Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA damage in wounded, hypoxic and acidotic human skin fibroblast cell cultures after low laser irradiation

Phototherapy has become more popular and widely used in the treatment of a variety of medical conditions. To ensure sound results as evidence of its effectiveness, well designed experiments must be conducted when determining the effect of phototherapy. Cell culture models such as hypoxic, acidotic and wounded cell cultures simulating different disease conditions including ischemic heart disease, diabetes and wound healing were used to determine the effect of laser irradiation on the genetic integrity of the cell. Even though phototherapy has been found to be beneficial in a wide spectrum of conditions, it has been shown to induce DNA damage. However, this damage appears to be repairable. The risk lies in the fact that phototherapy may help the medical condition initially but damage DNA at the same time leaving undetected damage that may result in late onset, more severe, induced medical conditions including cancer. Human skin fibroblasts were cultured and used to induce a wound (by the central scratch model), hypoxic (by incubation in an anaerobic jar, 95% N2 and 5% O2) and acidotic (reducing the pH of the media to 6.7) conditions. Different models were irradiated using a Helium-Neon (632.8 nm) laser with a power density of 2.07 mW/cm2 and a fluence of 5 J/cm2 or 16 J/cm2. The effect of the irradiation was determined using the Comet assay 1 and 24 h after irradiation. In addition, the Comet assay was performed with the addition of formamidopyrimidine glycosylase (FPG) obviating strand brakes in oxidized bases at a high fluence of 16 J/cm2. A significant increase in DNA damage was seen in all three injured models at both 1 and 24 h post-irradiation when compared to the normal un-injured cells. However, when compared to non-irradiated controls the acidotic model showed a significant decrease in DNA damage 24 h after irradiation indicating the possible induction of cellular DNA repair mechanisms. When wounded cells were irradiated with higher fluences of 16 J/cm2, there was a significant increase in DNA damage in irradiated cells with and without the addition of FPG. These results are indicative of the importance of both cell injury model as well as fluence when assessing the effect of phototherapy on DNA integrity.
Effects of sediment disturbance on the structure of benthic fauna in a subtropical tidal creek of southeastern Brazil

An experimental analysis of benthic response to sediment disturbance by the blue crab Callinectes danae was carried out in an unvegetated flat adjacent to a salt marsh of the tidal Perequ& Creek (Paranagua Bay, SE Brazil). In order to mimic the natural pits dug by C. danae, we made randomly arranged holes, which were subsequently sampled together with undisturbed control sites on 6 different sampling dates, up to 18 d after disturbance. Analyses of variance were performed to determine if significant differences in macrobenthic population densities and abiotic parameters existed at different sampling times, and between control and disturbed areas. Apart from water content, physical variables did not differ significantly between disturbed and control areas, suggesting that adaptive strategies of the organisms themselves were the maln structuring factor of the recolonization process. We provide evidence that active immigration, together with passlve deposition, is a major colonization vector for the fauna of local low-energy tidal flats. Recolonization rates of the local fauna paralleled the mobility degrees of individual species or taxa. The numerically dominant surface crawler Heleobia australis and the burrower Lumbrineris tetraura, which are the more mobile species of local macrofauna, also exhibited the more rapid recolonization. There was no evidence that the catchment action of pits actually concentrated food resources, since sediment organic content was essentially similar between disturbed and control sites. Evidence for passive deposition was shown for the sedentariate species Laeonereis acuta, Capitella capitata and an unidentified nematode, whose recolonization rates were moderate and followed the sediment infill of pits. The only species to exhibit evidence of exploiting conditions created by pit simulation was the suspension-feeding bivalve Anomalocardia brasiliana that exhibited fast recolonization rates and higher abundance at disturbed sites. The infaunal predator Sigambra grubji was the only species present at significantly lower densities in pits throughout the experiment, probably due to the removal of its putative food source. Disturbances made by blue crabs, though short-lived, are abundant and frequent enough actually to maintain high densities of species that are otherwise scarce in similar tidal habitats. Such biogenic disturbances can be considered as a mechanism that allows for the persistence and numerical dominance of opportunistic species in tidal flats of local tidal creeks.
Effects of Monensin and Fish Oil on Conjugated Linoleic Acid Production by Rumen Microbes in Holstein Cows Fed Diets Supplemented with Soybean Oil and Sodium Bicarbonate

