Miracle-dz/UniFAR-FTUs huggingface dataset:
Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain.

PURPOSE In radiotherapy (RT) based on magnetic resonance imaging (MRI) as the only modality, the information on electron density must be derived from the MRI scan by creating a so-called pseudo computed tomography (pCT). This is a nontrivial task, since the voxel-intensities in an MRI scan are not uniquely related to electron density. To solve the task, voxel-based or atlas-based models have typically been used. The voxel-based models require a specialized dual ultrashort echo time MRI sequence for bone visualization and the atlas-based models require deformable registrations of conventional MRI scans. In this study, we investigate the potential of a patch-based method for creating a pCT based on conventional T1-weighted MRI scans without using deformable registrations. We compare this method against two state-of-the-art methods within the voxel-based and atlas-based categories. METHODS The data consisted of CT and MRI scans of five cranial RT patients. To compare the performance of the different methods, a nested cross validation was done to find optimal model parameters for all the methods. Voxel-wise and geometric evaluations of the pCTs were done. Furthermore, a radiologic evaluation based on water equivalent path lengths was carried out, comparing the upper hemisphere of the head in the pCT and the real CT. Finally, the dosimetric accuracy was tested and compared for a photon treatment plan. RESULTS The pCTs produced with the patch-based method had the best voxel-wise, geometric, and radiologic agreement with the real CT, closely followed by the atlas-based method. In terms of the dosimetric accuracy, the patch-based method had average deviations of less than 0.5% in measures related to target coverage. CONCLUSIONS We showed that a patch-based method could generate an accurate pCT based on conventional T1-weighted MRI sequences and without deformable registrations. In our evaluations, the method performed better than existing voxel-based and atlas-based methods and showed a promising potential for RT of the brain based only on MRI.
Finding 16S rRNA gene-based SNPs for the genetic traceability of commercial species belonging to Gadiformes

Abstract A SNPs (Single Nucleotide Polymorphism) based analysis was developed to differentiate four economically important species belonging to the Gadiformes order: Pacific cod Gadus macrocephalus, Atlantic cod Gadus morhua, Haddock Melanogrammus aeglefinus and Ling Molva molva. A 430bp fragment of the 16s rRNA gene was amplified using interspecific conserved primer and sequenced. The sequences were aligned and analyzed for the presence of SNPs; three SNPs (MerSNP1, MerSNP7 and MerSNP9) were identified and selected to allow discrimination between the four species. Aplotypes were TCC, CCC, CAT and CAC for Pacific cod, Atlantic cod, Haddock and Ling respectively. Confirmation of results was achieved by sequencing 16s rRNA gene fragments of 16 G. morhua, 7 G. macrocephalus, 15 M. aeglefinus and 5 M. molva samples collected at different fish catching campaign. Nucleotide sequence of 16s rRNA mitochondial gene has been shown to be a useful tool to allow rapid reliable and fully automatable for discrimination of 4 economically important species in fisheries industry.
The taxonomic status of Megalurothrips Bagnall (Thysanoptera : Thripidae)

Abstract Megalurothrips Bagnall, hitherto treated as a synonym of Taeniothrips A. & S. , is here re-elevated to generic rank and characterized. The genus is reviewed and eight nominal species are included. Taeniothrips ditissimus A. & J. is synonymised with Megalurothrips morosus (Pr.); Taeniothrips distal is var. infernalis Pr. is considered a synonym of M. distalis (Ka.); while Pongamiothrips Anan. is sunk under Megalurothrips.
Evidence of deep genetic divergence between populations of an important recreational fishery species, Lichia amia L. 1758, around southern Africa

Lichia amia is an important coastal recreational fishery species with a cosmopolitan distribution in the eastern Atlantic. In southern Africa, it is distributed from southern Angola to northern KwaZulu-Natal in South Africa. A recent biological survey revealed differences between Angolan and South African individuals suggesting that they may represent separate stocks. As fishery management decisions should be based on accurate knowledge of population structure, an initial survey of the genetic substructuring of L. amia was conducted on samples collected in southern Angola and South Africa. Assessment of genetic diversity and population structure was conducted using a fragment of the mitochondrial Control Region. Obtained genetic diversity levels were within the expected range for marine teleosts (h = 0.867, π = 0.007), and two deeply divergent (southern Angolan and South African) populations were identified (average φ ST = 0.78) across the Benguela Current system. These results suggest that Angolan and South African L. amia should be managed as two independent stocks. This work represents the first assessment of population genetic substructuring across the Benguela Current of a valuable coastal fishery resource, and has application for future fisheries management.
Regulation of plant nitrate assimilation: from ecophysiology to brain proteins

