Miracle-dz/UniFAR-FTUs huggingface dataset:
Alpines, trees, and refugia in Europe

Refugia were critically important for species survival in both glacial and interglacial stages of the Quaternary. The classical view of glacial stages is that alpine and arctic plants were widespread in the lowlands of central Europe and around the margins of the continental and alpine ice-sheets, whereas trees were restricted to localised refugial areas in southern Europe and the Mediterranean basin. New palaeobotanical evidence in Europe suggests, however, that this classical view is incomplete and that tree distributional ranges during the glacial stages were more extensive and included many local areas of small populations in central and eastern Europe growing in so-called ‘cryptic’ refugia. We argue that this concept of ‘cryptic’ refugia is also applicable to arctic and alpine plants during temperate interglacial stages where small localised populations grow in naturally open habitats that are not beyond or above the forest limit. Determination of the whereabouts of these cold- and warm-stage ‘cryptic’ refugia is very important in our understanding of the spatial patterns of present day genetic diversity and the possible rates of spread of trees in response to future climate change.
Dangers in testing statistical hypotheses

SUMMARY Most experiments are intended for the estimation of the size of effects rather than for the testing of a hypothesis of whether or not an effect occurs. Hypothesis testing is often inapplicable, is over-used and is likely to lead to misinterpretations of results. The two types of error possible in hypothesis testing are discussed. Whereas Type I error is usually examined as a matter of course, Type II error is almost always ignored. Investigations in which zero differences are important should recognise the possibility of Type II error in their interpretation. A nonsignificant result should not be interpreted as evidence of a lack of effect. Statistical significance is not synonymous with economic or scientific importance. The importance of choosing the most appropriate design is emphasised and some suggestions are made as to how important sources of error can be avoided.
Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems

Whether new combinations of genes that result from hybridization and introgression between wild and cultivated taxa are maintained, with the resultant development of populations with new characteristics, depends on natural selection, and in the case of crops, on human selection. While many cases of deliberate introgression of desirable traits into crop cultivars as part of breeding programmes are known, the extent and significance of natural or farmer‐assisted introgression is uncertain. A range of techniques have been used to document natural hybridization and introgression of agricultural crops and their wild relatives in many crops including maize, wheat, barley, oats, pearl millet, foxtail millet, quinoa, hops, hemp, potato, cocona, casava, common bean, cowpea, pigeon pea, carrots, squash, tomato, radish, letuce, chilli, beets, sunflower, cabbage, and rasberries. However, the majority of these studies are based on morphological characters, and few have investigated the frequency with which such new types are produced and retained in natural and agroecosystems for farmer selection. Even more limited is information on the role of farmers in recognizing and selecting new genetic variation from the natural introgression of crops with their wild relatives, and the impact, once selected, of these new genetic combinations on the crop diversity. Molecular evaluation of natural introgression linked to investigations of farmer recognition and use of introgressed types provide ways of evaluating whether farmer selection for introgressed types is a significant process in increasing the genetic diversity of crop plants.
Mango Malformation: One Hundred Years of Research

Malformation, arguably the most important disease of mango (Mangifera indica L.) worldwide, is of growing concern because it is widespread and destructive and because its etiology and control are not well understood. Numerous studies have attempted to determine the nature of the disease since its recognition in India in 1891 (75), producing over 150 publications since 1910 (7), although many of these add little to our knowledge of either etiology or control. A recent chapter (28) on mango malformation deals comprehensively with the disease, including its physiology. This review aims to consolidate and clarify existing knowledge, particularly on etiology and control, and to identify future areas of research that might be useful in solving this "century-old" disease.
Forest productivity increases with evenness, species richness and trait variation: a global meta‐analysis

1. Although there is ample support for positive species richness–productivity relationships in planted grassland experiments, a recent 48‐site study found no diversity–productivity relationship (DPR) in herbaceous communities. Thus, debate persists about diversity effects in natural versus planted systems. Additionally, current knowledge is weak regarding the influence of evenness on the DPRs, how DPRs are affected by the variation in life‐history traits among constituent species in polycultures and how DPRs differ among biomes. The impacts of these factors on DPRs in forest ecosystems are even more poorly understood.
Using the randomisation in specifying the ANOVA model and table for properly and improperly replicated grazing trials

