Miracle-dz/UniFAR-FTUs huggingface dataset:
Intrinsic functional reorganisation of the attention network in the blind

Attention can bias visual perception by modulating the neuronal activity of visual areas. However, little is known if blindness can reshape the intrinsic functional organisation within the attention networks and between the attention and visual networks. A voxel-wise network-based functional connectivity strengthen mapping analysis was proposed to thirty congenitally, thirty early and thirty late blind subjects, and thirty sighted controls. Both the blind and sighted subjects exhibited similar spatial distributions of the intrinsic dorsal (DAN) and ventral (VAN) attention networks. Moreover, compared to the sighted controls, the blind subjects showed increased functional coupling within the DAN, and between the DAN and VAN, and between the attention sub-networks and visual areas, suggesting an increased information communication by visual deprivation. However, the onset age of blindness had little impact on the functional coupling of the attention network, indicating that non-visual sensory experience is enough for driving the development of intrinsic functional organization of the attention network. Finally, a positive correlation was identified between the duration of blindness and the functional coupling of the posterior inferior frontal gyrus with the visual network, representing an experience-dependent reorganisation after visual deprivation.
Male chemical cues mediate the female preference for egg deposition site in Rhynchophorus ferrugineus.

The choice of a suitable oviposition site is critical for the reproductive success of many animals. In insects, oviposition site choice is often driven by chemicals: oviposition-deterring pheromones are well known for many insects, whereas oviposition-stimulating pheromones have only been reported for a few species. Here, we investigate which cues trigger the choice of a deposition site in the Red Palm Weevil, Rhynchophorus ferrugineus (Olivier) (Coleoptera Dryophthoridae), the worst palm pest. Our experiments clearly showed that females prefer to lay eggs in a substrate already used for the same purpose. To provide evidence for cues mediating this preference, we carried out a series of bioassays following a binary-choice test paradigm. Our results showed that neither the presence of eggs nor the polar or apolar compounds extracted from the egg surface affected female preference. Moreover, experiments in which the body of adults was rubbed on the substrate allowed us to exclude that body surface compounds are involved in this process. Bioassays preventing male-substrate contact suggested a role of the male in determining the female’s choice of the oviposition site. Our results suggest the male aggregation pheromone as the best candidate to mediate such female preference. Further studies will be necessary to clarify whether female preference represents a simple by-product of the aggregation pheromone effect or is due to a specific compound of the pheromone that triggers the female behaviour.
Inhibition of monocarboxylate transporter 1 by AZD3965 as a therapeutic approach in oncology

i Acknowledgements . iii List of Figures and Tables . xi List of Abbreviations . xiv Chapter 1. Introduction . 1 1.1. Cellular metabolism . 1 1.1.1. Glycolysis . 1 1.1.2. Oxidative phosphorylation . 3 1.2. Reprogramming energy metabolism ‐ An emerging hallmark of cancer . 6 1.2. 1. The Warburg effect . 6 1.2. 2. Regulation of cellular metabolism in cancer . 8 1.3. Therapeutic targeting of tumour metabolism . 11 1.3. 1. Nucleotide biosynthesis . 13 1.3. 2. Amino acid metabolism . 13 1.3. 3. Oxidative phosphorylation . 14 1.3. 4. Glycolysis . 14 1.4. Monocarboxylate transporter 1 . 16 1.4. 1. Structure . 16 1.4. 2. Function of monocarboxylate transporters 1‐4 . 16 1.4. 3. Mechanism of lactate transport . 18 1.4. 4. Regulation . 18 1.5. MCT1 as a therapeutic target in cancer . 20 1.5. 1. Differential expression of MCTs in cancer . 20 1.5. 2. Lactate shuttle hypothesis . 21 1.5. 3. MCT1 inhibition in in vitro and in vivo cancer models . 21
Spatial characteristics of species distributions as drivers in conservation prioritization

