Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Scots pine (Pinus sylvestris L.) log diameter under bark by using shape and image data

The sawmilling industry stores and measures logs in bark in order to maximize efficiency, quality conservation and preservation. However, billing is based on the diameter under bark, which it is necessary to estimate based on manual or automatic bark detection. Recently, an approach for automatic determination of diameter under bark based on a multi-sensor approach, including shape data, colour image data and tracheid effect data has been presented, including promising results for logs of the species Norway spruce (Picea abies (L.) H. Karst) and Silver fir (Abies alba Mill.). This paper extends this approach to Scots pine (Pinus sylvestris L.). The comparison of the estimated diameters under bark of 270 pine logs with the respective diameters after debarking shows that the method works well and reliably. Estimation errors are in general close to zero and are below ±10 mm for 98% of the logs. In comparison with manual bark detection, the automatic approach is clearly an improvement. Influences of season or characteristics like discolouration are mostly small. Applying a bark detection algorithm trained on spruce to the pine logs leads to acceptable results, but using a separate algorithm for pine leads to an even better performance.
New Pillars of Evolutionary Theory in the Light of Genomics

The evolutionist theory proposed by Darwin is one of the fundamental pillars in biology. Darwin’s theory was solidified with the Modern synthesis of evolutionary biology thanks to the rediscovery of Mendel’s work, which laid the genetic basis of heredity. In recent years, great progress has been acquired in the sequencing and analyses of complete genomes, which have provided several elements to discuss some Darwinists tenets of evolution. The evidence of gene duplication and whole-genome duplication, the horizontal gene transfer and the endosymbiosis process question the idea that evolution proceeds through the gradual accumulation of infinitesimally small random changes. The new evidence of neutral selection on the genomics context reveals other mechanisms of evolution not necessarily related with the idea of progress or with an adaptationist
Caps on Eukaryotic mRNAs

A 5′-terminal cap is added to most eukaryotic cellular and viral messenger ribonucleic acids (mRNAs) at an early stage of transcription. Capping is essential and modulates several subsequent events in gene expression including pre-mRNA splicing, 3′-poly(A) addition, overall stability, nuclear exit to cytoplasm, protein synthesis, and mRNA turnover initiated by decapping. These and other effects involve cap-binding proteins that recognise the m7GpppN cap structure. Capping proceeds by a similar series of enzymatic steps in a wide range of systems, but differences exist between metazoans and unicellular eukaryotes and viruses, pointing to capping enzymes as potential targets for the development of selective drugs against some fungal, viral and parasitic infections. Moreover, the unique structural features of caps enable us to define the initiation sites and promoter regions of gene transcription, and provide a basis for advanced sequencer-mediated high-throughput genome-wide profiling of gene expression in a wide range of cell types. Key Concepts: mRNA caps are now known to be essential components of gene expression in eukaryotic organisms. The history of the discovery of the presence of 5′ caps on messenger RNA and its subsequent scientific flowering is a good example of how a seemingly small biochemical observation can lead to the deeper understanding of a wide range of fundamental molecular biological phenomena. Evolution has resulted in wide variations in capping structure and function among organisms ranging from viruses to humans; the selective forces underlying such variation requires more research. Research that has documented viral-specific capping reactions in viruses should prove to be a fertile source of research leading to new and novel anti-viral agents. The ‘cap-snatching’ strategies of influenza viruses is a remarkable example of an apparent adaptation to enhance infectivity and is a particularly compelling target for therapeutic intervention. The NMD mRNA surveillance pathway, which includes a pioneer round of translation with cap-binding proteins, results in a striking decrease of defective mRNA in cells of patients with genetic diseases containing premature termination codons. Methylation of genomic DNA and mRNA is now widely accepted as a major pathway of the regulation of both transcription and translation in eukaryotes. Protein synthesis is a major field of gene expression where many players work for mRNA capping, decapping, decoding, quality control of gene transcripts and peptide elongation. Micro RNAs are now widely accepted as major players in the translational control of protein synthesis. The analysis of cap-trapped sequences by high-throughput sequencers enables one to carry out a genome-wide identification of promoters together with quantification of their expression, thus elucidating a promoter-based network of transcriptional regulation. Keywords: RNA capping and decapping; RNA methylation; cap-binding proteins; translation; mRNA stability; CAGE (cap analysis of gene expression); next-generation sequencer
Biogeology of Wallacea: geotectonic models, areas of endemism, and natural biogeographical units

