Miracle-dz/UniFAR-FTUs huggingface dataset:
Basin-scale latitudinal patterns of copepod grazing in the Atlantic Ocean

Size-fractionated copepod abundance and ingestion rates were investigated along a 50°S-50°N latitudinal transect, during the Atlantic Meridional Transect (AMT) 4, 5 and 6 cruises (boreal spring-autumn 1997, boreal spring-summer 1998). Copepod abundance was higher at high latitudes in spring, near northwest Africa, in the equatorial and Benguela upwelling systems, and in the Subtropical Convergence, and lower in oligotrophic gyres. Gut contents were not related to phytoplankton biomass or production. Gut evacuation rate averaged 0.03 min -1 , and was not related to latitude or body size. Conservative estimates of copepod community total ingestion rates ranged between 3.4 and 173 mg C m -2 day -1 for AMT4, 1.6-252 mg C m -2 day -1 in AMT5 and 10-160 mg C m -2 day -1 in AMT6. Maximum values were always in the upwelling regions, the subtropical convergence and high latitudes in the Northern Hemisphere during boreal spring. Calculated ingestion rates translate into average daily minimal consumption values of 2. 07%, 1.89% and 2.6% of total chlorophyll stock, or 8. 02%, 14.5% and 12.9% of total primary production ingested daily on AMT4, 5 and 6 respectively. Grazing impact increases considerably if we consider ingestion of phytoplankton larger than 2 μm, especially under the influence of the Equatorial and North African upwellings, where copepod ingestion represents up to 30% of the biomass and >100% of production by large cells.
Perfluorinated Compounds and Polybrominated Diphenyl Ethers in Great Blue Heron Eggs from Three Colonies on the Mississippi River, Minnesota

Abstract. Archived Great Blue Heron (Ardea herodias) eggs (N = 16) collected in 1993 from three colonies on the Mississippi River in Minnesota were analyzed in 2007 for perfluorinated compounds (PFCs) and polybrominated diphenyl ethers (PBDEs). One of the three colonies, Pig's Eye, was located near a presumed source of PFCs. Based on a multivariate analysis, the pattern of nine PFC concentrations differed significantly between Pig's Eye and the upriver (P = 0.002) and downriver (P = 0.02) colonies; but not between the upriver and downriver colonies (P = 0.25). Mean concentrations of perfluorooctane sulfonate (PFOS), a major PFC compound, were significantly higher at the Pig's Eye colony (geometric mean = 940 ng/g wet weight) than at upriver (60 ng/g wet weight) and downriver (131 ng/g wet weight) colonies. Perfluorooctane sulfonate concentrations from the Pig's Eye colony are among the highest reported in bird eggs. Concentrations of PFOS in Great Blue Heron eggs from Pig's Eye were well below the toxicity thresholds estimated for Bobwhite Quail (Colinus virginianus) and Mallards (Anas platyrhynchos), but within the toxicity threshold estimated for White Leghorn Chickens (Gallus domesticus). The pattern of six PBDE congener concentrations did not differ among the three colonies (P = 0.08). Total PBDE concentrations, however, were significantly greater (P = 0.03) at Pig's Eye (geometric mean = 142 ng/g wet weight) than the upriver colony (13 ng/g wet weight). Polybrominated diphenyl ether concentrations in two of six Great Blue Heron eggs from the Pig's Eye colony were within levels associated with altered reproductive behavior in American Kestrels (Falco sparverius).
Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI

Investigation of genetic diversity and the relationships among varieties and breeding lines is of great importance to facilitate parental selection in the development of inbred and hybrid rice varieties and in the construction of heterotic groups. The technology of single nucleotide polymorphism (SNP) is being advanced for the assessment of population diversity and genetic structures. We characterized 215 widely cultivated indica rice varieties developed in southern China and at the International Rice Research Institute (IRRI) using IRRI-developed SNP oligonucleotide pooled assay (OPA) to provide grouping information of rice mega-varieties for further heterotic pool study. The results revealed that the Chinese varieties were more divergent than the IRRI varieties. Two major subpopulations were clustered for the varieties using a model-based grouping method. The IRRI varieties were closely grouped and separated clearly from the majority of the Chinese varieties. The Chinese varieties were subclustered into three subgroups, but there was no clear evidence to separate the Chinese varieties into subgroups geographically, indicating a great degree of genetic integration of alleles and shared ancestries among those high-yielding modern varieties.
The role of caspases in cryoinjury: caspase inhibition strongly improves the recovery of cryopreserved hematopoietic and other cells

