Miracle-dz/UniFAR-FTUs huggingface dataset:
Substantial labile carbon stocks and microbial activity in deeply weathered soils below a tropical wet forest

Contrary to large areas in Amazonia of tropical moist forests with a pronounced dry season, tropical wet forests in Costa Rica do not depend on deep roots to maintain an evergreen forest canopy through the year. At our Costa Rican tropical wet forest sites, we found a large carbon stock in the subsoil of deeply weathered Oxisols, even though only 0.04–0.2% of the measured root biomass (>2 mm diameter) to 3 m depth was below 2 m. In addition, we demonstrate that 20% or more of this deep soil carbon (depending on soil type) can be mobilized after forest clearing for pasture establishment. Microbial activity between 0.3 and 3 m depth contributed about 50% to the microbial activity in these soils, confirming the importance of the subsoil in C cycling. Depending on soil type, forest clearing for pasture establishment led from no change to a slight addition of carbon in the topsoil (0–0.3 m depth). However, this effect was countered by a substantial loss of C stocks in the subsoil (1–3 m depth). Our results show that large stocks of relatively labile carbon are not limited to areas with a prolonged dry season, but can also be found in deeply weathered soils below tropical wet forests. Forest clearing in such areas may produce unexpectedly high C losses from the subsoil.
A cytogenetic study of bilateral sexual polyploidization in cassava (Manihot esculenta Crantz)

Microsporogenesis and megasporogenesis were cytogenetically and histologically analysed in three cassava clones:‘Rayong 1′,‘Rayong 60′,‘M. mga’ and two hybrid lines,‘OMR 3641-1’ and ‘OMR 3641-1’ to elucidate the evolution of sexual polyploids in cassava. At telophase II, formation of 17-21 micronuclei per pollen cell plate was observed in 16 out of 351 cell plates in ‘M. mga’. Micronuclei were observed at low (0.3-2.3%) frequencies, at the sporad stage in all clones. Monads, dyads, triads and tetrads, which are established sources of high ploidy levels were observed at low (2.6%) and high (22.2%) frequencies. Megasporogenesis in ‘Rayong 1’ and ‘Rayong 60’ showed a lack of second meiotic divisions after a successful first division that resulted in partly unreduced embryo sacs with 2n eggs, suggesting another unrecognized and, as yet, unreported source of sexual polyploid formation in cassava. Meiotic abnormalities during microsporogenesis and megasporogenesis are implicated as being responsible for the formation of mixoploids (triploids and tetraploids) in cassava breeding programmes. A cytogenetic mechanism resulting in bilateral sexual polyploids through different gametic fertilization pathways in cassava is suggested and its role in breeding is briefly discussed.
Biotechnological Potential of Streptomyces Siderophores as New Antibiotics.

BACKGROUND Siderophores are small molecule iron-chelators produced by microorganisms and plants growing mostly under low iron conditions. Siderophores allow iron capture and transport through cell membranes into the cytoplasm, where iron is released for use in biological processes. These bacterial iron uptake systems can be used for antibiotic conjugation or as targets for killing pathogenic bacteria. Siderophores have been explored recently because of their potential applications in environmental and therapeutic research. They are present in Streptomyces, Gram-positive bacteria that are an important source for discovering new siderophores. OBJECTIVE This review summarizes siderophore molecules produced by the genus Streptomyces emphasizing their potential as biotechnological producers and also illustrating genomic tools for discovering siderophores useful for treating bacterial infections. METHODS The literature search was performed using PUBMED and MEDLINE databases with keywords siderophore, secondary metabolites, Trojan horse strategy, sideromycin and Streptomyces. The literature research focused on bibliographic databases including all siderophores identified in the genus Streptomyces. In addition, reference genomes of Streptomyces from GenBank were used to identify siderophore biosynthetic gene clusters by using the antiSMASH platform. RESULTS This review has highlighted some of the many siderophore molecules produced by Streptomyces, illustrating the diversity of their chemical structures and wide spectrum of bioactivities against pathogenic bacteria. Furthermore, the possibility of using siderophores conjugated with antibiotics could be an alternative to overcome bacterial resistance to drugs and could improve their therapeutic efficacy. CONCLUSION This review confirms the importance of Streptomyces as a rich source of siderophores, and underlines their potential as antibacterial agents.
Growth and resilience responses of Scots pine to extreme droughts across Europe depend on predrought growth conditions

