Miracle-dz/UniFAR-FTUs huggingface dataset:
Non‐climatic variations in the oxygen isotopic compositions of plants

The 18O content of leaf water strongly influences the 18O contents of atmospheric CO2 and O2. The 18O signatures of these atmospheric gases, in turn, emerge as important indicators of large‐scale gas exchange processes. Better understanding of the factors that influence the isotopic composition of leaf water is still required, however, for the quantitative utilization of these tracers. The 18O enrichment of leaf water relative to local meteoric water, is known to reflect climatic conditions. Less is known about the extent variations in the 18O content of leaf water are influenced by nonclimatic, species‐specific characteristics. In a collection of 90 plant species from all continents grown under the same climatic conditions in the Jerusalem Botanical Garden we observed variations of about 9‰ in the δ18O values of stem water, δs, and of about 14‰ in the mid‐day δ18O enrichment of bulk leaf water, δLW–δs. Differences between δ18O values predicted by a conventional evaporation model, δM, and δLW ranged between – 3.3‰ and + 11.8‰. The δ18O values of water in the chloroplasts (δch) in leaves of 10 selected plants were estimated from on‐line CO2 discrimination measurements. Although much uncertainty is still involved in these estimates, the results indicated that δch can significantly deviate from δM in species with high leaf peclet number. The δ18O values of bulk leaf water significantly correlated with δ18O values of leaf cellulose (directly) and with instantaneous water use efficiency (A/E, inversely). Differences in isotopic characteristics among conventionally defined vegetation types were not significant, except for conifers that significantly differed from shrubs in δ18O and δ13C values of cellulose and in their peclet numbers, and from deciduous woodland species in their δ18O and δ13C values of cellulose. The results indicated that predictions of the δ18O values of leaf water (δLW, δM and δch) could be improved by considering plant species‐specific characteristics.
Redescription and three-dimensional reconstruction of the limnic acochlidian gastropod Strubellia paradoxa (Strubell, 1892) (Gastropoda: Euthyneura) from Ambon, Indonesia

This study is the first to examine the entire microanatomy of a representative of the limnic family Acochlidiidae s.l. , belonging to the otherwise marine mesopsammic Acochlidia. A paratype of Strubellia paradoxa (Strubell, 1892) was reconstructed three-dimensionally from serial semi-thin sections using the software Amira; additional material recently collected close to the type locality on Ambon Island, Indonesia was examined by scanning electron microscopy. Results are critically compared with the original description by Küthe of 1935. The genital system of S. paradoxa is monaulic, with two allosperm receptacles in the male phase, suggesting that the species is a sequential, protandric hermaphrodite rather than gonochoric; an open seminal groove connects to a complex cephalic copulatory apparatus. The two-chambered heart with conspicuous epicardium, the elongated kidney and the looped nephroduct are interpreted as possible adaptations to the freshwater habitat. Differences from S. “paradoxa” sensu Wawra 1974 and 1988 from the Solomon Islands are discussed.
A Bioenergetics Simulation of the Potential Effects of Angler Harvest on Growth of Largemouth Bass in a Catch-and-Release Fishery

Abstract Catch-and-release regulations in warmwater fisheries have the potential to limit growth and reduce the average size of harvestable fish as a result of density-dependent interactions. We assessed the effect of angler harvest on growth of largemouth bass Micropterus salmoides in Stonewall Jackson Lake where fishing for black bass Micropterus spp. was regulated with a no-harvest restriction. Using bioenergetic simulations, we estimated the amount of prey that would be made available for growth of remaining fish at harvest rates of 28.4 and 56.8% of the population. Simulation results indicated that consumption by age- 1 through age-6 largemouth bass in Stonewall Jackson Lake was 41 metric tons of forage in 1990. Juvenile largemouth bass (ages 1–3) consumed 57% of the forage eaten. Except for brief time periods for age-4 fish, foraging success for all age-classes of harvestable largemouth bass was relatively low; consumption rates were below 50% of maximum potential. Modeling showed that increasing fi.
Estimating the zone of influence of industrial developments on wildlife: a migratory caribou Rangifer tarandus groenlandicus and diamond mine case study

