Nanofabrication of Gate-defined GaAs/AlGaAs Lateral Quantum Dots

A quantum computer is a computer composed of quantum bits (qubits) that takes advantage of quantum effects, such as superposition of states and entanglement, to solve certain problems exponentially faster than with the best known algorithms on a classical computer. Gate-defined lateral quantum dots on GaAs/AlGaAs are one of many avenues explored for the implementation of a qubit. When properly fabricated, such a device is able to trap a small number of electrons in a certain region of space. The spin states of these electrons can then be used to implement the logical 0 and 1 of the quantum bit. Given the nanometer scale of these quantum dots, cleanroom facilities offering specialized equipment- such as scanning electron microscopes and e-beam evaporators- are required for their fabrication. Great care must be taken throughout the fabrication process to maintain cleanliness of the sample surface and to avoid damaging the fragile gates of the structure. This paper presents the detailed fabrication protocol of gate-defined lateral quantum dots from the wafer to a working device. Characterization methods and representative results are also briefly discussed. Although this paper concentrates on double quantum dots, the fabrication process remains the same for single or triple dots or even arrays of quantum dots. Moreover, the protocol can be adapted to fabricate lateral quantum dots on other substrates, such as Si/SiGe.     

Review: Assessing fish welfare in research and aquaculture,with a focus on European directives

The number of farmed fish in the world has increased considerably. Aquaculture is a growing industry that will in the future provide a large portion of fishery products. Moreover, in recent years, the number of teleost fish used as animal models for scientific research in both biomedical and ecological fields has increased. Therefore, it is increasingly important to implement measures designed to enhance the welfare of these animals. Currently, a number of European rules exist as requirements for the establishment, care and accommodation of fish maintained for human purposes. As far as (teleost) fish are concerned, the fact that the number of extant species is much greater than that of all other vertebrates must be considered. Of further importance is that each species has its own specific physical and chemical requirements. These factors make it difficult to provide generalized recommendations or requirements for all fish species. An adequate knowledge is required of the physiology and ecology of each species bred. This paper integrates and discusses, in a single synthesis, the current issues related to fish welfare, considering that teleosts are target species for both aquaculture and experimental models in biological and biomedical research. We first focus on the practical aspects, which must be considered when assessing fish welfare in both research and aquaculture contexts. Next, we address husbandry and the care of fish housed in research laboratories and aquaculture facilities in relation to their physiological and behavioural requirements, as well as in reference to the suggestions provided by European regulations. Finally, to evaluate precisely which parameters described by Directive 2010/63/EU are reported in scientific papers, we analysed 82 articles published by European researchers in 2014 and 2015. This review found that there is a general lack of information related to the optimal environmental conditions that should be provided for the range of species covered by this directive.     

THE ASSESSMENT OF COMPETITION BETWEEN SEALS AND COMMERCIAL FISHERIES IN THE NORTH SEA AND THE ANTARCTIC1

Most of the exploited fish stocks in the North Sea are also used as a food supply by a number of seal species; the same is true for some fish and invertebrate stocks in the Antarctic—although the fisheries there are, at present, much smaller than those in the North Sea. The information needed for a critical assessment of such interactions is reviewed. Using existing techniques it is possible to estimate the quantity and size-classes of each fish or invertebrate species consumed by seals and to compare this with the commercial catch. If fishing mortality is known, these estimates can be used to calculate the level of mortality imposed by the seals. However, a realistic evaluation requires information on the distribution and movements of the fish, the seals' feeding effort, and the fisheries effort in time and space. At present it is difficult or impossible to obtain this information, but recent technological developments in telemetry equipment will soon make it feasible. To assess the economic effects of changes in seal numbers on the fishery, or the ecological effects of changes in fisheries effort on seal populations, requires additional information on the responses of the fishery and the seals to changes in fish abundance, and of the commercial market to changes in the supply of fish.     