The concepts of biogeographical regions and areas of endemism are briefly reviewed prior to a discussion of what constitutes a natural biogeographical unit. It is concluded that a natural biogeographical unit comprises a group of endemic species that share a geological history. These natural biogeographical units are termed Wallacean biogeographical units in honour of the biogeographer A.R. Wallace. Models of the geological development of Indonesia and the Philippines are outlined. Areas of endemism within Wallacea are identified by distributional data, and their relationship to each other and to the adjacent continental regions are evaluated using molecular phylogenies from the literature. The boundaries of these areas of endemism are in broad agreement with earlier works, but it is argued that the Tanimbar Islands are biologically part of south Maluku, rather than the Lesser Sundas, and that Timor (plus Savu, Roti, Wetar, Damar, and Babar) and the western Lesser Sundas form areas of endemism in their own right. Wallacean biogeographical units within Wallacea are identified by congruence between areas of endemism and geological history. It is concluded that although Wallacea as a whole is not a natural biogeographical region, neither is it completely artificial as it is formed from a complex of predominantly Australasian exotic fragments linked by geological processes within a complex collision zone. The Philippines are argued to be an integral part of Wallacea, as originally intended.
Morphological and genetic differentiation of Eremina desertorum (Gastropoda, Pulmonata, Helicidae) in Egypt

To understand the processes that result in morphological and genetic diversity, we studied the differentiation of the land snails Eremina d. desertorum and Eremina desertorum irregularis in the deserts of northern Egypt. These two taxa are differentiated with regard to shell size and shape and are separated by a narrow hybrid zone west of Alexandria. The lack of differences in the genitalia and the lack of reciprocal monophyly of the mitochondrial haplotypes of E. d. desertorum and E. desertorum irregularis support their classification as subspecies rather than distinct species. Low genetic distances indicate that the differentiation is probably less than half a million years old. The genetic data indicate a population expansion in agreement with other evidence that the Nile region in northern Egypt was more humid well into historical times than today. Shell size and shape are correlated with a climatic gradient from cooler and more humid conditions along the Mediterranean coast to arid and hot conditions in the interior. The decrease of body size with decreasing precipitation and increasing temperature might be explained by limited time for food intake in the more arid regions. The shape differences between the taxa are partly an indirect consequence of selection for body size, but are also directly affected by selection for reduction of aperture size.
Habitat restoration facilitates an ecological trap for a locally rare, wetland‐restricted butterfly

Abstract. 1. Ecological traps occur when organisms preferentially reproduce in low quality reproductive habitats because the co‐evolved cues associated with high quality habitat become re‐associated with low quality habitat due to anthropogenically mediated habitat changes. Although the proximate mechanisms underpinning nearly all empirical examples of ecological traps involve exotic species, agriculturalization, or artificial structures, habitat restoration may also facilitate ecological traps because it directly targets species assemblages with a long‐standing co‐evolutionary history.
A useful new insecticide bioassay using first-instar larvae of a net-spinning caddisfly, Cheumatopsyche brevilineata (Trichoptera: Hydropsychidae)

A new insecticide bioassay for assessing the effects of acute insecticide toxicity on lotic insects was developed. It uses first-instar larvae of a net-spinning caddisfly, Cheumatopsyche brevilineata. The test method was suitable for 30 insecticides with a range of action mechanisms. Caddisfly larvae were much more sensitive than daphnids to neonicotinoids. The new bioassay is thus a useful and reliable method for assessing the impact of chemicals such as neonicotinoids, whose risks for lotic insects might be underestimated by the daphnid bioassay.
Effects of enzymes on ester production during the course of a Chinese liquor fermentation as discussed by correlation analysis and path analysis