Wildlife species may respond to industrial development with changes in distribution. However, discerning a response to development from differences in habitat selection is challenging. Since the early 1990s, migratory tundra Bathurst caribou Rangifer tarandus groenlandicus in the Canadian Arctic have been exposed to the construction and operation of two adjacent open-pit mines within the herd's summer range. We developed a statistical approach to directly estimate the zone of influence (area of reduced caribou occupancy) of the mines during mid-July-mid-October. We used caribou presence recorded during aerial surveys and locations of satellite-collared cow caribou as inputs to a model to account for patterns in habitat selection as well as mine activities. We then constrained the zone of influence curve to asymptote, such that the average distance from the mine complex where caribou habitat selection was not affected by the mine could be estimated. During the operation period for the two open-pit mines, we detected a 14-km zone of influence from the aerial survey data, and a weaker 11-km zone from the satellite-collar locations. Caribou were about four times more likely to select habitat at distances greater than the zone of influence compared to the two-mine complex, with a gradation of increasing selection up to the estimated zone of influence. Caribou are responding to industrial developments at greater distances than shown in other areas, possibly related to fine dust deposition from mine activities in open, tundra habitats. The methodology we developed provides a standardized approach to estimate the spatial impact of stressors on caribou or other wildlife species.
Bacterial Iron Oxidation in Circumneutral Freshwater Habitats: Findings from the Field and the Laboratory

Lithotrophic Fe-oxidation at neutral pH is becoming recognized as an important microbial process. An overview of the microbial iron cycle is presented with an emphasis on the role of microbes that grow under microaerobic conditions at oxic-anoxic transition zones where Fe(II) is abundant. Examples of these environments from freshwater are considered. Contrary Creek is a spring-fed wetland in Virginia. Measurements over the course of a year showed that it had a consistent pH around 6, and Fe(II) concentrations ranged from 25 to 300 μ M, with the highest concentrations in the summer months. At all times abundant flocs of Fe-oxides composed principally of Lepthothrix ochracea sheaths were present. Based on observations at this site, and other sites, a model for microbial Fe mat formation is presented. A thermal site in Yellowstone National Park that had consistent circumneutral pH and high Fe(II) concentrations was also studied. This site did not have evidence for Fe-oxidizing bacteria, but was, instead, dominated by a cyanobacterial photosynthetic mat. Consideration is given to growth conditions for pure cultures of Fe-oxidizing bacteria (FeOB) in the laboratory. A novel method of growing FeOB on gradient plates was developed. This led to an increase of cell yields to 2 × 108 cells/ml, which is nearly an order of magnitude greater than previous methods have yielded. Finally, speculation is made as to the potential for conditions on Mars that might have been conducive for microbial Fe-oxidation.
Rodent population and community responses to forest‐based biofuel production

Intensively managed forests in the southeastern United States are a potential source of cellulosic bioenergy and, as conversion technologies improve and demand increases, a greater land area may be required to produce biofuel feedstocks. However, responses of wildlife to forest-based biofuel production are largely unknown. We examined the 4-year response of rodent populations and assemblages to a range of biofuel production regimes, including harvesting residual woody debris and intercropping switchgrass (Panicum virgatum), in an intensively managed loblolly pine (Pinus taeda) forest in eastern North Carolina, USA. We investigated abundance, demography, and community response of rodents in a randomized and replicated field experiment using mark-recapture techniques during 2009–2012. Whereas removal of downed woody biomass did not affect abundance, diversity, or demography of rodents, we detected species-specific effects of incorporating switchgrass. After switchgrass was well established, invasive house mice (Mus musculus) were most abundant in plots with switchgrass. In contrast, white-footed mice (Peromyscus leucopus) were commonly captured in plots without switchgrass and other rodents were not affected by biofuel treatments. Across the study, natural succession exerted greater effects on rodent species and the rodent community than biofuel production regimes. As remaining logs and stumps decay and become limiting, downed wood may become more important to rodents. Our results indicate that intercropping switchgrass and harvesting residual woody material had limited effects on rodents in the Coastal Plain of North Carolina, USA within 4 years of stand establishment.
Bacterial Indigo Reduction