Nitrogenous inorganic compounds impact plants as nutrients, signals and toxins. We are dissecting a regulatory network that controls nitrate assimilation at the level of nitrate reductase (NR) activity. The identification of protein kinase cascades, protein phosphatases and 14-3-3 proteins as regulators of NR are giving clues about how plants sense their nutrient availability, and use the information to signal changes in their metabolism and developmental strategies to cope with supplies. We hope that understanding these controls might lead to the design of transgenic plants with deregulated signalling networks, which would make them more efficient in using nitrogen fertilizers, and improving quality and yield of crops. There are circumstantial indications that gaseous anthropogenic nitrogenous emissions might also have complex regulatory influences on plant growth and development.
Modélisation du comportement vibro-acoustique des structures

Le manuscrit est decompose en trois parties. Dans la premiere partie sont decrits les travaux de recherches portant sur l'elaboration de methodes qui reposent sur une description du champ de deplacement des structures et du champ de pression des parties acoustiques. Il s'agit de methodes de syntheses modale propres au groupe de recherche auquel j'appartiens et que j'ai eu l'occasion d'etudier lors de ma these de doctorat. La seconde partie est consacree aux methodes energetiques, et plus particulierement a la Methode \'Energetique Simplifiee (MES) developpee au laboratoire LTDS. Il s'agit essentiellement de reformulations de la methode permettant de l'adapter a des problemes de detection de source, d'optimisation de caracteristiques de materiaux et d'optimisation de forme. La derniere partie regroupe les techniques permettant d'effectuer des etudes large bande au moyen de formulations hybrides qui reposent sur les travaux des deux premieres parties. Differentes approches sont proposees, et une methode particuliere est developpee pour l'etude du bruit rayonne par un systeme de freinage automobile.
Low reproductive output of isolated, self-fertilizing snails: inbreeding depression or absence of social facilitation?

Inbreeding depression has been studied extensively in many animals, but the potential of ‘social facilitation' (a response to the presence of conspecifics in the environment) to influence reproduction has received little attention. Studies of reproductive output in freshwater hermaphrodite snails have implicated inbreeding depression, but never social facilitation, in the reduced reproductive output of isolated compared with paired/grouped snails. In this experiment, isolated, self-fertilizing Biomphalaria glabrata snails had reduced reproductive output compared with paired, predominantly cross-fertilizing snails. However, the reproductive output of control snails (paired, but prevented from cross-fertilizing) was similar to that of paired, cross-fertilizing snails, suggesting that the low reproductive output of snails in isolation was not simply due to inbreeding depression with self-fertilization. I suggest that an absence of social facilitation, caused by deprivation of social communication as a result of isolation, may play a role in reducing reproductive output of isolated B. glabrata, and that future studies of inbreeding depression using isolated and paired/grouped hermaphrodite snails should be designed to control for possible effects of social facilitation.
COLUBROID SYSTEMATICS: EVIDENCE FOR AN EARLY APPEARANCE OF THE VENOM APPARATUS FOLLOWED BY EXTENSIVE EVOLUTIONARY TINKERING

Colubroids or advanced snakes form a monophyletic group comprising four families: Atractaspididae (11 genera, 70 species), “Colubridae” (300 genera, 1850 species), Elapidae (65 genera, 270 species) and Viperidae (33 genera, 240 species). A preliminary classification of colubroids based both on morphological and molecular data is presented and all extant genera of “Colubridae” are listed accordingly. The front-fanged venom system (displayed by some Atractaspididae, all Elapidae and all Viperidae) evolved several times independently and appeared early within colubroids. The rear-fanged venom system (displayed by some Atractaspididae and many “Colubridae”) has been studied less than the front-fanged system, although it is clear that opisthoglyph “Colubridae” constitute a polyphyletic group. The other components of the venom apparatus, the glands and the secretions, also show great variability, rendering the reconstruction of the evolutionary history of the venom apparatus difficult. Nevertheless, the presence of serous secretory cells in the supralabial region and of a differentiated maxillary dentition within the most basal extant lineages of advanced snakes strongly suggest that the venom apparatus is a synapomorphy of the Colubroidea and that its absence in a few “Colubridae” results from secondary losses.
Drought‐stress and plant resistance affect herbivore performance and proteome: the case of the green peach aphid Myzus persicae (Hemiptera: Aphididae)

