Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating carbon carrying capacity in natural forest ecosystems across heterogeneous landscapes: addressing sources of error

Evaluating contributions of forest ecosystems to climate change mitigation requires well‐calibrated carbon cycle models with quantified baseline carbon stocks. An appropriate baseline for carbon accounting of natural forests at landscape scales is carbon carrying capacity (CCC); defined as the mass of carbon stored in an ecosystem under prevailing environmental conditions and natural disturbance regimes but excluding anthropogenic disturbance. Carbon models require empirical measurements for input and calibration, such as net primary production (NPP) and total ecosystem carbon stock (equivalent to CCC at equilibrium). We sought to improve model calibration by addressing three sources of errors that cause uncertainty in carbon accounting across heterogeneous landscapes: (1) data‐model representation, (2) data‐object representation, (3) up‐scaling. We derived spatially explicit empirical models based on environmental variables across landscape scales to estimate NPP (based on a synthesis of global site data of NPP and gross primary productivity, n=27), and CCC (based on site data of carbon stocks in natural eucalypt forests of southeast Australia, n=284). The models significantly improved predictions, each accounting for 51% of the variance. Our methods to reduce uncertainty in baseline carbon stocks, such as using appropriate calibration data from sites with minimal human disturbance, measurements of large trees and incorporating environmental variability across the landscape, have generic application to other regions and ecosystem types. These analyses resulted in forest CCC in southeast Australia (mean total biomass of 360 t C ha−1, with cool moist temperate forests up to 1000 t C ha−1) that are larger than estimates from other national and international (average biome 202 t C ha−1) carbon accounting systems. Reducing uncertainty in estimates of carbon stocks in natural forests is important to allow accurate accounting for losses of carbon due to human activities and sequestration of carbon by forest growth.
CLOCK is involved in the circadian transactivation of peroxisome-proliferator-activated receptor α (PPARα) in mice

PPARα (peroxisome-proliferator-activated receptor α) is a member of the nuclear receptor superfamily of ligand-activated transcription factors that regulate the expression of genes associated with lipid metabolism. In the present study, we show that circadian expression of mouse PPARα mRNA requires the basic helix–loop–helix PAS (Per-Arnt-Sim) protein CLOCK, a core component of the negative-feedback loop that drives circadian oscillators in mammals. The circadian expression of PPARα mRNA was abolished in the liver of homozygous Clock mutant mice. Using wild-type and Clock-deficient fibroblasts derived from homozygous Clock mutant mice, we showed that the circadian expression of PPARα mRNA is regulated by the peripheral oscillators in a CLOCK-dependent manner. Transient transfection and EMSAs (electrophoretic mobility-shift assays) revealed that the CLOCK–BMAL1 (brain and muscle Arnt-like protein 1) heterodimer transactivates the PPARα gene via an E-box-rich region located in the second intron. This region contained two perfect E-boxes and four E-box-like motifs within 90 bases. ChIP (chromatin immunoprecipitation) also showed that CLOCK associates with this E-box-rich region in vivo. Circadian expression of PPARα mRNA was intact in the liver of insulin-dependent diabetic and of adrenalectomized mice, suggesting that endogenous insulin and glucocorticoids are not essential for the rhythmic expression of the PPARα gene. These results suggested that CLOCK plays an important role in lipid homoeostasis by regulating the transcription of a key protein, PPARα.
Detecting juvenile survival effects of habitat actions: power analysis applied to endangered Snake River spring-summer chinook (Oncorhynchus tshawytscha)

Using 10 years of parr-to-smolt survival rate estimates for passive integrated transponder (PIT) tagged, endangered wild Snake River chinook (Oncorhynchus tshawytscha) (measured in eight spawning streams), we demonstrate that moderate increases in base-case survival may be detectable quickly, as required by recent U.S. National Marine Fisheries Service regulations. The regulations require that effects of tributary habitat actions on juvenile salmonid survival rates be detectable within 5 to 8 years. Simple log-linear regression models were employed where the natural log of survival is a function of parr size, parent stock abundance, tagging location, and year. The analysis uses beforeafter controlimpact (BACI) statistical techniques. The results suggest that multiplicative survival rate changes of 30% should be detectable within 7 years, and increases of 50% within 3 years. Models with higher information-theoretic weights were more powerful than less plausible models. Models using juvenile survival were.
Alternatives to Robinson and Redford’s Method of Assessing Overharvest from Incomplete Demographic Data

