Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional genomics of ageing and its modulation by diet

Ageing is a widespread phenomenon limiting the lifespan of almost all species. Virtually all organisms age, however what controls the ageing process remains enigmatic. A lot of human disease and death are affected by ageing or age-related diseases. Understanding the ageing process is crucial to benefit humanity including intervention of human disease or life extension. The work presented here allows to gain insights into the ageing process which can be manipulated by targeting ageing genes via genetic modifications, environmental factors, or pharmacological interventions. Biological information is increasing at an exponential pace. Information technology is also advancing at a fast pace. The combination of these two trends may allow us to understand biological processes such as ageing. Ageing is plastic; many studies have shown that the ageing process can be sped up, slowed down, stopped, or even reversed. For example, the ageing process can be slowed down by dietary restriction (DR), the most powerful non-genetic intervention known to counteract the basic ageing process. In addition, the ageing process can be modulated by genetic as well as environmental means including dietary as well as pharmacological interventions. Here it is hypothesized that ageing genes do not only play an important role in the ageing process but also in its modulation by diet. In this thesis, functional genomics approaches are applied to genomic data such as transcriptomics and interactomics. Graph theoretic concepts like guilt-by-association and shortest path are applied on ageing and its dietary manipulations. This methodology enabled to gather new insights into the underlying mechanisms of the ageing process and its interference with interventions like dietary restriction, as well as to predict original hypotheses, new ageing genes, and novel pharmaceuticals. Firstly, a curated knowledge base was established which includes lossand gain-of-function experiments that impact on lifespan of organisms including human, mouse, fruit fly, nematode, and yeast, among others. Genes controlling the ageing process (ageing genes) were classified based on their effect on lifespan resulting from genetic manipulations in the common biomedical model organisms as well as in humans. Those classes were characterized for common associations and potential novel ageing genes were predicted by applying graph theory like the guilt-by-association principle. Specifically, this thesis classifies ageing genes that control the ageing process into two main classes: 1) gerontogenes that mediate the ageing process, therefore decrease lifespan of the organism; 2) ageing-suppressor genes that suppress the ageing process, thus increase lifespan of the organism. Further analysis shows that: Gerontogenes are associated with translation, positive regulation of apoptosis, inflammation, TOR signalling, positive regulation of multicellular organism growth and development, as well as transcription
Image-Aided Navigation Using Cooperative Binocular Stereopsis

Abstract : This thesis proposes a novel method for cooperatively estimating the positions of two vehicles in a global reference frame based on synchronized image and inertial information. The proposed technique - cooperative binocular stereopsis - leverages the ability of one vehicle to reliably localize itself relative to the other vehicle using image data which enables motion estimation from tracking the three dimensional positions of common features. Unlike popular simultaneous localization and mapping (SLAM) techniques, the method proposed in this work does not require that the positions of features be carried forward in memory. Instead, the optimal vehicle motion over a single time interval is estimated from the positions of common features using a modified bundle adjustment algorithm and is used as a measurement in a delayed state extended Kalman filter (EKF). The developed system achieves improved motion estimation as compared to previous work and is a potential alternative to map-based SLAM algorithms.
Compound maximal motor unit response is modulated by contraction intensity, but not contraction type in tibialis anterior