Little is known about the simultaneous effects of drought stress and plant resistance on herbivorous insects. By subjecting the green peach aphid Myzus persicae Sulzer to well‐watered and drought‐stressed plants of both susceptible and resistant peach (Prunus persica), the effects of both stressors on aphid performance and proteomics are tested. Overall, the influence of the water treatment on aphid performance is less pronounced than the effect of host plant genetic resistance. On the susceptible cultivar, aphid survival, host acceptance and ability to colonize the plant do not depend on water treatment. On the resistant cultivar, aphid survival and ability to colonize are higher on drought‐stressed than on well‐watered plants. A study examining the pattern of protein expression aiming to explain the variation in aphid performance finds higher protein expression in aphids on the drought‐stressed susceptible cultivars compared with the well‐watered ones. In the susceptible cultivar, the regulated proteins are related to energy metabolism and exoskeleton functionality, whereas, in the resistant cultivar, the proteins are involved with the cytoskeleton. Comparison of the protein expression ratios for resistant versus susceptible plants reveals that four proteins are down‐regulated in well‐watered plants and 15 proteins are down‐regulated in drought‐stressed plants. Drought stress applied to the susceptible cultivar induces the regulation of proteins in M. persicae that enable physiological adaptation to maintain an almost unaltered aphid performance. By contrast, for aphids on the resistant cultivar subjected to drought stress, the down‐regulation of proteins responds to an induced host susceptibility effect.
Seed Dispersal by South Africa's Only Forest-Dwelling Guenon, the Samango Monkey (Cercopithecus mitis)

Primate seed dispersal in South African forests and its potential benefit to forest plants has not been extensively investigated. South African forests are inhabited by only one exclusively forest-dwelling, large-bodied, diurnal, frugivorous primate, the samango monkey (Cercopithecus mitis). Our study presents first insights into seed dispersal by samango monkeys in an Afromontane forest in their northernmost South African distribution. Through focal animal sampling we found that samango monkeys were predominantly frugivorous (72% of observed feeding time), consuming fruits of 25 plant species and dispersing the seeds of 13 (52%) of them through defecation, carrying in cheek pouches and spitting and dropping. The overall ratio of seed predation was relatively low (16%). Although our study spanned the wet season only, our findings demonstrate that samango monkeys may be potentially important seed dispersers for certain plant species (Ficus spp. and Searsia chirindensis making up 44% of the diet) in this part of their range.
Gonioinfradens paucidentatus (A. Milne Edwards, 1861) (Crustacea, Decapoda, Portunidae): a new alien crab in the Mediterranean Sea

The first record for the Mediterranean Sea of the Red Sea/Indo-Pacific portunid Gonioinfradens paucidentatus (red swimming crab) is documented. A detailed description of the specimens collected at Rodos Island (southeastern Aegean Sea) is given, while possible introduction vectors of the species in the area are discussed.
CARACTERIZAÇÃO BIOQUÍMICA DA ENZIMA ADENINA FOSFORIBOSILTRANSFERASE (APRT) DE MYCOBACTERIUM TUBERCULOSIS

