Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal management of metapopulations across space and time

iii Declaration . v Acknowledgments . vi List of Figures . xii List of Tables. xxv Preface . xxvi Chapter 1: General introduction . 1 1.1 Overview . 2 1.2 What is a metapopulation? 2 1.3 Types of metapopulations . 3 1.3. 1 Levins metapopulation . 3 1.3. 2 Mainland-island metapopulation . 5 1.3. 3 Non-equilibrium and patchy populations . 5 1.4 Managing metapopulations . 6 1.5 Factors complicating decision-making . 7 1.6 Model-based decision-making . 8 1.7 Metapopulation modelling . 9 1.8 Decision theory . 11 1.9 Stochastic dynamic programming . 12 1.10 Motivation . 14 1.11 Thesis aim . 15 1.12 Thesis outline . 15 Chapter 2: Learning about colonisation when managing metapopulations under an adaptive management framework . 19 2.1 Abstract . 20 2.2 Introduction . 21 2.3 Methods . 24
Identifying varying magnetic anomalies using geomagnetic monitoring

We are concerned with the inverse problem of identifying magnetic anomalies with varying parameters beneath the Earth using geomagnetic monitoring. Observations of the change in Earth's magnetic field–the secular variation–provide information about the anomalies as well as their variations. In this paper, we rigorously establish the unique recovery results for this magnetic anomaly detection problem. We show that one can uniquely recover the locations, the variation parameters including the growth or decaying rates as well as their material parameters of the anomalies. This paper extends the existing results in [ 9 ] by two of the authors to the more practical and challenging scenario with varying anomalies.
Evaluation of six diets fed to redclaw, Cherax quadricarinatus (von Martens), held in pond enclosures

Five formulated pelleted diets and one natural diet were led to redclaw crayfish held within 9 m2 cages fixed to the bottom of an earthen pond in a 6x4 randomised block experiment. Crayfish were stocked at a mean weight of 9.7 ± 0.13 and a density of 6. 7 per m2 in June and harvested 5 months later in November. Formulated diets varied considerably in composition, particularly crude protein which ranged from 18 to 42%. A sixth natural diet consisted of a combination of whole rice, lupin seed and raw potato. Food was provided to each cage 3 times per week to excess. Numbers harvested from each cage were severely affected by escape and to a lesser extent by water rat predation. In excess of 500 of the 1,440 experimental crayfish were captured outside the enclosures. Considerable growth was achieved in all cages, with one of the pellet diets significantly out-performing all others. Size at harvest from this superior diet averaged 45.8 g. Average size lor the other live diets ranged from 31.3 to 38.5 g. The mean size of escaped crayfish was 49 g. Due to the significant reduction in density in each cage because of losses attributed to escape and predation, the nutritional value of each diet was not completely tested. Nevertheless, the results suggest that at the densities which prevailed at harvest, the total protein level of the diet is of minimal significance, and other characteristics including those of a non-nutritional nature may be of greater importance. This supports the notion that a simple diet formulation which feeds the benthic microbial biomass is required for redclaw aquaculture, rather than a nutritionally complete diet formulation which feeds the animal.
The structure of kaliophilite KAlSiO4, a long-lasting crystallographic problem

The elusive structure of the mineral kaliophilite has been determined by 3D electron diffraction and refined using single-crystal X-ray data. Despite its simple formula, ideally KAlSiO4, the structure of this mineral remained a mystery for over a century as a result of pseudo-symmetry and twinning, which reduce the coherent crystalline domain size to a few hundreds of nanometres.
Motion Analysis on Depth Camera Data to Quantify Parkinson’s Disease Patients’ Motor Status Within the Framework of I-Prognosis Personalized Game Suite