Spatial prioritization, based on the biogeographical identification of priority areas for conservation actions, is an important aspect of conservation planning. Although the influence of factors such as costs, threats or use of surrogates on the resulting priorities has been studied extensively, relatively little is known about how the spatial characteristics of species distributions drive the spatial pattern of priorities in multi‐species conservation plans. Using datasets from Australia and Finland, we explore how excluding or including a given species changes spatial priorities in a multi‐species prioritization. We develop three metrics to quantify changes in priorities, and explore how these changes depend on the total number of species used in the prioritization, the spatial characteristics of the given species distribution, and how species share their space with other species used in the prioritization. We randomly selected 12 set of 10 species from each dataset, and explore the influence of each of these species in prioritizations done for a total of 10, 20, 50 or 100 species. We show that spatial priorities become increasingly stable as the number of species is increased, and that the stability of highest and lowest priority areas behave differently. When less than 50 species were used in a prioritization, intermediately rare species that occupy mostly species‐poor habitats tend to have the greatest influence on priorities, whereas very rare and common species that co‐occur with many other species tend to have a small influence. Our results present a systematic method to explore the stability of spatial priorities to changes in the species pool used for a conservation plan. Although the analysed two datasets differed in data type, location, scale and species composition, they both showed how using a small number of species leads to unstable spatial solutions, where the choice to include or exclude an individual species can strongly influence the conservation outcome. Our results also show that conservation planners should carefully assess the use of spatial prioritizations for identifying least important areas (e.g. for development) as these can be particularly unstable when the prioritization is based on a small number of species.
Population connectivity: combining methods for estimating avian dispersal and migratory linkages

We use a variety of methods to study population connectivity. In Chapter 1, we use stable isotope ratios in feathers to make Bayesian inferences about the migratory connectivity between breeding and wintering grounds of Henslow’s sparrows. We use hydrogen and carbon stable isotope ratios (deltaH and deltaC). We compare the deltaH and deltaC of feathers from wintering sparrows to five breeding region deltaH and deltaC to estimate the probability that each individual wintering sparrow originated from each of the five regions. Breeding bird abundances are used as prior probabilities of breeding region origin. We conclude that there are no clear linkages between specific breeding regions and wintering sites. In Chapter 2, we use three methods to estimate dispersal in Henslow’s sparrows. 1)deltaH in feathers are used to determine whether an individual breeding bird has a deltaH signature characteristic of the breeding site. 2) Song structure is used as the signature of an individual’s previous breeding-ground origin. 3) Genetic markers are used to evaluate population structure. Genetic structure is evaluated using three estimates. Fst estimates and private alleles are used too calculate the number of migrants per generation (Nm) between sites. Private alleles are evaluated to determine if they are truly private. A Bayesian clustering method is used to infer the number of populations. All methods revealed high rates of dispersal.
Phytochemistry of hydroxycoumarins from Manihot esculenta Euphorbiaceae (cassava)

This is an interdisciplinary research project on cassava (Manihot esculenta Crantz, Euphorbiaceae) ultimately working towards producing cassava roots which are long-lasting, free of post-harvest physiological deterioration (PPD). It aims to contribute to ensuring food security. In cassava, scopoletin and its -glycoside scopolin are considered phytoanticipants, not phytoalexins, due to their increasing accumulation during the PPD process compared to their barely detectable levels in fresh roots. Starting with a focussed literature review on the potential of cassava, contrasted with its limitations on harvesting due to PPD, and biosynthesis along the phenylpropanoid pathway of key hydroxycoumarins, e.g. scopoletin and esculetin, the associated gaps in our current knowledge have been set out. Whether scopoletin is biosynthesized de novo from L-phenylalanine in response to stress, or whether stress prompts its release from the corresponding glycoside is unknown. Therefore, assessing hydroxycoumarin biosynthesis and quantifying their accumulation patterns have been undertaken in wild-type and transgenic plants in order to elucidate the divergence in scopoletin biosynthetic pathways. The identification of key genes on each pathway leading to scopoletin in cassava, and then exploring their functional identities using the model plant A. thaliana and genetically engineered E. coli, where the genes were isolated, cloned, and expressed, were also undertaken. Transgenic A. thaliana lines with no activity of the key enzymes on the proposed pathway, namely F6ʹH1, CCoAOMT, and EOMT, were developed. Competition feeding experiments using stable isotopically labelled potential biosynthetic intermediates showed the incorporation of labelled ferulate into scopoletin in transgenic A.t-F6´H1 and M.e-F6´H. This confirmed the activity of other hydroxylase enzymes rather than F6´H1 in the ortho-hydroxylation steps. The hydroxycoumarins of interest were isolated, characterized, and quantified in the wild type and mutant lines using chromatographic and spectroscopic techniques, mainly NMR, HR-MS, and LC-MS. Taken together, a significant contribution to knowledge about hydroxycoumarin biosynthesis has been made.
Neotropical Orchid Miscellanea