Determining a single compound maximal motor response (MMAX) or an average superimposed MMAX response (MSUP) are commonly used reference values in experiments eliciting raw electromyographic, motor evoked potentials, H‐reflexes, and V‐waves. However, existing literature is limited in detailing the most appropriate method to normalize these electrophysiological measures. Due to the accessibility of assessment from a cortical and spinal perspective, the tibialis anterior is increasingly used in literature and hence investigated in this study. The aims of the present study were to examine the differences and level of agreement in MMAX/MSUP under different muscle actions and contraction intensities. Following a familiarization session, 22 males visited the laboratory on a single occasion. MMAX was recorded under 10% isometric and 25% and 100% shortening and lengthening maximal voluntary contractions (MVC) at an angular velocity of 15° sec−1. MSUP was also recorded during 100% shortening and lengthening with an average of five responses recorded. There were no differences in MMAX or MSUP between contraction types. All variables showed large, positive correlations (P < 0.001, r2 ≥ 0.64). MMAX amplitude was larger (P < 0.001) at 100% shortening and lengthening intensity compared to MMAX amplitude at 10% isometric and 25% lengthening MVC. Bland‐Altman plots revealed a bias toward higher MMAX at the higher contraction intensities. Despite MSUP being significantly smaller than MMAX (P < 0.001) at 100% MVC, MSUP showed a large positive correlation (P < 0.001, r2 ≥ 0.64) with all variables. It is our recommendation that MMAX should be recorded at specific contraction intensity but not necessarily a specific contraction type.
Nectar and pollen production of Helianthus tuberosus L. – an exotic plant with invasiveness potential

Abstract In Central Europe, Helianthus tuberosus L. is a late summer/autumn bloomer (August/November). The disc florets produce both nectar and pollen. Floral reward is available in male-phase flowers (pollen and nectar) and in female-phase flowers (nectar). The floral reward is attractive to a variety of insect visitors (honey bees, wasps, flies and butterflies). The season of blooming as well as the total sugar yield (25.4 – 47.4 kg ha−1) and pollen yield (57.8 – 212.7 kg ha−1) indicate that H. tuberosus is important in the enhancement of food resources for pollinators. The generative reproduction in H. tuberosus is impaired (the species does not set seeds/fruits). However, due to its attractiveness for a variety of pollinators in both rural and urban areas, the spread of H. tuberosus should be monitored. Moreover, its propagation needs to be attended with restrictions.
New insights into the evolution of lateral compound eyes in Palaeozoic horseshoe crabs

Vision allows animals to interact with their environment. Aquatic chelicerates dominate the early record of lateral compound eyes among non-biomineralizing crown-group euarthropods. Although the conservative morphology of lateral eyes in Xiphosura is potentially plesiomorphic for Euarthropoda, synziphosurine eye organization has received little attention despite their early diverging phylogenetic position. Here, we re-evaluate the fossil evidence for lateral compound eyes in the synziphosurines Bunodes sp. , Cyamocephalus loganensis, Legrandella lombardii, Limuloides limuloides, Pseudoniscus clarkei, Pseudoniscus falcatus and Pseudoniscus roosevelti. We compare these data with lateral eyes in the euchelicerates Houia yueya, Kasibelinurus amicorum and Lunataspis aurora. We find no convincing evidence for lateral eyes in most studied taxa, and Pseudoniscus roosevelti and Legrandella lombardii are the only synziphosurines with this feature. Our findings support two scenarios for euchelicerate lateral eye evolution. The elongate-crescentic lateral eyes of Legrandella lombardii might represent the ancestral organization, as suggested by the phylogenetic position of this taxon in stem-group Euchelicerata. Alternatively, the widespread occurrence of kidney-shaped lateral eyes in stem-group Xiphosura and stem-group Arachnida could represent the plesiomorphic condition; Legrandella lombardii eyes would therefore be derived. Both evolutionary scenarios support the interpretation that kidney-shaped lateral eyes are ancestral for crown-group Euchelicerata and morphologically conserved in extant Limulus polyphemus.
Curau genetic diversity in germplasm banks and natural populations

Ananas comosus var. erectifolius (L. B. Sm.) Coppens & F. Leal, populary known as curaua, is a bromeliaceae, found in the Amazonian flora. It is of great commercial interest, mostly for the automobile industry. Despite the curaua’s potential, little has been done to conserve its germplasm. For this, it’s necessary to know its genetic variability. An efficient way of knowing it is to use molecular markers because they are polymorphic and not influenced by the environment. Thus, this work is aimed to evaluate the genetic diversity in curaua’s access of different germplasm banks and its natural populations, using simple sequence repeat (SSR) and random amplified polymorphic DNA (RAPD) molecular markers. The similarity between the cultivars was calculated based on the Dice coefficient. From the similarity analysis, the cultivars grouping dendrogram was constructed using the unweighted pair group mean average method (UPGMA). High genetic similarity was observed between the individuals of each group and most of the variability found was between the groups. The low variability found within the groups is due to the way in which A. comosus var. erectifolius has been multiplied, through asexual reproduction in plantation areas. The data suggest that the conservation strategies of this species should focus on the largest possible number of collections in different geographic regions to increase the variability of the banks. Key words: Ananas comosus var. erectifolius, conservation
Automated recognition of functional compound-protein relationships in literature