We have examined bacterial indigo reduction to provide a basis for the development of a sustainable alternative to the present chemical methods used to reduce indigo for denim dyeing. Indigo was reduced by Clostridium isatidis, but not by the related Clostridium aurantibutyricum, Clostridium celatum nor Clostridium papyrosolvens. However C. papyrosolvens could, like C. isatidis, reduce the soluble dye, indigo carmine. Of the bacteria examined only the supernatant from C. isatidis cultures decreased indigo particle size. An anthraquinone-rich madder root extract, the soluble anthraquinone-2,6-disulfonic acid and humic acid all stimulated the reduction of indigo by C. isatidis, without affecting the redox potential of the cultures. C. isatidis cultures generated redox potentials from −476 to −602 mV vs SCE, which were about 100 mV more negative than those of the other bacteria examined. The mechanism of bacterial indigo reduction remains unknown, but the unique features of the indigo-reducing C. isatidis indicate possible mechanisms.
Morfologia e aspectos hidrológicos da bacia hidrográfica do rio Preto, divisa dos estados do Rio de Janeiro e de Minas Gerais

Neste trabalho, determinaram-se as caracteristicas morfometricas do relevo e da rede de drenagem da Bacia Hidrografica do Rio Preto, com a finalidade de prever do comportamento hidrologico da area. A partir da delimitacao da area da bacia, da digitalizacao das curvas de nivel e do sistema de drenagem, foram obtidas caracteristicas geometricas do relevo e da hidrografia da BHRP e das suas seis sub-bacias. Concluiu-se que a area apresentava forma alongada e estreita, aliada a uma alta densidade de drenagem, evidenciando menor possibilidade de ocorrencia de cheias. Porem, foram observadas enchentes justificadas pelos solos rasos, pelos intensos processos de desmatamento e uso da terra e pelo relevo acidentado, sendo 73,1% da area caracterizada como de relevo forte-ondulado a montanhoso. Quanto as sub-bacias, verificou-se que em todas essas unidades menos de 28% da area era compreendida de relevo plano, facilitando a erosao hidrica.
The size relationship between insects and their hosts

Abstract. 1 Regressions of adult insect size on host size were tested. The analysis was restricted to highly host‐specific insects that had thus been exposed to a narrow range of host size. 2 The phylogenetic regression method was used to analyse the data, so as to allow for the possible phylogenetic effects in cross‐species data. 3 Significant positive regressions were found in all the groups tested: female flower thrips, Meligethes species of pollen beetle, tephritid flies, and male and female fleas. They were also found by standard regressions within. and between Actornithophilus species of bird louse. 4 The regression of thrips size on pollen size was not significant, providing evidence against a hypothesis involving food size. 5 The regression of flea body size on host hair/feather length was significant, which is consistent with a hypothesis involving the size of spaces on the host. 6 The relationships may have implications for the understanding of evolutionary host shifts.
PRELIMINARY OBSERVATIONS ON THE ULTRASTRUCTURE OF MATURING CORK-CELLS FROM TUBERS OF SOLANUM TUBEROSUM L.

Summary The normal cork of young tubers of Solanum tuberosum L. cv. ‘King Edward’ was used as a source of maturing cork-cells. The cells are periclinally flattened and highly vacuolated. Electron-micrographs reveal that the cytoplasm, although sparse, is rich in mitochondria, ribosomes and membrane-bound vesicles. Electron-opaque crystals and endoplasmic reticulura are also present, but neither the plasmalemma, nor the tonoplast, are visible. Microtubules are seen at the interface between the cell wall and the cytoplasm. The layered appearance of the cell wall is compatible with the observations of other workers. No pits are visible but there is evidence that plasmadesmata were present earlier in the ontogeny of the cell. The significance of these observations is discussed in the light of existing information on cork-cell differentiation.
Indicator variables for a robust estimation of an acoustic index of abundance

