Miracle-dz/UniFAR-FTUs huggingface dataset:
Challenges associated with modeling low-oxygen waters in Chesapeake Bay: a multiple model comparison

Abstract. As three-dimensional (3-D) aquatic ecosystem models are used more frequently for operational water quality forecasts and ecological management decisions, it is important to understand the relative strengths and limitations of existing 3-D models of varying spatial resolution and biogeochemical complexity. To this end, 2-year simulations of the Chesapeake Bay from eight hydrodynamic-oxygen models have been statistically compared to each other and to historical monitoring data. Results show that although models have difficulty resolving the variables typically thought to be the main drivers of dissolved oxygen variability (stratification, nutrients, and chlorophyll), all eight models have significant skill in reproducing the mean and seasonal variability of dissolved oxygen. In addition, models with constant net respiration rates independent of nutrient supply and temperature reproduced observed dissolved oxygen concentrations about as well as much more complex, nutrient-dependent biogeochemical models. This finding has significant ramifications for short-term hypoxia forecasts in the Chesapeake Bay, which may be possible with very simple oxygen parameterizations, in contrast to the more complex full biogeochemical models required for scenario-based forecasting. However, models have difficulty simulating correct density and oxygen mixed layer depths, which are important ecologically in terms of habitat compression. Observations indicate a much stronger correlation between the depths of the top of the pycnocline and oxycline than between their maximum vertical gradients, highlighting the importance of the mixing depth in defining the region of aerobic habitat in the Chesapeake Bay when low-oxygen bottom waters are present. Improvement in hypoxia simulations will thus depend more on the ability of models to reproduce the correct mean and variability of the depth of the physically driven surface mixed layer than the precise magnitude of the vertical density gradient.
Mozambique and natural disasters: human capital under threat

This paper assesses the effect of a sequence of natural disasters on children’s health that hit Mozambique at the start of the 21st Century. The disasters in question were the floods of 2000 and the droughts of the years 2002 and 2003. Height-for-age z-scores of children between 1 and 3 years old is used to capture the cumulative effects of this sequence of natural disasters. It was found that the effect of the disasters on these children’s height was, on average, -0.4236 standard deviations, which corresponds to the affected children being more than 1.5 cm shorter by the time of the survey. The findings in this paper are important because of the long term economic cost associated with the disasters, and urge the need for further public intervention to mitigate the damage caused by the shocks. This paper also contributes to the existing literature on the subject of the impact of shocks on child health in the developing world by focusing on measurement errors, differences in physical stature among ethnic groups and migratory movements.
Identifying Assets Associated with Quality Extension Programming at the Local Level

County Extension offices are responsible for the majority of programming delivered in the United States. The purpose of this study was to identify and explore assets influencing the quality of county Extension programs. A basic qualitative research design was followed to conduct constant comparative analysis of five Extension county program review reports. Using the appreciative inquiry process as the lens through which to view the county program review reports revealed multiple assets leading to quality programming. Assets of the reviewed county Extension programs were found to cluster within the following themes: competent and enthusiastic Extension faculty, community partnerships, engaged and supportive stakeholders, effective resource management, sufficient and stable workforce, meeting stakeholder needs, positive reputation, access to facilities, positive relationships between county and state faculty, and innovative practices. The use of both needs-based and assets-based paradigms will provide Extension organizations with a more holistic understanding of its assets and a research-based foundation from which to make decisions about strengthening the organization at all levels.
CHEMICAL ECOLOGY OF INSECTS AND TRITROPHIC INTERACTIONS

This paper reviews the chemical ecology of insects to explain the role of semiochemicals in plant-herbivore, herbivore-carnivore and plant-carnivore interactions. The semiochemicals, mediating tritrophic interactions may be produced by plants, herbivores or their natural enemies (carnivores). Some semiochemicals attract the herbivores and carnivores and mediate interaction among them, while on the other hand some repel them. The semiochemicals are used by herbivores, parasites and predators as cues to locate food, host or prey. The same chemicals are also used for defensive purpose by some herbivores against their natural enemies as they are sequestered through their bodies.
Informal Workers Across Europe: Evidence from 30 Countries

The European Social Survey data are used to analyze informal employment at the main job in 30 countries. Overall, informality decreases from South to West to East to North. However, dependent work without contract is more prevalent in Eastern Europe than in the West, except for Ireland, the UK and Austria. Between 2004 and 2009, no cases found when unemployment and dependent informality rates in a country went up together, suggesting that work without contract is pro-cyclical in Europe. Dependent informality rate is inversely related to skills (measured by either schooling or occupation). The low-educated, the young (especially students), the elderly, and persons with disabilities are more likely to work informally, other things equal. In Southern and Western Europe, immigrants from CEE and FSU feature the highest dependent informality rate, whilst in Eastern Europe this group is second after minorities without immigrant background. In Eastern, Southern and part of Western Europe, immigrants not covered by EU free mobility provisions are more likely to work without contracts than otherwise similar natives. We provide evidence that exclusion and discrimination play important role in pushing employees into informality, whilst this seems not to be the case for informal self-employed. Both on average and after controlling for a rich set of individual characteristics, informal employees in all parts of Europe are having the largest financial difficulties among all categories of employed population (yet they fare much better than the unemployed and discouraged), whilst informal self-employed are at least as well off as formal employees.
Infiltrated Photonic Crystal Fibers for Sensing Applications