The present study was conducted with four ruminally canulated Holstein cows to observe the effects of monensin or fish oil on diet fermentation and production of conjugated linoleic acids (CLAs) in the rumen when fed diets supplemented with soybean oil and sodium bicarbonate. Cows of the control treatment were fed a basal diet (CON) consisting of 60% commercial concentrate and 40% chopped rye grass hay. Cows of other treatments were fed the same diet as CON, but the concentrate was supplemented with 7% of soybean oil and 0.5% of sodium bicarbonate (SO-B), SO-B supplemented with monensin (30 ppm, SO-BM) or concentrate supplemented with 6.3% of soybean oil, 0.5% of sodium-bicarbonate, 30 ppm of monensin and 0.7% of fish oil (SO-BMF). Dry matter (DM) intake of the cows was significantly (p<0.011) reduced by feeding the SO-BMF diet compared to the other diets which did not differ in DM intake. Whole tract digestibility of major dietary components was significantly (p<0.004-0.027) higher for SO-BMF than the other supplement-containing diets. Dietary supplements did not clearly affect rumen pH and ammonia concentrations compared to the CON diet. Significantly reduced (p<0.05) total VFA concentration was obtained by the addition of fish oil to the diet (SO-BMF) compared to other diets. No differences, however, were obtained in major VFA proportions as well as in total VFA between the supplemented diets. The SO-BM diet increased (p<0.01-0.05) the concentrations of trans-1 C 18:1 and linoleic acid in rumen fluid. Total CLA concentration was also increased by the feeding of SO-B and SO-BM diets during early fermentation times (up to 3 h) post-feeding. Cis-9, trans-11 CLA concentration in rumen fluid was highest (p<0.05) for SO-B up to 1 h while the highest (p<0.01) value for SO-BM occurred at 3 h post-feeding. An increased trans-10, cis-12 CLA concentration was obtained from the SO-B and SO-BM diets at 1 and 3 h post feeding compared to the other diets. Supplementation of oils with monensin and sodium bicarbonate increased (p<0.05) the proportions of C 18:1 and CLA in the plasma of cows, but the effect of monensin and/or fish oil was limited to trans-10, cis-12 CLA.
Copper tolerance of Acer pseudoplatanus L. (sycamore) in tissue culture.

The growth of Acer pseudoplatanus L. (sycamore) callus tissue on solid and liquid growth media containing elevated copper concentrations was studied in an attempt to understand the responses of trees to metal contamination and to provide an index of tolerance which may show a parallel expression of tolerance to the whole plant. Callus growth on solid media was very variable, but was significantly reduced at 10 mg l-1 , with necrosis occurring at 20 mg l-1 ; copper was readily removed from the media in direct proportion to its concentration. Cell suspension cultures differed in their response to copper according to their site of origin. In cultures originating from uncontaminated sites, growth was inhibited at 12.5 and 15.0 mg l-1 Cu, but cultures originating from mature trees at a metal-contaminated site were not affected by these concentrations. This metal tolerance trait was stable in cell culture through repeated sub-culturing on uncontaminated media for periods of more than 12 months. The trait was not present in a culture derived from a (non-tolerant) seedling at the metal-contaminated site, but it was induced in one non-tolerant culture by repeated exposure to high metal levels. The significance of these findings is discussed in the context of the possession of appropriate genetic variation in trees for surviving the impact of metal contamination.
Energetics and thermoregulation of the Gouldian Finch (Erythrura gouldiae)