Abstract. Literature and herbarium studies of various orchid taxa that occur in the New World leads to the recognition of four new species, epitypification, lectotypification, and synonymisation of some neglected names, and the transfer of three names. Furthermore, reviews are presented on the synonymy and identity of the red-orange flowered Fernandezia species in Colombia and Venezuela, and the circumscription of Odontorrhynchus chilensis in Chile. The new species proposed are Aspidogyne jussariensis, Liparis vasquezii, L. yanachagae, and Microchilus tunquianus ; new combinations are Bulbophyllum pinelianum, Maxillaria humilis, and Microstylis section Chrysanthera; new lectotypifications and synonymy are Epidendrum acinacifolium (= Tolumnia variegata), E. calcaratum (= Ionopsis utricularioides), E. minimum (= Polystachya foliosa), and E. obtusifolium (= E. nocturnum); Polystachya extinctoria (= P. concreta) is neotypified; new synonyms are Centropetalum lanceolatum (= Fernandezia sanguinea), Fernandezia aurantiaca, F. ortiziana (both = F. myrtillus), Fernandezia tica (= F. sanguinea), Gomesa stricta (= Pleurothallis quadrifida), Nasonia hartwegii (= Fernandezia myrtillus), Odontorrhynchus domeykoanus, O. erosus, O. variabilis (all = O. chilensis), and Pachyphyllum favosifolium (= Fernandezia sanguinea).
Health effects of resistant starch

The merits of a fibre-rich diet are well documented. Resistant starch (RS) is a form of starch that resists digestion in the small intestine and, as such, is classified as a type of dietary fibre. RS can be categorised as one of five types (RS1–5), some of which occur naturally in foods such as bananas, potatoes, grains and legumes and some of which are produced or modified commercially, and incorporated into food products. This review describes human evidence on the health effects of RS consumption, with the aim of identifying any benefits of RS-rich foods and RS as a functional ingredient. The reduced glycaemic response consistently reported with RS consumption, when compared with digestible carbohydrate, has resulted in an approved European Union health claim. Thus, RS-rich foods may be particularly useful for managing diabetes. There appears to be little impact of RS on other metabolic markers, such as blood pressure and plasma lipids, though data are comparatively limited. Promising results on markers of gut health suggest that further research may lead to the classification of RS as a prebiotic. Microbial fermentation of RS in the large intestine to produce short-chain fatty acids likely underpins some of its biological effects, including increasing satiety. However, effects on appetite have not resulted in notable changes in bodyweight after long-term consumption. Emerging research suggests potential for RS as an ingredient in oral rehydration solutions and in the treatment of chronic kidney disease. Overall, RS possesses positive properties as a healthy food component.
Use of passive acoustic monitoring to characterize fish spawning behavior and habitat use within a complex mosaic of estuarine habitats

Structurally complex estuarine habitats, such as seagrass beds, salt marshes, and oyster reefs, are used by fish for foraging, avoiding predators, and spawning. Here, we used passive acoustics to characterize spatiotemporal patterns in the soundscape of an estuarine reserve that contained a mosaic of habitat types, and focused on relating characteristics of the soundscape [e.g., low-frequency (150–1500 Hz) sound pressure levels (SPLs), amount of fish chorusing] to patterns in the seascape (percent cover of estuarine habitats surrounding the recording sites). Over a 3-mo period, 2-min duration underwater sound recordings were made every 20 min at eight sites within Middle Marsh in Back Sound, North Carolina, USA. While habitat composition was not related to spatial patterns in low-frequency SPLs, there was a positive and statistically significant relationship between the percent recordings with fish chorusing, and percent cover of seagrass for silver perch [Bairdiella chrysoura (Lacepede, 1802)], spotted seatrout [Cynoscion nebulosus (Cuvier, 1830)], and other fish, irrespective of spatial scale (10 vs 25 m). Moreover, silver perch and spotted seatrout, soniferous species that share similar spawning locations, exhibited temporal partitioning in the soundscape with seatrout calls occurring just before sunset and peaking several hours after sunset, and declining sharply as perch chorusing increased after sunset with a peak at midnight. Overall, local habitat composition and the soundscape at these sites were not highly correlated; where major sound producing fish species are transient, other seascape characteristics, such as proximity to channels, likely have a larger influence on the resulting soundscape.
Initiation à la génétique des populations naturelles : Applications aux parasites et à leurs vecteurs