Effect of position-fixing interval on estimated swimming speed and movement pattern of fish tracked with a stationary positioning system

Ultrasonic telemetry using stationary positioning systems allows several fish to be tracked simultaneously, but systems that are incapable of sampling multiple frequencies simultaneously can record data from only one transmitter (individual) at a time. Tracking several individuals simultaneously thus results in longer intervals between successive position fixes for each fish. This deficiency leads to loss of detail in the tracking data collected, and may be expected to cause loss of accuracy in estimates of the swimming speeds and movement patterns of the fish tracked. Even systems that track fish on multiple frequencies are not capable of continuous tracking due to technical issues. We determined the swimming speed, area occupied, activity rhythm and movement pattern of cod (Gadus morhua) using a stationary single-channel positioning system, and analysed how estimates of these behavioural parameters were affected by the interval between successive position fixes. Single fish were tracked at a time, and position fixes were eliminated at regular intervals in the original data to generate new data sets, as if they had been collected in the course of tracking several fish (2–16). In comparison with the complete set, these data sets gave 30–70% decreases in estimates of swimming speed depending on the number of fish supposedly being tracked. These results were similar for two individuals of different size and activity level, indicating that they can be employed as correction factors to partly compensate for underestimates of swimming speed when several fish are tracked simultaneously. Tracking `several' fish only slightly affected the estimates of area occupied (1–15%). The diurnal activity rhythm was also similar between the data sets, whereas details in search pattern were not seen when several fish were tracked simultaneously.     

Measuring Complex Behavior Patterns in Fish—Effects of Endocrine Disruptors on the Guppy Reproductive Behavior

An obstacle in behavioral research is in obtaining unbiased measurements and presenting them in numerical terms, independent of human interpretation and observational endurance. Simple locomotory behavior can be relatively easily quantified with existing computerized vision systems, whereas it is much more difficult to obtain unbiased measurements of complex behavior patterns. We have developed a computerized vision system (DISPLAY), which identifies and quantifies complex behavior patterns and interactions in fish. In short, the fish scenery is viewed from above by a camera. At a frame-rate of 12 s^{? 1}, the fish silhouettes are stored in a frame file. Subsequently, the position and orientation of each fish relative to the other(s), the distance between them, and their body curvature are determined in each frame. Further, frame-to-frame comparisons enable calculation of speed and direction of fish movements. With these measurements available, composite behavior patterns can now be entered graphically by the user as distinct classifiers. The system has been used for studying the effects of endocrine disruptors on the reproductive behavior of the male guppy (Poecilia reticulata). Both estrogenic and antiandrogenic substances significantly suppress the number and duration of posturing behavior and sigmoid displays, two distinct elements in the courtship behavior of the male guppy.     

Bands against stripes on the backs of mackerel,Scomber scombrus L.

A thin band of reflecting platelets overlies the central parts of the light and dark stripes found on each side of the dorsal surfaces of the body of the mackerel (Scomber scombrus L.). When this fish has its antero-posterior axis horizontal and its mid-dorsal and mid-ventral lines in the same vertical plane, V, the surfaces of the reflecting platelets in these bands are within a few degrees of being vertical. These surfaces are, however, tipped about 17 degrees from plane V towards the tail. In the angular distributions of radiance commonly found in the sea, the reflections from these bands can mask parts of the pattern of light and dark stripes seen by neighbours in ways that depend on the orientation of the fish in the external light field and the position of the fish relative to its neighbours. With this arrangement, when the fish changes its orientation and/or its velocity with respect to neighbouring fish, this is signalled to the neighbours as changes in the patterns of brightness of its dorsal surfaces. Relatively small changes in roll, pitch and yaw can produce large changes in appearance and, as vision is a most important sense in the mackerel, it seems likely that these changes are important for signalling.     

Pain perception, aversion and fear in fish

There is now compelling evidence that teleost fish possess similar nociceptive processing systems to those found in terrestrial vertebrates. Noxious stimulation of these nociceptors--specialised pain receptors -in the skin around the snout of fish generates neural activity that can be electrophysiologically recorded, and induces a number of behavioural and physiological changes. To determine whether changes in behaviour are more than simple responses to the noxious stimulation it is necessary to demonstrate that higher order cognitive processes such as mental state or 'affective state' are involved. However, quantifying the 'motivational affected state' of an animal--a concept encompassing not just pain but also fear, hunger, thirst and pleasure - is difficult owing to its subjectivity. Recent empirical work is beginning to test these concepts in fish, and we review a number of these studies and suggest how these general methodologies could be used to further our understanding of fish cognition and the capacity for fish to experience mental states such as fear or suffering.     

