Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights into pig taxonomy, domestication and human dispersal in Island South East Asia: molar shape analysis of Sus remains from Niah Caves, Sarawak

Despite the almost ubiquitous presence of Holocene Sus remains in Island South East Asia (ISEA), the domestication of pigs and their dispersal in this region remains somewhat confused. Using molar shape geometric morphometric analysis, archaeological Sus dental series from the Sarawak caves of Niah (Aceramic, Neolithic) and Lobang Kudih (Ming period), are compared with extant ISEA wild pigs to establish their taxonomic status and to further explore the evidence for local domestication or introduction of allochthonous populations. Results on modern data-sets show that outline analysis of the third lower molar achieves highly significant inter- and intra-specific differentiation among ISEA wild pigs, with a phenotypic divergence structure displaying congruence with molecular phylogenies. Both tooth shape and mtDNA evidence strongly suggest the so-called wild pigs of New Guinea to be the descendants of pigs domesticated in mainland South East Asia and introduced by early farmers to ISEA. None of our data provide clear evidence for a Neolithic introduction of domesticated pigs, or for the local domestication of indigenous bearded pigs, since all Aceramic and Neolithic pigs from Niah cave have been identified as indigenous bearded pig (Sus barbatus). Local domestication experiments by foragers have not been ruled out, since evidence of hypoplasia as a marker of domestication processes has been observed. Introduction of allochthonous domestic pigs between the Late Neolithic and the Metal Age is suggested, since this small domestic breed from Lobang Kudih cave displays strong phenetic relationships with S. scrofa of New Guinea, recognised by molecular phylogeography as part of the ‘Pacific Clade’ linked both with Lapita and Polynesian dispersals. Introduction of celebensis-like species has also been suggested. Future studies should incorporate broader time-scale and geographical framework data-sets to strengthen these assumptions. Copyright © 2008 John Wiley & Sons, Ltd.
Simulation modelling as a tool for examining the consequences of spatial structure and connectivity on local and regional population dynamics

Kerr, L. A. , Cadrin, S. X. , and Secor, D. H. 2010. Simulation modelling as a tool for examining the consequences of spatial structure and connectivity on local and regional population dynamics. - ICES Journal of Marine Science, 67: 1631-1639.An understanding of the mechanisms underlying population persistence makes fisheries management more effective. A model framework is described, which can test hypotheses about spatial structure and connectivity within and between populations and their influence on the productivity (spawning-stock biomass, SSB), stability (variation in SSB), resilience (time to rebuild SSB after environmental disturbance), and sustainability (maximum sustainable fishing mortality and yield) of systems. The general model consists of linked age-structured submodels that incorporate the unique demographics and dynamics of population components, along with the degree and type of connectivity between them. The flexibility of this framework is illustrated with three case studies examining (i) spatial structure within a population of white perch, (ii) different types and degrees of connectivity between populations of Atlantic herring, and (iii) spatial heterogeneity and connectivity within a stock of Atlantic cod. System variance is reduced by abundant, stable population components, and the asynchronous responses of those components. Components with high productivity contributed disproportionately to the resilience of systems. Increased synchrony of component responses to environmental forcing decreased the stability of the overall system. Simulation modelling is a useful approach to evaluate the consequences of spatial structure and connectivity, and can be used to understand better the productivity and dynamics of local and regional populations.
Survival rates of thermotolerant Campylobacter species in a transport and enrichment medium under different environmental conditions

Determinou-se a sobrevida de Campylobacter jejuni subsp. jejuni e C. coli no meio de transporte e enriquecimento TEC, mantido sob diferentes condicoes de temperatura e concentracao de oxigenio. A sobrevida da maioria das amostras foi superior a cinco dias, obtendo-se os periodos de sobrevida mais prolongados (sete a 15 dias), quando o meio foi incubado em microaerofilia a temperatura ambiente, condicoes nas quais o tempo de sobrevida de C. coli foi superior ao de C. jejuni subsp. jejuni.
A minimal receptor-Ig chimera of human FcεRI α-chain efficiently binds secretory and membrane IgE

