Miracle-dz/UniFAR-FTUs huggingface dataset:
PARENT SELECTION IN TOMATO BASED ON MORPHO-PHYSIOLOGICAL TRAITS

The objectives of this study were to determine if a relationship exists between selected morpho-physiological traits and general combining ability for yield in determinate and indeterminate tomato inbred lines, to determine if a relationship exists between these traits and the average probability that an inbred can produce transgressive segregates, and to determine if the levels of some physiological traits that contribute to yield differ between growth habits. Among determinate inbreds, general combining ability for yield is significantly correlated with yield and fruit number but not with harvest index, photosynthesis, specific leaf weight, or average fruit size. Among indeterminates, general combining ability for yield is significantly correlated only with yield. Regression analysis indicates that inbred yield is the best predictor of general combining ability for yield among determinate inbreds. Inbred yield is also a good predictor of general combining ability for yield among indeterminate inbreds. However, the addition of harvest index, fruit number, and average fruit size as independent variables to the regression model increases the accuracy of this prediction. The predictive model for determinate inbreds accurately estimates general combining ability for yield when tested using four additional determinate inbreds. No test was made of the predictive model for indeterminate inbreds. The average probability that a determinate inbred can produce transgressive segregates when crossed with other lines is significantly correlated with harvest index and fruit number. Although the correlation between this probability and inbred yield is high, it is not significant. It can be concluded from these results that none of the morpho-physiological traits studied can be used to screen large amounts of parental material for possible use in breeding programs. Breeders should continue to select parental inbreds on the basis of their yields when trying to improve yield. It is possible that harvest index may provide an additional criterion for evaluating parental material provided a method is found for reliably measuring this trait. A comparison between determinate and indeterminate inbred lines indicates that the determinate inbreds have, on average, higher photosynthetic rates, higher specific leaf weights, and higher harvest indices than the indeterminate inbreds. Since the determinate and indeterminate inbreds produce the same total yield, these results indicate that the relative efficiencies of some of the physiological processes that contribute to these yields differ between growth habits.
Foliar secretory structures in Melia azedarach (Meliaceae), a widely cultivated and often invasive tree

ABSTRACT Melia azedarach (chinaberry; syringa), a tree with bipinnately compound leaves, is one of the most widely cultivated of all tropical trees, but has become naturalised in several parts of the world. New observations are presented on the morphology and anatomy of extrafloral nectaries (EFNs). These should serve as baseline information in ecological studies on the invasiveness of the species, as well as its potential biocontrol. We report, for the first time, extrafloral nectaries (EFNs) on the leaflet lamina, as well as capitate glands on very young leaflets. A sugar analysis of the exudate of the former confirmed it to be nectar. In addition, known EFNs occurring in paired recesses at the petiole base were studied anatomically and developmentally. These so-called paired glands were found to be groups of individual and separate EFNs, for which the new term ‘compound EFN’ is suggested. Each EFN making up a compound EFN is similar in structure to the laminar EFNs except that they tend to protrude beyond the epidermal surface to a greater degree and to be composed of cells which differ slightly in shape. The secretory tissue of both petiolar and laminar EFNs originates from protoderm and ground tissues, albeit with slightly different initial cell divisions. Capitate glands were found on very young leaflets. Ants were frequent visitors to mainly the petiolar EFNs, less often the laminar ones. Members of the Meliaceae (including M. azedarach) are well known sources of limonoids, compounds with insect antifeedant properties. It is suggested that petiolar and laminar EFNs may attract different preferential nectar feeders, thus providing a first line of indirect defence, resulting in the removal or deterring of potential herbivores even before any damage is inflicted on the plant. Additionally, nectar from the EFNs may protect against co-evolved or other herbivores tolerant of limonoids.
A direct comparison of four high risk human papilloma virus tests versus the cobas test for detecting cervical intraepithelial neoplasia and cervical cancer

