Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporating cointegration relations in a short-run model of the Finnish sawlog market

This paper reports on the results of a simultaneous equations sawlog market model using monthly data for Finland in 1985-1997. Johansen's multivariate method is used to estimate cointegration vectors, which are then included in a dynamic error-correction model. Rank tests indicate two cointegrating vectors, which is theoretically consistent with the demand and supply equations. In the sawlog demand, the equilibrium is established for sawlog stumpage price and quantity and sawn wood price and capital stock, while the supply function in a perfect capital market entails sawlog price and quantity, real interest rate, and the effect of increasing timber stock as captured by a linear trend. Contrary to earlier findings, stumpage price seems to have a positive effect on sawlog supply, both in the short and long run, while only the long-run price effect is present in the sawlog demand. Disequilibrium in demand is corrected within one quarter, while the speed of adjustment is found to be slow in the sawlog supply.
Patterns and controlling factors of species diversity in the Arctic Ocean

Aim The Arctic Ocean is one of the last near‐pristine regions on Earth, and, although human activities are expected to impact on Arctic ecosystems, we know very little about baseline patterns of Arctic Ocean biodiversity. This paper aims to describe Arctic Ocean‐wide patterns of benthic biodiversity and to explore factors related to the large‐scale species diversity patterns.
Bi-temporal Query Optimization Techniques in Decision Insight

The complexity of dynamic environments in which companies work requires their managers to take rapid and relevant decisions. A business activity monitoring application should be able to implement complex bi-temporal queries on real-time data and historical data in order to detect business trends and anomalies. However, accessing both real-time and historical data is costly and can hardly meet the application’s requirements of fast responses for analysts.In this paper, we propose Decision Insight, a platform developed by a French software editor, that solves this problem. It consists in redefining such a complex bi-temporal query into: 1) a set of continuous queries in charge of handling real-time data (whose results are materialized) and 2) a query that accesses both historical and materialized results of the previous continuous queries. Thus, Decision Insight can provide analysts with timely answers through a convenient GUI.Decision Insight is based on a column-store bi-temporal DBMS that handles these two types of data and implements a simple and efficient bi-temporal query optimization technique. We demonstrate the interest of our approach using an adapted version of TPCBiH, a bi-temporal extension of the TPC-H benchmark. Extensive experiments have been conducted, pointing out the interest of Decision Insight for delivering timely information based on historical and real-time data.
Sexual selection and sex allocation in the gregarious parasitoid wasp Nasonia vitripennis

Sex allocation and sexual selection have been heavily studied, but rarely linked. In this thesis I investigated the interface between them in the gregarious parasitoid wasp Nasonia vitripennis, both directly and through their interactions with the mating system and sexual conflict. Chapter 2 investigated sexual selection and mating at the natal site: earlier eclosing males mated more females independently of body size. Nasonia follows Local Mate Competition, which describes how a female laying eggs alone on a patch of resources (a so-called single-foundress) should lay an extremely female-biased brood to minimise competition between her sons, yet ensure all her daughters are fertilised. Based on this I predicted that males with with fewer brothers would be better inseminators. Despite finding significant among-strain variation in (1) single-foundress sex ratio, (2) mate competitiveness when alone and (3) when in competition, (4) sperm resources, but not (5) sperm-depletion (Chapters 3 & 4), I did not find the predicted relationship. Conversely males from strains with more brothers had a higher mating success under competition (Chapter 3) leading to the question: does mating success select on sex ratio or vice versa? Either way it is a result of an interaction between sexual selection and sex allocation. Chapter 5 investigated the role of male post-copulatory courtship on female re-mating, and found that amongstrain variation in female re-mating was not associated with variation in the duration of the post-copulatory courtship. Chapter 6 reviewed sexual conflict in the Hymenoptera: their haplodiploid genetics, newly sequenced genomes and varied lifehistories provides a base for future research to build on. Finally I highlight the novel links between sexual selection, sex allocation, sexual conflict and the mating system found during my studies that will hopefully prompt future research on this topic.
Zooplankton Distribution and Transport in the California Current off Oregon