Shoals and schools: back to the heuristic definitions and quantitative references

The terms ??shoal??, ??swarm?? and ??school?? are very frequently used in research on collective behaviours in animals. Pitcher??s definitions are accepted as the authority in the field but are based on a conceptual criterion of sociability. Without call into question the basis of these definitions, they do not provide tools to determine these behaviours quantitatively. To compare studies between populations, species, taxa or different experimental treatments, and between different authors, quantitative references are necessary. Quantitative measurements of collective behaviours can also test and validate the predictive capacity of computer models by comparing real data from nature so that different models can be compared. The first part of this paper succinctly reviews the definitions and meanings of these behaviours, with particular attention paid to quantitative aspects. This review underlines a series of conceptual confusions concerning these behavioural terms observed in the scientific literature and oral scientific communications. The second part reviews the quantitative parameters developed by biologists studying collective fish behaviours, mainly fish shoals, and by theoretical biologists and physicists studying computer modelling of collective behaviours. The parameters reviewed herein make no attempt to explain the mechanisms and causes that create a shoal, a swarm or a school, but rather try to describe these collective behaviours, and to connect local and global properties with individual and collective behaviours. Recent development over the last decade in technology, data processing capacity, cameras, and video tracking tools have provided the opportunity to obtain quantitative measures of collective dynamic behaviours in animals both rapidly and precisely.     

Automated Reconstruction of Three-Dimensional Fish Motion,Forces, and Torques

Fish can move freely through the water column and make complex three-dimensional motions to explore their environment, escape or feed. Nevertheless, the majority of swimming studies is currently limited to two-dimensional analyses. Accurate experimental quantification of changes in body shape, position and orientation (swimming kinematics) in three dimensions is therefore essential to advance biomechanical research of fish swimming. Here, we present a validated method that automatically tracks a swimming fish in three dimensions from multi-camera high-speed video. We use an optimisation procedure to fit a parameterised, morphology-based fish model to each set of video images. This results in a time sequence of position, orientation and body curvature. We post-process this data to derive additional kinematic parameters (e.g. velocities, accelerations) and propose an inverse-dynamics method to compute the resultant forces and torques during swimming. The presented method for quantifying 3D fish motion paves the way for future analyses of swimming biomechanics.     

LPFC: an Internet library of protein family core structures.

As the number of protein molecules with known, high-resolution structures increases, it becomes necessary to organize these structures for rapid retrieval, comparison, and analysis. The Protein Data Bank (PDB) currently contains nearly 5,000 entries and is growing exponentially. Most new structures are similar structurally to ones reported previously and can be grouped into families. As the number of members in each family increases, it becomes possible to summarize, statistically, the commonalities and differences within each family. We reported previously a method for finding the atoms in a family alignment that have low spatial variance and those that have higher spatial variance (i.e., the "core" atoms that have the same relative position in all family members and the "non-core" atoms that do not). The core structures we compute have biological significance and provide an excellent quantitative and visual summary of a multiple structural alignment. In order to extend their utility, we have constructed a library of protein family cores, accessible over the World Wide Web at http:/ /www-smi.stanford.edu/projects/helix/LPFC/. This library is generated automatically with publicly available computer programs requiring only a set of multiple alignments as input. It contains quantitative analysis of the spatial variation of atoms within each protein family, the coordinates of the average core structures derived from the families, and display files (in bitmap and VRML formats). Here, we describe the resource and illustrate its applicability by comparing three multiple alignments of the globin family. These three alignments are found to be similar, but with some significant differences related to the diversity of family members and the specific method used for alignment.     