During the course of a Chinese liquor fermentation, the enzyme activities in the fermenting grains have important effects on ester production. Activities of six kinds of major hydrolases (including amylase, glucoamylase, protease, cellulase, pectinase and lipase) and the production of esters (including total esters, ethyl acetate, ethyl butyrate, ethyl caproate and ethyl lactate) were measured in the fermenting grains. The correlation coefficient between enzyme activities and ester production was calculated through correlation analysis, and the direct and indirect path coefficients of enzyme activities on ester production were obtained by path analysis. The results showed that enzymes had not only direct effects, but also indirect effects via other enzymes on ester production, indicating that the origin and composition of the enzyme effects on ester production were specific. Copyright © 2014 The Institute of Brewing & Distilling
Enzymatic production of D-alanine from DL-alaninamide by novel D-alaninamide specific amide hydrolase

Enzymatic production of D-alanine from DL-alaninamide was investigated. A bacterial strain, NJ-26, which was identified as Arthrohacter sp. , was isolated from activated sludge as a producer of a D-alaninamide specific amide hydrolase (D-amidase). This strain produced D-amidase in the presence of alaninamide as an inducer. The enzyme was purified about 260-fold to near homogeneity. The enzyme is a monomer polypeptide with a molecular weight of about 67,000 as estimated by gel filtration column chromatography. The optimal pH for activity was 7.5. It showed a high D-stereospecificity toward alaninamide. The relative velocity toward L-alaninamide was about 0.7% of that toward D-alaninamide. The Km for D- and L-alaninamide were 4.2 mM and 26.1 mM, respectively. After optimization of the reaction conditions, 105 g/liter of D-alanine was generated from 210 g/liter DL-alaninamide with over 99% enatiomeric excess as a result of cellular reaction and all of the L-alaninamide remained in the reaction mixture.
Chemical Composition of the Essential Oils of Six Hypericum Species (Hypericaceae) from Iran

The genus Hypericum is one of the most important medicinal plants that contain 17 species in Iran, three of them are endemics. This paper reports the essential oil composition of six Hypericum species from Iran. The essential oil analysis of a number of the studied plants has already been reported but their report from Iran may be valuable for scientists. Samples collected between June and August 2007. The composition of the essential oils from Hypericum was investigated on flower and leaf. Essential oils were obtained by hydrodistillation method and then were analyzed by GC and GC/MS. Main components obtained in H. dogonbadanicum (endemic of Iran) on flower were phenyl ethyl octanoate(29.0%), terpin-4-ol (20.0%), and -phellandrene (12.9%), and on leaf were -pinene (54.3%), -pinene (12.0%) and p-cymene (11.0%), in H. helianthemoides on flower were -pinene (55.9%), Z-ocimene (8.7%) and -pinene (7.5%), and in H. hyssopifolium on flower were -pinene (49.5%), -pinene (12.9%) and n-tetradecan (5.2%) and on leaf were E-nerolidol (21.0%), n-tetradecane (15.8%) and -himachalene(13.3%), in H. lysimachioides on flower were -pinene (55.0%), Z--ocimene (30.7%) and n-tetradecane (2.7%), in H. perforatumon flower were E--farnesene (14.7%), n-hexadecanal (9.1%) and E-nerolidol (7.8%), and in H. triquetrifolium on flower were n-tetradecane (21.3%), -himachalene (14.2%) and -pinene (10.7%), and on leaf were -himachalen (27%), n-tetradecane (25.7%) and n-pentadecane (7.0%).
Studies on the optimization of growth and indole alkaloid production by hairy root cultures of Catharanthus roseus

Catharanthus roseus hairy root cultures, genetically transformed with Agrobacterium rhizogenes, produce a wide variety of indole alkaloids. The effect of sucrose, phosphate, nitrate, and ammonia concentrations on growth and indole alkaloid production of C. roseus hairy root cultures were studied by using statistical experimental designs and linear regression analysis. Contradictory effects of these nutrients on growth and indole alkaloid production were found. The maximal growth was obtained by having 77. 8 mg NaH2PO4 · H2O/L and 1. 311 g KNO3/L in the medium, whereas the specific production of alkaloids was highest at the lowest levels of all the nutrients studied. The maximal dry weight was obtained with high values of sucrose and ammonia, but clear optimum concentrations could not be found. When having enough nutrients to support reasonable growth, it appeared difficult to affect the specific alkaloid production rates considerably. The growth (dry wt.) with the optimized nutrient concentrations in the medium was more than 50% better than in the control medium with about the same alkaloid production.
Inhibition of nuclear factor‐κB activation induces apoptosis in cerebellar granule cells