Photonic crystal fibers (PCFs) are a special class of optical fibers with a periodic arrangement of microstructured holes located in the fiber’s cladding. Light confinement is achieved by means of either index-guiding, or the photonic bandgap effect in a low-index core. Ever since PCFs were first demonstrated in 1995, their special characteristics, such as potentially high birefringence, very small or high nonlinearity, low propagation losses, and controllable dispersion parameters, have rendered them unique for many applications, such as sensors, high-power pulse transmission, and biomedical studies. When the holes of PCFs are filled with solids, liquids or gases, unprecedented opportunities for applications emerge. These include, but are not limited in, supercontinuum generation, propulsion of atoms through a hollow fiber core, fiber-loaded Bose–Einstein condensates, as well as enhanced sensing and measurement devices. For this reason, infiltrated PCF have been the focus of intensive research in recent years. In this review, the fundamentals and fabrication of PCF infiltrated with different materials are discussed. In addition, potential applications of infiltrated PCF sensors are reviewed, identifying the challenges and limitations to scale up and commercialize this novel technology.
Experimentally exploring how the awareness of existential freedom influences support for autocratic leadership styles among individuals high and low in neuroticism

The present dissertation builds on classic existential philosophy and psychological theory to suggest that personal freedom can be burdensome to the self and may, ironically, motivate people to displace their freedom to an autocratic (vs. democratic) authority who would make decisions on behalf of such individuals rather than democratically involve them in the decision-making process. The present analysis further suggests that low neurotics are especially likely to actively “escape” their freedom by displacing it, whereas high neurotics instead employ inactive strategies and are unlikely to actively displace their freedom. Three preliminary studies explore and demonstrate these processes. A fourth study then proposes that the process of displacing personal responsibility for one’s freedom is an important part of maintaining psychological equanimity, and offers an experiment designed to test whether displacement to autocratic authority helps reduce anxiety among low neurotics perceiving increased personal freedom. Results of this study did not support the hypothesis: displacement did not relieve explicit anxiety—reported anxiety was greater among low neurotics reminded of freedom whether or not they were first allowed to displace to authority. Instead, the displacement effect emerged when leadership style was measured first (replicating the preliminary studies), yet was eliminated when measured after participants reported on their explicit anxiety. The implications of these findings are considered in terms of alternative explanations, theoretical refinements, and future research efforts.
Thermal expansion in dispersion-bound molecular crystals

We explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with $ab$ $initio$ molecular dynamics yields cell parameters accurate to within 2% of experiment for a set of pyridine-like molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I ($\approx 40$% more than classical thermal expansion at $153$ K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. When predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and sophisticated treatments of Pauli repulsion are needed in dispersion-bound molecular crystals.
The nature of the multi-wavelength emission of 3C 111

Aims. We attempt to determine the nature of the high energy emission of the radio galaxy 3C 111, by distinguishing between the effects of the thermal and non-thermal processes. Methods. We study the X-ray spectrum of 3C 111 between 0.4 keV and 200 keV, and its spectral energy distribution, using data from the Suzaku satellite combined with INTEGRAL, Swift/BAT data, and Fermi/LAT data. We then model the overall spectral energy distribution by including radio and infrared data. Results. The combined Suzaku, Swift and INTEGRAL data are represented by an absorbed exponentially cut-off power-law with reflection from neutral material with a photon index Γ= 1.68± 0.03, a high-energy cut-off Ecut = 227 +143 −67 keV, a reflection component with R = 0.7 ± 0.3 and a Gaussian component to account for the iron emission-line at 6.4 keV with an equivalent width of EW = 85 ± 11 eV. The X-ray spectrum appears dominated by thermal, Seyfert-like processes, but there are also indications of non-thermal processes. The radio to γ-ray spectral energy distribution can be fit with a single-zone synchrotron-self Compton model, with no need for an additional thermal component. Conclusions. We suggest a hybrid scenario to explain the broad-band emission, including a thermal component (iron line, reflection) that dominates in the X-ray regime and a non-thermal one to explain the spectral energy distribution.
Spadis: selecting predictive and diverse SNPS in GWAS