Species composition,abundance and diversity of Ichthyofauna of Ikere-Gorge,Oyo State,Nigeria

Anthropogenic activities in inland water can cause species loss and displacement. Therefore, there is a need to regularly examine species composition, abundance and diversity of freshwater ecosystem as a means to monitor its health. Ichthyofauna of Ikere-gorge, Iseyin, Oyo State was studied for a period of 24 month, from January 2017 to December 2018. Ikere-gorge was divided into four strata, each comprises three fishing villages. One village in each stratum was randomly selected as sampling site. The catches were sorted into taxonomic groups (species and families) using standard fish identification keys. Forty-one fish species from 13 families were identified in which species richness varied among the sampling villages. Asamu had 34, Agatu had 30, Spillway had 39 and Irawote had 29 species. The freshwater fish species of Nigeria is the richest in West Africa and more than 15% of these fish species are found in Ikere-gorge. Mormyridae family was the most represented with 10 species. Cichlidae was the most abundant by catch and by weight. Sarotherodon galilaeus has the highest abundance by catch and by weight. Gnathonemus brucii was identified as a vulnerable species. The result obtained from this study show that conservation program should be urgently put in place to prevent some fish from extinction. There should be introduction of closed season to allow for proper recruitment of fish population. Likewise, minimum mesh size should be set to allow juvenile and immature fish to escape and allow them to spawn at least once before being vulnerable to gear. There should regulation to set maximum number of fishermen to be allowed to fish at a particular day, this is to reduce fishing pressure.     

Fishes as models in studies of sexual selection and parental care

Fishes are by far the most diverse group of vertebrates. This fact is in no way, however, reflected in their use as model organisms for understanding sexual selection or parental care. Why is this so? Is it because fishes are actually poor models? The usefulness of fishes as models for sexual selection and parental care is discussed by emphasizing some problems inherent in fish studies, along with a number of reasons why fishes are indeed excellently suited. The pros and cons of fishes as models are discussed mainly by comparison with birds, the most popular model organisms in animal behaviour. Difficulties include a lack of background knowledge for many species, and the problems of marking and observing fishes in their natural environment. Positive attributes include the diversity of lifestyles among fishes, and the ease with which they can be studied experimentally in the laboratory. How useful fish models can be is briefly illustrated by the impressive and broadly relevant advances derived from studies of guppies Poecilia reticulata and three‐spined sticklebacks Gasterosteus aculeatus . A selection of topics is highlighted where fish studies have either advanced or could greatly enhance, the understanding of processes fundamental to animal reproductive dynamics. Such topics include sex role dynamics, the evolution of female ornamentation and mate choice copying. Finally, a number of potential pitfalls in the future use of fish as models for sexual selection and parental care are discussed. Researchers interested in these issues are recommended to make much more extensive use of fish models, but also to adopt a wider range of models among fishes.     

Diversification, Sympatric Speciation, and Trophic Polymorphism of Arctic Charr, Salvelinus Alpinus Complex, in Transbaikalia

In northern Transbaikalia, independently evolving landlocked populations of Arctic charr are found in mountain lakes. To assess the diversity of charr in this region, speciation modes involved in the evolution of charr forms, and the role of trophic polymorphism in their divergence, we studied the morphology and feeding of dwarf, small, and large forms of Arctic charr from a number of Transbaikalian lakes. Meristic data on charr from five lakes support the earlier conclusion that the three forms do not represent separate lineages but have independently diverged in sympatry in each of the lakes. In 10 lakes, the dwarf form showed varying degrees of differentiation from normal (small and large) charr in meristic characters (up to morphologically distinct and presumably reproductively isolated groupings), which is viewed as various levels of sympatric divergence. Indexes of gill raker length in fish from 20 lakes vary among populations of both dwarf and normal charr, with forms having short and long rakers being sympatric in some of these lakes. However, the index can be used only for comparing charr of different forms up to about 32cm fork length (FL) because it is strongly negatively correlated with size in larger fish. The study of charr diets in 21 lakes indicates that large charr are piscivorous whereas dwarf and small charr feed on a wide range of invertebrates, partitioning these resources in different ways. Planktivores, including very specialized ones, and non-planktivores (benthic feeders, insectivores) can be identified within the small and dwarf forms. The proportion of plankton in the diets of dwarf and small charr is positively correlated with the number and length of gill rakers while the proportion of benthos is negatively correlated. Allopatric planktivorous and non-planktivorous small charr differ in body proportions; parallel emergence of such morphotypes in different parts of the range is a characteristic feature of the Salvelinus alpinus complex.     