The nuclear factor (NF)‐κB family of transcription factors plays important roles in the regulation of many activities of neuronal cells, such as synaptic transmission, inflammation, neuroprotection, and neurotoxicity. In resting cells, NF‐κB activity is present both in the cytoplasm, as an inducible‐inactive complex, and in the nucleus, as a constitutive form. Regulation of its inducible activity relies on processing of IκB(s), which occurs through the proteasome. Here we show that in cerebellar granule cells (CGC) the induction of apoptosis, by potassium withdrawal (5 mM KCl), decreases the amount of nuclear NF‐κB. To understand whether NF‐κB was required for CGC survival, these cells, maintained under depolarizing conditions (25 mM KCl and serum), were treated with proteasome inhibitors. The results show that these treatments reduce the nuclear amount of NF‐κB and increase p65 cytoplasmic levels, a process partially regulated via IκBα degradation. These events are also associated with an impairment in CGC survival, with changes in nuclear morphology, induction of DNA laddering, and oligonucleosome formation, consistent with apoptosis. According to the K+ deprivation model, PSI‐induced apoptosis is reversed by inhibitors of transcription and translation as well as by specific caspase inhibitors. Together our results show an important role for NF‐κB in maintaining CGC survival. Indeed, under conditions of mild depolarization (K25) necessary for CGC survival, NF‐κB is distributed between cytosol and nucleus, whereas, under apoptotic conditions (K5), it is depleted from the nucleus, such as after proteasome inhibitor treatment. Therefore, NF‐κB nuclear deprivation is involved in the induction of CGC apoptosis. J Neurosci. Res. 66:1064–1073, 2001. © 2001 Wiley‐Liss, Inc.
Genetic and biological characterization of Toxoplasma gondii from Uganda

Toxoplasma gondii is a widely distributed protozoan parasite, estimated to infect 25-50% of the global human population. While most infections are asymptomatic, AIDS-associated toxoplasmic encephalitis causes a high level of morbidity and mortality and this is a particular problem in sub-Saharan Africa, where HIV affects a substantial part of the population. Despite the scale of the problem, virtually nothing has been known about the T. gondii strains present in Africa. The work presented in this thesis showed for the first time that all the three main clonal lineages of T. gondii are present and cause disease in African HIV-patients, and that genotype II was the most common in Uganda. Subsequent isolation of eight strains revealed that the T. gondii parasites in Uganda are highly similar to the strains found in Europe and North America, but over 1,200 novel mutations were identified and many of these were indicative of positive selection of genes active in the interface with the host. An important finding was the discovery of a rare natural recombinant strain, which possessed genetic elements from both genotype II and III and displayed an intermediate in vivo growth rate, compared with the genuine type II and III strains from the same area. Whole genome sequencing of this isolate revealed that sexual recombination may be more frequent than previously thought, but that selective pressures appear to favour a conserved genetic composition. The studies included in this thesis provide novel insight into the genotype and phenotype of T. gondii strains from Africa, and describe for the first time the genomics of a natural recombinant T. gondii strain.
Agronomic challenges from novel pathotypes of Albugo candida to the emerging Brassica juncea industry in Western Australia.