Conservation biologists often must make decisions about the sustainability of harvest rates based on minimal demographic information. To assist them Robinson and Redford (1991) formulated a method to estimate maximum rates of production which could be used to detect overharvesting based on only age at first reproduction, fecundity, and maximum longevity. By assuming constant adult survival, we reduced the Euler equation to a simple form that allows calculation of population growth from the same minimal demographic data, but that can incorporate empirical prereproductive and adult survival rates if available. With this formula, we computed growth rates using various explicit survival schedules, and we compared these rates and those from Robinson and Redford’s (1991) method to rates calculated from 19 relatively complete mammalian life tables gleaned from the literature. When we applied our method (assuming 1% survival to maximum longevity) and that of Robinson and Redford (1991) to the same minimal demographic data, we found that our growth rates were closer to those from complete life tables. We therefore reexamined the data of Fa et al. (1995) and Fitzgibbon et al. (1995) , who analyzed overharvesting of several populations of commercially exploited African mammals based on Robinson and Redford’s (1991) methods. Our reanalysis indicates that several additional populations may be overharvested. Our analysis also suggests that data on survival to age at first reproduction improves estimates of population growth rates more than data on age‐specific adult survival. Regardless of the method, approximate growth rates based on incomplete life tables can be used to detect when populations are overharvested, but one should not conclude that harvest rates are sustainable when they are less than approximate production rates because simplifying assumptions often lead to overestimates.
Water potential, turgor and cell wall properties in elongating tissues of the hydrotropically bending roots of pea (Pisum sativum L.)

The hydrotropic bending of roots of an ageotropic pea mutant, ageotropum, was studied in humid air in a chamber with a steady humidity gradient. We examined the effects of atmospheric humidity around the root on the water status of root tissues, as well as the wall growth and the hydraulic properties of the elongating tissues. Atmospheric humidity at the surface of the root was clearly lower on the side orientated towards the air with lower humidity than on the side orientated towards the air with higher humidity. However, there were no differences in water potential and osmotic potential between the tissues that faced air with higher and lower humidities in the elongating and mature regions. Plastic extensibility was higher in the tissues that faced the air with lower humidity than in the tissues that faced the air with higher humidity. No differences in turgor pressure and yield threshold were observed between the tissues that faced air with higher and lower humidities. Therefore, the extensibility of the cell wall appeared to be responsible for the different growth rates of tissues in root hydrotropism. A further probable cause of the hydrotropical bending of roots is changes in the hydraulic conductance in the elongating tissues. Since the hydrotropic bending of roots occurred only when a root tip was exposed to a humidity gradient, hydrotropism might occur after perception of difference in humidity by the root tip, with accompanying changes in cell wall extensibility and hydraulic conductance.
Theileria parva apical membrane antigen-1 (AMA-1) shares conserved sequences with apicomplexan homologs

The apical membrane antigen-1 (AMA-1) is a leading malaria vaccine candidate that is expressed in mature stage parasites and is thought to be essential for invasion. In Plasmodium falciparum , AMA-1 is localized initially to the micronemes, apical organelles of the parasite. A similar apicomplexan parasite, Theileria parva infects and transforms lymphocytes of cattle and African buffalo causing the disease called East Coast fever (ECF). The AMA-1 homolog in T. parva was isolated, cloned and sequenced. The predicted amino acid sequence was further analyzed. The partial gene sequence, which is 1422 bp long and encoding 473 amino acid residues, is located on chromosome 1 of the T. parva genome. The AMA-1 homolog in T. parva shares conserved sequences with apicomplexan homologs. It is 64% similar to the AMA-1 in Babesia bigemina , and 56% similar to the homolog in P. falciparum . Given the importance of AMA-1 in invasion and the central role invasion plays in pathogenesis, the T. parva AMA1 may likely have implications for vaccine design in the East Coast fever disease.
BcSKS11, a SKS gene from pollinated pistils of Chinese cabbage pak choi, is expressed continuously during the male gametophyte development, pollen germination and pollen-tube growth processes