We constructed a soluble minimal receptor-Ig chimera in which the two extracellular domains of human FceRI αchain (D1 and D2) were fused to the dimerizing C-terminal domain of human IgG1 heavy chain (γ1-CH3). The protein was expressed and actively secreted by Chinese hamster ovary (CHO) cells as a fully glycosylated soluble dimeric protein. It showed efficient binding both to human membrane-bound IgE isoforms and to the two secretory IgE isoforms. Moreover, the dimeric receptor binds IgE with the expected 1:2 stoichiometry. The receptor-Ig chimera, in 2-fold molar excess, inhibited engagement of secretory IgE to rat basophilic leukemia cells expressing the human αβγ receptor. Full self-nature and inability to bind Fcγ receptors make this protein an attractive candidate for clinical applications and a novel biotechnological tool for atopic allergy research.
The identification of quality antibacterial drug discovery targets: a case study with aminoacyl-tRNA synthetases

Although there is a clearly established need for new antibiotics, the route to their discovery is anything but clear or defined. One possible approach is target-based drug discovery. Adhering to this strategy, appropriate targets must first be selected. Even this early stage step in the process is not straightforward. As described here, numbers of genomics targets are available and a subset of those have been linked to infection. However, only a further subset of these targets will prove amenable to drug discovery. Here we profile two approaches to identify quality drug discovery targets from within a family of enzymes known as aminoacyl-tRNA synthetases. Targets were selected based on (i) high throughput screening data or (ii) protein sequence similarity analyses. The merits of each approach are discussed. Although some measure of success was achieved using sequence similarity to prioritise targets, high throughput screening data and the subsequent profiling of hits resulted in the selection of higher quality targets for further study.
Lignin-modifying enzymes from selected white-rot fungi: production and role from in lignin degradation

Abstract White-rot fungi produce extracellular lignin-modifying enzymes, the best characterized of which are laccase (EC 1.10.3.2), lignin peroxidases (EC 1.11.1.7) and manganese peroxidases (EC 1.11.1.7). Lignin biodegradation studies have been carried out mostly using the white-rot fungus Phanerochaete chrysosporium which produces multiple isoenzymes of lignin peroxidase and manganese peroxidase but does not produce laccase. Many other white-rot fungi produce laccase in addition to lignin and manganese peroxidases and in varying combinations. Based on the enzyme production patterns of an array of white-rot fungi, three categories of fungi are suggested: (i) lignin-manganese peroxidase group (e.g.P. chrysosporium and Phlebia radiata), (ii) manganese peroxidase-laccase group (e.g. Dichomitus squalens and Rigidoporus lignosus), and (iii) lignin peroxidase-laccase group (e.g. Phlebia ochraceofulva and Junghuhnia separabilima). The most efficient lignin degraders, estimated by 14CO2 evolution from 14C-[Ring]-labelled synthetic lignin (DHP), belong to the first group, whereas many of the most selective lignin-degrading fungi belong to the second, although only moderate to good [14C]DHP mineralization is obtained using fungi from this group. The lignin peroxidase-laccase fungi only poorly degrade [14C]DHP.
Introductions of seaweeds: accidental transfer pathways and mechanisms

Abstract Macroalgae are a significant component of historic and modern invasions, with association to a wide variety of transport mechanisms. These transport mechanisms pose specific constraints on the ways by which species can be taken up, transported and released into a new environment. Currently operating transport mechanisms for marine macroalgae are either associations with intentional introductions (translocations for aquaculture, aquarium or live seafood trade) or accidental introductions (mainly as hull-fouling). A number of potential management options exist, including the development of international instruments and regional agreements. The development of treatment options for hull fouling, the most significant and poorly managed transport mechanism for macroalgae, is of urgent need. Our current ability to identify which species are likely to invade next is limited. However, an examination of the synergies between species' functional traits, transport constraints, and recipient community attributes will likely provide possible options in the future.
Expression of Nav1.6 sodium channels by Schwann cells at neuromuscular junctions: Role in the motor endplate disease phenotype