Transport and retention of zooplankton biomass in the shelf and slope regions off Oregon, USA, were studied in June 2002, using high-resolution measurements of temperature, salinity, depth, fluorescence, water current and zooplankton abundance. We employed 2 different analytical methods for minimizing divergence in the geostrophic current fields based on measurements from a vessel using an acoustic Doppler current profiler. We detected high zooplankton biomass in coastal upwelling areas on the shelf, and exchanges between shelf waters with high zooplankton biomass and offshelf waters with low zooplankton biomass via cross-isobath currents. In the shelf area of Heceta Bank off Newport bounded by the 153 m isobath, the standing zooplankton biomass was ~4 × 104 t C. The major flux of zooplankton biomass into the area occurred at the northern boundary at a rate of 1 × 103 to 2.5 × 103 t C d−1 or a specific rate of 0.03 to 0.06 d−1 based on 2 different analytical methods. The flux at the southern boundary was 1 order of magnitude lower, and a significant flux out of the area occurred at the 153 m isobath at a rate of ~0.8 × 103 to 3.7 × 103 t C d−1 or a specific rate of 0.02 to 0.09 d−1. These rates are comparable with the zooplankton growth and mortality rates of ~0.1 d−1 previously reported for this region. Offshelf transport of zooplankton contributes significantly to biomass losses in shelf ecosystems and in turn fuels offshelf ecosystems.
Factors that influenced multiple ovulation results of zebu donors.

INTRODUCTION Despite Multiple ovulation and embryo transfer technique (MOET) has spread all over the country, aspects influencing MOET efficiency were little evaluated. It become more important when considered the breeding and conservation programs in MOET nucleus (Nicholas and Smith, 1983). Different factors have been pointed as responsible for MOET results (Monniaux et al., 1983 ; Callesen et al., 1986 ; Lamberson and Lambeth, 1986 ; Walton and Stubbings, 1986 ; Bastidas and Randel, 1987 ; Armstrong, 1993 ; Woolliams et al., 1995). The complexity of superovulation response variation, according to authors, is evident. Thus, the objective of this study was to verify the influence of breed, herd, year of birthday, age at superovulation, age at 1 calving, month, season and year of superovulation, flushing order, drug, dose, number of inseminations and interactions on the number of corpora luteous (CL), total of structures per flushing (SF) and number of viable embryos (VE).
Molecular Evidence of Long Wavelength Spectral Sensitivity in the Reverse Sexually Dichromatic Convict Cichlid (Amatitlania nigrofasciata)

The Convict Cichlid, Amatitlania nigrofasciata, is a popular model organism for behavioral ecologists to study mate choice, monogamy, and parental care. This freshwater Central American fish displays the rare phenotype of reverse sexual dichromatism, and despite the species’ pervasiveness in behavioral laboratories, the role of female ornamentation in this system is uncertain. To better understand the function of female ornamentation, this study characterizes the visual sensitivity of A. nigrofasciata with particular attention to the long wavelength spectral sensitivity needed to perceive female coloration. We find Convict Cichlids to express a trichromatic complement of opsin proteins: SWS2A, SWS2B, and LWS. After confirming the expression of a LWS opsin gene, we inspected the LWS gene in order to speculate on directional selection potentially resulting in heightened sensitivity to female ornamentation. We examined seven tuning residues in the coding sequence of the LWS opsin gene of A. nigrofasciata and present sequence data that suggest Convict Cichlids have heightened long wavelength sensitivity that is tuned to the female ornament present.
Recontextualising Cellular Respiration in Upper Secondary Biology Education. Characteristics and Practicability of a Learning and Teaching Strategy