Trade-off between number and length of remote videos for rapid assessments of reef fish assemblages

Remote underwater videos are widely employed to assess the structure and composition of reef fish assemblages but the sampling effort employed on each survey differs considerably, indicating that both the number of assessments and video length could be optimized. We searched for this optimal sampling effort in remote video samples to conduct rapid assessments of community composition and discussed the relation between number of replicates and video length, and how it impacts the method's efficiency to characterize species assemblages. Remote video recordings from tropical reefs in northeastern Brazil were used to investigate how fish species richness and composition builds across time and number of assays. Videos as short as 5 min successfully recorded species richness, requiring about five repetitions to record most species that compose 80% of the total biomass. Recording species composition required even less time in these reefs, setting a minimum of 3 min with the same five videos. By comparing the detected richness per analysed time unit, we found several shorter videos recorded for more species than a few longer videos, indicating that increasing the sampling coverage in the reef area might be better than just extending the video length for rapid assessments.     

Ontogenetic variation in fin ray segmentation between latitudinal populations of the medaka, <Emphasis Type="Italic">Oryzias latipes</Emphasis>

Fin rays of ray-finned fishes are composed of multiple bony segments, and each fin ray elongates by adding a new segment to the tip. Therefore, fin ray length is determined by the number of segments and the length of each segment. A comparison of the anal fin rays of a northern and southern wild population of the medaka, Oryzias latipes, revealed that southern fish had more segments per fin ray, resulting in longer anal fins than the northern fish. When fish were reared in a laboratory common environment, segmentation of the fin rays started earlier with respect to body size in the southern fish. In the southern males, moreover, the rate of segment addition accelerated after a certain body size, indicating sexual maturity. These patterns of segment addition during ontogeny were consistent with the patterns of fin ray elongation. Although distal segments tended to be longer, except for the most proximal segment, in both populations, the southern fish had shorter segments than the northern fish at any position on fin rays. These results indicate that the interpopulation variation in fin length is largely due to genetically-based differences in the control of segment addition, and that the length of each segment does not contribute to it. We suspect that fin ray segmentation is regulated by thyroid and sex hormones that differ between populations. We also found that some segments fuse with each other at the base of each fin ray, the functions and mechanisms of which remain unclear.     

Costs and benefits of a cleaning mutualism

Juvenile Atlantic salmon or parr ( Salmo salar L.) maintain station at certain locations in flowing stream water. This position choice is assumed to involve the maximization of energy intake, based upon food availability which is usually directly related to water flow rate. Conversely energy expenditure, including station holding behaviour, foraging and defending preferred sites, is inversely related to water flow rate. Adaptations of parr to life in fast flows implies that station holding is energetically inexpensive at water speeds up to the maximum sustained holding speed, which is fish specific, thus the most important energetic consideration for parr is the ability to maximize food intake. Ten groups of three parr were each observed for 60 min within an artificial stream tank over a heterogeneous substratum. Individual position choice and behaviour were recorded continuously. For each location chosen by the parr the potential upstream line‐of‐sight (LOS), defined as the maximum distance upstream that the water surface would be visible, was calculated. At those sites where foraging behaviour was observed, the mean upstream potential LOS was significantly greater than at sites where other behaviours were observed and at 400 randomly generated sites within the tank. When foraging, parr usually take food from the stream drift and there is a significant time expenditure on food location, identification and catching. Results presented here would seem to confirm that to maximize time available to make these decisions, a fish would be expected to maximize the distance over which it can observe potential food particles.     

The Processing of Symbolic and Nonsymbolic Ratios in School-Age Children

This study tested the processing of ratios of natural numbers in school-age children. Nine- and eleven-year-olds were presented collections made up of orange and grey dots (i.e., nonsymbolic format) and fractions (i.e., symbolic format). They were asked to estimate ratios between the number of orange dots and the total number of dots and fractions by producing an equivalent ratio of surface areas (filling up a virtual glass). First, we tested whether symbolic notation of ratios affects their processing by directly comparing performance on fractions with that on dot sets. Second, we investigated whether children’s estimates of nonsymbolic ratios of natural numbers relied at least in part on ratios of surface areas by contrasting a condition in which the ratio of surface areas occupied by dots covaried with the ratio of natural numbers and a condition in which this ratio of surface areas was kept constant across ratios of natural numbers. The results showed that symbolic notation did not really have a negative impact on performance among 9-year-olds, while it led to more accurate estimates in 11-year-olds. Furthermore, in dot conditions, children’s estimates increased consistently with ratios between the number of orange dots and the total number of dots even when the ratio of surface areas was kept constant but were less accurate in that condition than when the ratio of surface areas covaried with the ratio of natural numbers. In summary, these results indicate that mental magnitude representation is more accurate when it is activated from symbolic ratios in children as young as 11 years old and that school-age children rely at least in part on ratios of surface areas to process nonsymbolic ratios of natural numbers when given the opportunity to do so.     