Cell wall-related genes and proteins are crucial for fertilisation-related events such as pollen germination and pollen-tube growth. Recent studies have focussed on the molecular mechanism of cell-wall synthesis and regulation of these processes; however, limited information is available on the mechanism and modification of the crucial cell-wall materials. We isolated a gene that is potentially involved in cell-wall metabolism from pollinated pistils of the male sterile line ‘Bcajh97-A’ in Chinese cabbage pak choi (Brassica campestris SKewed5 Similar 11, BcSKS11). BcSKS11 has several features of SKewed5 Similar (SKS) proteins, which are structures that are similar to plant multicopper oxidase but lack the 10 necessary residues of two copper-binding sites. A phylogenetic tree constructed from 49 SKS proteins found four clades, with BcSKS11 being in a clade with tobacco sequences. Reverse transcription–polymerase chain reaction and in situ hybridisation revealed that BcSKS11 was specifically expressed in uninucleate microspores, mature pollen grains and growing pollen tubes of pollinated pistils. These results suggest that BcSKS11 might be stored in mature pollen grains, in preparation for pollen germination and pollen-tube growth.
CHARACTERIZATION OF XANTHOMONAS ARBORICOLA pv. JUGLANDIS ISOLATED FROM WALNUTS IN LITHUANIA

SUMMARY This study records the presence of bacterial walnut blight, caused by Xanthomonas arboricola pv. juglandis (Xaj), on walnuts (Juglans spp.) in Lithuania and confirms that its geographic distribution has been underestimated. The pathogen caused the most serious symptoms on J. cinerea and J. mandshurica trees. DNA typing methods (rep-PCR and MLST) used for characterization of Xaj isolates disclosed a high similarity among them. Strains from Lithuania, however, showed a still not fully understood difference from Xaj strains from Poland, a neighbouring country, that needs further investigation.
Long-distance dispersal in migratory pied flycatchers Ficedula hypoleuca is relatively common between the UK and the Netherlands

Long-distance dispersal can potentially have important consequences for evolutionary change, but is difficult to quantify. We present quantitative estimates of natal dispersal between the UK and the Netherlands in a long-distance migratory bird, the pied flycatcher. Due to over 90 000 individual ringed adults caught and 730 000 ringed nestlings we are able to estimate that dispersal of young born in the UK to breeding in the Netherlands occurs on average 43 times yr−1, and probably even more recently. We estimated that between 2000 and 2009 about 0.70% of the Dutch adult population could be immigrants from the UK. No cases of dispersal from the Netherlands to the UK were observed. Dispersing individuals bring new genes to the Netherlands, as males in the UK have a darker plumage than Dutch males. We found a good qualitative match between the proportion of dark males breeding in two Dutch populations and the estimated immigration rate from the UK. This and potentially other genetic differences may allow for new evolutionary directions if these genes are beneficial in the new population. The causes of dispersal are unknown, but it is striking that especially birds from the northern range limit dispersed.
Egg load and the decision to host feed in the parasitoid Aphytis melinus

We make and test predictions about how the number of eggs a female parasitoid is carrying (her «egg load») influences her propensity for'host-feeding', the consumption of host body fluids. We first develop a simple dynamic state variable model that predicts that parasitoids should host-feed only when completely empty of eggs. This result reflects an important assumption of the simple model, namely the absence of a delay between host-feeding and the maturation of eggs. We therefore develop two additional models that incorporate a delay by adding extra «pre-egg» state variables to the simple model. Adding even a short delay makes possible a non-zero threshold egg number at and below which the parasitoid host-feeds. We then compare the results of the models with behavioural observations of host-feeding by Aphytis melinus DeBach (Hymenoptera: Aphelinidae)
α‐Lipoic acid inhibits TNF‐a‐induced NF‐κB activation and adhesion molecule expression in human aortic endothelial cells