Thierry De Meeûs est chercheur à l’IRD, spécialisé en écologie évolutive et en génétique des populations dans les systèmes hôte-parasite-vecteur (laboratoire Intertryp, UMR 177 IRD/Cirad). Il mène en parallèle une activité d’enseignement et de recherche et travaille actuellement au Cirdes (Burkina Faso) sur les trypanosomoses africaines et les mouches tsétsé. Il est co-auteur de nombreuses publications dans différentes revues ou ouvrages collectifs.
Agent-Based Modelling in Multicellular Systems Biology

This chapter aims at discussing the content of multi-agent based simulation (MABS) applied to computational biology i.e., to modelling and simulating biological systems by means of computational models, methodologies, and frameworks. In particular, the adoption of agent-based modelling (ABM) in the field of multicellular systems biology is explored, focussing on the challenging scenarios of developmental biology. After motivating why agent-based abstractions are critical in representing multicellular systems behaviour, MABS is discussed as the source of the most natural and appropriate mechanism for analysing the self-organising behaviour of systems of cells. As a case study, an application of MABS to the development of Drosophila Melanogaster is finally presented, which exploits the ALCHEMIST platform for agent-based simulation.
Impact of Ejaculate Frequencies on the Quality of Red Jungle Fowl (Gallus gallus murghi) semen

The Red Jungle Fowl (Gallus gallus murghi), a native species of Southern Asia is threatened by habitat destruction, egg collection, predation and genetic hybridisation. Semen banking is one of the reproductive techniques used for the conservation of endangered species. To develop a semen bank for Red Jungle Fowl, the impact of semen collection frequencies on spermatozoa must be known. The study evaluated the impact of four ejaculate collection frequencies (once in 12, 24, 48 and 72 hours) on semen quality parameters (volume, motility, concentration, live/dead ratio, acrosomal integrity and plasma membrane integrity) of Red Jungle Fowl semen. Sperm motility and concentration was higher (P < 0.05) at 24, 48 and 72 hours of collection period compared to 12 hours. Semen volume increased (P < 0.05) at 48 and 72 hours of collection compared to 12 and 24 hours of collection frequency. The sperm acrosomal integrity was higher (P < 0.05) at 72 hours of collection compared to 12, 24 and 72 hours of collection frequency. The plasma membrane integrity was not affected by the frequency of collection (P > 0.05). The number of live sperm were observed to be higher (P > 0.05) at 12 hours of collection compared to 24, 48 and 72 hours. The overall semen output of all cocks was theoretically similar at a collection frequency of once in 48 hours and 72 hours in all of the semen quality parameters evaluated in this study. It is concluded that semen of optimum quality may be collected at 48 and 72 hours of interval for captive breeding programs of Red Jungle Fowl.
Toward a comprehensive taxonomic revision of the “hirculus” group of American Onthophagus Latreille, 1802 (Coleoptera, Scarabaeidae, Scarabaeinae)

