Miracle-dz/UniFAR-FTUs huggingface dataset:
Occurrence and geographic distribution of Squash leaf curl virus in the Baja California Peninsula, Mexico

Abstract Squash leaf curl (SLC) disease causes serious damage in a great diversity of horticultural crops worldwide and is due to infection by different ssDNA bipartite begomoviruses (Family Geminiviridae). Symptoms of leaf yellowing, stunting and curling have been observed in squash crops in the southern region of the Baja California (BC) Peninsula in the northwestern region of Mexico for at least a decade. The damage estimated for all localities showed disease incidence of 73.3% to 97.7% and severity of 49%. Infected plants were collected in three localities in addition to adult whiteflies for species determination. Squash leaf curl virus (SLCuV) was detected in both infected plants and whiteflies by PCR using specific primers that amplified a 601 bp fragment. The full-length DNA-A sequence was 99.1% identical to sequences in GenBank. Phylogenetic studies using the core CP region showed that the BC isolate grouped within a well-defined clade together with SLCuV from the Mediterranean Middle East and USA. The molecular analysis in individual adult whiteflies determined that all populations belonged to Bemisia tabaci (MEAM1) (biotype B) species. No evidence of the Mediterranean (MED) species (biotype Q) was found. The SLC disease has prevailed in squash in the region in several growing cycles and in geographically separated localities. To the best of our knowledge, this is the first report of SLCuV associated with squash plants in BCS, Mexico.
Density-based spatial clustering methods for very large datasets

Spatial data mining, or knowledge discovery in spatial databases, refers to the extraction from spatial databases of implicit knowledge, of spatial relations, or of other patterns that are not explicitly stored. Finding clusters in spatial data is an active research area in spatial data mining. The first part of this thesis proposes a novel density-based spatial clustering method called DBRS. The algorithm can identify clusters of widely varying shapes, clusters that depend on non-spatial attributes, and approximate clusters in very large databases. DBRS achieves these results by repeatedly picking an unclassified point at random and examining its neighborhood. If the neighborhood is sparsely populated or the purity of the points in the neighborhood is too low, the point is classified as noise. Otherwise, if any point in the neighborhood is part of a known cluster, this neighborhood is joined to that cluster. If neither of these two possibilities applies, a new cluster is begun with this neighborhood. The experimental results show that DBRS is not only efficient but also can produce high-quality clusters. The second part of this thesis develops a constraint-based spatial clustering algorithm dealing with constraints due to obstacles and facilitators. Typically, a clustering task consists of separating a set of objects into different groups according to a measure of goodness. A common measure of goodness is Euclidean distance (i.e. straight-line distance). However, in many applications, the use of Euclidean distance has a weakness because of the presence of obstacles and facilitators. An obstacle is a physical object that obstructs the reachability among the data objects, and a facilitator is also a physical object that connects distant data objects or connects data objects across obstacles. Handling these constraints can lead to effective and fruitful data mining by capturing application semantics. We extend DBRS to a new spatial clustering method, called DBRS+, which can handle any combination of intersecting obstacles and facilitators. DBRS+ is simple and efficient. Without any preprocessing, the constraints are handled during the clustering process. DBRS+ has been empirically evaluated using synthetic and real data sets. The third part of this thesis emphasizes that domain knowledge can play a key role in spatial clustering. We propose a framework called ONTO_CLUST to combine the domain ontology with the clustering algorithms. In the framework, we show that the clustering process should occur at the knowledge level so that users can identify their goals and understand the results. In ONTO_CLUST, the spatial clustering ontology component is used when identifying the clustering problem and the relevant data. Users' goals are used to search in the ontology. The results of these queries identify the proper clustering methods and the appropriate datasets. Based on these results, clustering is conducted. The clustering result can be used for statistical analysis or it can be interpreted using the ontology. The final result is returned to the user in an understandable format.
Assessing allele specific expression across multiple tissues from RNA-seq read data

Motivation: RNA sequencing enables allele specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression project (GTEx) is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data. Results: We present a statistical method to compare different patterns of ASE across tissues and to classify genetic variants according to their impact on the tissue-wide expression profile. We focus on strong ASE effects that we are expecting to see for protein-truncating variants, but our method can also be adjusted for other types of ASE effects. We illustrate the method with a real data example on a tissue-wide expression profile of a variant causal for lipoid proteinosis, and with a simulation study to assess our method more generally. Availability: MAMBA software: http://birch.well.ox.ac.uk/∼rivas/mamba/ R source code and data examples: http://www.iki. fi/mpirinen/ Contact: matti.pirinen@helsinki.fi rivas@well.ox.ac.uk
From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon

Abstract The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next‐generation sequencing approaches have prompted the transition to genome‐wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double‐digest restriction‐associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild‐born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.
Perception of aversive stimuli of different gustatory modalities in an haematophagous insect, Rhodnius prolixus

Sensory aversion is an essential link for avoiding potential dangers. Here, we studied the chemical perception of aversive compounds of different gustatory modalities (salty and bitter) in the haematophagous kissing bug, Rhodnius prolixus. Over a walking arena, insects preferred a substrate embedded with 0.3 M NaCl or KCl rather than with distilled water. Same salts were avoided when prepared at 1 M. When NaCl and KCl were confronted, no preferences were evinced by insects. A pre-exposure to amiloride interfered with the repellency of NaCl and KCl equally, suggesting that amiloride-sensitive receptors are involved in the detection of both salts. Discriminative experiments were then performed to determine if R. prolixus can distinguish between these salts. An aversive operant conditioning involving either NaCl or KCl modulated the repellency of the conditioned salt, but also of the novel salt. A chemical pre-exposure to the salts did not to modify their repellency levels. When we crossed gustatory modalities by confronting NaCl to caffeine (i.e. a bitter stimulus) no innate preferences were evinced. Aversive operant conditionings with either NaCl or Caf rendered unspecific changes in the repellency of both compounds. A chemical pre-exposure to Caf modulated the response to Caf but not to NaCl, suggesting the existence of two independent neural pathways for the detection of salts and bitter compounds. Overall results suggest that R. prolixus cannot distinguish between NaCl and KCl but can distinguish between NaCl and Caf and generalizes the response between these two aversive stimuli of different gustatory modality. Summary statement Kissing-bugs use contact chemo-perception to avoid aversive substrates. They can sensory distinguish between salty (sodium chloride) and bitter (caffeine) tastes, but not between different salts (sodium and potassium chloride).
Lossless data compression methods based on neural network

No lossless data compression method based on neural network has been found before. A lossless compression method based on BP network for the long character-string of 0 and 1 is given by establishing specific mapping Y and specific integer function and with the non-linear approximation capability of concrete three-layer BP network in this paper. The compression and decompression algorithms of the lossless compression method are provided. Experiments show that the compression ratio of the lossless compression method is usually around 16/11 and the method can effectively compress the data which have been compressed by Huffman coding, arithmetic coding or dictionary coding.
Vascular Inflammation and Oxidative Stress: Major Triggers for Cardiovascular Disease

Cardiovascular disease is a leading cause of death and reduced quality of life, proven by the latest data of the Global Burden of Disease Study, and is only gaining in prevalence worldwide. Clinical trials have identified chronic inflammatory disorders as cardiovascular risks, and recent research has revealed a contribution by various inflammatory cells to vascular oxidative stress. Atherosclerosis and cardiovascular disease are closely associated with inflammation, probably due to the close interaction of inflammation with oxidative stress. Classical therapies for inflammatory disorders have demonstrated protective effects in various models of cardiovascular disease; especially established drugs with pleiotropic immunomodulatory properties have proven beneficial cardiovascular effects; normalization of oxidative stress seems to be a common feature of these therapies. The close link between inflammation and redox balance was also supported by reports on aggravated inflammatory phenotype in the absence of antioxidant defense proteins (e.g., superoxide dismutases, heme oxygenase-1, and glutathione peroxidases) or overexpression of reactive oxygen species producing enzymes (e.g., NADPH oxidases). The value of immunomodulation for the treatment of cardiovascular disease was recently supported by large-scale clinical trials demonstrating reduced cardiovascular mortality in patients with established atherosclerotic disease when treated by highly specific anti-inflammatory therapies (e.g., using monoclonal antibodies against cytokines). Modern antidiabetic cardiovascular drugs (e.g., SGLT2 inhibitors, DPP-4 inhibitors, and GLP-1 analogs) seem to share these immunomodulatory properties and display potent antioxidant effects, all of which may explain their successful lowering of cardiovascular risk.
A toolbox of nanobodies developed and validated for diverse neuroscience research applications