Summary. A method for deriving the analysis of variance for an experiment is presented and applied to grazing trials. A special feature of grazing trials, specifically utilised by our method, is that they involve at least 2 randomisations: treatments are randomised to field units (for example paddocks or plots), and field units are randomised to animals. Randomisation results in the confounding (‘mixing up’) of terms and our method includes separate terms in the analysis of variance table for confounded terms so that all sources of variability in the experiment have terms for them included in the table and the confounding between the sources of variability in the experiment is explicitly displayed in the table. This information is used in determining the valid error terms and we will present examples that show how to ascertain these for effects of interest and hence which effects can be tested. In this it fulfils the same role as the contentious process of identifying the experimental unit. It will be demonstrated that the inclusion of separate terms for confounded terms results in improper replication in grazing trials being automatically signalled, and makes its ramifications clear.
Does difference exist between epitope and non-epitope residues? Analysis of the physicochemical and structural properties on conformational epi-topes from B-cell protein antigens.

Background As an essential step of adaptive immune response, the recognition between antigen and antibody triggers a series of self-protection mechanisms. Therefore, the prediction of antibody-binding sites (B-cell epitope) for protein antigens is an important field in immunology research. The performance of current prediction methods is far from satisfying, especially for conformational epitope prediction. Here a multi-perspective analysis was carried on with a comprehensive B-cell conformational epitope dataset, which contains 161 immunoglobulin complex structures collected from PDB, corresponding to 166 unique computationally defined epitopes. These conformational epitopes were described with parameters from different perspectives, including characteristics of epitope itself, comparison to non-epitope surface areas, and interaction pattern with antibody. Results According to the analysis results, B-cell conformational epitopes were relatively constant both in the number of composing residues and the accessible surface area. Though composed of spatially clustering residues, there were sequentially linear segments exist in these epitopes. Besides, statistical differences were found between epitope and non-epitope surface residues with parameters in residual and structural levels. Compared to non-epitope surface residues, epitope ones were more accessible. Amino acid enrichment and preference for specific types of residue-pair set on epitope areas have also been observed. Several amino acid properties from AAindex have been proven to distinguish epitope residues from non-epitope surface ones. Additionally, epitope residues tended to be less conservative under the environmental pressure. Measured by topological parameters, epitope residues were surrounded with fewer residues but in a more compact way. The occurrences of residue-pair sets between epitope and paratope also showed some patterns. Conclusions Results indicate that, certain rules do exist in conformational epitopes in terms of size and sequential continuity. Statistical differences have been found between epitope and non-epitope surface residues in residual and structural levels. Such differences indicate the existence of distinctiveness for conformation epitopes. On the other hand, there was no accordant estimation for higher or lower values derived from any parameter for epitope residues compared with non-epitope surface residues. This observation further confirms the complicacy of characteristics for conformational epitope. Under such circumstance, it will be a more effective and accurate approach to combine several parameters to predict the conformation epitope. Finding conformational epitopes and analysing their properties is an important step to identify internal formation mechanism of conformational epitopes and this study will help future development of new prediction tools.
Host Factors Influencing the Eradication Rate of Helicobacter Pylori

Currently, the resistance of Helicobacter pylori to antibacterial is considered as a major factor negatively affecting the effectiveness of anti-Helicobacter therapy (AHT). However, treatment success may depend on a series of host (a patient) factors alongside with the antibiotic resistance. This paper summarizes and analyzes the main host factors, affecting the efficiency of modern AHT regimens: conditions caused by hypersecretion of hydrochloric acid; polymorphisms in the genes (CYP2C19, MDR1, IL-1 ); low compliance; smoking; overweight/obesity and diabetes mellitus.
Ecology of the cattle tick (Boophilus microplus) in subtropical Australia. III. Modelling populations on different breeds of cattle