This study is to evaluate performances and genotyping capabilities of four human papilloma virus (HR-HPV) tests based on real-time polymerase chain reaction (PCR) technology platforms compared with the cobas test. Discordant results were further analyzed using INNO-LiPA HPV genotyping test, the gold standard laboratory test to determine presence and type of HPV infection. Over 200 samples from Hospital patients were collected and analyzed using five HR-HPV tests. Women with positive test results were referred directly to colposcopy. If a positive result was returned, biopsies were administered for pathological classification. Clinical performances and genotyping capabilities between the four HR-HPV and cobas tests were compared and contrasted. High levels of agreement were observed, though all HR-HPV tests presented discrepancies compared with the cobas test. Cervical intraepithelial neoplasia Grade 2 or higher lesions (CIN2+) was set as the threshold, and all five tests performed with equally high sensitivity. Lower levels of specificity were observed across all five tests. Results suggest the four HR-HPV tests analyzed are as effective as the cobas test in genotyping capacities and diagnosing CIN. Therefore, these test kits should be used for HPV screening, especially in developing nations because they are cost effective and reliable. Minor discrepancies between tests are generally unavoidable though this may add complexity to the clinical decision-making process. As such, we recommend that efforts be made to standardize HPV genotyping tests as well as to optimize clinical sensitivity and specificity. Focusing on these issues will drive the development of HPV detection techniques, therefore save lives.
How to best threshold and validate stacked species assemblages? Community optimisation might hold the answer

The popularity of species distribution models (SDMs) and the associated stacked species distribution models (S‐SDMs), as tools for community ecologists, largely increased in recent years. However, while some consensus was reached about the best methods to threshold and evaluate individual SDMs, little agreement exists on how to best assemble individual SDMs into communities, that is, how to build and assess S‐SDM predictions. Here, we used published data of insects and plants collected within the same study region to test (a) if the most established thresholding methods to optimize single species prediction are also the best choice for predicting species assemblage composition, or if community‐based thresholding can be a better alternative, and (b) whether the optimal thresholding method depends on taxa, prevalence distribution and/or species richness. Based on a comparison of different evaluation approaches, we provide guidelines for a robust community cross‐validation framework, to use if spatial or temporal independent data are unavailable. Our results showed that the selection of the “optimal” assembly strategy mostly depends on the evaluation approach rather than taxa, prevalence distribution, regional species pool or species richness. If evaluated with independent data or reliable cross‐validation, community‐based thresholding seems superior compared to single species optimisation. However, many published studies did not evaluate community projections with independent data, often leading to overoptimistic community evaluation metrics based on single species optimisation. The fact that most of the reviewed S‐SDM studies reported over‐fitted community evaluation metrics highlights the importance of developing clear evaluation guidelines for community models. Here, we move a first step in this direction, providing a framework for cross‐validation at the community level.
Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma

The identification of somatic alterations with a cancer promoting role is challenging in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we developed a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously (mutations, copy number alterations and structural rearrangements). Analysing 261 EACs from the OCCAMS Consortium, we discovered a large number of novel cancer genes that, together with well-known drivers, help promote cancer. Validation using 107 additional EACs confirmed the robustness of the approach. Unlike known drivers whose alterations recur across patients, the large majority of the newly discovered cancer genes are rare or patient-specific. Despite this, they converge towards perturbing cancer-related processes, including intracellular signalling, cell cycle regulation, proteasome activity and Toll-like receptor signalling. Recurrence of process perturbation, rather than individual genes, divides EACs into six clusters that differ in their molecular and clinical features and suggest patient stratifications for personalised treatments. By experimentally mimicking or reverting alterations of predicted cancer genes, we validated their contribution to cancer progression and revealed EAC acquired dependencies, thus demonstrating their potential as therapeutic targets.
A check-list of the benthic marine macroalgae on the eastern Adriatic coast: II. Heterokontophyta (Phaeophyta): Phaeophyceae