A tuberculose humana e uma das doencas mais preocupantes da atualidade. A cada ano, esta patologia faz 1,7 milhoes de vitimas em todo o mundo. Alem disso, de acordo com o ultimo levantamento da OMS, em 2009, 9,4 milhoes de individuos desenvolveram a doenca. Baseado nesses dados, e fundamental buscar novos alvos para combater o principal agente causador desta doenca em humanos, o Mycobacterium tuberculosis. A busca por novos alvos pode permitir o desenvolvimento de drogas mais eficazes, que diminuam o tempo de tratamento da tuberculose e que oferecam menos reacoes adversas. Uma proteina ainda nao explorada no bacilo e a adenina fosforibosiltransferase (APRT). Esta enzima e responsavel por catalisar uma reacao entre PRPP e base adenina livre, para formar AMP e PPi. Sabe-se que esta enzima tem um papel bastante importante na via de salvamento de purinas, uma rota metabolica dentro do metabolismo de nucleotideos. Ela ja foi estudada em diversos organismos, incluindo seres humanos, a bacteria Escherichia coli e diferentes eucariotos basais como especies do genero Leishmania. Este projeto tem como objetivo caracterizar os processos bioquimicos basicos desta enzima. Para isso, o gene apt da cepa laboratorial H37Rv de Mtb precisa ser amplificado por PCR e clonado em vetores plasmidiais. A proteina entao sera superexpressa em celulas de E. coli, purificada por HPLC para remover os contaminantes e caracterizada por ensaios enzimaticos utilizando um espectrofotometro.
Nitrogen and carbon limitation of planktonic primary production and phytoplankton–bacterioplankton coupling in ponds on the McMurdo Ice Shelf, Antarctica

We compared planktonic primary and secondary production across twenty meltwater ponds on the surface of the McMurdo Ice Shelf in January 2007, including some ponds with basal brines created by meromictic stratification. Primary production ranged from 1.07 to 65.72 mgC m−3 h−1 in surface waters. In stratified ponds primary production was always more than ten times higher in basal brines than in the corresponding mixolimnion. Regression tree analysis (r2 = 0.80) identified inorganic nitrogen (as NH 4 + ? > ) as the main factor limiting planktonic primary production. However, there was also evidence of inorganic carbon co-limitation of photosynthesis in some of the more oligotrophic waters. Neither C nor N limited carbon fixation at [NH4–N] > 50 mg m−3, with photoinhibition the factor most likely limiting photosynthesis under such conditions. Primary production was the only factor significantly correlated to bacterial production and the relationship (r2 = 0.56) was non-linear. Nitrogen limitation and tight coupling of planktonic primary and bacterial production is surprising in these ponds, as all have large pools of dissolved organic carbon (1.2–260 g m−3) and organic nitrogen (all >130 mg m−3). The dissolved pools of organic carbon and nitrogen appear to be recalcitrant and bacterial production to be constrained by limited release of labile organics from phytoplankton.
Distributed heterogeneous systems for large-scale graph processing

Graph processing is increasingly popular in a variety of scientific and engineering domains. Consequently, graphs and graph-processing algorithms have become increasingly more diverse. Following the big data trend in every computer-related domain, graphs have also become increasingly larger. Processing graphs is requiring more sophisticated computer systems. Important for this thesis, graph-processing systems now need to combine scalability (a grand challenge in computer science) and raw processing power (an endless race), with efficiency especially in cost and energy requirements (a difficult to define and ensure non-functional property for computer systems). New trade-offs between these elements are offered by two important trends in computer systems. First, distributed systems have grown in popularity and cost-efficiency. Second, GPUs offer an excellent performance-energy ratio and are included in most modern computers. By combining distributed CPU-based systems and non-distributed GPU-enabled systems into distributed heterogeneous systems, large-scale graph processing may become possible and efficient. However, many challenges still exist in the area of graph processing before distributed heterogeneous systems can be well understood. In this thesis, we conduct fundamental and applied research to address three major challenges in three research directions of graph processing: application (understanding new data characteristics and sharing graphs), knowledge (evaluating and comparing the performance of various graphprocessing systems), and design (designing new partitioning policies and entire graphprocessing systems that can use both CPUs and GPUs on multiple machines).
Food quality for Daphnia in humic and clear water lakes

1. Growth and reproduction of Daphnia fed lake seston were measured in two categories of meso- to eutrophic lakes differing with respect to terrestrial organic matter influence (humic and clear water lakes). The content of highly unsaturated fatty acids (HUFA), P and N, as well as the taxonomical composition of seston were analysed.2. Seston HUFA and C : P ratios were similar between lake categories, whereas C : N ratios were lower in the clear water lakes in both spring and summer. Despite the similarity in HUFA and P content of seston, Daphnia growth rate, clutch size and the proportion of gravid females were, respectively, about 1.5, 3 and 6 times higher in the clear water lakes.3. Differences in growth and reproduction were related to a combination of higher N content and good fatty acid quality of the seston in the clear water lakes. Relatively high biomass of edible algae, such as Rhodomonas sp. and Cryptomonas sp. , in the clear water lakes, and differences in water pH likely contributed to the observed differences in Daphnia growth and reproduction between lake categories. Additionally, it is possible that Daphnia was energy limited in the humic lakes despite high particulate organic carbon (POC) concentrations, as the contribution of non-algal and detrital C to the POC pool was high.4. Our results suggest that dietary HUFA content has the potential to improve herbivore growth and reproduction if N and P are not limiting. N merits more attention in studies of zooplankton nutrition. (Less)
Identification of novel SNPs in INHBB gene of Indian goat

