Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine tuning of trehalose biosynthesis and hydrolysis as novel tools for the generation of abiotic stress tolerant plants

The impact of abiotic stress on plant growth and development has been and still is a major research topic. An important pathway that has been linked to abiotic stress tolerance is the trehalose biosynthetic pathway. Recent findings showed that trehalose metabolism is also important for normal plant growth and development. The intermediate compound – trehalose-6-phosphate (T6P) – is now confirmed to act as a sensor for available sucrose, hereby directly influencing the type of response to the changing environmental conditions. This is possible because T6P and/or trehalose or their biosynthetic enzymes are part of complex interaction networks with other crucial hormone and sugar-induced signaling pathways, which may function at different developmental stages. Because of its effect on plant growth and development, modification of trehalose biosynthesis, either at the level of T6P synthesis, T6P hydrolysis, or trehalose hydrolysis, has been utilized to try to improve crop yield and biomass. It was shown that alteration of the amounts of either T6P and/or trehalose did result in increased stress tolerance, but also resulted in many unexpected phenotypic alterations. A main challenge is to characterize the part of the signaling pathway resulting in improved stress tolerance, without affecting the pathways resulting in the unwanted phenotypes. One such specific pathway where modification of trehalose metabolism improved stress tolerance, without any side effects, was recently obtained by overexpression of trehalase, which results in a more sensitive reaction of the stomatal guard cells and closing of the stomata under drought stress conditions. We have used the data that have been obtained from different studies to generate the optimal plant that can be constructed based on modifications of trehalose metabolism.
G-PARE: A visual analytic tool for comparative analysis of uncertain graphs

There are a growing number of machine learning algorithms which operate on graphs. Example applications for these algorithms include predicting which customers will recommend products to their friends in a viral marketing campaign using a customer network, predicting the topics of publications in a citation network, or predicting the political affiliations of people in a social network. It is important for an analyst to have tools to help compare the output of these machine learning algorithms. In this work, we present G-PARE, a visual analytic tool for comparing two uncertain graphs, where each uncertain graph is produced by a machine learning algorithm which outputs probabilities over node labels. G-PARE provides several different views which allow users to obtain a global overview of the algorithms output, as well as focused views that show subsets of nodes of interest. By providing an adaptive exploration environment, G-PARE guides the users to places in the graph where two algorithms predictions agree and places where they disagree. This enables the user to follow cascades of misclassifications by comparing the algorithms outcome with the ground truth. After describing the features of G-PARE, we illustrate its utility through several use cases based on networks from different domains.
Hydrated salt minerals on Europa's surface from the Galileo near‐infrared mapping spectrometer (NIMS) investigation

We reported evidence of heavily hydrated salt minerals present over large areas of Europa's surface from analysis of reflectance spectra returned by the Galileo mission near infrared mapping spectrometer (NIMS) [McCord et al., 1997a, b, 1998a, b]. Here we elaborate on this earlier evidence, present spatial distributions of these minerals, examine alternate water-ice interpretations, expand on our hydrated-salts interpretation, consider salt mineral stability on Europa, and discuss the implications. Extensive well-defined areas on Europa show distinct, asymmetric water-related absorption bands in the 1 to 2.5-μm region. Radiative transfer modeling of water ice involving different particle sizes and layers at Europa temperatures does not reproduce the distinctive Europa water bands. However, ice near its melting temperature, such as in terrestrial environments, does have some characteristics of the Europa spectrum. Alternatively, some classes of heavily hydrated minerals do exhibit such water bands. Among plausible materials, heavily hydrated salt minerals, such as magnesium and sodium sulfates, sodium carbonate and their mixtures, are preferred. All Europa spectral features are present in some salt minerals and a very good match to the Europa spectrum can be achieved by mixing several salt spectra. However, no single or mix of salt mineral spectra from the limited library available has so far been found to perfectly match the Europa spectrum in every detail. The material is concentrated at the lineaments and in chaotic terrain, which are technically disrupted areas on the trailing side. Since the spectrum of the material on Europa is nearly the same everywhere so-far studied, the salt or salt-mixture composition may be nearly uniform. This suggests similar sources and processes over at least a near-hemispheric scale. This would suggest that an extensive subsurface ocean containing dissolved salts is the source, and several possible mechanisms for deposit emplacement are considered. The hydrogen bonds associated with hydration of these salts are similar or greater in strength and energy to those in pure water ice. Thus, once on the surface, the salt minerals should be as stable to disruption as water ice at the Europa temperatures, and mechanisms are suggested to enhance the stability of both materials. Spectra obtained of MgSO4·6H2O at 77 K show only small differences from room temperature spectra. The main difference is the appearance of the individual absorptions composing the broad, composite water features and associated with the several different H2O sites in the salt hydrate molecule. This suggests that the Europa absorption bands are also composites. Thus higher spectral resolution may reveal these diagnostic features in Europa's spectrum. The specific salts present and their relative abundances would be indicators of the chemistry and conditions of an ocean environment, and areas of fresh, heavy concentration of these minerals should make ideal lander mission sampling sites.
Phosphoenolpyruvate synthetase and pyruvate, phosphate dikinase of Thermoproteus tenax: key pieces in the puzzle of archaeal carbohydrate metabolism