A chec-klist of brown algae (Heterokontophyta ; Phaeophyta) from the eastern Adriatic coast, based on records published from 19480 to 2008, is presented. For geographic analysis the coast is divided into three parts: northern, central, and southern. A total of 186 macroalgal taxa (species and lower taxonomic categories) are recognized, in wich is 11 new combinations proposed.
In silico analysis and homology modelling of coat-protein of garlic common latent virus isolated from India

Garlic is affected by several diseases incited by viruses, fungi, bacteria and nematodes. In this study, coat-protein sequence was analyzed and modelled to explore properties and structure of garlic common latent virus (GarCLV). Since no structural information is available for majority of protein sequences available in Protein Data Bank (PDB), computational methods for protein structure prediction have been of much interest in recent years. Physico-chemical properties of the protein under study were computed. The grand average of hydropathy (GRAVY) value and instability index were found to be -0.513 and 44.39, respectively, supporting the protein to have better interaction with water. The modelling was performed Swiss model web server and found was that 84.2% of the amino acid residues in most favored region. The model was validated using structural analysis and verification server (SAVS). Coat-protein structure of GarCLV obtained through computational modelling was found congruent with their protein structure obtained by X-ray crystallography or nuclear mag nifty resonance (NMR).
Comparison of the Essential Oils of Ferula orientalis L., Ferulago sandrasica Peşmen and Quézel, and Hippomarathrum microcarpum Petrov and Their Antimicrobial Activity

Objectives: To determine the chemical composition and antimicrobial activity of the essential oils of the aerial parts of Ferula orientalis L. , roots of Ferulago sandrasica Peşmen and Quézel, and aerial parts of Hippomarathrum microcarpum Petrov. Materials and Methods: Essential oils were analyzed by gas chromatography and gas chromatography/mass spectrometry. The antimicrobial activity of the essential oils was determined by bioautography assay. Results: α-Pinene (75.9%) and β-pinene (3.4%) were the major components of the aerial parts of F. orientalis; with limonene (28.9%), α-pinene (15.6%), and terpinolene (13.9%) for F. sandrasica; and β-caryophyllene (31.4%) and caryophyllene oxide (23.1%) for the aerial parts of H. microcarpum. Essential oils from the aerial parts of F. orientalis, the roots of F. sandrasica, and the aerial parts of H. microcarpum were active against Staphylococcus aureus and Candida albicans strains. However, essential oils were not active against Pseudomonas aeruginosa or Escherichia coli. Conclusion: The antimicrobial activities against S. aureus and C. albicans of these species may be attributed to the presence of the main components in the essential oils.
When the Microenvironment Talks, Do Neural Stem Cells Listen? Novel Roles for Complement and Immune Interactions in Autocrine Regulation and Paracrine Modulation of Neural Stem Cells

Author(s): Benavente Perez, Francisca | Advisor(s): Anderson, Aileen J | Abstract: Neural stem cell (NSC) therapies offer promising potential for promoting neurorepair following a variety of neurodegenerative disorders and central nervous system (CNS) injuries. As the use of NSC in clinical trials increases, it is critical to understand the basic biology underlying the neural stem cell capacity for self-renewal, migration, differentiation and final integration in the neural circuitry. Even though there is a great understanding of the molecules and factors involved in neurogenesis in the developmental neurogenic niche, little is known about how the changes in the neurogenic niche in response to disease, injury or aging, may modulate endogenous as well as transplanted NSC and their final capacity for neurorepair. Historically the CNS has been seen as an immuno-privileged organ, with limited interaction with immune components from the rest of the organism. However, it is clear that this view is incomplete and fails to encompass the dynamic and persistent immune response observed in the pathogenesis associated with many types of CNS diseases (e.g., Alzheimer’s disease, traumatic CNS injury, stroke, aging, etc.). We have shown that the inflammatory microenvironment affects NSC fate and migration, influencing their final capacity for neurorepair. We have previously identified a direct and interactive effect of complement components C1q and C3a on NSC mediating proliferation, migration and fate potential in vitro as well as in vivo with function blocking antibodies. In this dissertation I investigate the molecular mechanisms associated with the effects of C1q and C3a on NSC, focusing on the ligand-receptor interactions responsible for this novel effect between the immune system and NSC populations. This dissertation is composed of an Introduction (Chapter 1), and three data chapters (Chapters 2-4) investigating a novel proposed cellular mechanism in which complement molecules modulate NSC migration, proliferation, fate, and final functional integration through direct interaction with cell surface receptors. Elucidating NSC inflammatory microenvironment interactions (i.e, signaling molecules, receptors, intracellular pathways) will provide a better understanding of the impact of the inflammatory microenvironment on NSC populations. Understanding these mechanisms may be a key approach to enabling effective NSC therapies in CNS trauma, disease and aging.
Association mapping in rice: basic concepts and perspectives for molecular breeding