Inhibin ï¢B (INHBB) gene is considered as a possible candidate gene for the prolificacy trait based on the important role of inhibin in reproduction. A mutation (A782G) in exon 2 of INHBB gene has significant effect on litter size in Jining Grey goats. Thus the objective of the present study was to explore polymorphism (SNP) in exon 2 region of INHBB in a panel of Indian goats consisting of high, medium and low prolificacy goat breeds. Two pairs of primers, P1 and P2 were designed according to the exon 2 sequence of bovine INHBB with amplified product size of 244bp and 296bp respectively. Polymerase chain reaction followed by direct DNA sequencing revealed absence of already reported SNP (A782G) in Indian goats where favorable A allele was fixed. Two novel SNPs were identified in the amplified products of primer P2 in Indian goats. These included Gï‚®A mutation at base 693 and Cï‚®T mutation at base 840 of exon 2 (numbering is with respect to U16241 sequence) in Indian goats, which did not cause any amino acid change. Allele distribution was of similar magnitude in Indian goats with predominance of wild allele (G=0.93 and C=0.96). Heterozygote was observed for G693A mutation in one animal each of Beetal, Osmanabadi, Sangamneri and Ganjam breeds, however heterozygotes of C840T mutations were observed in 4 animals of Osmanabadi breed only. Novel SNPs need further investigations for association with prolificacy trait that would have important implications for the goat industry.
Studies on the induction of chlorophyll fluorescence in barley protoplasts. I. Factors affecting the observation of oscillations in the yield of chlorophyll fluorescence and the rate of oxygen evolution

Chlorophyll fluorescence and oxygen evolution have been measured in suspensions of protoplasts isolated from barley leaves. Like the parent tissue, the protoplasts exhibit transients in both fluorescence and the rate of oxygen evolution upon illumination and before a steady state rate of photosynthesis is reached. The two signals are anti-parallel and slightly phase shifted with fluorescence changes preceeding alteration in the rate of oxygen evolution by 10-15 s. Fast (t ≈ 15 s) and a slow (t ≈ 2 min) fluorescence peaks were observed, the latter strongly resembling the oscillations described in leaves (Walker, Horton, Sivak & Quick, Photobiochem. Photobiophys. 5, 35 (1983)). The amplitude of the oscillation was most pronounced in strong light, and at high (more than 8.0) pH whereas the period was temperature dependent. Antimycin A was found to suppress the slow oscillation but to exaggerate the fast transient, whereas low ( < 0.1 μM) DCMU had the reverse effect. These results are discussed in terms of a proposed mechanism to account for these transients and it is suggested that cyclic electron flow may have an important role.
Response of Antioxidative Enzymes to Cadmium Stress in Leaves and Roots of Radish (Raphanus sativus L.)

Presented study has demonstrated that exposure of plants to toxic heavy metal Cd results a reduction in plant growth. Varied concentrations of CdCl2, ranging from 0.0 to 50 ppm in the germinating media reduced leaf area of radish plant, chlorophyll and carotenoid contents. Greater loss of chlorophyll b content than chlorophyll a was observed especially under 50 ppm Cd exposure. With regards to the distribution of Cd in roots and leaves, the obtained data showed that the maximum accumulation of Cd occurred in roots followed by leaves. Generally, Fe, Zn, Mn and Cu declined in leaves compared to the roots. Furthermore, substantial increases were observed in antioxidant enzymes, such as catalase (CAT), glutathione S-transferase (GST) and peroxidase (POD), in Cd-stressed plants in comparison with control. The Cd stress also induced several changes in CAT and POD isozyme profiles and enhanced their activities. The results suggest that the reduction of leaf area and pigment content together with antioxidant enzymes and isozyme patterns can be used as indicators to Cd contamination.