Marking zebrafish, Danio rerio (cyprinidae), using scale regeneration

Tagging or marking small laboratory-bred fish species is not an easy task. This also holds for the zebrafish, Danio rerio, which is widely used throughout the world as a model organism for genetics, developmental biology, etc. We present a simple marking technique based on scale regeneration. A comparative morphological study of various types of zebrafish scales indeed shows that regenerated scales are easily distinguishable from nonregenerated ones. We propose to take advantage of this typical morphology to mark a single or several individuals. This technique, based on a natural biological process, is easy to perform and does not enhance fish mortality in laboratory breeding conditions. It permits assembly of several specimens in a single tank with the possibility of identifying each of them by regenerated-scale coding. Nevertheless, a prerequisite is that the species does not lose and regenerate scales in large numbers in laboratory breeding conditions. To check this, 5,200 scales were removed from a large region of the left flank in 100 zebrafish and the number and position of regenerated scales were statistically analysed. Our results indicate that (1) laboratory-bred zebrafish have only a few regenerated scales (7.48%), (2) the probability of finding a regenerated scale is similar whatever its position in a row (antero-posterior axis), but (3) it differs from one row to another (scales from the back are more frequently lost than those from the pectoral region). This paper presents a procedure to mark small breeding colonies of zebrafish using scale regeneration with the number and position of the scales to be removed with high probability of marking success. J. Exp. Zool. 286:297-304, 2000.     

Crimson Spotted Rainbowfish (Melanotaenia duboulayi) Change Their Spatial Position according to Nutritional Requirement

Decision making in moving animal groups has been shown to be disproportionately influenced by individuals at the front of groups. Therefore, an explanation of state-dependent positioning of individuals within animal groups may provide a mechanism for group movement decisions. Nutritional state is dynamic and can differ between members of the same group. It is also known to drive animal movement decisions. Therefore, we assayed 6 groups of 8 rainbowfish foraging in a flow tank. Half of the fish had been starved for 24h and half had been fed 1h prior to experimental start. Groups were assayed again one week later but individuals were allocated to the opposite nutritional treatment. During the assay the positions of individually identified fish were recorded as were the number of food items they each ate and the position within the group they acquired them from. Food-deprived fish were more often found towards the front of the shoal; the mean weighted positional score of food-deprived fish was significantly larger than that of well-fed fish. Individuals were not consistent in their position within a shoal between treatments. There was a significant positive correlation between mean weighted positional score and number of food items acquired which displays an obvious benefit to front positions. These results suggest that positional preferences are based on nutritional state and provide a mechanism for state-dependent influence on group decision-making as well as increasing our understanding of what factors are important for group functioning.     

Impact of Great Crested Grebes (Podiceps cristatus L.) on fish ponds

Because Great Crested Grebes (Podiceps cristatus L.) mainly feed on fish, fish-farmers sometimes claim that economic losses are caused by grebes (EIFAC, 1988). Such claims were not based on scientific research.Therefore, a study was carried out to measure the impact of Great Crested Grebes on a fish-farm, managed by the Organization for the Improvement of Inland Fisheries (O.V.B.) in Valkenswaard (The Netherlands) during the period 1986–1988. The O.V.B. provided fish data for each pond including fish density and fresh fish weight for each fish species. The number of grebes was counted at least once a week. Activity patterns, including nocturnal activity, were determined both for the period with and without young. No nocturnal foraging activity was observed. Furthermore, fish biomass consumed per 1000 s foraging time by adult birds and chicks was calculated.In some fish-ponds grebes ate coarse fish, and chicks especially were fed these fish. The average daily fish consumption was 222 g for adults and 108 g for juveniles.Based on available fish data, it can be concluded that grebes consumed fewer fish than the number expected to die, and only marginally influenced the fish populations in the aquaculture ponds studied.