Global climate change is expected to further raise the frequency and severity of extreme events, such as droughts. The effects of extreme droughts on trees are difficult to disentangle given the inherent complexity of drought events (frequency, severity, duration, and timing during the growing season). Besides, drought effects might be modulated by trees’ phenotypic variability, which is, in turn, affected by long‐term local selective pressures and management legacies. Here we investigated the magnitude and the temporal changes of tree‐level resilience (i.e., resistance, recovery, and resilience) to extreme droughts. Moreover, we assessed the tree‐, site‐, and drought‐related factors and their interactions driving the tree‐level resilience to extreme droughts. We used a tree‐ring network of the widely distributed Scots pine (Pinus sylvestris) along a 2,800 km latitudinal gradient from southern Spain to northern Germany. We found that the resilience to extreme drought decreased in mid‐elevation and low productivity sites from 1980–1999 to 2000–2011 likely due to more frequent and severe droughts in the later period. Our study showed that the impact of drought on tree‐level resilience was not dependent on its latitudinal location, but rather on the type of sites trees were growing at and on their growth performances (i.e., magnitude and variability of growth) during the predrought period. We found significant interactive effects between drought duration and tree growth prior to drought, suggesting that Scots pine trees with higher magnitude and variability of growth in the long term are more vulnerable to long and severe droughts. Moreover, our results indicate that Scots pine trees that experienced more frequent droughts over the long‐term were less resistant to extreme droughts. We, therefore, conclude that the physiological resilience to extreme droughts might be constrained by their growth prior to drought, and that more frequent and longer drought periods may overstrain their potential for acclimation.
Profiles of Cognitive Change in Preclinical and Prodromal Alzheimer's Disease Using Change-Point Analysis.

BACKGROUND Alzheimer's disease (AD) is now understood to have a long preclinical phase in which pathology starts to accumulate in the absence of clinical symptoms. Identifying the temporal stages of accelerated cognitive decline in this phase may help in developing more sensitive neuropsychological tools for early screening of preclinical cognitive decline. Change-point analyses are increasingly used to characterize the temporal stages of accelerated cognitive decline in the preclinical stages of AD. However, statistical comparisons of change-points between specific cognitive measures have not been reported. OBJECTIVE To characterize and compare the temporal stages of accelerated decline in performance on multiple cognitive tests in a sample of participants from the Baltimore Longitudinal Study on Aging (BLSA) who later developed AD. METHODS 165 older adults (baseline age range: 61.1-91.2) from the Baltimore Longitudinal Study of Aging developed AD during follow-up. Linear and non-linear mixed models were fit for 11 cognitive measures to determine change-points in rates of decline before AD diagnosis. Bootstrapping was used to compare the timing of change-points across cognitive measures. RESULTS Change-points followed by accelerated decline ranged from 15.5 years (Standard Error (S.E.) = 1.72) for Card Rotations to 1.9 years (S.E. = 0.68) for the Trail-Making A test before AD diagnosis. Accelerated decline in Card Rotations occurred significantly earlier than all other measures, including learning and memory measures. CONCLUSION Results suggest that visuospatial ability, as assessed by Card Rotations, may have the greatest utility as an early predictive tool in identifying preclinical AD.
Integrating Convolutional Neural Networks and Multi-Task Dictionary Learning for Cognitive Decline Prediction with Longitudinal Images.

BACKGROUND Disease progression prediction based on neuroimaging biomarkers is vital in Alzheimer's disease (AD) research. Convolutional neural networks (CNN) have been proved to be powerful for various computer vision research by refining reliable and high-level feature maps from image patches. OBJECTIVE A key challenge in applying CNN to neuroimaging research is the limited labeled samples with high dimensional features. Another challenge is how to improve the prediction accuracy by joint analysis of multiple data sources (i.e., multiple time points or multiple biomarkers). To address these two challenges, we propose a novel multi-task learning framework based on CNN. METHODS First, we pre-trained CNN on the ImageNet dataset and transferred the knowledge from the pre-trained model to neuroimaging representation. We used this deep model as feature extractor to generate high-level feature maps of different tasks. Then a novel unsupervised learning method, termed Multi-task Stochastic Coordinate Coding (MSCC), was proposed for learning sparse features of multi-task feature maps by using shared and individual dictionaries. Finally, Lasso regression was performed on these multi-task sparse features to predict AD progression measured by the Mini-Mental State Examination (MMSE) and the Alzheimer's Disease Assessment Scale cognitive subscale (ADAS-Cog). RESULTS We applied this novel CNN-MSCC system on the Alzheimer's Disease Neuroimaging Initiative dataset to predict future MMSE/ADAS-Cog scales. We found our method achieved superior performances compared with seven other methods. CONCLUSION Our work may add new insights into data augmentation and multi-task deep model research and facilitate the adoption of deep models in neuroimaging research.
Cytological Effects of a Gene in Datura which Causes Dyad Formation in Sporogenesis