Nanobodies (nAbs) are small, minimal antibodies that have distinct attributes that make them uniquely suited for certain biomedical research, diagnostic and therapeutic applications. Prominent uses include as intracellular antibodies or intrabodies to bind and deliver cargo to specific proteins and/or subcellular sites within cells, and as nanoscale immunolabels for enhanced tissue penetration and improved spatial imaging resolution. Here, we report the generation and validation of nAbs against a set of proteins prominently expressed at specific subcellular sites in brain neurons. We describe a novel hierarchical validation pipeline to systematically evaluate nAbs isolated by phage display for effective and specific use as intrabodies and immunolabels in mammalian cells including brain neurons. These nAbs form part of a robust toolbox for targeting proteins with distinct and highly spatially-restricted subcellular localization in mammalian brain neurons, allowing for visualization and/or modulation of structure and function at those sites.
Speech processing and short term memory in children with normal and atypical speech and language development.

This thesis is motivated by research evidence of significant relationships between short-term memory and speech and language development, and by clinical observations of poor short-term memory skills in some children with developmental language difficulties. It addresses the question ‘to what degree do speech processing skills underpin short-term memory and language development’? A series of experiments were carried out, collecting data from children, aged 7 years and under, who were developing normally, and from children with speech and / or language difficulties. Performance on tasks of speech production and auditory discrimination were found to show significant developmental differences, and these speech processing skills were significantly correlated with non-word repetition performance. Different presentation and response mechanisms, and the phonological complexity o f words to be recalled significantly affected short-term memory performance. These findings implicate speech input and output processing in short-term memory performance. Data from a longitudinal study showed that auditory discrimination skills significantly predicted the development of both short-term memory and receptive language development, but speech production skills were not related to short -term memory or language development. Short-term memory skills significantly predicted grammatical development. A series of case studies of children with speech and / or language difficulties demonstrated a range of individual, longitudinal profiles of performance across speech processing, short term memory and standardised language measures. Findings from the normative data did not explain the patterns o f development in clinical cases, however, short-term memory skills were broadly in line with the level of receptive language development attained. Relationships between short-term memory, speech and language in normal development may not reflect the mechanisms by which short-term memory and language is impaired in disordered individuals.
Signalling mechanisms and epigenetic regulation of seed development in Arabidopsis thaliana

In flowering plants, seed development starts with a double fertilisation event, leading to the formation of the embryo and the endosperm. Though only the embryo contributes to the next generation, control of endosperm proliferation, as well as the timing of its cellularisation are crucial for embryo viability. Both the embryo and the endosperm are enclosed by the seed coat, a maternal tissue that serves as a protective layer and is important for various aspects of seed development. Despite not arising directly from a fertilization event, the seed coat responds to fertilization by expanding and differentiating, accompanying the growth of the embryo and the endosperm. Therefore, successful seed development requires a set of signalling networks that coordinate growth between the embryo, the endosperm, and the seed coat. In this thesis, I show that auxin is a key player in these signalling networks. Its biosynthesis occurs in the endosperm, depends on the activity of imprinted paternally expressed genes, and serves two purposes: i) it triggers and sustains endosperm proliferation, and ii) it is exported to the integuments, which kick-starts seed coat development. In later stages of seed development, a reduction of auxin activity in the endosperm is required to initiate endosperm cellularisation, and the seed abortion phenotypes observed in interploidy crosses are connected with atypical levels of this hormone. The present work also identified two endosperm-expressed MADS-box transcription factors (TFs) as the upstream transcriptional regulators of auxin biosynthesis and transport genes. Interestingly, one of these TFs – the imprinted paternally expressed PHERES1 – controls the expression of several other imprinted genes, and accesses its targets through specific DNA-binding sites, which are significantly associated with transposable elements (TEs). TEs were previously implicated in providing epigenetic landscapes conducive to imprinted gene expression. I further propose that these elements have been co-opted as cis-regulatory sequences that facilitate PHERES1 binding to promoters of imprinted genes. Overall, this thesis makes important contributions to further increase our understanding of seed development: not only it uncovers the hormone auxin as a key factor that coordinates the development of different seed components, but also clarifies the previously elusive role of MADS-box genes in the transcriptional networks controlling endosperm development.
Plant mixed lineage kinase domain-like proteins limit biotrophic pathogen growth