Since concepts may have different meanings in different contexts, students have to learn to recontextualise them, i.e. to adapt their meanings to a new context. It is unclear, however, what characteristics a learning and teaching strategy for recontextualising should have. The study aims to develop such a learning and teaching strategy for cellular respiration. The strategy consists of a storyline, consisting of three contexts, with embedded cognitive elements and some episodes focussed on recontextualising cellular respiration. Testing the strategy in two classes in upper secondary biology education showed that the strategy was largely practicable.
Using DNA taxonomy to investigate the ecological determinants of plankton diversity: explaining the occurrence of Synchaeta spp. (Rotifera, Monogononta) in mountain lakes

Summary 1. The occurrence of unresolved complexes of cryptic species may hinder the identification of the main ecological drivers of biodiversity when different cryptic taxa have different ecological requirements. 2. We assessed factors influencing the occurrence of Synchaeta species (monogonont rotifers) in 17 waterbodies of the Trentino-South Tyrol region in the Eastern Alps. To do so, we compared the results of using unresolved complexes of cryptic species, as is common practice in limnological studies based on morphological taxonomy, and having resolved cryptic complexes, made possible by DNA taxonomy. 3. To identify cryptic species, we used the generalised mixed Yule coalescent (GMYC) model. We investigated the relationship between the environment and the occurrence of Synchaeta spp. by multivariate ordination using two definitions of the units of diversity, namely (i) unresolved species complexes (morphospecies) and (ii) putative cryptic species (GMYC entities). Our expectation was that resolving complexes of cryptic species could provide more information than using morphospecies. 4. As expected, DNA taxonomy provided greater taxonomic resolution than morphological taxonomy. Further, environmental-based multivariate ordination on cryptic species explained a significantly higher proportion of variance than that based on morphospecies. Occurrence of GMYC entities was related to total phosphorus (TP), whereas no relationship could be found between morphospecies and the environment. Moreover, different cryptic species within the same morphospecies showed different, and even opposite, preferences for TP. In addition, the wide geographical distribution of haplotypes and cryptic species indicated the absence of barriers to dispersal in Synchaeta.
CEGAR for Computing High-Level Counterexamples for Probabilistic Systems

In this thesis we present a technique to compute high-level counterexamples for probabilistic systems as described in [Wimmer et al., 2013]. High-level counterexamples operate on the description of probabilistic automata in a guarded command language inspired by the input language of the probabilistic model checker PRISM [Kwiatkowska et al., 2011]. While minimal high-level counterexamples provide valuable feedback for debugging a probabilistic model, their computation is computationally hard. Hence, we aim at deriving such counterexamples on an abstraction of the model. Following the ideas of [Wachter et al., 2007], we show how to apply the well-known paradigm of counterexample guided abstraction refinement to probabilistic systems in a way that enables us to derive a high-level counterexample for the concrete model on a potentially coarse abstraction without having to build an explicit representation of the full system. We show the correctness of the approach and present experimental results showing the possible speed-up obtained in practice.
Integrating multiple species connectivity and habitat quality into conservation planning for coral reefs

Incorporating connectivity into the design of marine protected areas (MPAs) has met with conceptual, theoretical, and practical challenges, which include: 1) the need to consider connectivity for multiple species with different dispersal abilities, and 2) the role played by variable habitat quality in determining the spatial patterns of connectivity. We propose an innovative approach, combining biophysical modeling with a routinely-used tool for marine-reserve design (Marxan), to address both challenges by using ecologically-informed connectivity parameters. We showed how functional demographic connectivity for four candidate reef-associated species with varying dispersal abilities and a suite of connectivity metrics weighted by habitat quality can be used to set conservation objectives and inform MPA placement. Overall, the strength of dispersal barriers varied across modeled species and, also across species, we found a lack of spatial concordance of reefs that were high-quality sources, self-persistent, and stepping-stones. Including spatially-heterogeneous habitat quality made a considerable difference to connectivity patterns, significantly reducing the potential reproductive output from many reefs. We also found that caution is needed in combining connectivity data from modeled species into multi-species matrices, which do not perform reliably as surrogates for all connectivity metrics of individual species. We then showed that restricting the habitat available for conservation has an inequitable impact on different connectivity objectives and species, with greatest impact on betweenness centrality and long-distance dispersers. We used Brazilian coral reefs as a case study but our approach is applicable to both marine and terrestrial conservation planning, and offers a holistic way to design functionally-connected reserves to tackle the complex issues relevant to planning for persistence.
Additive main effects and multiplicative interaction analysis of European linseed Linum Ustatissimum L cultivars under South African conditions

