporic Africans as well. In this paper, I use many of Mazrui's publications that discuss various Islamic issues in Africa, the West, and globally.
Investigating tRNA abundance as a determinant of decoding speed in Saccharomyces cerevisiae.

There are two main points that control the rate of translation, translation initiation which controls the rate of recruitment of ribosomes to the mRNA, and translation elongation which controls the speed with which ribosomes decode the mRNA. When initiation is not limiting, ribosomal queues can build up, reducing ribosomal clearance from the start codon. The dynamics of elongation control are largely determined by the decoding speed of individual codons. One way in which the system controls the rate and efficiency of translation is through codon bias, taking advantage of the differences in decoding speed. Our aim in this study is to investigate the role of tRNA abundance in determining decoding speed for the synonymous codons of threonine. Using Saccharomyces cerevisiae, we build codon reporter constructs where a codon optimised Renilla luciferase gene was preceded by ten codon repeats of one of the four threonine codons, in such a way that the decoding speed of the codon repeats determined the expression levels of the luciferase. Our analyses showed that the observed protein levels of RLuc correlated with the predicted order of decoding speeds, based on our knowledge of threonyl-tRNA populations, in descending order ACT, ACA, ACC and ACG. However, RNA analyses suggest that only one out of the four threonine reporters, ACG10_Rluc was limited at the level of translation thus able to report on decoding speed. Our current data suggest that decoding speed reporters based on the principle tested here are of limited usefulness, because of unanticipated interactions between codon usage and mRNA levels.
The Radicals Scavenging Activity of Yogurt Fortified with Rose Hip Marmalade During 21 Days of Storage Period

In this study, the handmade rose hip marmalade was added to regular yogurt (before or after fermentation) and in different concentrations (5, 10, 15%). The physico-chemical, micro-biological, antioxidant activity and phenolic compounds properties of yogurt fortified with rose hip marmalade were determined during 21 days of storage period. Practical experiments show that the rose hip marmalade participate in enhancing the radical scavenging activity, phenolic compounds and water holding capacity of yogurt. While gradually the conditions and duration of storage contribute to significant decreases in radical scavenging activity, phenolic compounds and water holding capacity as well as the sensory evaluation. Results show that the 15% concentration of rose hip marmalade increased the radical scavenging activity in comparing with other concentrations. On the other hand the best effect of marmalade concentrations in overall properties was recorded in 10% concentration; also the shelf life of yogurt fortified with rose hip marmalade was determined in 14 days. Keywords: antioxidant, radical scavenging activity, free radicals, rose hip marmalade, yogurt.
Growing Up Shuar: Life History Tradeoffs and Energy Allocation in the Context of Physical Growth Among an Indigenous Amazonian Population

Life history theory assumes that organisms allocate energetic resources (i.e., calories) to primary life functions such as maintenance, growth, reproduction, and physical activity in a manner that maximizes fitness. Under this conceptual framework, energy is limited, resource allocation is dynamic, and functional tradeoffs between competing metabolic processes are expected to occur. Life history tradeoffs have been invoked to explain biological variation across a range of species and ecological contexts. However, few studies have examined patterns of energy allocation and tradeoffs during human development, restricting fundamental understandings of human life history, phenotypic plasticity, and health. This dissertation investigates human energy allocation and life history tradeoffs in the context of physical growth among the Shuar, a small-scale indigenous population from Amazonian Ecuador. Mixed-longitudinal anthropometric data were collected from 2,553 Shuar between the ages of 0-29 years. Additional market integration (i.e., production for and consumption from a market-based economy) and immune activity (i.e., finger-prick blood biomarker) data were obtained from a subset of children and adolescents. Analysis was performed to explore variation in physical growth at the population, regional, household, and individual levels. Results demonstrate that, as a population, the Shuar grow significantly more slowly than international references and experience several unique developmental characteristics that may be
Phototropism in light-grown mustard (sinapis alba l.) seedlings.

This thesis is an investiga tion of the mechanisms of b lu e l ig h t mediated phototropism in higher p lants. Phototropism was analysed in light-grown mustard (Sinapis alba L.) seedlings under low pressure sodium (SOX) lamps to minimise the involvement o f phytochrome. L igh tgrown mustard seedlings do not show a blue-light-mediated in h ib i t io n o f axis extension growth and the Blaauw theory must therefore be rejected as an explanation of phototropism. Phototropic curvature was established by an in h ib i t io n of growth on the il lum inated side of the hypocotyl accompanied by an equal but opposite acceleration on the shaded side, w ith l i t t l e or no change in net growth. This pattern o f d i f fe re n t ia l growth can be modified by l ight-grow th responses separate from those involved in phototropism. Preliminary resu lts from a biophysical analysis o f ce l l growth using micro-pressure probes indicates phototropic growth responses are caused by changes in wall rheological properties, possibly by wall e x te n s ib i l i ty alone. There is a complex re la tionsh ip between the k ine t ics o f phototropism and stimulus fluence ra te . The lag time is independent o f fluence ra te . The i n i t i a l rate of curvature was d ire c t ly proportional to log fluence rate between threshold and saturation fluence ra tes. Following th is i n i t i a l phase, gravi t ro p ic compensation and auto­ tro p ic stra ightening modify curvature, which can no longer be used as a qu an t ita t ive measure of phototropism. Implications fo r measurement o f the response and selection of appropriate photobiological conditions are outlined The magnitude o f the internal l ig h t gradient influences the rate o f curvature The experimental resu lts are discussed in re la t io n to other knowledge o f the phototropic transduction chain. The resu lts are not inconsistent w ith the Cholodny-Went theory o f phototropism. Preliminary data ind ica ting phytochrome-mediated phototropism are presented, and the comparison of lag times in p lant physiology is also discussed.