In addition to their role in action potential generation and fast synaptic transmission in neurons, voltage‐dependent sodium channels can also be active in glia. Terminal Schwann cells (TSCs) wrap around the nerve terminal arborization at the neuromuscular junction, which they contribute to shape during development and in the postdenervation processes. Using fluorescent in situ hybridization (FISH), immunofluorescence, and confocal microscopy, we detected the neuronal Nav1.6 sodium channel transcripts and proteins in TSCs in normal adult rats and mice. Nav1.6 protein co‐localized with the Schwann cell marker S‐100 but was not detected in the SV2‐positive nerve terminals. The med phenotype in mice is due to a mutation in the SCN8A gene resulting in loss of Nav1.6 expression. It leads to early onset in postnatal life of defects in neuromuscular transmission with minimal alteration of axonal conduction. Strikingly, in mutant mice, the nonmyelinated pre‐terminal region of axons showed abundant sprouting at neuromuscular junctions, and most of the α‐bungarotoxin‐labeled endplates were devoid of S‐100‐ or GFAP‐positive TSCs. Using specific antibodies against the Nav1.2 and Nav1.6 sodium channels, ankyrin G and Caspr 1, and a pan sodium channel antibody, we found that a similar proportion of ankyrin G‐positive nodes of Ranvier express sodium channels in mutant and wild‐type animals and that nodal expression of Nav1.2 persists in med mice. Our data supports the hypothesis that the lack of expression of Nav1.6 in Schwann cells at neuromuscular junctions might play a role in the med phenotype. © 2005 Wiley‐Liss, Inc. © 2005 Wiley‐Liss, Inc.
Proximate composition and mineral analysis of cinnamon.

A study was conducted to know the nutritive value of cinnamon in the Department of Huma n Nutrition, NWFP Agricultural University, Peshawar. The standard procedures of AOAC (2003) were followed to analyze the proximate composition and mineral analysis. The caloric value was calculated from crude protein, crude fat, crude fiber, carbohydrate, moisture and ash content. The iron (Fe), zinc (Zn), calcium (Ca), chromium (Cr), manganese (Mn) and magnesium (Mg) were determined by Atomic Absorption Spectrophotometer, sodium (Na) and potassium (K) by Flame Photometer and phosphorus (P) by Spectrophotometer. The results revealed that cinnamon contained ash (2.4%), crude protein (3.5%), crude fat (4%), crude fiber (33.0%), moisture (5.1%) and carbohydrate (52.0%). While the mineral determination gave the data that cinnamon contained iron (7.0 mg/g), Zinc (2.6 mg/g), Calcium (83.8 mg/g), Chromium (0.4 mg/g), Manganese (20.1 mg/g) and Magnesium (85.5 mg/g), sodium (0.0 mg/g), Potassium (134.7 mg/g) and Phosphorus (42.4 mg/g). This study concluded that the tested cinnamon contained highest amount of carbohydrate and lowest amount of ash. Similarly, among minerals the tested cinnamon contained highest amount of potassium and no sodium at all.
Effect of sugar alcohol on physicochemical properties of wheat starch

Effects of sugar alcohol (maltitol, erythritol, and xylitol) at different concentration levels (sugar alcohol/starch ratio 0.1:1, 0.2:1, 0.5:1, 1:1, 2:1, w/w, db) on the physicochemical properties of wheat starch were studied.The swelling power decreased significantly with sugar alcohols content increasing at 95°C. Rapid visco-analyser (RVA) breakdown and setback of wheat starch decreased with increasing sugar alcohol content. Texture measurements showed that hardness of wheat starch gel rose with increasing content of sugar alcohols, indicating that sugar alcohols probably facilitated the retrogradation of amylose following the order of xylitol>maltitol>erythritol at a sugar alcohol/starch ratio of 2:1. The gelatinization temperature and enthalpy of wheat starch increased significantly at higher maltitol, erythritol, and xylitol concentrations (� 1:1). Such effects might be contributed to more hydrogen bonds formed between sugar alcohols hydroxyl groups and starch chains and the granule needed greater energy to break away during gelatinization.
Testing a Microwave Device for the Treatment of Plant Materials by Various Technologies