It can be difficult to predict the outcome when a newly introduced crop is challenged by a specialized obligate phytopathogen. This case study explores the potential of Albugo candida, which causes white blister (WB) of Brassicas, to evolve into a major challenge to the broad acre crop Brassica juncea in the Western Australian (W.A.) ag- ricultural landscape. Brassica juncea is currently emerging as a viable replacement oilseed crop to B. napus, especially in parts of W.A. with diminishing rainfall. WB is known to be a greater threat to B. juncea than to B. napus. Studies to date indicate significant genetic diversity of A. candida populations in this region, with many pathotypes evolv- ing on exotic and native weed flora, and these may result in the development of strains that pose increased threats to B. juncea crops than those already encountered. Information gathered on pathogenic behaviour and defense mechanisms will assist understanding the nature of the appearance of novel pathotypes, and enable development of strategies to enhance host resistance to A. candida in B. juncea. Strategies to manipulate agronomic practices, such as weed control, may also help to reduce the hazards posed by newly evolving pathotypes in this region.
The Griffoniasimplicifolia I Isolectin B4 and Tomato Lectin Recognize Astrocytes instead of Microglia in Adult Hamster Retina

Two lectins, Griffonia simplicifolia I isolectin B4 (GS-I lectin) and Lycopersicon esculentum (LE) lectin, reported to be specific microglia markers in a number of animals including rodents, were used to stain hamster retinas. In the adult hamster retina, both of them failed to stain microglia but instead labeled astrocytes (in addition to endothelial cells). GS-I lectin-positive astrocytes were mainly located at peripheral regions of the retina but were variable in number and staining intensity, while LE lectin stained most astrocytes as judged by co-localization with anti-glial fibrillary acidic protein staining. To see whether astrocytes (and/or microglia) would be labeled by the lectins during postnatal retinal development, retinas from newborns all the way to adults were studied. Starting from P0, GS-I lectin selectively labeled astrocytes located adjacent to and peripheral to the tips of developing blood vessels, suggesting a functional association of glycoproteins containing α-D-galactose (the terminal sugar residue with binding affinity to GS-I) with the migration of the astrocytic front during development. The GS-I lectin staining on this population of astrocytes became reduced as the astrocytic front reached the retinal periphery, so that in the adult only astrocytes in the periphery became positive for GS-I. In contrast, LE lectin stained most astrocytes in the developing retina, starting from P2 and with maximum staining intensity achieved around P14, which continued unchanged to adulthood. During early postnatal retinal development, both lectins could label microglia, but the staining was abolished well before the retina became mature. GS-I could label microglia until P18, and the stained cells were mainly confined to the retinal periphery where blood vessels were absent, suggesting that expression of the terminal α-D-galactose residue is regulated by interaction with the developing vasculature (and/or astrocytes). LE could mark microglia till P6, but the labeling was weaker compared with GS-I. The results indicate that at least in the hamster, GS-I and LE lectin may be a more selective marker for retinal astrocytes than microglia. It would be interesting to see whether some other animals will exhibit a similar picture, and whether the expression of the sugar residues (specific for GS-I and LE lectin binding) on astrocytes instead of microglia will confer any functional consequences uniquely different from those animals with specific microglia binding.
Comparison of Nitrogen and Oxygen Demands of Enological Yeasts: Technological Consequences

Nitrogen and oxygen requirements of commercial yeasts were compared. Nitrogen demands were measured by calculating the amounts of ammoniacal nitrogen necessary to keep the fermentation rate constant during the stationary phase. Oxygen demands were studied by (i) running anaerobic fermentations and (ii) measuring the effect of adding 1 mg/L oxygen at the beginning of the stationary phase. Substantial differences were found and their technological impact was discussed. Because of the importance of nitrogen and oxygen in enology, using such tests may be of great interest, especially when there are risks of (i) slow fermentations, due to nitrogen deficiencies or (ii) sluggish fermentations, mainly due to oxygen limitations.
Reflexed flowers in Aeschynomene amorphoides (Fabaceae: Faboideae): a mechanism promoting pollination specialization?

This study aims to understand the role of floral traits in determining the reproductive biology of the leguminous shrub Aeschynomene amorphoides, endemic to western Mexico, which has unusually orientated flowers. We investigated the floral biology, pollination and breeding system based on a combination of morphological studies and field experiments, using controlled pollinations in a natural environment. The architecture and reflexed position of A. amorphoides flowers facilitate precise placement of pollen on the body of the pollinator, but this has a cost to A. amorphoides in terms of available flower resources. These costs to reproduction success are set against the attraction of a specialized pollinator, Tetraloniella jaliscoensis, which is capable of manipulating this unique pollination system in papilionoid (or flag) flowers. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177, 657–666.