The interconversion of phosphoenolpyruvate and pyruvate represents an important control point of the Embden–Meyerhof–Parnas (EMP) pathway in Bacteria and Eucarya, but little is known about this site of regulation in Archaea. Here we report on the coexistence of phosphoenolpyruvate synthetase (PEPS) and the first described archaeal pyruvate, phosphate dikinase (PPDK), which, besides pyruvate kinase (PK), are involved in the catalysis of this reaction in the hyperthermophilic crenarchaeote Thermoproteus tenax. The genes encoding T. tenax PEPS and PPDK were cloned and expressed in Escherichia coli, and the enzymic and regulatory properties of the recombinant gene products were analysed. Whereas PEPS catalyses the unidirectional conversion of pyruvate to phosphoenolpyruvate, PPDK shows a bidirectional activity with a preference for the catabolic reaction. In contrast to PK of T. tenax, which is regulated on transcript level but exhibits only limited regulatory potential on protein level, PEPS and PPDK activities are modulated by adenosine phosphates and intermediates of the carbohydrate metabolism. Additionally, expression of PEPS is regulated on transcript level in response to the offered carbon source as revealed by Northern blot analyses. The combined action of the differently regulated enzymes PEPS, PPDK and PK represents a novel way of controlling the interconversion of phosphoenolpyruvate and pyruvate in the reversible EMP pathway, allowing short‐term and long‐term adaptation to different trophic conditions. Comparative genomic analyses indicate the coexistence of PEPS, PPDK and PK in other Archaea as well, suggesting a similar regulation of the carbohydrate metabolism in these organisms.
Measurement of the Forward–backward Asymmetry in Top Quark–antiquark Production in P ¯ P Collisions Using the Lepton+jets Channel (the D0 Collaboration

We present a measurement of the forward–backward asymmetry in top quark–antiquark production using the full Tevatron Run II dataset collected by the D0 experiment at Fermilab. The measurement is performed in lepton+jets final states using a new kinematic fitting algorithm for events with four or more jets and a new partial reconstruction algorithm for events with only three jets. Corrected for detector acceptance and resolution effects, the asymmetry is evaluated to be AFB = (10.6 ± 3.0) %. Results are consistent with the standard model predictions which range from 5.0% to 8.8%. We also present the dependence of the asymmetry on the invariant mass of the top quark–antiquark system and the difference in rapidities of top quark and antiquark.
Developmental buffering: how many genes?