Endothelial activation and monocyte adhesion are initiating steps in atherogenesis thought to be caused in part by oxidative stress. The metabolic thiol antioxidant a‐lipoic acid has been suggested to be of therapeutic value in pathologies associated with redox imbalances. We investigated the role of (R)‐a‐lipoic acid (LA) vs. glutathione and ascorbic acid in tumor necrosis factor a (TNF‐a) ‐induced adhesion molecule expression and nuclear factor KB (NF‐κB) signaling in human aortic endothelial cells (HAEC). Preincubation of HAEC for 48 h with LA (0.05–1 mmol/l) dose‐dependently inhibited TNF‐a (10 U/ml) ‐induced adhesion of human monocytic THP‐1 cells, as well as mRNA and protein expression of E‐selectin, vascular cell adhesion molecule 1 and intercellular adhesion molecule 1. LA also strongly inhibited TNF‐a‐induced mRNA expression of monocyte chemoat‐tractant protein‐1 but did not affect expression of TNF‐a receptor 1. Furthermore, LA dose‐dependently inhibited TNF‐a‐induced IκB kinase activation, subsequent degradation of IκB, the cytoplasmic NF‐κB inhibitor, and nuclear translocation of NF‐κB. In contrast, TNF‐a‐induced NF‐κB activation and adhesion molecule expression were not affected by ascorbic acid or by manipulating cellular glutathione status with L‐2‐oxo‐4‐thiazolidinecarboxylic acid, N‐acetyl‐L‐cys‐teine, or D,L‐buthionine‐S,R‐sulfoximine. Our data show that clinically relevant concentrations of LA, but neither vitamin C nor glutathione, inhibit adhesion molecule expression in HAEC and monocyte adhesion by inhibiting the IκB/NF‐κB signaling pathway at the level, or upstream, of IκB kinase. —Zhang, W. ‐J., Frei, B. α‐Lipoic acid inhibits TNF‐α‐induced NF‐κB activation and adhesion molecule expression in human aortic endothelial cells. FASEB J. 15, 2423–2432 (2001)
An effective method for obtaining high quality messenger ribonucleic acid (mRNA) with minimal ribosomal ribonucleic acid (rRNA) contents

Plant transcriptomes are very complex in nature and includes overlapping transcripts, transcribed intergenic regions, and abundant non-coding ribonucleic acids (RNAs). With RNA-Seq approach using next generation sequencing technology, complementary deoxyribonucleic acid (cDNA) library constructed either from Messenger ribonucleic acid (mRNA) or from ribosomal ribonucleic acid (rRNA) minus total RNA can be directly sequenced for transcriptome studies. The transcriptome analysis is mainly hampered by presence of unwanted abundant rRNA transcripts in cDNA library, which may represent majority species in RNA-Seq if not removed carefully from the total RNA. Though many commercial kits are available in the market for isolation of high quality mRNA from total RNA and their efficiency to remove rRNA contaminants from mRNA may vary. In the present study an effort has been made to isolate high quality mRNA with minimal rRNA contamination through designing an experiment with the use of two commercially available kits.
β-Amyloid Stimulation of Microglia and Monocytes Results in TNFα-Dependent Expression of Inducible Nitric Oxide Synthase and Neuronal Apoptosis

Reactive microglia associated with the β-amyloid plaques in Alzheimer's disease (AD) brains initiate a sequence of inflammatory events integral to the disease process. We have observed that fibrillar β-amyloid peptides activate a tyrosine kinase-based signaling response in primary mouse microglia and the human monocytic cell line, THP-1, resulting in production of neurotoxic secretory products, proinflammatory cytokines, and reactive oxygen species. We report that most of the amyloid-induced tyrosine kinase activity was stimulated after activation of Src family members such as Lyn. However, transduction of the signaling response required for increased production of the cytokines TNFα and IL1-β was mediated by the nonreceptor tyrosine kinase, Syk. Additionally, β-amyloid stimulated an NFκB-dependent pathway in parallel that was required for cytokine production. Importantly, TNFα generated by the monocytes and microglia was responsible for the majority of the neuorotoxic activity secreted by these cells after β-amyloid stimulation but must act in concert with other factors elaborated by microglia to elicit neuronal death. Moreover, we observed that the neuronal loss was apoptotic in nature and involved increased neuronal expression of inducible nitric oxide synthase and subsequent peroxynitrite production. Selective inhibitors of inducible nitric oxide synthase effectively protected cells from toxicity associated with the microglial and monocytic secretory products. This study demonstrates a functional linkage between β-amyloid-dependent activation of microglia and several characteristic markers of neuronal death occurring in Alzheimer's disease brains.
Effects of the Microcystis aeruginosa Strain RST9501 from Patos Lagoon, RS, on Growth and Reproduction of the Cladocera Ceriodaphnia dubia