The taxonomy of the American Onthophagus Latreille, 1802 included in the “ hirculus ” group is revised, and a study of their morphology allows for the delineation of five species-complexes. Herein, we provide a diagnosis of the “ hirculus ” group, an illustrated key to the complexes, along with a descriptive overview of their taxonomy and geographic distribution. Onthophagus hirculus Mannerheim, 1829 is considered to be a junior synonym of O. hircus Billberg, 1815, which is here demonstrated to be a valid species name. Thus, the “ hirculus ” group is here renamed the “ hircus ” group. Furthermore, a general scheme of the genital organs of American Onthophagus is provided, including names of different anatomical parts and a brief discussion on the need for nomenclatural stability for the genitalia of scarab beetles.
Alkaloidy - naturalne substancje kardioaktywne

wraz z pokarmem stanowią ochronę przed drapieżnikami (KołodziejczyK 2004). Alkaloidy wykazują wysoką i zróżnicowaną aktywność biologiczną. Aktualnie w lecznictwie surowce roślinne zawierające alkaloidy stosowane są rzadko. Wykorzystywane są natomiast czyste alkaloidy, zarówno wyodrębnione z roślin, jak i uzyskane w sposób syntetyczny. W ostatnich latach intensywność badań nad właściwościami alkaloidów znacznie wzrosła. Stwierdzono, iż wiele związków stosowanych w dawnej medycynie ludowej, w leczeniu schorzeń układu sercowo-naczyniowego, wykazuje zdolność do blokowania kanałów wapniowych, podobnie jak odbywa się to za pomocą blokerów syntetycznych. Leki te, poprzez zahamowanie napływu jonów wapnia do komórek mięśnia sercowego, zmniejszają jego kurczliwość, co skutkuje obniżeniem ciśnienia krwi, poprawą krążenia wieńcowego i obwodowego, efektem chronoi inotropowym oraz działaniem antyarytmicznym (chrobot i MatKowsKi 2007). Choroby kardiologiczne są główną przyczyną zgonów w Polsce i na świecie. Poznanie jak największej liczby substancji zarówno pochodzenia naturalnego, jak i syntetycznego, modyfikujących oraz normalizujących aktywność serca, stanowi podstawę do rozwoju badań nad sposobami leczenia chorób serca.
Phenotypic evaluation and molecular profiling of Brassica juncea (L.) lines carrying introgressions from Erucastrum abyssinicum

Introgression lines (ILs), created in Brassica juncea, following hybridization with Erucastrum abyssinicum were studied to catalogue their genetic diversity and crop performance under stressed ecologies. Molecular data generated following amplification with 72 SSR markers (35 (A genome) and 37 (B genome)) suggested the occurrence of high genetic diversity. ILs like JA-85, JA-128, JA-77, JA-30, JA-72, JA-96, JA-196, JA-95, JA-75 fell in Cluster 1 along with E. abyssinicum and were amongst those lines that carried a very large chunk of genomic information from the wild donor species. Graphical genotyping revealed that percent introgression varied from 12.5% to 40% with maximum introgression in JA-30, followed by other ILs like JA-85 (39.9%), JA53 (38.3%), JA-128 (37.4%), JA-75 (37.4%), JA-77 (36%), JA-96 (35.9%), JA-95 (35.1%), JA-72 (34.9%), JA-196 (34.1%), JA-245 (33.7%). Least introgression from the donor parent was recorded in JA-24 (12.5%). On the whole, maximum introgression was seen in chromosome 3 of ‘B’ genome which had 43.2 percent introgression from the donor parent. Morphological evaluation helped to identify useful ILs for earliness and components associated with crop productivity. Some of the ILs like JA-344 (number of primary branches), JA-92 (number of siliqua on main shoot), JA42 (siliqua length), JA-159 and JA-235 (seeds per pod), JA-192 (seed yield) performed equally well in both the environments. Grain yield was positively associated with flowering, plant height, leaf area index etc. which indicated that higher yield can be achieved by bringing changes in these parameters. GG Biplot analysis also confirmed a high level of variation for all the traits studied. Morphological data for test characters was also used to generate Euclidean distance graphs based on Mahalanobis D analysis and the ILs were clustered in 10 groups. The growing unpredictability of climate requires breeding of cultivars adapted to broad environments. Three ILs namely JA-59, JA-65, JA-240 were able to tolerate high temperature while 16 ILs viz. JA-22, JA-31, JA-35, JA-38, JA-45, JA-65, JA-127, JA-147, JA-149, JA174, JA-193, JA-233, JA-331, JA-343, JA-352 and JA-36 could tolerate low temperature stress during flowering. These ILs can further be used in future breeding programmes suited for the development of varieties for stressed ecologies.