The numbers of cattle ticks, Boophi1u.s microplu. ~, were counted on cattle, with diffcrcnt Bos indicus (zebu) content in central and southern Queensland, from Noven~bcr 1977 to May 1982. Conc~~rrently, mcasure- menis werc made of the survival rates of parasitic stages of the tick and of the success of free-living stages in producing larval progeny. These measurements were related to the tick burdens on the cattle in order to test current understanding of the ecology of the tick. Tick numbers increased exponentially with decreasing Bos indicus content. Tick numbers built up very rapidly on the Bos taurus cattle and resulted in deaths early in the first season, so the herd was replaced with animals of 25% zebu content. The pure zebu animals carried an average of five ticks per animal per day in central Queensland and only one in southern Queensland. The 50% zebu herds carried 65 ticks per day in central Queensland and 1 l in southern Queensland, compared with 79 and 37 on the 25% zebu herds at the two locations. During their brief time in the experiment the B. taurus animals carried 465 and 302 ticks per day in central and southern Queensland respectively. The observed tick infestation levels were estimated to cause annual losses of liveweight gain of 1, 14 and 17 kg in zebu, 50% zebu and 25% zebu animals respectively in central Queensland. Comparative figures for southern Queensland were 0, 2 and 8 kg. Compensatory liveweight gain would have reduced these losses by up to 6 kg. These data relate to animals which were breeding most of the time and hence were less resistant than dry cattle. The results indicate that B. microplus has been reduced to a marginal problem on animals with 50% zebu genes in the region. It is therefore difficull to justify any control measures in southern areas, particularly when they could increase the risk of babesiosis. Owners of B. taurus cattle will continue to be at risk of major losses in productivity. Changes in the tick burden on the herd5 were explained mostly by changes in survival rates of parasitic ticks in central Queensland and by changes in availability of larvae on the pastures in southern Queensland. Additional keywords: census; model; zebu; economic loss.
Leaf Element Content and Utilization of Maple and Elm as Hosts by the Potato Leafhopper (Homoptera: Cicadellidae)

Abstract Feeding injury and performance of the potato leafhopper, Empoasca fabae (Harris), was measured on two red maple clones (Acer rubrum L.), a Freeman maple cultivar (A. × freemanii E. Murray), two elm cultivars (Ulmus spp.), and an American elm clonal selection (U. americana L.), and was related to the leaf content of important nutritional elements. Significantly more eggs were laid and more nymphs became adults on American and Patriot elms than on the other clones. Although the mean number of eggs laid was not significantly different among the maple clones, nymphal survivorship was significantly higher on red maple 56026 than on the other maple clones. Although the number of eggs laid was linearly related to foliar nitrogen and phosphorus, survival of nymphs to adulthood was linearly related to foliar nitrogen. Significantly more leafhoppers from the wild population were collected from American elm, followed by Patriot elm and red maple 56026. Although none of the elms showed any evidence of feeding injury, the maple trees varied from tolerant (i.e., ‘Indian Summer’) to susceptible (i.e., red maple 56026). Leafhoppers may need to increase feeding on red maple 56026 as a compensatory response to the limited nutritional quality of this clone. Because the sex ratio of the wild population was close to 1:1, and consistent across clones, it appears that differences in the behavior of the potato leafhopper among clones were not a function of gender bias associated with each species. Resistance against the potato leafhopper among maples and elms is influenced, in part, by the nutritional content of the leaves. Yet, feeding injury is not a good indicator of host resistance against the potato leafhopper.
Understanding behavioural responses and their consequences