Cryopreserved cells and tissues are increasingly used for stem cell transplantation and tissue engineering. However, their freezing, storage, and thawing is associated with severe damage, suggesting the need for better cryopreservation methods. Here, we show that activation of caspase‐3 is induced during the freeze‐thaw process. Moreover, we demonstrate that prevention of caspase activation by the caspase inhibitor zVAD‐fmk strongly improves the recovery and survival of several cryopreserved cell types and hematopoietic progenitor cells. A short preincubation with the caspase inhibitor after thawing also enhances the colony‐forming activity of hematopoietic progenitor cells up to threefold. Furthermore, overexpression of Bcl‐2, but not the blockade of the death receptor signaling, confers protection, indicating that cryoinjury‐ associated cell death is mediated by a Bcl‐2‐controlled mitochondrial pathway. Thus, our data suggest the use of zVAD‐fmk as an efficient cryoprotective agent. The addition of caspase inhibitors may be an important tool for the cryopreservation of living cells and advantageous in cell transplantation, tissue engineering, and other genetic technologies.
Immune responses and gut morphology in Senegalese sole (Solea senegalensis) fed dietary probiotic supplementation and following exposure to Photobacterium damselae subsp. piscicida

The aim of this study was to determine the effect of a dietary multi-species probiotic on growth, gut morphology and immune parameters in Senegalese sole (Solea senegalensis). Fish were fed with two experimental diets, a control diet and the same diet supplemented with the probiotic for 72 days. A sub-lethal bath challenge with Photobacterium damselae subsp. piscicida was performed after the growth trial. Intestine and blood samples were collected to study gut structure and plasmatic immune parameters. No significant differences were found in growth performance. The analysis of gut morphology showed a significant increase in intestinal villi height of Senegalese sole fed the probiotic. Regarding circulating leucocytes, dietary probiotic supplementation increased thrombocytes levels whereas a decrease in the proportion of lymphocytes was observed. No significant differences were observed in humoural immune parameters. Bath challenge differentially affected leucocyte counts and increased peroxidase activity. This study presents the possibility of using dietary probiotic supplementation to increase Senegalese sole welfare since gut morphology was positively affected. Although the immune response after a bacterial challenge was not modulated by dietary treatment, further studies would be instrumental to unravel eventual dietary benefits on immune mechanisms.
p38 Kinase rescues failing myocardium after myocardial infarction: evidence for angiogenic and anti‐apoptotic mechanisms

As a leading cause of heart failure, postinfarction left ventricular remodeling represents an important target for therapeutic interventions. Mitogen‐activated protein kinases regulate critical cellular processes including stress response and survival, but their role in left ventricular remodeling is unknown. In the present study, rats were subjected to myocardial infarction by ligating the left anterior descending coronary artery. Western blot and kinase assay analysis revealed an inactivation of p38 kinase after myocardial infarction. Local adenovirus‐mediated cotransfection of wild‐type (WT) p38 kinase and constitutively active MKK3b reduced infarct size (26±3% vs. 47±4%, P<0.05 vs. LacZ‐treated control) associated with improved ejection fraction (66.9±5.5% vs. 44.4±4.0%, P<0.001), fractional shortening (30.2±2.1% vs. 19.7±2.2%, P<0.001), and decreased left ventricular diastolic diameter (8.5±0.4 mm vs. 9.5±0.2 mm, P<0.01). p38 kinase gene transfer increased capillary density (2423±107/mm2 vs. 1934±86/mm2, P<0.001) and resulted in microvessel enlargement in the ischemic border zone. Apoptosis (35±7 vs. 69±13 cells, P<0.01) and fibrosis (16±3% vs. 34±8%, P<0.05) were reduced, while the number of c‐kit positive cardiac stem‐like cells remained unchanged. These results indicate that reduced p38 signaling predisposes to adverse postinfarction remodeling. The rescue of failing myocardium with p38 kinase may be a potential new therapy for heart failure after myocardial infarction. —Tenhunen, O. , Soini, Y. , Ilves, M. , Rysä, J., Tuukkanen, J., Serpi, R. , Pennanen, H. , Ruskoaho, H. , Leskinen, H. p38 Kinase rescues failing myocardium after myocardial infarction: evidence for angiogenic and anti‐apoptotic mechanisms. FASEB J. 20, E1276‐E1286 (2006)
Effect of purple (Cyperus rotundus) and yellow nutsedge (C. esculentus) on growth and reflectance characteristics of cotton and soybean