ABSTRACT In the last decade, association mapping (AM) has become a well-established method to detect genes and quantitative trait loci (QTLs) associated with agronomically important traits. The identification of a large number of single nucleotide polymorphisms (SNPs) from genome sequencing and concurrent development of high-throughput genotyping platforms has led to AM being widely used for a range of crops. These technologies have been used in rice (Oryza sativa) to explore the abundant diversity and there is enormous potential to identify novel QTLs for traits of interest. Due to the availability of cost-effective high-throughput SNP genotyping methods and rapid developments in rice genomics, it is inevitable that these AM approaches will become more popular in the future, especially in the context of genome-wide association studies (GWASs). In this paper, we review the fundamental concepts, critical considerations and limitations of AM focusing on rice, and reiterate the importance of accurate phenotypic data. We also include a section about connecting GWAS to molecular breeding, covering practical consideration for breeders, which is required to use GWAS results in actual rice molecular breeding programs and which has not received adequate attention in the scientific literature.
Effect of plant diversification on pest abundance and tomato yields in two cropping systems in Burkina Faso: farmer practices and integrated pest management

In Burkina Faso, pests are the main constraint to tomato production because they can cause a complete loss of yields. To protect their crops, producers use extensively chemical pesticides. However, this method can be ineffective and creates collateral effects on public health and on environment. To mitigate this problem, Integrated Pest Management (IPM) trials based on tomato crop in association with basil, garlic or onion were compared with the usual practices of producers in field trials in 2017. The tomato-onion association provided both the best protection of the fruits and the highest yield (3 kg / m²) compared with peasant and other IPM practices. No pesticide residue was detected in samples (tomatoes and soils) from IPM practices. However, several active substances (profenofos, lambda-cyhalothrin and chlorpyrifos-ethyl) were detected in samples from farmers' practices. Only chlorpyrifos-ethyl showed a residue level above its Maximum Residue Limit (MRL) in tomatoes (360% of MRL), without acute intoxication risk for consumers according to the calculations of the Predictable Short Term Intake (PSTI). Awareness-raising and producer training on the better agricultural and phytosanitary practices are necessary to protect public health and environment against adverse effects of pesticides in Burkina Faso. Keywords : Tomato, peasant practices, IPM, cultural association, Burkina Faso.
Reinstatement of the Southern Andean Genus Stenodraba (Brassicaceae) Based on Molecular Data and Insights from its Environmental and Geographic Distribution