The primary manifestations of Parkinson Disease (PD) concern abnormalities of movement associated with the constant deterioration of motor skills. Such motor impairment affects patients’ movement accuracy and coordination, disrupting their daily life. Taking into account recent studies stating that computer-based physical therapy games can be used as a PD rehabilitation option, we propose a novel Exergame, the iPrognosis Warming up Game (http://www.i-prognosis.eu/), as a user-friendly tool that could both serve as a computer-based physical therapy game, as well as a means of accurately and automatically identifying the severity of PD motor symptoms. To this regard, we propose a novel deep learning methodology for motor impairment stage prediction that relies solely on human body motion data extracted from the recorded game sessions. Experimental results using a dataset of both early and advanced PD patients reveal a good classification performance of the proposed methodology, predicting the motor impairment stage of PD patients and paving the way for additional research in the field.
Sex ratio and maturity of orange-dotted tuskfish Choerodon anchorago Bloch, 1791 in Wallace Line at Spermonde Archipelago

Orange-dotted tuskfish Choerodon anchorago was a Labridae family that could be found in coral reef and seagrass ecosystems. Orange-dotted tuskfish has a wide distribution in Indo-Pacific waters which has an important economic value that needs to be managed sustainably. This study aims to analyze the sex-ratio and maturity of orange-dotted tuskfish. The samples were collected from fishermen catches that were landed at the Rajawali Makassar Fishing Port at Makassar city. The orange-dotted tuskfish sex ratio was not balanced between males and female. Macroscopically, it was seen that orange-dotted tuskfish was a hermaphrodite. The synchronicity of maturity stages between male and female, both based on the sampling period, and the length class indicated that the process of reproduction, especially fertilization, was relatively safe. Female orange-dotted tuskfish that reach the first maturity earlier than male; suggest that orange-dotted tuskfish was most likely a protogyny.
Essential oil effects on rumen fermentation, animal performance, and meat quality of beef steers

Efficiency in ruminants has historically been improved by using antibiotics and ionophores to alter rumen fermentation. Nutritionists, however, have begun searching for alternative rumen modifiers due to the negative attention received by non-therapeutic antibiotic use. Plant extracts, like essential oils, are being explored as a potential alternative to alter fermentation and improve growth and efficiency in ruminants. Essential oils are naturally occurring, secondary metabolites that can be distilled or extracted from most plants and possess antimicrobial properties. Next Enhance ® (NE, Novus International Inc.) is comprised of garlic (diallyl disulfide) and cinnamon (cinnamaldehyde) extracts; both have demonstrated the ability to modify fermentation. A series of experiments was conducted to determine how feeding NE affects in vitro fermentation, site and extent of nutrient digestion, feedlot performance, carcass traits, meat quality, and consumer sensory characteristics of LM steaks from beef steers. The first experiment in this thesis examined how feedlot steer performance and carcass traits were affected by NE feeding. ADG and G:F were improved early in the feeding period by 150 mg·hd −1 ·d −1 targeted NE inclusion. DMI, overall ADG, and overall G:F were not
Oocyte Atresia Characteristics and Effect on Reproductive Effort of Manila Clam Tapes philippinarum (Adams and Reeve, 1850)

ABSTRACT The histological characteristics of oocyte atresia were examined in the Manila clam Tapes philippinarum (Adams and Reeve, 1850), at Croisic Traict on the French Atlantic coast, over 4- and 5-month gametogenic periods (May to August 2015 and April to September 2016). Atresia was found at all stages of gametogenesis, as well as in residual oocytes, and was characterized by several characteristics: loss of the nucleolus, nuclear degradation, altered cytoplasmic staining affinities, cytoplasmic retraction, and finally the loss of all cellular content. Histological observations indicated that T. philippinarum partially spawned repeatedly over the gametogenic period. Stereological counts showed that at least 15% of the oocyte volume was occupied by atresic oocytes (AO) at the onset of gametogenesis before any spawning activity; this increased to 30% in the middle of the gametogenic period (including both pre- and postspawning oocytes) and 80% at the end of the gametogenic period (postspawning atresia). Of all oocytes whose fate could be determined during active gametogenesis, nearly half were atresic. Similar observations were made for smaller sample sizes of clams from two other sites in nearby Bourgneuf Bay over a 26-mo period. Both AO and nonatresic oocytes were observed in the same gonad acini, suggesting that the process was either not propagated or not synchronized. The considerable proportion of oocytes affected by atresia underscores the need for better recognition, documentation, and integration of this process into models of reproductive effort and fecundity in this species. In particular, condition indices based on tissue : shell weights should be interpreted as estimations of reproductive investment, not as indications of potential reproductive outcome.
The complete chloroplast genome of Nomocharis pardanthina