Abstract Because of interest in monitoring crop response to weed interference, greenhouse experiments were conducted to evaluate interference of purple and yellow nutsedge on the growth, development, and spectral response of cotton and soybean. Cotton fresh weight was reduced 9 to 42% compared with the control when grown with yellow and purple nutsedge. Fresh weight of soybean was reduced 27 to 60% when it emerged simultaneously with yellow nutsedge and 45 to 63% when it emerged 7 d after yellow nutsedge. Soybean fresh weight was reduced 30 to 35% when it emerged simultaneously with purple nutsedge and 44 to 72% when it emerged 7 d after purple nutsedge. Reflectance data were analyzed using wavelet transformation techniques with the HAAR mother wavelet. Nine extracted features from the cotton and soybean leaf reflectance measurements were used to classify single-leaf cotton and soybean reflectance measurements to predict whether cotton or soybean was growing in the presence or absence of purple and yellow nutsedge. After training the system, the ability to separate leaf reflectance measurements of crops growing weed free from those growing in the presence of purple and yellow nutsedge was tested using cross-validation with the nearest mean classifier. Cross-validation accuracy results for cotton were 62 to 70%. Cross-validation accuracy for soybean and yellow nutsedge was similar, regardless of emergence, and ranged from 60 to 71%. Features extracted from the soybean reflectance measurements were not as effective in classifying soybean leaf reflectance measurements based on the presence or absence of purple nutsedge. A decrease in accuracy was observed for both simultaneous and delayed soybean emergence in purple nutsedge fresh weight categories from more than 2,560 g to more than 3,420 g. Overall, the system correctly classified soybean emerging simultaneously with purple nutsedge 58 to 74% and soybean emerging 7 d after purple nutsedge 53 to 67%. These results indicate the potential of differentiating crops under stress using spectral reflectance, although refinements to the system must be made before it is field ready. Nomenclature: Yellow nutsedge, Cyperus esculentus L. CYPES; purple nutsedge, Cyperus rotundus L. CYPRO; soybean, Glycine max (L.) Merr. ; cotton, Gossypium hirsutum L.
Effect of soil waterlogging on below‐ground biomass allometric relations in Norway spruce

Abstract An increasing importance is assigned to the estimation and verification of carbon stocks in forests. Forestry practice has several long‐established and reliable methods for the assessment of above‐ground biomass; however, we still miss accurate predictors of below‐ground biomass. A major windthrow event exposing the coarse root systems of Norway spruce trees allowed us to assess the effects of contrasting soil stone and water content on below‐ground allocation. Increasing stone content decreases the root/shoot ratio, while soil waterlogging leads to an increase in this ratio. We constructed allometric relationships for below‐ground biomass prediction and were able to show that only soil waterlogging significantly impacts model parameters. We showed that diameter at breast height is a reliable predictor of below‐ground biomass and, once site‐specific parameters have been developed, it is possible to accurately estimate below‐ground biomass in Norway spruce.
Spatial and Temporal Variation of the Freshwater Mussel Dreissena blanci (Westerlund, 1890) Larvae in Greek Lakes