Since the very inception of evolutionary theory, animal behaviour has been seen as a trait upon which selection can act. Darwin’s theory of sexual selection, exposed in the Descent of Man ( Darwin 1871 ), sparked some of the earliest research on the adaptive value of behaviours (e.g. Noble and Bradley 1933 ), yet the modern synthesis of the 1940s didn’t pay much attention to traits that one would nowadays call behaviours ( Birkhead and Monaghan 2010 ; Kokko and Jennions 2010 ). It took close to a century before the adaptive framework began to dominate the study of behaviour—thanks to the work of Niko Tinbergen and Konrad Lorenz ( Tinbergen 1963 ). This solidifi ed the link between evolutionary biology and the behavioural sciences that Charles Darwin had suggested. Like organs, behaviours represent adaptations to the environment. Tinbergen, for instance, demonstrated that the sticklebacks’ fi erce reaction against the colour red represents an adaptation to exclude attractive sexual competitors ( Tinbergen 1963 ), while Lorenz studied the impulse of goslings to follow the fi rst object they see after hatching, which ensures they remain safe with their mother and learn how to be adult geese. These landmark studies sparked decades of search for the adaptive function of different behaviours ( Owens 2006 ), which later translated into the behavioural ecologists’ modern obsession with fi tness consequences of behaviour, ideally in the real ecological context. Behavioural ecology was born (see Birkhead and Monaghan 2010 ; Kokko and Jennions 2010 ). There is, however, some irony in the images that these early studies of adaptation convey. There are famed pictures of geese, which happened to be imprinted on Konrad Lorentz’s boots on hatching, courting the ethologist as if they were conspecifi c adults; and stories of Niko Tinbergen’s sticklebacks wasting energy on aggressive displays towards the refl ection of red cars which would pass by the window next to their tank. It is hard to see the adaptive value of those behaviours. Naturally, we all know that humans are rarely present when goslings hatch, CHAPTER 1
Apparent digestibility, rumen fermentation and nitrogen balance in Tibetan and fine-wool sheep offered forage-concentrate diets differing in nitrogen concentration

SUMMARY A comparative study of the effect of dietary nitrogen (N) content [Low: 11·0; Medium-Low (MLow): 16·7; Medium-High (Mhigh): 23·1; High: 29·2 N g/kg dry matter (DM)] on apparent digestibilities, rumen fermentation and N balance was conducted in coarse wool Tibetan sheep and Gansu Alpine fine-wool sheep at Wushaoling in the northeast of the Qinghai-Tibetan Plateau. It was hypothesized that responses would differ between breeds and that responses would favour Tibetan over fine-wool sheep at low N intakes. Eight wethers [four Tibetan sheep and four fine-wool sheep, 20–24 months old; body weight ± standard deviation was 52 ± 3·2 kg] were used in two concurrent 4 × 4 Latin square designs. Dry matter, organic matter, neutral detergent fibre and acid detergent fibre digestibilities were higher in Tibetan than fine-wool sheep when fed the Low, MLow and High N diets while N retention was higher when the animals were fed the Low and MLow N diets. Tibetan sheep had a higher rumen pH than fine-wool sheep; however, total volatile fatty acids were similar between breeds. Molar proportions of acetate were higher but propionate and butyrate lower in Tibetan than fine-wool sheep. In addition, Tibetan sheep had higher concentrations of ruminal free amino acid-N and soluble protein-N than fine-wool sheep. Plasma and saliva urea-N concentrations were higher in Tibetan than fine-wool sheep when supplied with the Low N diet. It was concluded that Tibetan sheep were better able to cope with low N feed than fine-wool sheep because of the higher N retention and higher DM and fibre digestibilities with Low and MLow diets.
Wavelet Based Adaptive Detection of Automotive Radar Single Target with Low SNR

We propose an adaptive detection algorithm combining two signal processing methods: ordered statistics and wavelet based denoising, with the purpose of detecting low SNR single automotive radar target. The detection is realized by denoising the Range-Doppler map obtained for the Rapid Chirps waveform, using a Hard-Thresholding filter applied in the wavelet domain. The threshold is selected as the maximum value of the medians of the Range-Doppler map resolution cells. We quantify by simulations the merits of each of the two signal processing methods used.
Visual Activation in α‐Chloralose‐anaesthetized Cats Does Not Cause Lactate Accumulation in the Visual Cortex as Detected by [1HINMR Difference Spectroscopy