Motivation Much effort has been invested in the identification of protein-protein interactions using text mining and machine learning methods. The extraction of functional relationships between chemical compounds and proteins from literature has received much less attention, and no ready-to-use open-source software is so far available for this task. Method We created a new benchmark dataset of 2,753 sentences from abstracts containing annotations of proteins, small molecules, and their relationships. Two kernel methods were applied to classify these relationships as functional or non-functional, named shallow linguistic and all-paths graph kernel. Furthermore, the benefit of interaction verbs in sentences was evaluated. Results The cross-validation of the all-paths graph kernel (AUC value: 84.2%, F1 score: 81.8%) shows slightly better results than the shallow linguistic kernel (AUC value: 81.6%, F1 score: 79.7%) on our benchmark dataset. Both models achieve state-of-the-art performance in the research area of relation extraction. Furthermore, the combination of shallow linguistic and all-paths graph kernel could further increase the overall performance. We used each of the two kernels to identify functional relationships in all PubMed abstracts (28 million) and provide the results, including recorded processing time. Availability The software for the tested kernels, the benchmark, the processed 28 million PubMed abstracts, all evaluation scripts, as well as the scripts for processing the complete PubMed database are freely available at https://github.com/KerstenDoering/CPI-Pipeline. Author summary Text mining aims at organizing large sets of unstructured text data to provide efficient information extraction. Particularly in the area of drug discovery, the knowledge about small molecules and their interactions with proteins is of crucial importance to understand the drug effects on cells, tissues, and organisms. This data is normally hidden in written articles, which are published in journals with a focus on life sciences. In this publication, we show how text mining methods can be used to extract data about functional interactions between small molecules and proteins from texts. We created a new dataset with annotated sentences of scientific abstracts for the purpose of training two diverse machine learning methods (kernels), and successfully classified compound-protein pairs as functional and non-functional relations, i.e. no interactions. Our newly developed benchmark dataset and the pipeline for information extraction are freely available for download. Furthermore, we show that the software can be easily up-scaled to process large datasets by applying the approach to 28 million abstracts.
Repertoire of morphable proteins in an organism

All living organisms have evolved to contain a set of proteins with variable physical and chemical properties. Efforts in the field of structural biology have contributed to uncovering the shape and the variability of each component. A set of experimental coordinates for a given protein can be used to define the “morphness/unmorphness”. Here we show the results of global analysis of more than a thousand E. coli proteins, demonstrating that it would be a comprehensive method of understanding the evolved repertoire in an organism. By collecting “UnMorphness Factor” (UMF) determined for each of the proteins, the lowest and the highest boundaries of the experimentally observable structural variation are understood. The distribution of UMFs obtained for an organism is expected to represent how rigid and flexible components are balanced. The present analysis extends to evaluate the growing data from single particle cryo-electron microscopy, providing valuable information on effective interpretation to structural changes of proteins and the supramolecular complexes. The data and the method presented here also conform to FAIR data principles, having potential significance to advance the field of structural and molecular cell biology.
Meta-analysis Shows That Rapid Phenotypic Change in Angiosperms in Response to Environmental Change Is Followed by Stasis