ABSTRACT Recent molecular studies on dreissenid species in southern Europe found that Dreissena blanci (Westerlund, 1890) resides in several lakes where previous studies identified it as Dreissena polymorpha (Pallas, 1771). Because D. blanci seems to constitute a “new record” in the Balkans, the present study provides novel information on the biology and ecology of its planktonic larvae in four natural lakes and one reservoir located in western Greece. Dreissena blend larvae were present in all lakes and their abundance varied between 3.4 and 440 ind. I-1. The larvae were present all year round, having greater abundance in spring and summer and lesser in winter. The species seems to have an extended reproductive period from early spring until late summer. The larvae are distributed mainly in the upper 20 m of the deep lakes Amvrakia and Trichonis, while are aggregated close to or within the thermocline layer in the latter lake. A size-specific depth distribution was observed, with larger larvae residing in deeper strata during the stratification period. Temperature appears to be the most important parameter affecting the abundance variation of the larvae in the natural lakes, while water retention time is the major parameter in Stratos reservoir. In contrast, the soft, muddy substratum of Lake Lysimachia seems to be the inhibiting factor for the existence of a viable population here. The great similarities in larval ecology between D. blanci and D. polymorpha must be taken into consideration, as D. blanci could become another invasive species in freshwater ecosystems. Therefore, more research is required on the life cycle of this species, and the ecological and economic consequences of its presence in lakes and reservoirs of southeastern Europe.
Evidence for natural hybridization between Primula beesiana and P. bulleyana, two heterostylous primroses in NW Yunnan, China

Natural hybridization was assumed to play an essential role for the diversification of Primula; however, only one study of hybridization in the region of the Himalayas has been undertaken. In the present study, we examined another natural hybrid zone where morphologically putative hybrids as well as P. beesiana Forrest, P. bulleyana Forrest, and P. poissonii Franch. co‐occurred. We used molecular data to confirm the parental species of putative hybrids and the unidirectional hybridization pattern between P. beesiana and P. bulleyana. Moreover, with reference to synthetic F1s, most hybrids examined are possibly advanced generations, although the possibility of F1 hybrids currently examined could not be completely excluded. In addition, pollinator observations on experimental arrays of transplanted parental species showed interspecific pollen flows during visitations of shared pollinators, indicating an incomplete pre‐zygotic barrier between P. beesiana and P. bulleyana. Seed productions from both flower morphs of putative hybrids were significantly lower than parental species, suggesting lower reproductive success in these hybrids. Combined with the evidence of recent habitat disturbance in the study area, we might witness the early process of hybridization between P. beesiana and P. bulleyana.
Human trampling as a threat factor for the conservation of peripheral plant populations

Abstract In recent years, peripheral plant populations have been gaining more and more interest from a conservation point of view, as they normally grow in non-optimal ecological conditions and, consequently, are more sensitive to environmental stresses if compared to the core population. In a 7-year study (1999–2005) we examined the effects of human trampling on an alpine plant species (Senecio incanus subsp. incanus) at the southern extreme of its distribution (Northern Apennines), where it occurs in only one isolated and fragmented population. Two trampled and two untrampled permanent plots, monitored yearly, showed highly significant differences relative to S. incanus cover and reproduction, and cover by other plant species. Specifically, S. incanus cover and sexual reproduction were lowest in the trampled plots. The evidence of human trampling damage was also clearly demonstrated in a logistic regression analysis, since S. incanus cover and reproduction were significant variables. On the basis of these results, for the first time, human trampling has been identified as a real threat for the conservation of small and isolated peripheral populations, especially if coupled with climate warming. Finally, in situ and ex situ management recommendations are suggested.
A Computational Approach of Benzimidazole Containing Pyrazoline-5-one Derivatives as Targeted Antifungal Activity

14α-demethylase enzyme is a primary target in treatment of fungal infections in organisms ranging from humans to plants, and development of more potent and selective 14α-demethylase inhibitors is an important biological objective. Molecular docking is routinely used for understanding drug-receptor interaction in modern drug design. Here we described the docking of benzimidazole containing pyrazoline-5-one derivatives as inhibitors of 14α-demethylase. The inhibitory activities against 14α-demethylase were investigated by molecular docking using the HEX docking software. These compounds docked into the active site of receptor (PDB code, 1E9X) using Hex docking tools software which showed good affinity for the enzyme when compared with the binging energies of standard drugs such as clotrimazole (-24.05) and griseofulvin (-36.57). Among all the designed compounds, the compound 7 shows more binding energy values (-59.85). Further we planned to synthesis these benzimidazole derivatives and screen for in-vitro anti fungal effect on different fungal organisms.
Memory decline in healthy older people