1. Dyad formation in sporogenesis in Datura, owing to a recessive gene, was found among the F2 offspring from radium-treated pollen. 2. During megasporogenesis the first meiotic division is present, but the second meiotic division is regularly absent. As a result only two megaspores (dyads) are formed. 3. One of the megaspores disintegrates; the other undergoes three successive mitotic divisions. Its nucleus contains 12 pairs of chromosomes instead of 12 single chromosomes. 4. An embryo sac is formed containing eight nuclei, each with 24 chromosomes. 5. During microsporogenesis the same meiotic abnormality is found in the pollen mother cell. There is a failure of the second division, and after the first division a thick cell wall develops between the two nuclei, forming a dyad of microspores. 6. Each microspore, containing 12 pairs of chromosomes, develops into the male gametophyte. 7. A small percentage (about 1 to 5 per cent) of megasporocytes and microsporocytes in dyad plants develops normally. Since both meiotic divisions are present, a "tetrad" of microspores instead of a "dyad" is formed. Each gamete that results from these exceptional cases contains 12 single chromosomes. 8. The formation of 2n and 3n normal offspring from the cross dyad x normal confirms the occurrence of both 1n and 2n egg cells. Dyad 2n offspring have come from parthenogenesis of a 2n dyad egg. 9. The occurrence of large and normal sized pollen grains in dyad plants confirms the occurrence of both 1n and 2n sperms.
CONTRIBUTION TO THE KNOWLEDGE OF MICROTUS GUENTHERI HARTINGI FROM THEBES, GREECE

Etude des variations individuelles chez des Microtus guentheri hartingi collectes pres de Thobes, Grece, en 1960-61. Pas de difference morphologique sexuelle. La sous-espece etudiee est une des plus petites. Sex-ratio : 1,69 9 pour 1 tf. Le cinquieme des 9 sont gestantes et il y a une moyenne de 5,6 embryons (de 4 a 8). Etude de la structure des molaires, de la variation de la 3 molaire suporieure. Composition du terrier.
Plant growth promotion by phosphate solubilizing fungi – current perspective

Phosphorus is abundant in soils in both organic and inorganic forms; nevertheless, it is unavailable to plants. Accordingly, soil becomes phosphorus (P)-deficient, making P one of the most important nutrient elements limiting crop productivity. To circumvent the P deficiency, phosphate-solubilizing microorganisms could play an important role in making P available for plants by dissolving insoluble P. The dissolution of inorganic P by microbial communities including fungi is though common under in vitro conditions; the performance of phosphate-solubilizing microbes in situ has been contradictory. Fungi exhibit traits such as mineral solubilization, biological control, and production of secondary metabolites. As such, their potential to enhance plant growth when present in association with the roots is clear. The challenge is how to make use of such biological resources to maintain soil health while increasing the crop productivity by providing P to plants through the application of phosphate-solubilizing fungi. The present review focuses on the mechanisms of phosphate solubilization, development and mode of fungal inoculants application and mechanisms of growth promotion by phosphate-solubilizing fungi for crop productivity under a wide range of agro-ecosystems, and the understanding and management of P nutrition of plants through the application of phosphate-solubilizing fungi will be addressed and discussed.
A flavonol synthase gene GtFLS defines anther-specific flavonol accumulation in gentian

Flavonoids are important for male gametophyte development. Here we report on the flavonoid components and their biosynthetic regulation in gentian anthers. Among flavonoids, flavonols, including kaempferol, quercetin and isorhamnetin derivatives, accumulated abundantly in gentian anthers. However, flavones and anthocyanins, which are the main flavonoids accumulating in petals, were not detected. Northern blot analysis of nine flavonoid biosynthetic genes showed that the ‘early’ flavonoid biosynthetic genes were expressed in both anthers and petals, and that flavonol synthase (FLS) transcripts were restricted to anthers. In contrast, flavone synthase II (FNSII) and ‘late’ flavonoid biosynthetic genes were expressed specifically in gentian petals. To confirm anther-specific expression of FLS, the 5′-upstream region of FLS (GtFLSpro) was cloned by inverse PCR and fused to the uidA (GUS) reporter gene. Tobacco, Arabidopsis and gentian plants, transformed with the GtFLSproGUS construct, exhibited anther-specific GUS expression. Expression was observed in the tapetum and in pollen at late stages of anther development in transgenic plants. These results revealed that flavonol accumulation in gentian anthers was regulated by the spatial expression of GtFLS. Our results also suggest that anther-specific regulation of FLS is conserved among higher plants and the GtFLS promoter is useful for induction of specific gene expression in anthers.
Low‐severity fire as a mechanism of organic matter protection in global peatlands: Thermal alteration slows decomposition