Flax (Linum ustatissimum L.) is a multipurpose crop cultivated for both the fibre in the stem (fibre flax) or for its oil pressed from the seed (linseed). The natural qualities of flax make it a desirable commodity for manufacturers seeking alternative solutions to chemical and plastic-based products. As there is no production of flax in South Africa, ten linseed cultivars were imported from the Netherlands and the United Kingdom and evaluated for their adaptability under South African conditions. These cultivars were planted during the 2005 to 2009 season at six different localities (environments) in the Western Cape Province under rain fed conditions. The localities were, Bredasdorp, Caledon, Elsenburg, Koringberg, Langgewens and Napier. The Additive Main Effects and Multiplicative Interaction (AMMI) statistical method as well as the PCA (Principal Component Analysis) model were used to describe cultivar environment interaction on grain yield. Results indicated that the cultivars Sunrise, Capricorn, Bilstar, Virgo and Taurus were the most adapted cultivars for high potential environments.
Development of the thyroid gland: lessons from congenitally hypothyroid mice and men

Congenital hypothyroidism is the most common congenital endocrine disorder (one newborn in 3000) and represents the most common cause of preventable mental retardation. In 10–20% of cases, it is due to autosomal recessive functional disorders leading to goiter formation (thyroid dyshormonogenesis). In the remainder, it is due to thyroid dysgenesis, which comprises usually isolated defects in: (1) migration of the median thyroid anlage, leading to a round cluster of ectopic cells (usually in a sublingual position) with no other thyroid tissue present; (2) differentiation or survival of the thyroid follicular cells leading to athyreosis; and (3) growth of a thyroid with the normal bilobed shape and in the normal cervical position (orthotopic hypoplasia). Mouse knock‐outs have demonstrated that thyroid transcription factor‐1 (TTF‐1) and PAX8 are required for the survival and proliferation of thyroid follicular cell precursors, TTF‐2 for their downward migration and the thyrotropin receptor (TSHR) for post‐natal thyroid growth. In humans, thyroid dysgenesis is generally a sporadic malformation but an affected relative is found in 2% of cases, a figure 15‐fold higher than by chance alone. Pedigree analysis is most compatible with dominant inheritance with variable penetrance. However, mutations in TTF‐1, TTF‐2, PAX8 and TSHR are found in <10% of patients with congenital hypothyroidism and these predominantly have orthotopic thyroid hypoplasia, often associated with other malformations. This low yield and the discordance of >90% of monozygotic twin pairs suggests that isolated thyroid ectopy or athyreosis most often results from early somatic mutations, epigenetic modifications or stochastic developmental events.
Spatial, seasonal and individual variation in the diet of White-tailed Eagles Haliaeetus albicilla assessed using stable isotope ratios