Background: Criteria for mild cognitive impairment require objective evidence of a memory deficit but do not require objective evidence of memory decline. Application of these criteria may therefore result in the misclassification of older patients with memory decline as normal because their neuropsychological test performance at a single point in time may be within normal limits. This study aimed to identify and characterize older people with memory decline. Method: Word list delayed recall (WLDR) test performance was assessed on five occasions during a 2-year period in a cohort of healthy older individuals. Older people with declining (n = 35) and nondeclining (n = 66) WLDR scores were identified. Both subgroups were then compared on apoE genotype, Clinical Dementia Rating, and neuropsychological test performance at the fifth assessment. Results: Thirty-four percent of the group with declining memory recorded a Clinical Dementia Rating of 0.5, compared with 5% of the nondeclining memory group. No between-group differences were observed in cognitive domains other than memory, self-reported cognitive failures, or the proportion of each group carrying the apoE epsilon 4 allele. Conclusions: A large proportion of healthy older individuals show memory decline, which may represent the early stages of a potentially more severe cognitive impairment. Further investigation is necessary to determine the relationship between apoE genotype, self-reported cognitive impairment, and memory decline in older people.
Effects of systemic fungal endophytes on the performance of meadow fescue and tall fescue in mixtures with red clover

A symbiosis between grasses and systemic fungal endophytes exists in both natural and agricultural grassland communities. Our objective was to examine the effects of systemic endophytes on the competitive ability of two agronomically important grass species: meadow fescue [Festuca pratensis (Huds.) syn. Schedonorus pratensis (Huds.) P. Beauv] and tall fescue [Festuca arundinacea (Schreb.) syn. Schedonorus phoenix (Scop.)]. Plants of meadow and tall fescue were grown for 48 days in replacement series of interspecific mixture with a legume (red clover, Trifolium pratense L.) in different nutrient environments in a greenhouse. Neither of the grass species gained endophyte-promoted competitive advantage over red clover in grass–clover mixtures. Endophyte infection increased the growth of meadow fescue monocultures by 89% compared to endophyte-free monocultures in high-nutrient soils, but plant competition or the cost of endophyte infection to the meadow fescue decreased the yield in resource-limited conditions. On average, endophyte-infected and endophyte-free meadow fescues produced 0·15 and 0·17 g, and 0·14 and 0·14 g dry biomass per plant in mixtures with red clover in high- and low-nutrient soils respectively. In contrast to meadow fescue, endophyte-promoted growth of tall fescue monocultures was not detected. Endophyte-infected and endophyte-free tall fescue monocultures produced 0·76 and 0·95 g biomass per pot, respectively, in the high-nutrient environment. Endophyte infection can increase the performance of the host grass, but the positive effects depend on the host species, the species composition and soil nutrient availability.
Dilation of nanonatennas induced by an electromagnetic source

The illumination of plasmonic mesostructures produces high confinement of light in their vicinity. This confinement of light can be enhanced in the gap between the two metallic nanorods of a nanonantenna, in particular for the design of biosensors. The nanometric gap can be reduced if the elevation of temperature of the nanonantenna is sufficient, and therefore the fine tuning of the sensor requires the description of the photo-thermal induced dilation. The multiphysics problem associated to such photo-thermal and mechanical effects is modeled through a Finite Element Method (FEM). The problem consists in computing the electromagnetic field, the temperature and the induced dilation surface. This contribution consists in discussing the numerical efficiencies of a sequential, and a coupled approaches, especially in terms of adaptive meshing of the space of computation. The relationship between the field enhancement and the reduction of the gap is studied. Finally the validity of the 2D multiphysic model is discussed.