Abstract Nomocharis pardanthina Franchet (Liliaceae) is an endangered species naturally distributed in China. The complete chloroplast genome sequence of N. pardanthina was generated by de novo assembly using whole genome next generation sequencing data. The chloroplast genome of N. pardanthina was 152,718 bp in length and divided into four distinct regions, such as large single copy region (82,154 bp), small single copy region (17,524 bp) and a pair of inverted repeat regions (26,520 bp). The genome annotation predicted a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that N. pardanthina is nested in Lilium and has close relationship to L. bakerianum and L. taliense.
ST-LSTM: Spatio-Temporal Graph Based Long Short-Term Memory Network For Vehicle Trajectory Prediction

Autonomous vehicles need the ability to predict the trajectory of surrounding vehicles, so as to make a rational decision planning, improve driving safety and ride comfort. In this paper, a new hierarchical Long Short-Term Memory (LSTM) based on Spatio-Temporal (ST) graph is proposed for vehicle trajectory prediction. Our ST-LSTM uses three layers of different LSTMs to capture the information of spatial, temporal and trajectory data, and LSTM-based encoder-decoder model as a whole, which is capable of accurately predicting future trajectories for vehicles on the highway. Our model trained and validated on the publicly available NGSIM US-101 and I-80 datasets. In comparison to state-of-art methods, our method could achieve a more accurate prediction trajectory over 5s time horizon.
Social Resources as Cognitive Structures: Thinking about a Dense Support Network Increases Perceived Support

Two experiments examined how the ways in which people mentally represent their personal networks affect perceptions of social support. Social support research often uses “name generators” in which individuals are asked to choose how many people they receive support from, resulting in cognitive networks that confound size and density. Taking a fixed size approach, Study 1 showed that the density of chronically activated networks predicted perceived support in both emotional and informational domains. Study 2 assigned participants to think of a dense or sparse personal network of equal size to test whether experimentally manipulated density can influence perceived support. Results indicated that thinking of a dense (vs. sparse) network led to higher perceived support, which in turn promoted more confidence in coping with life stressors. Collectively, these studies highlight how moment-to-moment changes in cognitive networks can influence social resources and explicate key psychological mechanisms tied to cognitive social structures.
Seed Biology of Sulfonylurea-Resistant and -Susceptible Biotypes of Prickly Lettuce (Lactuca serriola)

The persistence of herbicide-resistant biotypes within a given weed population can be highly correlated with the longevity of its seed in the soil and its reproductive ability. This study compared seed longevity of sulfonylurea-susceptible (S) and -resistant (R) biotypes of prickly lettuce in soil at three depths and two locations. Seed longevity in soil was not different between R and S biotypes. Seed longevity was longer when seed were buried compared to seed placed on the soil surface. A field study on seed production showed that prickly lettuce plants produced an average of 14 flower heads and 181 seed per day. Average seed weight was 0.6 mg. No differences were observed in the fecundity or seed viability between the R and S biotypes. However, seed from R biotype plants germinated as fast or faster than seed from S biotype plants.
A Clinical Study Measuring Dental Aerosols with and without a HVE Device