The question of how phenotypic variation is regulated hasattracted an increasing amount of attention in recent years(Debat and David 2001; Flatt 2005). In particular, the dis-covery of the intriguing eﬀects of mutations of heat-shockprotein 90 (Hsp90) on phenotypic variability (Rutherford andLindquist 1998; Queitsch et al. 2002) sparked a great deal ofinterest in the question of whether there are speciﬁc genes withkey roles in the regulation of phenotypic variation and evolv-ability (e.g., Wagner et al. 1999). A number of studies have been published in the past sev-eral months that addressed a range of questions concerningthe buﬀering role of Hsp90 in ﬂies (Carey et al. 2006; Debatet al. 2006; Milton et al. 2006; Gibert et al. 2007), ﬁsh (Yeyatiet al. 2007) and plants (Sangster et al. 2007). Together withsome other recent studies, these articles oﬀer some new per-spectives on the genetic basis of developmental buﬀering.
Targeted killing of Leishmania donovani in vivo and in vitro with amphotericin B attached to functionalized carbon nanotubes.

OBJECTIVES This study describes the antileishmanial efficacy of the novel drug formulation of amphotericin B (AmB) attached to functionalized carbon nanotubes (f-CNTs) and compares it with AmB. METHODS f-CNTs were prepared in a two-step chemical carboxylation and amidation process. The AmB was then attached to make f-CNT-AmB and its construction was confirmed by Fourier transform infrared (FTIR) spectroscopy and transmission electron microscopy (TEM). The cytotoxicity of the constructed compound, f-CNT-AmB, was assessed in vitro using the J774A.1 macrophage cell line and in vivo using healthy BALB/c mice. Antileishmanial activity of AmB and f-CNT-AmB was assessed in vitro using a macrophage (J774A.1 cell line) model of Leishmania donovani infection. Antileishmanial activity was assessed in vivo by comparing the parasite load of hamsters treated with a 5 day course of AmB, f-CNTs or f-CNT-AmB initiated at 30 days after infection with L. donovani parasites. RESULTS The FTIR spectroscopy and TEM data demonstrate the successful attachment of AmB to f-CNTs. The in vitro cytotoxicity of AmB, f-CNTs and f-CNT-AmB was measured by the cytotoxic concentration required to kill 50% of the cells: 0.48±0.06 μg/mL; 7.31±1.16 μg/mL; 0.66±0.17 μg/mL, respectively, in the J774A.1 cell line. The in vivo toxicity assessment of the compounds in BALB/c mice revealed no hepatic or renal toxicity. Against intracellular amastigotes the in vitro antileishmanial efficacy of f-CNT-AmB was significantly higher than that of AmB (IC50 0.00234±0.00075 μg/mL versus 0.03263±0.00123 μg/mL; P≤0.0001). The percentage inhibition of amastigote replication in hamsters treated with f-CNT-AmB was significantly more than that with AmB (89.85%±2.93% versus 68.97%±1.84%; P=0.0004). CONCLUSIONS The results of these experiments clearly demonstrate that f-CNT-AmB has significantly greater antileishmanial efficacy than AmB and had no significant cytotoxic effects.
Owls May Use Faeces and Prey Feathers to Signal Current Reproduction

Background Many animals communicate by marking focal elements of their home range with different kinds of materials. Visual signaling has been demonstrated to play a previously unrecognized role in the intraspecific communication of eagle owls (Bubo bubo), in both territorial and parent-offspring contexts. Visual signals may play a role in a variety of circumstances in this crepuscular and nocturnal species. Methodology/Principal Findings Here, we report that a large amount of extremely visible white faeces and prey feathers appear during the breeding season on posts and plucking sites in proximity to the nest, potentially representing a way for eagle owls to mark their territory. We present descriptive and experimental evidence showing that faeces and prey remains could act as previously unrecognized visual signals in a nocturnal avian predator. This novel signaling behavior could indicate the owls' current reproductive status to potential intruders, such as other territorial owls or non-breeding floaters. Faeces and prey feather markings may also advertise an owl's reproductive status or function in mate-mate communication. Conclusions/Significance We speculate that faeces marks and plucking may represent an overlooked but widespread method for communicating current reproduction to conspecifics. Such marking behavior may be common in birds, and we may now be exploring other questions and mechanisms in territoriality.
The obese gene product, leptin: possible role in obesity‐related hypertension in adolescents