This study evaluates the toxicity of the Microcystis aeruginosa strain RST9501, isolated from Patos Lagoon, to cladocerans using standard tests with Ceriodaphnia dubia. The strain RST9501 was compared with the non-toxic M. aeruginosa strain NPJT-01. Chronic effects were estimated by evaluating reproduction and growth in C. dubia exposed to increasing concentrations of M. aeruginosa. Alternative food source constituted by Pseudokirchneriella subcapitata and Artemia chow was made available for all treatments. The presence of the two strains of M. aeruginosa inhibited both reproduction and growth in C. dubia. Also, regardless the presence of microcystin, there was an increase in toxicity as the cell concentration of both strains increased.
Supplement to the 2002 catalogue of Australian Crustacea: Malacostraca - Syncarida and Peracarida (Volume 19.2A): 2002-2004

Poore, G.C. B. 2005. Supplement to the 2002 catalogue of Australian Malacostraca – Syncarida and Peracarida (Volume 19.2A): 2002–2004. Museum Victoria Science Reports 7: 1–15. Publications in the period 2002 to 2004 dealing with Australian Syncarida and Peracarida have been reviewed and new taxa, new combinations and significant papers listed. Eighty species in 28 genera and seven families of Isopoda, seven new species in four genera and two families of Tanaidacea, and one new species of Spelaeogriphacea have been newly reported for Australia in the 3-year period. No publications dealing with Syncarida, Mictacea or Thermosbaenacea were found. This report does not deal with Amphipoda, Mysidacea or Cumacea. These updates have been made to the Zoological Catalogue of Australia Volume 19.2A on the Australian Biological Resources Study website.
The theoretical foundations for size spectrum models of fish communities

Size spectrum models have emerged from 40 years of basic research on how body size determines individual physiology and structures marine communities. They are based on commonly accepted assumptions and have a low parameter set, making them easy to deploy for strategic ecosystem-oriented impact assessment of fisheries. We describe the fundamental concepts in size-based models about food encounter and the bioenergetics budget of individuals. Within the general framework, three model types have emerged that differ in their degree of complexity: the food-web, the trait-based, and the community models. We demonstrate the differences between the models through examples of their response to fishing and their dynamic behavior. We review implementations of size spectrum models and describe important variations concerning the functional response, whether growth is food-dependent or fixed, and the density dependence imposed on the system. Finally, we discuss challenges and promising directions.
The thermal response of leaf extension rate in genotypes of the C4-grass Miscanthus: an important factor in determining the potential productivity of different genotypes

Thermal responses of plant extension rate are reported for 32 genotypes of the C4 grass Miscanthus. Displacement transducers were used to measure plant extension rate as temperatures were stepped between 20 C and 5 °C. Leaf extension accounted for 83% of the plant extension. The Q10 between 10C and 20 C for the genotypes varied from 3.0 to 4.7. The relationship between temperature (5-20 °C) and plant extension rate was found to be described adequately by fitting a third order polynomial. An estimate of the effect of differences in the thermal response of plant extension rate on the potential yield of the genotypes was calculated for Irish climatic conditions using a simple growth model. Potential yield varied between 3 and 231 ha"1 year"1. This demonstrates the critical role which differences in leaf expansion rate can play in the selection of more productive genotypes. The significance of vapour pressure deficit on the estimates of thermal response of plant extension rate are discussed.
Dramatherapy with Women Survivors of Domestic Abuse: A Small Scale Research Study

The aim of this inquiry was to ascertain the efficacy of a multi-modal model of short-term dramatherapy with women who had suffered domestic abuse. A small-scale study was carried out to compare women who received individual dramatherapy with women who received individual key worker intervention. The 15 women were assigned to either the experimental or the control group. The experimental group received up to 12 weekly dramatherapy sessions with a qualified dramatherapist and the control group received 12 weekly key worker sessions with an experienced domestic violence substance misuse worker. The CORE system was used for both groups to provide pre- and post-intervention scores to assess change. The findings from this study revealed that the women who received dramatherapy presented significant improvements in their CORE Outcome Measure (CORE-OM) scores compared to women who attended key worker sessions. Women in the control group also showed improvements but not to the same extent.