(1) Introduction: External high volume extraction devices may offer a way to reduce any aerosol particulate generated. The aim of this study was to measure the particle count during dental aerosol procedures and compare the results to when a High Volume Extraction device is used; (2) Methods: A comparative clinical study measuring the amount of PM1, PM2.5 and PM10 aerosol particulate with and without the use of an external High Volume Extraction device was undertaken. In total, 10 restorative procedures were monitored with an an industrial Trotec PC220 particle counter. The air sampler was placed at the average working distance of the clinicians involved in the study - 420mm. ; (3) Results: In the present study aerosol particulate was recorded at statistically significantly increased levels during dental procedures without an external high volume extraction device versus with the device. The null hypothesis was rejected, in that significant differences were found between the results of the amount of aerosol particle count with and without a High Volume Extraction device. ; (4) Conclusion: If the results of the present study are repeated in an in vivo setting, an external high volume suction device may potentially lower the risk of transmission of viral particulate.
Farmers’ attitude to standard production method based on Temanggung robusta coffee’s geographical indication

Temanggung Regency is one of the main producers of coffee in Central Java Province. Robusta coffee originating from this area has the potential to become a specialty coffee because it has a distinctive taste character that is indicated because of geographicaal factor. In an effort to improve competitiveness and protect their coffee, coffee farmers are motivated to produce and do post-harvest based on Geographical Indications (GI) standard. However, only around 170 farmers who implement production methods (on farm); harvest and post-harvest; and processing in accordance with standards. Attitudes are thought to have an important role in the behavior of these farmers. This publication will deliver part of the research results, namely the importance of farmers’ attitudes towards coffee production methods (on farm) that are appropriate to GI. For this reason, this study aims to analyze the attitude of farmers to the standard production methods according to the GI of Temanggung Robusta Coffee. The study was conducted in Kandangan Sub-district where the location of the MPIG-KRT secretariat was located. Respondents were 80 coffee farmers who were taken by simple random sampling. Data was collected by questionnaire, independent interview, observation, and documentation recording. The results showed that 1) the majority (51.25%) of farmers had good attitudes and 45% were very good towards the standards of coffee production methods, 2) There was a significant relationship between the influence of others and farmers’ attitudes toward the standard production methods, but there was no significant relationship between age, formal education, and non-formal education with the attitude of the farmer.
Phytomer growth and development, and nitrogen dynamics in a perennial C4 grass

The aim of the present thesis is the characterization of morphological features and nitrogen (N) dynamics of a perennial C4 grass, Cleistogenes squarrosa. Results revealed a strong coordination of elongation both within a phytomer and between successive phytomers on a tiller, that was virtually unaffected by nitrogen nutrition and vapor pressure deficit (VPD). N dynamics at the tiller level was integrated with that of the remainder of the shoot. N turnover of 0.36% per hour in mature blades assessed by N labeling was much higher that had been derived from observation of net changes in N content.
Discrete attractor dynamics underlying selective persistent activity in frontal cortex

Short-term memories link events separated in time, such as past sensation and future actions. Short-term memories are correlated with selective persistent activity, which can be maintained over seconds. In a delayed response task that requires short-term memory, neurons in mouse anterior lateral motor cortex (ALM) show persistent activity that instructs future actions. To elucidate the mechanisms underlying this persistent activity we combined intracellular and extracellular electrophysiology with optogenetic perturbations and network modeling. During the delay epoch, both membrane potential and population activity of ALM neurons funneled towards discrete endpoints related to specific movement directions. These endpoints were robust to transient shifts in ALM activity caused by optogenetic perturbations. Perturbations occasionally switched the population dynamics to the other endpoint, followed by incorrect actions. Our results are consistent with discrete attractor dynamics underlying short-term memory related to motor planning.
Effect of Rosmarinus officinalis Essential Oil and Nisin on Streptococcus iniae and Lactococcus garvieae in a Food Model System