Objective The mechanism of the association between obesity and hypertension is not clear. The recently discovered obese gene product, leptin, the levels of which increase in obese subjects, has been shown to reduce food intake and increase sympathetic nervous system activity in animal studies. The present study was undertaken to elucidate the relationship between blood pressure and factors related to obesity, including leptin, in different age groups. Methods The subjects were 348 Japanese male adolescents (15–17 years old) and 165 men (40–59 years old) not taking medication for hypertension, diabetes mellitus or hyperlipidaemia. Height, weight, blood pressure, heart rate, plasma glucose, lipid profiles, serum insulin and leptin levels were measured in the morning after an overnight fast. Results Body mass index (BMI), serum leptin level and the homeostasis model insulin resistance index increased in the order of blood-pressure category (i.e. normotensive < high normal < hypertensive) in both the male adolescents and the middle-aged men. In addition, simple linear regressions revealed that both systolic and diastolic blood pressure correlated significantly with serum leptin and the insulin resistance index in both groups. Even after adjustment for age and BMI, the correlation of mean blood pressure with leptin remained in the obese adolescents (r2 = 0.390, P = 0.02). The heart rate also correlated with leptin in the adolescents (r = 0.18, P < 0.001), but not in the middle-aged subjects (r = 0.04). Even after adjustment for age and BMI in adolescents, serum leptin correlated significantly with heart rate. Conclusion These results suggest a role for leptin in obesity-related hypertension, especially in adolescents.
Design, Synthesis, and Biological Evaluation of Prenylated Chalcones as Vasorelaxant Agents

Five prenylated chalcones and one allylated chalcone were prepared according to the analysis based on support vector machine (SVM) classification model. Most of the synthesized chalcones showed potent vasorelaxant activities through evaluation in aortic rings with the endothelium pre‐contracted by phenylephrine (PE), indicating that the experimental activities were in good agreement with the theoretical ones. Structure‐activity relationship of these compounds showed that the substituent pattern and number of hydroxyl groups were crucial for their vasorelaxant activities and that the replacement of prenyl group with allyl group retained the potent activity.
Differentiation of Acacia koa forest stands across an elevation gradient in Hawai‘i using fine-resolution remotely sensed imagery

Koa (Acacia koa) forests are found across broad environmental gradients in the Hawaiian Islands. Previous studies have identified important environmental factors controlling stand structure and productivity at the plot level, but these have not been applied at the landscape level because of small-scale spatial variability. The goal of this study is to compare the differentiation of koa forest types across an elevation/temperature gradient ranging from 1200 to 2050 m asl (17–13°C mean annual temperature (MAT)) through the analysis of field measurements of forest structure and fine-resolution remotely sensed imagery. Several vegetation indices (VIs) (atmospherically resistant vegetation index (ARVI), enhanced vegetation index (EVI), normalized difference vegetation index (NDVI), soil-adjusted vegetation index (SAVI), modified soil-adjusted vegetation index (MSAVI), simple ratio (SR) and modified simple ratio (MSR)) are calculated from IKONOS satellite imagery of these stands and analysed using supervised classification techniques. This procedure allows a clear differentiation of koa stands from areas dominated by grasses, shrubs and bare lava. Across the elevation gradient, VIs allow differentiation of three koa forest stand classes at upper, intermediate and lower elevations. In agreement with the image classification, analysis of variance (ANOVA) of tree height and leaf phosphorus (P) suggests that there are also three significantly different groups of koa stands at those elevations. A landscape-scale map of land cover and koa stand classes demonstrates both the general trend with elevation and the small-scale heterogeneity that exists across the elevation gradient. Application of these classification techniques with fine spatial resolution imagery can improve the characterization of different koa stand types across the islands of Hawai‘i, which should aid both the conservation and utilization of this ecologically important species.
Impact of instantaneous sea ice removal in a coupled general circulation model