In North West Africa, pelagic fisheries are an essential economic sector. However, the scientific community fails to perform satisfactory assessments of key pelagic species like sardinella, owing to a lack of relevant indices of abundance to tune the model. This paper provides an alternative acoustic index based on a semiquantitative modelisation of acoustic densities. Acoustic energy is split into binomial variables coding for null, low, medium, large, and very large densities. A multivariate geostatistical approach allows (i) mapping the spatial distribution of classes of densities and (ii) computing a new acoustic index of abundance for Sardinella aurita and Sardinella maderensis. We used the surveys of RV Fridtjof Nansen (1995–2006) and RV Al-Awam (2007–2010). Our results indicated that empirical spatial structures were highly stable over time for both between areas and surveys. Co-kriging maps also showed that sardinella had stable hot spots of distribution. The indices of abundance developed in the .
The ND1 gene of complex I is a mutational hot spot for Leber's hereditary optic neuropathy

A novel mitochondrial DNA (mtDNA) transition (3733G→A) inducing the E143 K amino acid change at a very conserved site of the NADH dehydrogenase subunit 1 (ND1) was identified in a family with six maternally related individuals with Leber's hereditary optic neuropathy (LHON) and in an unrelated sporadic case, all negative for known mutations and presenting with the canonical phenotype. The transition was not detected in 1,082 control mtDNAs and was heteroplasmic in several individuals from both pedigrees. In addition, the mtDNAs of the two families were found to belong to different haplogroups (H and X), thus confirming that the 3733G→A mutation occurred twice independently. Phosphorus magnetic resonance spectroscopy disclosed an in vivo brain and skeletal muscle energy metabolism deficit in the four examined patients. Muscle biopsy from two patients showed slight mitochondrial proliferation with abnormal mitochondria. Biochemical investigations in platelets showed partially insensitive complex I to rotenone inhibition. We conclude that the 3733G→A transition is a novel cause of LHON and, after those at positions 3460 and 4171, is the third ND1 mutation to be identified in multiple unrelated families. This finding shows that, in addition to ND6, the ND1 subunit gene is also a mutational hot spot for LHON. Ann Neurol 2004;56:631–641
Phytoplankton Ecology of the Strait of Georgia, British Columbia

Observations of phytoplankton production, abundance, and distribution were made at 16 stations in the Strait of Georgia from 1975 to 1977. The discharge of turbid Fraser River water exerts a strong influence on phytoplankton production and distribution in surface waters by rapid light attenuation and horizontal advection. At plume boundaries and back eddies where light conditions improve, very high production occurs (> 4–5 g C∙m−2∙d−1), because of rapidly replenished nutrients supplied by the Fraser River. Advection, turbulence, zooplankton grazing, and summer nitrate depletion collectively impart a heterogeneous distribution pattern to phytoplankton in the surface waters of the Strait of Georgia. Mean annual production varies from lows of 150 g C∙m−2 in Fraser River plume to highs of over 500 g C∙m−2 in sheltered boundary waters of inlets. Recent increases in ammonia and nitrate from land drainage and domestic sewage, mainly through the Fraser River, are related to increases in phytoplankton standing sto.
Distribution patterns and taxonomy of some legume-feeding psyllids (Hemiptera: Psylloidea) and their hosts from the Iberian Peninsula, Morocco and Macaronesia

Distribution patterns between continental and continental-island sister taxa are compared for some legume-feeding psyllids (Arytaininae, Psylloidea) and their host plants (Genisteae, Leguminosae). The host plant genera Adenocarpus, Chamaecytisus, Retama and Teline are characterized by distribution disjunctions, which sometimes match the disjunctions in the associated psyllids. Sister taxa pairs of Retama- and Teline-feeding psyllids from the continent and Macaronesian islands exhibit a similar geographic disjunction as their host plants, but this pattern is not found in Adenocarpus- or Chamaecytisus-feeding psyllids and their hosts. In addition, three closely related continental psyllids reflect the distribution of their Adenocarpus hosts in the montane regions of Morocco and Andalusia, but are not related to other Adenocarpus-feeding species. These examples suggest that among the Genisteae-feeding psyllids, shared distribution patterns with their hosts are localized rather than characteristic of the group as a whole. Six new species of psyllid, which feed on legume shrubs in the Genisteae, and are endemic to the Iberian Peninsula and Morocco, are described and illustrated. These species are in two taxonomically complex arytainine genera, Arytainilla and Livilla. Immature stages provide additional morphological characters useful for resolving taxonomic relationships within the Arytaininae, and the 5th instar nymphs of several species are described and illustrated. Genistoid-feeding psyllids are not known from all genera in the Genisteae but this may be due to incomplete sampling of rarer genistoid legumes. The majority of psyllids newly described here are narrow range endemics in either Andalusia or Morocco; one species occurs in both Andalusia and Morocco, and one species is more widespread in the Iberian Peninsula.
Integration of soil solarization with Brassica carinata seed meals amendment in a greenhouse lettuce production system