The amount and rate of phenotypic change at ecological timescales varies widely, but there has not been a comprehensive quantitative synthesis of the patterns and causes of such variation for plants. Present knowledge is based predominantly on animals, whose differences with plants in the origin of germ cells and the level of modularity (among others) could make it invalid for plants. We synthesized data on contemporary phenotypic responses of angiosperms to environmental change and show that if extinction does not occur, quantitative traits change quickly in the first few years following the environmental novelty and then remain stable. This general pattern is independent from life span, growth form, spatial scale, or the type of trait. Our work shows that high amounts and rates of phenotypic change at contemporary timescales observed in plants are consistent with the pattern of stasis and bounded evolution previously observed over longer time frames. We also found evidence that may contradict some common ideas about phenotypic evolution: (1) the total amount of phenotypic change observed does not differ significantly according to growth form or life span; (2) greater and faster divergence tends to occur between populations connected at the local scale, where gene flow could be intense, rather than between distant populations; and (3) traits closely related to fitness change as much and as fast as other traits.
Hierarchical vs non-hierarchical audio indexation and classification for video genres

In this paper, Support Vector Machines (SVMs) are used for segmenting and indexing video genres based on only audio features extracted at block level, which has a prominent asset by capturing local temporal information. The main contribution of our study is to show the wide effect on the classification accuracies while using an hierarchical categorization structure based on Mel Frequency Cepstral Coefficients (MFCC) audio descriptor. In fact, the classification consists in three common video genres: sports videos, music clips and news scenes. The sub-classification may divide each genre into several multi-speaker and multi-dialect sub-genres. The validation of this approach was carried out on over 360 minutes of video span yielding a classification accuracy of over 99%.
Deletion of calcineurin from GFAP-expressing astrocytes impairs excitability of cerebellar and hippocampal neurons through astroglial Na+/K+ ATPase

Astrocytes perform important housekeeping functions in the nervous system including maintenance of adequate neuronal excitability, although the regulatory mechanisms are currently poorly understood. The astrocytic Ca2+/calmodulin-activated phosphatase calcineurin (CaN) is implicated in the development of reactive gliosis and neuroinflammation, but its roles, including the control of neuronal excitability, in healthy brain is unknown. We have generated a mouse line with conditional knockout (KO) of CaN B1 (CaNB1) in glial fibrillary acidic protein (GFAP)-expressing astrocytes (astroglial calcineurin knock-out, ACN-KO). Here we report that postnatal and astrocyte-specific ablation of CaNB1 did not alter normal growth and development as well as adult neurogenesis. Yet, we found that specific deletion of astrocytic CaN selectively impairs intrinsic neuronal excitability in hippocampal CA1 pyramidal neurons and cerebellar granule cells (CGCs). This impairment was associated with a decrease in after-hyperpolarization in CGC, while passive properties were unchanged, suggesting impairment of K+ homeostasis. Indeed, blockade of Na+/K+-ATPase (NKA) with ouabain phenocopied the electrophysiological alterations observed in ACN-KO CGCs. In addition, NKA activity was significantly lower in cerebellar and hippocampal lysates and in pure astrocytic cultures from ACN-KO mice. While no changes were found in protein levels, NKA activity was inhibited by the specific CaN inhibitor FK506 in both cerebellar lysates and primary astroglia from control mice, suggesting that CaN directly modulates NKA activity and in this manner controls neuronal excitability. In summary, our data provide formal evidence for the notion that astroglia is fundamental for controlling basic neuronal functions and place CaN center-stage as an astrocytic Ca2+-sensitive switch.
In vitro breeding – shortcut to Pseudomonas syringae pv. actinidiae (Psa) tolerant kiwifruit

Abstract Pseudomonas syringae pv. actinidiae (Psa) causes the bacterial canker disease on kiwifruit vines. The disease outbreak has been reported in several countries worldwide, including New Zealand. Here, we briefly reviewed the current situation of Psa infection of kiwifruit vines in New Zealand, the effects of Psa on the New Zealand’s kiwifruit industry, and the disease control and breeding programmes undertaken in response to the outbreak of Psa in New Zealand. Then the methodology of an alternative breeding approach or in vitro breeding, which is a non-GM approach to obtain useful plant tissue culture-derived genetic variation in crop plants, was discussed. As a specific example of potential application of in vitro breeding, a novel plant breeding project idea based on the elemental defence mechanism is to generate Cu/Zn tolerant kiwifruit varieties that exhibit improved Psa tolerance.
Characterization of ruminal bacteria in grazing Nellore steers