We have tested the microwave device of continuous operation for the thermal treatment of plant materials, which was developed and designed to implement microwave technologies in the industry. The purpose of the tests was to assess the effectiveness of the microwave device by the indicators of quality of the obtained material and energy consumption determined by the efficiency of the conversion of microwave energy into the internal energy of the material. The effects of microwave treatment of a straw substrate for tree-destroying fungi were studied. The treatment quality was determined by the yield of Oyster (Pleurotus) mushrooms, grown on the obtained substrate. Microwave treatment was carried out in various modes, which differed in the value of specific power. When analyzing the effectiveness of microwave treatment, the results were compared with the data obtained during the application of the traditional technology of straw sterilization. It was shown that the harvest of Oyster mushrooms increased by 11 %. It was found that under the optimal mode, specific power was q v =8.68·10 5 W/m 3 , final temperature was t=96 °С, duration of treatment was 180 s. Based on the thermal calculations, the values of the microwave chamber efficiency η c were calculated; under the optimal mode, η c =62 %. The influence of the microwave treatment on the sowing characteristics of seed wheat grain was studied. The effectiveness of the microwave treatment was determined by the values of laboratory germination and seed germination energy. Under the optimal mode, the output power of magnetrons was ΣP out =0.6 kW, the grain consumption was G=2.1·10 -2 kg/s. The study of the microwave device operation showed that for this design, in order to ensure stable and uniform movement of the material along the product pipeline, it is necessary to maintain the movement speed that is not higher than 0.5 m/min. It is recommended to apply the tested microwave device of continuous operation on specialized farms
How reliable and robust are current biomarkers for copper status

Cu is an essential nutrient for man, but can be toxic if intakes are too high. In sensitive populations, marginal over- or under-exposure can have detrimental effects. Malnourished children, the elderly, and pregnant or lactating females may be susceptible for Cu deficiency. Cu status and exposure in the population can currently not be easily measured, as neither plasma Cu nor plasma cuproenzymes reflect Cu status precisely. Some blood markers (such as ceruloplasmin) indicate severe Cu depletion, but do not inversely respond to Cu excess, and are not suitable to indicate marginal states. A biomarker of Cu is needed that is sensitive to small changes in Cu status, and that responds to Cu excess as well as deficiency. Such a marker will aid in monitoring Cu status in large populations, and will help to avoid chronic health effects (for example, liver damage in chronic toxicity, osteoporosis, loss of collagen stability, or increased susceptibility to infections in deficiency). The advent of high-throughput technologies has enabled us to screen for potential biomarkers in the whole proteome of a cell, not excluding markers that have no direct link to Cu. Further, this screening allows us to search for a whole group of proteins that, in combination, reflect Cu status. The present review emphasises the need to find sensitive biomarkers for Cu, examines potential markers of Cu status already available, and discusses methods to identify a novel suite of biomarkers.
Spore production of Beauveria bassiana from agro-industrial residues

The purpose of this work was to produce Beauveria bassiana by Solid-State Fermentation using agro-industrial residues and optimizing the cultivation conditions. Refused potatoes, coffee husks and sugar-cane bagasse were tested. The blend of refused potatoes and sugar-cane bagasse (60-40%) with particle size in the range of 0.8-2 mm was used in the fermentation experiments. In Erlenmeyer flasks the best spore production was achieved with the following conditions: incubation temperature 26o C; initial pH 6.0; inoculum concentration 107 spores.g-1.dw and initial moisture 75%. In the column type reactor using forced aeration under the optimized conditions, the maximum production (1.07x1010spores.g-1.dw) was obtained at the 10th day of fermentation. The respirometric analyses of the fermentation showed a strong correlation between fungal growth and spore production.
Determinants of species evenness in a neotropical bat ensemble