The impact of extreme sea ice initial conditions on modelled climate is analysed for a fully coupled atmosphere ocean sea ice general circulation model, the Hadley Centre climate model HadCM3. A control run is chosen as reference experiment with greenhouse gas concentration fixed at pre‐industrial conditions. Sensitivity experiments show an almost complete recovery from total removal or strong increase of sea ice after four years. Thus, uncertainties in initial sea ice conditions seem to be unimportant for climate modelling on decadal or longer time scales. When the initial conditions of the ocean mixed layer were adjusted to ice‐free conditions, a few substantial differences remained for more than 15 model years. But these differences are clearly smaller than the uncertainty of the HadCM3 run and all the other 19 IPCC fourth assessment report climate model pre‐industrial runs. It is an important task to improve climate models in simulating the past sea ice variability to enable them to make reliable projections for the 21st century.
Stability evaluation of celecoxib nanoemulsion containing Tween 80

The aim of the present study was to evaluate the stability of celecoxib (CXB) using novel nanoemulsion formulation. Optimized nanoemulsion formulation of CXB was prepared by low energy emulsification method. Stability studies were performed for the period of 3 months. Droplet size, viscosity and refractive index (RI) were determined during storage. Shelf life of nanoemulsion formulation was also determined by accelerated stability testing. It was found that droplet size viscosity and RI were slightly increased at refrigerator and room temperature. The changes in these parameters were not significant (p ≥ 0.05). The shelf life of nanoemulsion formulation was found to be 2.73 years at room temperature. These results indicated that stability of CXB can be enhanced in nanoemulsion formulation using Tween 80 as surfactant.
Structural provinces offshore West Greenland and key geological variations influencing play assessment

A proposed subdivision of offshore West Greenland into four provinces is presented on the basis of regional variations in geological development, especially during the Cainozoic. The four provinces are from north to south: Baffin Bay, Disko West, Nuuk West, and Cape Farewell. In these provinces, play factors such as the petroleum-charge system, reservoir-seal system, and trap type must be viewed in close relation to two key processes: the influence of volcanic activity during the Palaeogene and Cainozoic exhumation. Caution is advised in using analogues and play evaluations across provinces without adjusting for key differences in geological evolution.
Stocks and dynamics of SOC in relation to soil redistribution by water and tillage erosion

Soil organic carbon (SOC) displaced by soil erosion is the subject of much current research and the fundamental question, whether accelerated soil erosion is a source or sink of atmospheric CO2, remains unresolved. A toposequence of terraced fields as well as a long slope was selected from hilly areas of the Sichuan Basin, China to determine effects of soil redistribution rates and processes on SOC stocks and dynamics. Soil samples for the determination of caesium‐137 (137Cs), SOC, total N and soil particle size fractions were collected at 5 m intervals along a transect down the two toposequences. 137Cs data showed that along the long slope transect soil erosion occurred in upper and middle slope positions and soil deposition appeared in the lower part of the slope. Along the terraced transect, soil was lost over the upper parts of the slopes and deposition occurred towards the downslope boundary on each terrace, resulting in very abrupt changes in soil redistribution over short distances either side of terrace boundaries that run parallel with the contour on the steep slopes. These data reflect a difference in erosion process; along the long slope transect, water erosion is the dominant process, while in the terraced landscape soil distribution is mainly the result of tillage erosion. SOC inventories (mass per unit area) show a similar pattern to the 137Cs inventory, with relatively low SOC content in the erosional sites and high SOC content in depositional areas. However, in the terraced field landscape C/N ratios were highest in the depositional areas, while along the long slope transect, C/N ratios were highest in the erosional areas. When the samples are subdivided based on 137Cs‐derived erosion and deposition data, it is found that the erosional areas have similar C/N ratios for both toposequences, while the C/N ratios in depositional areas are significantly different from each other. These differences are attributed to the difference in soil erosion processes; tillage erosion is mainly responsible for high‐SOC inventories at depositional positions on terraced fields, whereas water erosion plays a primary role in SOC storage at depositional positions on the long slope. These data support the theory that water erosion may cause a loss of SOC due to selective removal of the most labile fraction of SOC, while on the other hand tillage erosion only transports the soil over short distances with less effect on the total SOC stock.