ABSTRACT The effects of concentrations of Rosmarinus officinalis essential oil (EO) and nisin (N) as well as temperature and storage time on growth of Streptococcus iniae and Lactococcus garvieae in Oncorhynchus mykiss were evaluated. According to analysis of the rosemary EO, the 1, 8-cineol and α-pinene were the predominant components. The growth of S. iniae was significantly decrease by EO concentrations at 4 ºC. For L. garvieae, the viable count was significantly inhibited by EO and N singly and in combinations, incubated at bath storage of 0.25 and 0.5 µg/mL proved insufficient to act against S. iniae and L. garvieae. The combinations of the rosemary EO at 0.0015% with N at 0.5 µg/mL showed stronger antimicrobial effect against two bacterial than the rosemary EO at 0% but lower than the combination with N at 0.5 µg/mL and EO at 0.045% which in turn was lower than of the rosemary EO at 0.135%. In its turn, rosemary EO showed lower antimicrobial activity than its combinations with N, which showed a bactericidal effect against the pathogens. The best inhibitory effects of EO in combinations with N for two bacterial were obtained at combinations of EO=0.135% and N=0.5 µg/mL.
Properties of Water Ice and Dust Particles in the Atmosphere of Mars During the 2018 Global Dust Storm as Inferred From the Atmospheric Chemistry Suite

The properties of Martian aerosols are an integral part of the planetary climatology. Global dust storms (GDS) significantly alter spatial and vertical distributions of dust and water ice aerosols and their microphysical properties. We explored the 2018/Martian year 34 GDS with the Atmospheric Chemistry Suite instrument onboard the ESA‐Roscosmos Trace Gas Orbiter mission. Solar occultation observations of thermal infrared and near infrared channels in the 0.7–6 μm spectral range with >103 signal‐to‐noise ratio are used to constrain the vertical dependence and the temporal evolution of the particle properties of water ice and dust (effective radius, effective variance, number density, and mass loading) before the 2018 GDS and during its onset and decay phases. In most of the observations, the particle size of dust and water ice decreases with altitude. The effective radius of dust and water ice particles ranges in 0.1−3.5 μm and 0.1–5.5 μm, respectively. The largest aerosol particles (> 2.5 μm for dust and > 3.5 μm for water ice) are present below 10 km before the onset and during the GDS decay phase. During the peak of the GDS, dust reached altitudes of 85 km; the most frequently observed effective radius is 1–2 μm with 0.1–1 cm−3 number density and 0.1 effective variance. Detached layers of water ice composed of 0.1–1 μm particles are systematically observed at 50–100 km during this period. Below, at 0–50 km, we see the dust mixed with the main water ice layer comprising 1–4 μm particles.
Parasitoid phorid flies of leaf‐cutting ants are negatively affected by loss of forest cover

Habitat fragmentation can have a high impact on parasitoid–ant interactions. Phorid flies are among the most important groups of natural enemies of leaf‐cutting ants. We studied the effects of loss in forest cover upon phorids of the leaf‐cutting ant Acromyrmex nigerSmith (Hymenoptera: Formicidae: Attini) in a fragmented area in the Southeastern Atlantic Forest, Brazil. We sampled 10 forest fragments, five large (>75 ha) and five small (<20 ha), as well as three areas of continuous forest (>1 000 ha). We marked 1–5 colonies of A. niger in the interior of each forest location. At each nest, we collected all of the phorids in interaction with the worker ants for a period of 15 min. We then collected ca. 200 worker ants, which we maintained in the laboratory for rearing phorids from them. We identified three phorid genera – Apocephalus, Myrmosicarius, and Neodohrniphora – which we both observed in the field and reared in the laboratory. The abundance and parasitism percentage were significantly greater in continuous forest sites than in forest fragments, whereas there were no significant differences between fragments of different sizes. These results provide further evidence for the effects of habitat size on the phorid‐Acromyrmex system in a tropical rain forest, based on the abundance of parasitoids both as adults in the field and as reared immature phorids in the laboratory.