Evenness is an important property of communities. Species richness alone does not capture the fact that one or a few species may dominate total abundance and biomass of a community. This in turn has important consequences for ecosystem functioning and species interactions. Evenness has been observed to vary systematically along environmental and productivity gradients. However, a truly general theory about which factors control evenness in a community has yet to emerge. Prior research on evenness has suggested that high richness, biomass and abundance should lead to lower community evenness in our study system of bats in Panama. However, only few empirical studies examine the simultaneous effects of species richness, biomass or abundance on evenness. For the first time, we applied path analysis in the study of evenness to tease apart the relative importance and direction (positive or negative) of causality among these three factors. As predicted, we found that evenness decreases with increasing species richness, abundance and biomass. The negative effect of abundance was mediated by the positive joint effect of biomass and richness. The selected models varied in the strength of the correlation between the three variables with evenness but their direction was consistent. Overall, we argue that rarity, high mobility and differences in resource availability at sites with lower environmental stress can explain the negative effects of richness on evenness.
Function of the digestive system

Abstract The tremendous amounts of feed handled by commercial poultry breeds require an optimally functioning digestive tract. Functionality of the different segments of the digestive tract may be affected by diet and feeding systems, however. Retention time, moisture content, and pH of contents in the crop are, to a large extent, determined by feeding systems, where intermittent feeding is necessary for a stimulation of crop use. Retention time and pH of the gizzard contents are similarly affected by access to structural components, such as whole cereals or coarse fibers. These materials will stimulate normal development of the gizzard, increase retention time, and decrease pH. Less is known about characteristics of an optimally functioning small intestine, but stimulation of gizzard development will possibly improve functionality of the small intestine through a better feed flow regulation. Functionality of the digestive tract will possibly have a large effect on response to dietary manipulations (e.g., enzyme and pre- or probiotics addition), and therefore needs to be taken into consideration in experimental design and results interpretation.
Small habitat size and isolation can promote species richness: second-order effects on biodiversity in shallow lakes and ponds

Contemporary ecological landscape planning is often based on the assumption that small isolated habitat patches sustain relatively few species. Here, we suggest that for shallow lakes and ponds, the opposite can be true for some groups of organisms. Fish communities tend to be poor or even absent in small isolated lakes. However, submerged vegetation is often more abundant in such waterbodies. As a consequence of low fish biomass and high vegetation abundance, the richness of aquatic birds, plants, amphibians and invertebrates is often relatively high in small, shallow, isolated lakes. Although the rarity of fish is in line with expectations from the ruling paradigms about effects of habitat fragmentation in landscape ecology, the relative richness of various other groups of organisms in small ponds is opposite to these expectations. The case of shallow lakes illustrates that incorporating ecological interactions is essential to understanding the potential effects of habitat fragmentation. Single-species meta-population approaches may be misleading if ecological interactions are strong. A meta-community approach that explicitly incorporates biotic interactions, also those involving different trophic levels, is needed. Our diagnosis suggests that connection of isolated habitat fragments may in some cases reduce, rather than enhance, landscape-level biodiversity, and implies that biodiversity at the regional level will be maximized if the local habitat patches vary widely in size and degree of connectivity.
Drought affects the competitive interactions between Fagus sylvatica seedlings and an early successional species, Rubus fruticosus: responses of growth, water status and δ13C composition

Summary • Competitive interactions between European beech (Fagus sylvatica L.) seedlings and the early successional species Rubus fruticosus, and the role of water availability, are reported and discussed in relation to management practices and climatic changes in beech ecosystems of Central Europe. • Responses of growth, water status, gas exchange and carbon isotope composition (δ13C) to two competition and three irrigation treatments were examined in a factorial-design glasshouse study. • Under regular irrigation, coexistence with R. fruticosus did not significantly affect growth, water potential and gas exchange of beech seedlings. However, moderate water shortage caused a twofold reduction in beech biomass and changes in root : shoot ratios. Drought lowered transpiration rates and predawn water potentials (below the xylem embolism threshold) for F. sylvatica;δ13C of leaves and fine roots increased (discrimination was reduced). By contrast, significantly lower δ13C of R. fruticosus foliage indicated an improved water status. Competitive interference intensified the effects of reduced irrigation. • Water availability regulates the competitive interactions between beech seedlings and R. fruticosus. Natural regeneration of beech seedlings may be inhibited by interference from a species such as R. fruticosus, especially during summer drought, as predicted by actual climate models.