Abstract We examined the physiological responses of captive-bred Gouldian Finches (Erythrura gouldiae) to temperature by measuring their metabolic heat production (Hm, calculated from oxygen consumption), body temperature (Tb), and evaporative heat loss (He, calculated from evaporative water loss) at ambient temperatures (Ta) between 0 and 44°C. Overall, we found the Gouldian Finch to resemble other small tropical seed-eaters that forage in open, sunlit situations. Its active-phase basal metabolic rate (13.4 mW g−1; n = 11) was relatively low (61% of predicted allometrically) and it had only a modest capacity for evaporative cooling at high temperatures, dissipating evaporatively a maximum of 118% of its metabolic heat production above 40°C. Like other small tropical birds, the Gouldian Finch develops substantial hyperthermia at high temperature, maintaining its Tb an average of 1.4°C above Ta at Tas between 41.8 and 43.6°C. At Tas above the upper critical temperature (38°C), metabolic heat production increases linearly with Ta according to the relation: Hm (mW g−1) = -12.4 + 0.68 Ta. The slope of this relation, termed the coefficient of heat strain (hs), provides an integrated measure of the metabolic response to heat. For 38 bird species, hs (mW g−1 °C−1) varies with body size according to the relation: log(hs) = log(7.83)–0.54log(m), where m equals mass in grams. The Gouldian Finch's hs is only 40% of that predicted for a 17.1-g bird by this equation, proportionately the lowest value yet measured. Although aviculturalists widely regard the Gouldian Finch as cold intolerant, Ta in its northern Australian range sometimes falls to below freezing. Not surprisingly, we found that the Gouldian Finch is actually better insulated than the average songbird its size, its thermal conductance (0.184 mL O2 g−1 h−1 °C−1) being 81% of that predicted allometrically.
Global Gene Expression Changes by Several Phytochemicals in Human Colorectal Cancer Cell

Phytochemicals, non-nutrient chemicals derived from plants, have been shown to have anti-inflammation, anti-oxidation, and chemopreventive effects. In the current study, we investigated whether five different phytochemicals (resveratrol, genistein, epicatechin gallate, diallyl disulfide, and caffeic acid phenethyl ester) alter cell growth and gene expression in human colorectal cancer HCT116 cells. Using a cell viability assay, we found that each of the phytochemicals tested inhibited HCT116 cell growth in a dose-dependent manner. Additionally, using human oligo DNA microarray analysis, we found that only six genes were commonly up-regulated and seven genes were commonly down-regulated in response to each phytochemical treatment. For the commonly up-regulated genes, the microarray analysis was confirmed by reverse transcription.PCR using gene-specific primers. In addition, NAG-1 protein was up-regulated by all treated phytochemcials. The results of this study may help to enhance our understanding of the general molecular mechanisms of chemoprevention that are mediated by phytochemicals in human colorectal cancer.
Metabolic and genetic engineering of cyanobacteria for enhanced hydrogen production

There is an urgent need to develop sustainable solutions to convert solar energy into energy carriers used in society. In addition to solar cells generating electricity, there are several options to generate solar fuels, with molecular hydrogen being an interesting and promising option. Native and engineered cyanobacteria have been used as model systems to examine, develop and demonstrate photobiological hydrogen production. In the present review we present and discuss recent progress with respect to native biological systems to generate hydrogen, metabolic modulations, and genetic engineering of metabolic pathways, as well as the introduction of custom-designed, non-native enzymes and complexes for enhanced hydrogen production in cyanobacteria. In conclusion, metabolic and genetic engineering of native cyanobacterial hydrogen metabolism can significantly increase the hydrogen production. Introduction of custom-designed non-native capacities open up new possibilities to further enhance cyanobacterial-based hydrogen production.
How specific is the inhibition by methyl fluoride of acetoclastic methanogenesis in anoxic rice field soil