Many raptor species are considered to be generalists, taking a range of prey species. However, longitudinal dietary records are often scarce, although necessary for characterizing niche width of species at population and individual levels. Quantifying raptor diets at large spatio-temporal scales is often necessary for refining conservation efforts, although it can be particularly difficult and may involve a great effort by conventional means. Therefore, we adopted the analysis of stable isotopes in tissues of predators and their potential food sources as a complementary methodology for assessing animals’ diet. We examined the isotopic composition (d 13 C and d 15 N) of White-tailed Eagles Haliaeetus albicilla from Germany, Finland and Greenland to detect patterns of dietary variation and quantify diet composition. The isotopic analysis included liver and muscle samples from Eagles of the three populations together with 16 potential food sources in the German population. Our results suggested dietary differences between German and Greenlandic Eagles, in accordance with the availability of freshwater and marine habitats in each population. Within the German population, we found seasonal shifts in isotopic ratios, suggesting the birds responded to temporal changes in food availabilities, and agerelated isotopic differences, indicating different diets in adults and juveniles. Isotopic values of liver and muscle tissues collected from the same animal showed intra-individual short-term changes in the German and Finnish but not Greenlandic population. This suggests that local feeding niches of this generalist predator may vary with local food supplies, which determines the niche width (from generalist to specialist) at the individual level. Our results also revealed that game mammal carcasses constitute an important food source (29.5% of diet) for the German Eagle population during the winter half-year corresponding to the hunting season. This result is of relevance to management and conservation because the White-tailed Eagle and other raptor species are affected by the ingestion of lead ammunition from shot mammalian carcasses.
Can we explain regional abundance and road‐kill patterns with variables derived from local‐scale road‐kill models? Evaluating transferability with the European polecat

Aim We evaluated the transferability of variables previously found to have a significant effect on European polecat Mustela putorius road‐kills at a local scale (i.e. 50 m around location points) when we extrapolate them to a large scale [Universal Transverse Mercator (UTM) 100 km2] in a neighbouring area.
Isolation of high molecular weight DNA and double-stranded RNAs from fungi.

An efficient method for the extraction of DNA and RNA from fungi is described. Urediosporelings and sporidia of two basidiomycete species and mycellia from several species of Ascomycetes and Oomycetes were homogenized in a lysis buffer containing sodium dodecyl sulfate followed by cetyltrimethylammonium bromide extraction of carbohydrates in 1.4 M NaCl, leaving nucleic acids in the supernatant. After chloroform – isoamyl alcohol extraction of proteins, nucleic acids were precipitated with ethanol. Total nucleic acids prepared in this way contained nuclear, ribosomal, and mitochondrial DNA as well as double-stranded and single-stranded RNA. DNA was eluted from agarose gels and digested with endonucleases, labelled by nick translation, and used for hybridization without nonspecific background signal. A method is also described for RNase digestion of single-stranded and double-stranded RNA in agarose gels. Key words: DNA extraction, double-stranded RNA, cetyltrimethylammonium bromide, sodium dodecyl sulfate.
A significant range extension and sanctuary for the rare Open Bay Island skink (Oligosoma taumakae)

Abstract The Open Bay Island skink (Oligosoma taumakae) is one of New Zealand's rarest lizard species. Until 2010, it was known only from two small islands in the Open Bay Island Group, a Māori-owned wildlife sanctuary in South Westland, New Zealand. Skinks on these islands are threatened by predation from weka (Gallirallus australis), a flightless native rail thought to have been introduced to the Open Bay Islands c. 100 years ago. Here, we describe the discovery of Open Bay Island skinks on two vegetated rock stacks located off the coast of Barn Bay, 52 km southwest of the Open Bay Islands. Although small (c. 0.10 and 0.36 ha), the Barn Islands appear to be predator-free, providing an important sanctuary for the skinks. We recommend: (1) a survey of mainland sites with suitable habitat; and (2) an evaluation of the need for island biosecurity measures for detecting and responding to incursions of small mammals.
Cell Sorting and Chondrogenic Aggregate Formation in Limb Bud Recombinants and in Culture

The cartilage pattern of the developing chick limb changes along the proximal‐distal (PD) axis. It is assumed that these spatial changes are brought about by differences in the cellular properties of distal mesoderm, the progress zone (PZ). To examine whether these differences are actually maintained in the individual cells composing the PZ, we dissociated early (stage 20) and late (stage 25) PZ tissues into single cells, then mixed and recombined them with ectodermal jackets. The recombinants were grafted to limb bud stumps and allowed to develop into limb‐like structures. Early PZ cells were distributed within whole cartilage elements along the PD axis of the limb‐like structures, while cells from late PZ participated only in the formation of distal cartilage elements.