SPADIS: SELECTING PREDICTIVE AND DIVERSE SNPS IN GWAS Serhan Yılmaz M.S. in Computer Engineering Advisor: A. Ercüment Çiçek May 2018 Phenotypic heritability of complex traits and diseases is seldom explained by individual genetic variants identified in genome-wide association studies (GWAS). Many methods have been developed to select a subset of variant loci, which are associated with or predictive of the phenotype. Selecting connected Single Nucleotide Polymorphisms (SNPs) on SNP-SNP networks has been proven successful in finding biologically interpretable and predictive SNPs. However, we argue that the connectedness constraint favors selecting redundant features that affect similar biological processes and therefore does not necessarily yield better predictive performance. To this end, we propose a novel method called SPADIS that favors the selection of remotely located SNPs in order to account for their complementary effects in explaining a phenotype. SPADIS selects a diverse set of loci on a SNP-SNP network. This is achieved by maximizing a submodular set function with a greedy algorithm that ensures a constant factor (1 − 1/e) approximation to the optimal solution. We compare SPADIS to the state-of-the-art method SConES, on a dataset of Arabidopsis Thaliana with continuous flowering time phenotypes. SPADIS has better average phenotype prediction performance in 15 out of 17 phenotypes when the same number of SNPs are selected and provides consistent improvements across multiple networks and settings on average. Moreover, it identifies more candidate genes and runs faster. We also investigate the use of Hi-C data to construct SNP-SNP network in the context of SNP selection problem for the first time, which yields improvements in regression performance across all methods.
Employee Entitlements and Secured Creditors: Assessing the Effects of the Maximum Priority Proposal

Corporate failures and consequent default on obligations have, in some circumstances, led to significant losses for employees with accumulated unpaid leave entitlements. The Australian government responded initially to this problem by implementing a government-funded compensation scheme. Subsequently it announced a proposal involving legislating for seniority (maximum priority) of entitlements in corporate liquidation which has not been implemented. This paper analyses and provides quantitative estimates of the consequences of changing creditor priority in this manner. Contrary to conventional wisdom and arguments mounted in opposition to such a change, the effect on corporate funding costs would be extremely small. The paper argues that legislation to effect such a change warrants further consideration as a complement to the existing compensation scheme.
Ti Concentrations in Zircon from the Boggy Plain Zoned Pluton; Implications for Zircon Petrology and Hadean Tectonics

The Ti-in-zircon thermometer is employed in the zoned, high temperature (>1000°C) Boggy Plain Pluton. Measurements were made on zircon in rocks ranging in bulk compositions from gabbro to aplite. Apparent crystallization temperatures range from about 820-750°C (corrected for non-unity TiO2 activity). There is no correlation of Ti concentrations with rock type. The distributions of apparent crystallization temperatures are compared with a simple forward model. The model captures broad characteristics of the distributions, but has important differences. These differences may be the result of either sampling bias and/or a non-monotonic P-T-X history of the magma chamber during zircon crystallization. Titanium concentrations are generally higher than those in the Hadean zircon suite from the Jack Hills of Western Australia.
Evaluation of Reconstruction Parameters for 2-D Comb-Push Ultrasound Shear Wave Elastography

Shear wave elastography (SWE) is a noninvasive ultrasound imaging modality used in the assessment of the mechanical properties of tissues such as the liver, kidney, skeletal muscle, thyroid, and the breast. Among the methods used to perform SWE is the comb-push ultrasound shear elastography method. This method uses multiple focused ultrasound beams to generate push beams with acoustic radiation force. Applying these push beams generates propagating shear waves. The propagation motion is measured with ultrafast ultrasound imaging. The shear wave motion data are directionally filtered, and a 2-D shear wave velocity (SWV) algorithm is applied to create group velocity maps. This algorithm uses a moving window and a specified patch for performing cross-correlations of time-domain signals. We performed a parametric study of how the choice of the patch and window size affected the reconstruction of the SWV in homogeneous and inclusion phantoms. We quantified the mean velocity and coefficient of variation in the homogeneous phantoms. We measured the contrast-to-noise ratio and bias in the inclusion phantoms. In each of these cases, we found that particular combinations of the patch and window provided optimal values of these evaluation metrics for the phantoms tested. This study provides a basis to construct algorithms to produce optimal SWV reconstructions for various clinical applications.
The Stress Experience and Mental Health among Persons with Physical Disabilities: A Minority Stress Perspective