Abstract Stenodraba (Brassicaceae) included a group of eight species distributed along the Andes of South-Central Argentina and Chile. All of its species are currently treated in Pennellia (Tribe Halimolobeae) and Weberbauera (Tribe Thelypodieae). However, the phylogeny of Stenodraba and its tribal placement were never analyzed usingmolecular data. The lack of such studies, as well as the paucity of herbarium collections suggesting that some species are vulnerable and/or endangered, prompted us to address the molecular phylogeny of Stenodraba. For this purpose, we generated comprehensive molecular phylogenies using nuclear (ITS) and plastid (trnL-F and trnH-psbA) data and conducted different niche comparisons in the environmental and geographic spaces using climate data processed both by ordination and species distribution modelling (SDM) techniques. Results from phylogenetic analyses demonstrated that Stenodraba belongs to the South American tribe Eudemeae and is related to the genera Aschersoniodoxa, Brayopsis, Dactylocardamum, and Eudema. Stenodraba species formed two strongly supported clades, and although molecular data did not recover monophyly of the genus, this hypothesis could not be rejected with our data. The main clades were differentiated in their climatic niches (both in the environmental and geographical spaces), and niche overlap was greater within than between clades. Systematic implications, including a key distinguishing Stenodraba from the remaining genera of Eudemeae and a synopsis of its species, are also provided. The new combination S. lagunae is proposed.
A First Record of Anatrachyntis badia (Hodges 1962) (Lepidoptera: Cosmopterigidae) on Zamia integrifolia (Zamiaceae)

Summary This paper describes the first record of the cosmopolitan moth Anatrachyntis badia on the native Florida cycad Zamia integrifolia, and discusses its possible pollination benefit for this threatened plant. This new record is interesting due to the highly toxic nature of these endangered plants as well as their strict reliance on insect pollination for reproduction. It suggests that associations between species of Anatrachyntis and members of the Cycadales may be more widespread than currently known.
Computational investigation of protein surface polarity and pH-dependence: application to antibodies shows that antibody-antigen interfaces tend to be relatively polar

Protein instability leads to reversible self-association and irreversible aggregation which is a major concern for developing new biopharmaceutical leads. Protein solution behaviour is dictated by the physicochemical properties of the protein and the solution. Optimising protein solutions through experimental screens and targeted protein engineering can be a difficult and time consuming process. Here, we describe development of the protein-sol web server, which was previously restricted to protein solubility prediction from amino acid sequence. Tools are presented for calculating and mapping patches of hydrophobicity and charge on the protein surface. In addition, predictions of folded state stability and net charge are displayed as a heatmap for a range of pH and ionic strength conditions. Tools are evaluated in the context of antibodies, their fragments and interactions. Surprisingly, antibody-antigen interfaces are, on average, at least as polar as Fab surfaces. This benchmarking process provides the user with thresholds with which to assess non-polar surface patches, and possible solubility implications, in proteins of interest. Stability heatmaps compare favourably with experimental data for CH2 and CH3 domains. Display and quantification of surface polarity and pH / ionic strength dependence will be useful generally for investigation of protein biophysics.
Effect of harvest interval and intensity on the profitability of uneven-aged management of Norway spruce stands

This study evaluates the profitability of uneven-aged management in boreal forests, focusing on Norway spruce (Picea abies (L.) Karst. ). An individual-tree-based model EFIMOD is used to simulate the dynamics of soil organic matter, resource availability and forest growth. Considered management scenarios are constructed by varying the harvest interval and intensity (i.e. post-harvest basal area). Bare land, young stand and several uneven-aged managed mature stands are evaluated as initial stand states in the profitability analysis. The profitability of uneven-aged management is compared with traditional even-aged management. Uneven-aged management is profitable under all considered initial stand states and management scenarios with 3 per cent interest rate. Even-aged management is more profitable than uneven-aged management when the initial stand state is bare land or a young stand. The profitability is usually the opposite when uneven-aged managed mature stands are considered as the initial state. This, however, requires that the most profitable steady-state management regime, involving a 10-year harvest interval and 4 m² ha⁻¹ post-harvest basal area, is applied. Conversion of even-aged Norway spruce stand to uneven-aged is financially feasible when the stand structure of the even-aged stand has a wide diameter distribution of standing trees rather than the more restricted range usually associated with conventional management using thinning from below.