Acetoclastic methanogens have been described to be inhibited at much lower concentrations of methyl fluoride, CH3F, than H2/CO2-utilizing methanogens. Therefore, we tested whether CH3F inhibition may be used to determine, in anoxic rice field soil, the contribution of H2/CO2-dependent methanogenesis to the total CH4 production by comparing this technique with the incorporation of 14CO2 into CH4. In general, addition of 0.01–1% CH3F to the gas phase resulted in an immediate partial inhibition of the total CH4 production which lasted for at least 200 h. Inhibition increased with the logarithm of the initial CH3F concentration up to about 0.2–0.6%. The initial CH3F concentration slowly decreased with time, probably due to decomposition. CH4 production sometimes completely recovered during the course of the experiment. The presence of CH3F resulted in the accumulation of acetate, the final concentration of which was usually stoichiometrically related to the deficit in CH4 production and increased with the initial CH3F concentration. In some experiments, acetate accumulation was larger than expected from the CH4 deficit and a substantial incorporation of 14CO2 into acetate was observed. Hydrogen, on the other hand, was only slightly elevated in the presence of CH3F. Addition of increasing CH3F resulted in an increase of the percentage of H2-dependent methanogenesis (measured by conversion of 14CO2 to 14CH4) demonstrating that acetoclastic methanogenesis was preferentially inhibited by CH3F. However, the conversion of 14CO2 to 14CH4 was also slightly inhibited by CH3F. Apparently, CH3F inhibited the H2-dependent methanogenesis to some extent, depending on the concentration of CH3F applied. Indeed, the ratio between the residual CH4 production rate and the fraction of CH4 produced from 14CO2 decreased with an increasing CH3F concentration. A ratio of unity was obtained at initial CH3F concentrations of 0.2–0.6% (58–174 μM). Both methods, i.e. inhibition using 0.5% CH3F and conversion of 14CO2 to 14CH4, were applied to determine the temporal change of the contribution of H2/CO2-dependent methanogenesis to the total CH4 production in two different batches of Italian rice field soil during a 120-days anoxic incubation period. The results of the two methods agreed well within the error of the methods and showed a relatively constant contribution of H2/CO2-dependent methanogenesis of about 25–30% as soon as CH4 was produced at a steady rate and H2 partial pressures had stabilized at about 1.5–2.5 Pa.
Factors affecting the growth of Pennisetum purpureum in the wet tropics. II. Uninterrupted growth

Six plantings of elephant grass (Pennisetum purpureum) were made at 2-monthly intervals in the wet tropics of Queensland and grown for 6 months, ratooned and grown for a further 6 months. Yields of crop fractions were taken at monthly intervals. Dry matter yield attributes were all positively and significantly correlated with each other, and negatively correlated with nitrogen and phosphorus percentages. Stem height was strongly associated with total and stem dry matter yields. Time trends in dry matter yields could be well described by logistic growth curves. It was found that dry matter yields were linearly and significantly related to crop age, degree days, radiation receipt, energy-degree days, cumulative evapotranspiration and moisture stress-free days. The crop was well adapted to the environment and could be grown and harvested year-round for agro-industrial purposes.
The responses of pulmonary neuroendocrine cells in the lungs of Rana ridibunda to different experimental conditions

The study investigated the localisation and immunohistochemistry of neuroendocrine cells (PNECs) and their behaviour in the lungs of Rana ridibunda under experimental conditions and compared with control lungs. Serotonin- and bombesin-immunoreactive (IR) PNECs were observed as solitary cells or clusters of cells at the base of ciliated epithelium on the dilated apical parts of primary septa where incoming air first arrives, and in the respiratory epithelium. Serotonin-IR PNECs were predominantly present in the ciliated epithelium while bombesin-IR PNECs were found in the ciliated and respiratory epithelium. Additionally, bombesin-IR nerve fibres were found in the epithelium and among smooth muscle cells in the connective tissue. In frogs kept in a dry aquarium, serotonin- and bombesin-IR PNECs were characterised by various stages of secretion. Serotonin-IR PNECs released most of their secretory material, while bombesin-IR PNECs were stimulated for secretion. Moreover, bombesin secretions were raised. In conclusion, the cells were identified as members of the pulmonary epithelial endocrine system and can contribute to the pulmonary biology through a paracrine/endocrine pathway in the lungs of R. ridibunda.
Farmer Participation in On-Station Tree Species Selection for Agroforestry: a Case Study from Burundi