Tjelesni invaliditet / Physical disability Manjinski stres / Minority stress Diskriminacija / Discrimination Mentalno zdravlje / Mental health Osobe s tjelesnim invaliditetom često doživljavaju različite oblike diskriminacije te imaju povećan rizik za višu razinu stresa i negativnih ishoda mentalnog zdravlja. Do sada je stresno iskustvo osoba s invaliditetom u Hrvatskoj bilo slabo istraženo. Korištenjem manjinskog stresa kao konceptualnog okvira ovog istraživanja, cilj je bio istražiti iskustvo stresa kod osoba s tjelesnim invaliditetom i ispitati ulogu diskriminacije u oblikovanju tog iskustva te posljedične povezanosti s mentalnim zdravljem. U ovom su istraživanju provedeni individualni intervjui sa šest odraslih osoba s tjelesnim invaliditetom. Transkribirani intervjui analizirani su induktivno koristeći konstantan usporedni pristup. Sudionici su izvijestili kako su različiti stresori povezani s njihovim iskustvom življenja s tjelesnim invaliditetom negativno utjecali na njihov osobni osjećaj dobrobiti. Nadalje, sudionici su opisali brojna iskustva u kojima su posljedice diskriminacije, uključujući fizičku nepristupačnost, socijalnu izolaciju i ograničene mogućnosti zapošljavanja, izravno utjecali na njihovo iskustvo stresa. Preliminarna analiza ukazuje da manjinski stres pruža koristan okvir kroz koji se može dodatno ispitati i bolje razumjeti jedinstvene stresore koje doživljavaju osobe s tjelesnim invaliditetom i ulogu koju ima diskriminacija u njihovom iskustvu stresa.
Named Entity Recognition on Flemish audio-visual and newspaper archives

This paper describes a number of specific issues that we needed to deal with, in order to compose an accurate Named Entity Recognition tool on multimedia archives in Dutch. The considered data consists of archivation metadata from video collections, and large newspaper collections. For the video collections, the main challenge is to cope with a lack of capitalization in the metadata. To this end, specific capitalization features are calculated from Wikipedia. For the newspaper collections, the main concern is to create a system that maintains its performance over the course of many years. For that goal, special clustering features allow dealing with words that have not been encountered in training data. Results for the different components of the tool are reported on the target data, as well as on publicly available test data.
Ecohydraulics in the Mississippi River: Freshwater Mussel Dynamics Model

The family Unionidae (freshwater mussels) is geographically diverse with species found worldwide; their greatest diversity is found in North America. Zebra mussels (Dreissena polymorpha) are an exotic species introduced into North America in the 1980’s that has since become a threat to economic interests and native mussel species in the region. IIHR-Hydroscience and Engineering and WL|Delft Hydraulics are developing a numerical model of mussel population dynamics for the purpose of analyzing alternative management strategies of zebra mussels and Unionidae in the Upper Mississippi River (UMR). The Mussel Dynamics Model (MDM) simulates interaction of mussels and the hydraulic environment. This paper describes the approach taken in the MDM. Environmental conditions are defined by water quality parameters and using a 3D hydrodynamics model to solve for flow conditions. Incorporated is a habitat suitability index model (HSI) that uses basic rules of species tolerance to various environmental conditions, including host fish distributions. This information along with the biological and ecological characteristics of mussels is used in an individual based population dynamics model that simulates change of stage, competition, feeding and growth, reproduction, dispersal and settlement, motion, and mortality. The MDM has been run on a reach of pool 16 in the Mississippi River with positive results. Food competition between native and invasive species was simulated and the results are in agreement with observed survival rates of unionids reported in the literature. Currently efforts are underway to redesign the model to facilitate portability, to decrease computational time, allow for larger grid sizes, and to develop a user friendly interface. The HSI has been translated into C with an increase in processing speed and the ability to handle millions of grid points, a significant improvement over the original code.
On the influence of model physics on simulations of Arctic and Antarctic sea ice

Abstract. Two hindcast (1983–2007) simulations are performed with the global, ocean-sea ice models NEMO-LIM2 and NEMO-LIM3 driven by atmospheric reanalyses and climatologies. The two simulations differ only in their sea ice component, while all other elements of experimental design (resolution, initial conditions, atmospheric forcing) are kept identical. The main differences in the sea ice models lie in the formulation of the subgrid-scale ice thickness distribution, of the thermodynamic processes, of the sea ice salinity and of the sea ice rheology. To assess the differences in model skill over the period of investigation, we develop a set of metrics for both hemispheres, comparing the main sea ice variables (concentration, thickness and drift) to available observations and focusing on both mean state and seasonal to interannual variability. Based upon these metrics, we discuss the physical processes potentially responsible for the differences in model skill. In particular, we suggest that (i) a detailed representation of the ice thickness distribution increases the seasonal to interannual variability of ice extent, with spectacular improvement for the simulation of the recent observed summer Arctic sea ice retreats, (ii) the elastic-viscous-plastic rheology enhances the response of ice to wind stress, compared to the classical viscous-plastic approach, (iii) the grid formulation and the air-sea ice drag coefficient affect the simulated ice export through Fram Strait and the ice accumulation along the Canadian Archipelago, and (iv) both models show less skill in the Southern Ocean, probably due to the low quality of the reanalyses in this region and to the absence of important small-scale oceanic processes at the models' resolution (~1°).