Background: Rumen microorganisms have developed a series of complex interactions, representing one of the best examples of symbiosis between microorganisms in nature. Conventional taxonomic methods based on culture techniques are being replaced by molecular techniques that are faster and more accurate. Objective: To characterize rumen bacterial diversity of Nellore steers grazing on tropical pastures by sequencing the 16S rRNA gene using Illumina sequenctng. Methods: Three rumen-cannulated Nellore steers were used. The liquid and solid fractions of the rumen contents were processed to extract metagenomic DNA, and the VI and V2 hypervariable regions of the 16S rRNA gene were sequenced using Illumina sequencing. Results: A total of 11,407,000 reads of adequate quality were generated, and 812 operational taxonomic units (OTUs) were found at the species level. Twenty-seven phyla were identified, and the predominant phyla were Firmicutes (23%), Bacteroidetes (14%), Proteobacteria (10%), Spirochaetes (9%), Fibrobacteres (7%), Tenericutes (5%), and Actinobacteria (2%), which represented 70% of the total phyla identified in the rumen content. Conclusion: Rumen environment in grazing Nellore steers showed high bacterial diversity, with Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Fibrobacteres as the predominant phyla.
Patterns of coevolution between ambrosia beetle mycangia and the Ceratocystidaceae, with five new fungal genera and seven new species

Ambrosia beetles farm specialised fungi in sapwood tunnels and use pocket-like organs called mycangia to carry propagules of the fungal cultivars. Ambrosia fungi selectively grow in mycangia, which is central to the symbiosis, but the history of coevolution between fungal cultivars and mycangia is poorly understood. The fungal family Ceratocystidaceae previously included three ambrosial genera (Ambrosiella, Meredithiella, and Phialophoropsis), each farmed by one of three distantly related tribes of ambrosia beetles with unique and relatively large mycangium types. Studies on the phylogenetic relationships and evolutionary histories of these three genera were expanded with the previously unstudied ambrosia fungi associated with a fourth mycangium type, that of the tribe Scolytoplatypodini. Using ITS rDNA barcoding and a concatenated dataset of six loci (28S rDNA, 18S rDNA, tef1-α, tub, mcm7, and rpl1), a comprehensive phylogeny of the family Ceratocystidaceae was developed, including Inodoromyces interjectus gen. & sp. nov., a non-ambrosial species that is closely related to the family. Three minor morphological variants of the pronotal disk mycangium of the Scolytoplatypodini were associated with ambrosia fungi in three respective clades of Ceratocystidaceae: Wolfgangiella gen. nov., Toshionella gen. nov., and Ambrosiella remansi sp. nov. Closely-related species that are not symbionts of ambrosia beetles are accommodated by Catunica adiposa gen. & comb. nov. and Solaloca norvegica gen. & comb. nov. The divergent morphology of the ambrosial genera and their phylogenetic placement among non-ambrosial genera suggest three domestication events in the Ceratocystidaceae. Estimated divergence dates for the ambrosia fungi and mycangia suggest that Scolytoplatypodini mycangia may have been the first to acquire Ceratocystidaceae symbionts and other ambrosial fungal genera emerged shortly after the evolution of new mycangium types. There is no evidence of reversion to a non-ambrosial lifestyle in the mycangial symbionts.
COMPARATIVE ANALYSIS OF FIXED-GAIN RELAYING SCHEMES FOR INTER-RELAY COMMUNICATION OVER NAKAGAMI-M FADING CHANNEL

Analysis of Fixed-Gain relaying schemes for three time slot transmission protocol over Nakagami-m is presented. In this paper a profound analysis of two relaying schemes for inter-relay communication has been simulated and compared under different performance metrics. The performance is analyzed considering various relay locations in order to investigate the best relay location. The parameters used to analyze the system are Bit Error Rate, Outage capacity and Outage probability (BER).