Worldwide, regularly recurring wildfires shape many peatland ecosystems to the extent that fire‐adapted species often dominate plant communities, suggesting that wildfire is an integral part of peatland ecology rather than an anomaly. The most destructive blazes are smoldering fires that are usually initiated in periods of drought and can combust entire peatland carbon stores. However, peatland wildfires more typically occur as low‐severity surface burns that arise in the dormant season when vegetation is desiccated, and soil moisture is high. In such low‐severity fires, surface layers experience flash heating, but there is little loss of underlying peat to combustion. This study examines the potential importance of such processes in several peatlands that span a gradient from hemiboreal to tropical ecozones and experience a wide range of fire return intervals. We show that low‐severity fires can increase the pool of stable soil carbon by thermally altering the chemistry of soil organic matter (SOM), thereby reducing rates of microbial respiration. Using X‐ray photoelectron spectroscopy and Fourier transform infrared, we demonstrate that low‐severity fires significantly increase the degree of carbon condensation and aromatization of SOM functional groups, particularly on the surface of peat aggregates. Laboratory incubations show lower CO2 emissions from peat subjected to low‐severity fire and predict lower cumulative CO2 emissions from burned peat after 1–3 years. Also, low‐severity fires reduce the temperature sensitivity (Q10) of peat, indicating that these fires can inhibit microbial access to SOM. The increased stability of thermally altered SOM may allow a greater proportion of organic matter to survive vertical migration into saturated and anaerobic zones of peatlands where environmental conditions physiochemically protect carbon stores from decomposition for thousands of years. Thus, across latitudes, low‐severity fire is an overlooked factor influencing carbon cycling in peatlands, which is relevant to global carbon budgets as climate change alters fire regimes worldwide.
Short time guided bone regeneration using beta-tricalcium phosphate with and without fibronectin – An experimental study in rats

Background The aim of this histomorphometric study was to assess the bone regeneration potential of beta-tricalcium phosphate with fibronectin (β-TCP-Fn) in critical-sized defects (CSDs) in rats calvarial, to know whether Fn improves the new bone formation in a short time scope. Material and Methods CSDs were created in 30 Sprague Dawley rats, and divided into four groups (2 or 6 weeks of healing) and type of filling (β-TCP-Fn, β-TCP, empty control). Variables studied were augmented area (AA), gained tissue (GT), mineralized/non mineralized bone matrix (MBM/NMT) and bone substitute (BS). Results 60 samples at 2 and six weeks were evaluated. AA was higher for treatment groups comparing to controls (p < 0.001) and significant decrease in BS area in the β-TCP-Fn group from 2 to 6 weeks (p = 0.031). GT was higher in the β-TCP-Fn group than in the controls expressed in % (p = 0.028) and in mm2 (p = 0.011), specially at two weeks (p=0.056). Conclusions Both β-TCP biomaterials are effective as compared with bone defects left empty in maintaining the volume. GT in defects regeneration filed with β-TCP-Fn are significantly better in short healing time when comparing with controls but not for β-TCP used alone in rats calvarial CSDs. Key words:Bone regeneration, biomaterials, experimental design, histology.
Effect of ripening on the chemical composition of plantain peels and pulps (Musa paradisiaca)

The composition of minerals and organic contents of the peels and pulps of unripe (green) plantain (Musa paradisiaca L) through five different ripening stages were determined. Crude fibre, ash, fat, crude protein and moisture contents were higher in the peels than in the pulps whereas carbohydrate and dry matter contents were higher in the pulps than in the peels at different stages of ripening. Potassium is the most abundant mineral in both samples with estimated values of 37 g kg−1 in the green peel and 8.4 g kg−1 in the green pulp. Small increases in potassium content were found in both samples during ripening. Iron, calcium and sodium show similar variations but phosphorus levels decrease as ripening progressed. The concentrations of copper and magnesium ions remained fairly constant. The estimated values for copper were 13 mg kg−1 and 10 mg kg−1 for the peels and pulps, respectively. However, the magnesium content in the pulp of 41 mg kg−1 was constant whereas that of the peel increased as the fruit ripened. The low sodium content (350 mg kg−1) is an advantage in the treatment or prevention of hypokalaemia.
Methane metabolism in raised bogs of northern wetlands

Abstract Laboratory columns under continuous flow were packed with peat from the catotelm of an ombrotrophic bog to simulate the natural environment. Methane concentration increased from 1.4 to 47.8 μmol ml−1 due to anaerobic microbial degradation of the peat, while at the same time the water flow rate decreased from log ‐1.39 to ‐3.03 cm3 s−1 and the moisture content decreased from 85.7 to 56.6%. A control column sterilized by irradiation produced carbon dioxide, but, as the flow of water washed this soluble gas out of the column, the hydraulic conductivity and moisture content increased. These two results suggest that it is the volume of the gas (in the gas phase within the bog) that controls the hydraulic conductivity of peat bogs. Volume accounting at the end of the experiment showed no gas in the sterilized column but 17% gas by volume in the microbially active column. We suggest that as gas bubbles occlude the interstitial pores of the peat the water flow is impeded, reducing both the hydraulic cond.