The hypothesis that neuronal activation results in lactate accumulation due to mismatch between glucose and oxygen consumption was tested in the cat model of visual activation by monitoring cerebral metabolism with localized 1H nuclear magnetic resonance spectroscopy (MRS). Adult cats were anaesthetized with α‐chloralose, paralysed and mechanically ventilated. Visual evoked potentials measured over the occipital cortex showed maximal amplitude at 2 Hz stimulation, but the latencies of the early cortical potentials, N1 and P1, were independent of stimulation frequency. High signal‐to‐noise ratio, short echo time volume‐selected [1H]MRS was used to monitor cerebral lactate with a temporal resolution of 70 s. Difference proton spectroscopy unambiguously showed no lactate peak in the visual cortex during visual activation at stimulation frequencies ranging from 1 to 16 Hz. Absence of change in lactate concentration during visual stimulation was confirmed by averaging all the spectra acquired during activation and subtracting them from reference spectra collected in darkness, a procedure that had a calculated lactate detection limit of 0.17 mM. We also reduced the O2 in the inspired air to 13%, which decreased pO2 from 94.5 ± 8.9 to 47.0 ± 6.8 mmHg, during visual stimulation at 2 or 4 Hz. At this low pO2 level, visual stimulation did not cause lactate accumulation in the visual cortex, however. The present data show that neuronal activation to this degree in the cat brain is not associated with aerobic lactate production to an extent that can be detected with 1H MRS.
Aspects of selection for feed efficiency in meat producing poultry

Over the last five years, the costs of poultry feed ingredients have increased substantially. This has been due to an increased use of corn for ethanol production and a greater overall global feed grain demand. Across the poultry industry this has led to higher production costs and reaffirmed the importance of feed efficiency on profitability. The effect that an increase in feed costs has on profitability is a clear driver for the selection for birds with better feed efficiency. Feed efficiency selection can be achieved using a number of different analytical methods. Selection for feed conversion ratio (FCR) has been used to improve feed efficiency with success but using a ‘ratio’ trait has mathematical limitations because selection pressure tends to be placed on the component traits of FCR in a non-linear manner. Another measure, residual feed intake (RFI) shows moderate to high heritability and does not have the mathematical limitations associated with FCR. RFI has little to no correlation with production traits and this indicates that genetic improvement of RFI within a selection index can be done without the confounding issues inherent with FCR. Improvements in RFI or FCR have a favourable effect on environmental emissions and decreases the environmental impact of poultry production. The current global production of ammonia, CH4, and N2O by the poultry industry is significant, at levels of 2.1, 29.44 and 279 million tonnes CO2eq, respectively. Reductions in emissions can be achieved via improvements in feed efficiency by lowering amounts of manure excreted and decreasing emitted by-products such as ammonia and greenhouse gases (N2O, CO2 and CH4). Consequently, improvements in feed efficiency can not only increase profitability of the poultry industries by lowering production costs but also decrease environmental impact by reducing environmental emissions.
Environmental and fishing limitations to the rebuilding of the northern Gulf of St. Lawrence cod stock (Gadus morhua)

Time series of life history traits determining the reproductive potential and productivity of Atlantic cod (Gadus morhua) in the northern Gulf of St. Lawrence (nGSL) were obtained for the period covering the collapse and failure of the stock to recover. Decreasing trends in these traits were observed under unfavourable oceanographic conditions, with lowest values reached in the early 1990s. These changes had a negative impact on reproductive rate and instantaneous rate (r) of population growth. Estimates of r used as a proxy of stock productivity were negative when the stock collapsed, indicating that the biomass would have decreased even without fishing. Population abundance projections for the recent period suggest a potential increase in population size of 7.3% per year, with a doubling time of 10.5 years in the absence of exploitation and a near 0% rate with current fishing mortality, indicating that present harvesting does not allow any rebuilding of the stock. Given the similarities in environmental.