Abstract The use of integrated pest management is a valid alternative to conventional chemical treatments. This study was carried out to evaluate the effects of Brassica carinata seed meals amendment, combined with solarization, on soil activity and lettuce cultivation. B. carinata seed meals pellets are biofumigant plant tissues originated as byproducts of the biodiesel industry. Microbiological data combined with lettuce production results suggest that, after biofumigation, soil microbial communities change toward a new equilibrium that creates better root plant conditions to improve high lettuce yields. Moreover, Brassica seed meals, combined with solarization, preserved soil microflora against detrimental effects of heating, as revealed by enzymatic and functional analysis.
Environmental Sensitivity of Fish Otolith Microchemistry

A considerable aggregate of life-history, environmental and physiological information is incorporated within fish otoliths. This information may be discerned when appropriate analytical methods, based on an understanding of the mechanisms underlying changes in the structure and chemistry of otoliths, are utilized. Deposition of otolith carbonate may be regulated by many interacting factors, including age, physiology, environmental stress, availability of nourishment, ambient temperature, diurnal and seasonal cycles, and activity levels of individual fish. Complex interactions between genomic control and environmental conditions will ultimately govern depositional patterns. The chemical composition of otoliths is regulated by the physiological activity of fish, which in turn is influenced by environmental conditions. Interpretation of the chemical patterns in wild fishes must be validated by analysing the depositional patterns in fishes maintained under experimental conditions. Microchemistry analyses can provide life-history profiles and data on the environmental history of individual fish to clarify interpretation of age and growth trajectories. Several factors may contribute to the reported disparity in elemental studies, including suboptimal rearing environments, thermal effects on growth rate, and nutritional effects on otolith chemistry. Metabolic data describing growth and otolith crystallization obtained under artificial conditions that only grossly resemble the subtleties of the modelled environment may have a limited value and caution should be used when extrapolating results to natural systems.
Hybrid control for performance improvement of linear systems

In this introductory chapter, the research of this thesis is motivated. In particular, a different perspective on high performance control of linear (motion) systems is proposed by exploiting hybrid controllers instead of linear controllers. To motivate this paradigm shift towards hybrid control, linear control of linear (motion) systems together with its advantages and disadvantages will be (briefly) discussed in Section 1.1. In Section 1.2, the use of hybrid control for linear (motion) systems will be discussed along with the potential advantages that hybrid control can offer compared to linear control. The objectives and contributions of this thesis are presented in Section 1.3, followed by the outline of this thesis in Section 1.4. 1.1 Linear control of linear motion systems High-tech mechatronic systems, such as wafer scanners, printers, pick-and-place machines, electron microscopes, etc., have to perform their (motion) tasks with increasingly high performance demands on precision, throughput, etc., thereby requiring the utmost of the current mechatronic designs. In order to meet these stringent performance requirements, feedback/feedforward controllers are essential in any of these high-tech applications. To allow for a good interaction with feedback/feedforward controllers, the (mechanical) design of these systems is highly optimized such that their dynamic behavior can be regarded as approximately linear. Hence, in the scope of such applications linear (motion) systems form an important class of (motion) systems, which motivates the focus on this type of systems in this thesis. The vast majority of linear (motion) systems are being controlled by linear proportional-integral-derivative (PID) type controllers, which are based on the present (P), past (I) and future (D) control error, see, e.g., Astrom and Hagglund (2001), and can easily be designed using data-based frequency-domain 2 Chapter