Summary Surveys and on-farm trials are frequently used to facilitate farmer participation in agricultural research. This paper reports on a less common method-farmer involvement in on-station trials. Thirty-nine farmers were invited to multipurpose-tree screening trials in Burundi. Three different methods were used to determine which species the farmers wanted to test on their own farms. Private interviews and voting by a show of hands in plenary sessions gave very similar results whereas focus group interviews produced different and contradictory results. Researchers also learned what criteria farmers used to evaluate trees and the reasons for their choices. A supplementary survey of farmers’ preferences for trees grown on their own farms confirmed the findings and more clearly defined their criteria. In this survey, farmers used a local board game, Bao, to rate tree species across criteria they considered important. Overall, the visit to the trials and follow-up survey proved to be a useful and cost-effective method for getting farmer input and applying it in the screening process. La participación de los agricultores en la selección de especies de árboles
Overwinter Survival of Age‐0 Gizzard Shad in Missouri Reservoirs Spanning a Productivity Gradient: Roles of Body Size and Winter Severity

Abstract Survival through the first winter of life can be an important bottleneck in the recruitment of fishes and is commonly size dependent, with larger fish exhibiting higher survival than smaller fish. Body size and density of age-0 gizzard shad Dorosoma cepedianum, an ecologically important prey species, are reportedly influenced by reservoir productivity. These differences in age-0 demographics across a productivity gradient may influence overwinter survival and subsequent year-class strength of adults. I examined fall age-0 demographics (fall mean total length, mean density, and energy density), overwinter changes in these demographics, and factors that influenced overwinter survival among five age-0 cohorts in five Missouri reservoirs spanning a productivity gradient. I specifically wanted to determine whether (1) fall age-0 demographics varied along a reservoir productivity gradient, (2) fall age-0 demographics and winter severity were related to overwinter survival, and (3) variation in the abun.
Vegetation dynamics of the forest edge: trends in space and successional time

Forest herbs, shrubs, and tree seedlings were censused at five distances from human-generated edges at 14 sites in south-eastern Pennsylvania and northern Delaware, USA. Forest edges varied in orientation and in the degree of canopy closure, allowing comparisons of vegetation by aspect and successional stage. Soil depth and pH were measured at vegetation sampling points at a subset of sites; microclimate data were available from a parallel study. Edge-related pattern was observed in overall species composition, and in distributions of 15 individual species. At recently created forest edges, species abundances were correlated with steep climatic gradients. Although most edge-orientated species were clustered ≤ 5 m from the edge, some species consistently reached peak densities at distances up to 40 m, the greatest distance surveyed (.)
Environmental control of leaf water conductance in conifers

Diurnal measurements of leaf conductance, xylem water potential, temperature, humidity, and radiation were taken on six sites throughout Oregon. Xylem water potential was hypothesized to influence leaf conductance in two ways. First, predawn xylem water potential controlled the early-morning maximum leaf conductance of Pseudotsugamenziesii (Mirb.) Franco. Second, irrespective of predawn water potential, a threshold diurnal water potential was found. Whenever water potential of Pseudotsugamenziesii dropped below −20 bars (−20 × 105 Pa) during the day, a significant decrease in leaf conductance resulted. If the water potential threshold was not reached during the day, leaf conductance stayed at the morning maximum or decreased slightly in response to decreasing humidity.
Parâmetros cinéticos da degradação in vitro de alimentos incubados com inóculo microbiano de diferentes espécies de ruminantes

The estimation of the ruminal kinetic parameters of pumpkin, potato-sweet, beet, broccoli, carrot, alfalfa hay, alfalfa pellet and bean, currently used for feeding wild and domestic ruminants raised in the Rio de Janeiro Zoo, was made through in vitro incubation of the feedstuffs together with ruminal fluid obtained from aoudad (Ammotragus lervia), sambar deer (Cervus unicolor), eland (Taurotragus oryx), cattle (Bos taurus), buffalo (Bubalus bubalis), goat (Capra hircus) and sheep (Ovis aries). The gas production technique was used to obtain gas profiles, and the data were fitted by the mono or double compartmental model. The kinetic parameters were discrepant among both, animals and feedstuffs, and the double compartmental model gave the best estimation. Ruminal inocula from domestic ruminants can not be used to estimate the kinetic parameters of ruminal degradation of feedstuffs for wild ruminants.