Mixed lineage kinase domain-like (MLKL) protein mediates necroptotic cell death in vertebrates. We report here the discovery of a conserved protein family across seed plants that is structurally homologous to vertebrate MLKL. The Arabidopsis thaliana genome encodes three MLKLs with overlapping functions in limiting growth of obligate biotrophic fungal and oomycete pathogens. Although displaying a cell death activity mediated by N-terminal helical bundles, termed HeLo domain, AtMLKL-dependent immunity can be separated from host cell death. Cryo-electron microscopy structures of AtMLKLs reveal a tetrameric configuration, in which the pseudokinase domain and brace region bury the HeLo-domains, indicative of an auto-repressed complex. We also show the association of two AtMLKLs with microtubules. These findings, coupled with resistance-enhancing activity and altered microtubule association of a phosphomimetic mutation in the pseudokinase domain of AtMLKL1, point to a cell death-independent immunity mechanism. One Sentence Summary Plants have a protein family that is structurally homologous to vertebrate mixed lineage kinase domain-like protein, which induces necroptotic cell death, but these plant proteins can confer immunity without host cell death.
Molecular biological analysis of Bt-transgenic (Bt-9) rice and its effect on Daphnia magna feeding

Insect-resistant transgenic (Bt-9) rice was generated by inserting mCry1Ac1, a modified gene from the soil bacterium Bacillus thuringiensis, into the genome of a conventional variety of rice (Ilmi). With regard to potential problems such as safety, an evaluation of non-target organisms is necessary as an essential element of an environmental risk assessment of genetically modified (GM) crops. We studied the effects of the Bt-9 rice on the survival of cantor Daphnia magna, a commonly used model organism in ecotoxicological studies. D. magna fed on the Bt-transgenic rice (Bt-9) and its near non-GM counterparts (Ilmi) grown in the same environment (a 100% ground rice suspension). The Bt-9 rice was confirmed to have the inserted T-DNA and protein expression evident by the PCR and ELISA analyses. The feeding study showed a similar cumulative immobility and abnormal response of the Daphnia magna between the Bt-9 rice and Ilmi. Additionally, the 48 h-EC50 values of the Bt-9 and Ilmi rice were 4,400 mg/L (95% confidence limits: 3861.01 5015.01 mg/L) and 5,564 mg/L (95% confidence limits: 4780.03 6476.93 mg/L), respectively. The rice NOEC (No observed effect concentration) value for D. magna was suggested to be 1,620 mg/L. We conclude that the tested Bt-9 and Ilmi have a similar cumulative immobility for D. magna, a widely used model organism, and the growth of Bt-9 did not affect non-target insects.
Threatened vertebrate species: associations between conservation actions, funding and population trends

There are more species threatened with extinction now that at any point in recent history. However, resources for species conservation can be limited, and awareness of gaps in knowledge and conservation action implementation is important when allocating funds and planning conservation efforts. Here, we explore the relationships between conservation action implementation, funding allocation, and population trends for all vertebrate species listed under the US Endangered Species Act. The same core suite of conservation actions (monitoring, habitat protection, and educational awareness) was implemented for most species. Our assessment of the effectiveness of funding and implemented conservation actions was impeded, however, because population trend information was lacking for many species. For instance, we found that marine species received 3 times more annual funding on average than continental species and 10 times more annual funding than species that live on islands, yet the population trends for the majority of marine species are decreasing or unknown. Furthermore, the number of marine species with increasing population trends is not significantly higher. Thus, we conclude more monitoring and reporting is needed to improve population trend information before the appropriateness of funding allocation and efficacy of conservation actions can be properly assessed.
Biogenesis of a young, 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation

Phased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22 nt miRNAs. Most 22 nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21 nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous NB-LRRs, previously described as 21 nt in its mature form, primarily accumulates as a 22 nt isoform via monouridylation. We demonstrate that in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3’ terminus of miR1510 is only partially 2’-O-methylated, because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ~41 to 42 MYA with a conserved precursor structure yielding a 22 nt monouridylated form, yet a variant in mung bean is processed directly in a 22 nt mature form. This analysis of miR1510 yields two observations: (1) plants can utilize post-processing modification to generate abundant 22 nt miRNA isoforms to more efficiently regulate target mRNA abundances; (2) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.