Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal heterogeneity of prokaryotic micro-organism communities in sediment of traditional freshwater cultured fish ponds in Southwest China

ABSTRACT The temporal heterogeneity of prokaryotic microorganism communities in sediment of traditional freshwater cultured fish ponds in Southwest China were investigated by 16S rRNA clone libraries. The result indicated that a total of 47 archaea clones and 392 bacterial clones were recovered from three samples, among them, the bacteria Mitsuaria chitosanitabida, Prolixibacter bellariivorans and Flavihumibacter petaseus and archaea Methanoregula formicica were dominant in the cultivation 1 year (Y1) sample, the bacteria Cetobacterium somerae, Allochromatium vinosum and Rhabdochromatium marinum and archaea Methanolinea tarda were dominant in the cultivation 2 years (Y2) sample, the bacteria Cetobacterium somerae and Bacteroides fragilis and archaea Methanolinea tarda were dominant in the cultivation 4 years (Y4) sample. The Shannon–Wiener (H) diversity index and the Simpson dominancy index respectively varied from 2.23 to 2.37 and from 7.30 to 9.04 for three gene libraries. Maximum operational taxonomic unit (OTU) richness was respectively estimated with two different models SChao1 and SACE, and it revealed SChao1 15 and SACE 15 for Y1, SChao1 15.25 and SACE 15 for Y2, SChao1 12 and SACE 12 for Y4. However, the B. fragilis which was found in the Y4 sample was 99% similar to the human and animal pathogen B. fragilis. No pathogenic organisms related to humans or animals were found at any other sample. Mentionable, the more detailed information about the safety of fish pond cultivation environment should receive more attention and further studies.
Complete chloroplast genome of Ulleung Island endemic flowering cherry, Prunus takesimensis (Rosaceae), in Korea

Abstract Prunus takesimensis is an endemic flowering cherry on Ulleung Island, Korea. The complete chloroplast (cp) genome of P. takesimensis was generated by de novo assembly using whole-genome next-generation sequencing approach. The cp genome size was 157,948 bp in length consisting of four regions; large single copy region (85,959 bp), small single copy region (19,117 bp), and a pair of inverted repeat regions (26,436 bp). The genome contained a total of 128 genes, including 83 coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis for 20 reported genomes within the family Rosaceae showed the monophyly of the genus Prunus including newly sequenced P. takesimensis.
Inclusive Education at a South African University: Awakening the Sensitivities and Democratic Consciousness of Pre-Service Teachers

One of the chief goals of inclusive education is to provide pre-service teachers with a learning environment and prospects that enable them to become independent, responsible and critical educators. This study sought to determine how pre-service teachers at a South African university experienced inclusive education training. A purposeful sample of 6 pre-service teachers was selected. Data were collected using open-ended questionnaires which were exploratory in nature, and then analysed thematically. Findings showed inter alia that studying inclusive education proved to be an “eye opener”: students were enlightened to various aspects of being an educator: (i) curriculum differentiation, (ii) diversity, (iii) learners’ rights and (iv) the fact that learners experiencing various barriers to learning can be accommodated successfully in regular classrooms. It was revealed that studying inclusive education allowed pre-service teachers to appreciate the scope, value and higher purpose of teaching. The study shows that awareness of inclusive education enriches the training of pre-service teachers in South African schools.
EpiGraph: an open-source platform to quantify epithelial organization

During development, cells must coordinate their differentiation with their growth and organization to form complex multicellular structures such as tissues and organs. Healthy tissues must maintain these structures during homeostasis. Epithelia are packed ensembles of cells from which the different tissues of the organism will originate during embryogenesis. A large barrier to the analysis of the morphogenetic changes in epithelia is the lack of simple tools that enable the quantification of cell rearrangements. Here we present EpiGraph, an image analysis tool that quantifies epithelial organization. Our method combines computational geometry and graph theory to measure the degree of order of any packed tissue. EpiGraph goes beyond the traditional polygon distribution analysis, capturing other organizational traits that improve the characterization of epithelia. EpiGraph can objectively compare the rearrangements of epithelial cells during development and homeostasis to quantify how the global ensemble is affected. Importantly, it has been implemented in the open-access platform FIJI. This makes EpiGraph very user friendly, with no programming skills required. HIGHLIGHTS Epithelial images can be converted into graphs to quantify their topology. EpiGraph is a new simple method to capture epithelial organization. Epigraph can detect changes in tissue fluidity. EpiGraph has been designed as a plugin of FIJI to be accessible to any biology lab.
A Genetic Association Study of Glutamate Transporter Genes SLC1A1 and SLC1A3 in Tourette Syndrome and Attention-Deficit/Hyperactivity Disorder

Tourette syndrome (TS) is a heterogeneous disorder that may share etiological factors with attention-deficit/ hyperactivity disorder (ADHD) and obsessive-compulsive disorder (OCD). Genetic factors play a large role in the pathogenesis of these disorders and disruption of the glutamatergic system has been implicated through multiple lines of study. On this basis, the current investigation evaluates the role of two glutamate transporter genes: SLC1A1 and SLC1A3. SLC1A1 was selected for study based on its function and involvement in OCD, and was tested for association with TS and ADHD, using two independent samples. SLC1A3 was selected for study based on function and possible involvement in ADHD, and was tested for association using our TS sample. None of the genotyped markers remained significant following corrections for multiple testing. Considering that we observed several trends for association, studies using larger samples are required to determine whether these genes are associated with TS or ADHD.
Elaphoglossum doanense and Elaphoglossum tonduzii: New Members of Elaphoglossum Sect. Squamipedia (Dryopteridaceae) and Their Significance for Inferring the Evolution of Rhizome Habit and Nest-Forming Leaves within the Genus

Premise of research. Elaphoglossum is a large fern genus with about 600 species. Our continuing fieldwork and molecular investigations have revealed a surprising placement of two Elaphoglossum species in sect. Squamipedia. The two species differ from most others in the section by short-creeping rhizomes and large leaves. Their placement in sect. Squamipedia has implications for the evolution of rhizome form and nest-forming habit within the genus. Methodology. Phylogenetic relationships within Elaphoglossum were investigated using a three-locus plastid data set. Sampling encompassed representatives of all major clades in the genus, including all recognized species of sect. Squamipedia. We included all species of Elaphoglossum with nest-forming habit from which material was available. To better understand the evolution of rhizome form and nest-forming habit, those characters were scored and optimized onto the resulting phylogenetic tree. Pivotal results. Elaphoglossum doanense and Elaphoglossum tonduzii are resolved in sect. Squamipedia. They are sister to each other, and they in turn are sister to the rest of the Neotropical species in the section. Long-creeping rhizomes and non-nest-forming habit are plesiomorphic in Elaphoglossum. There have been several transitions in rhizome form within Elaphoglossum, either from short-creeping rhizomes to long-creeping ones or vice versa. For sect. Squamipedia, it is equivocal what the plesiomorphic rhizome form was. The nest-forming habit has evolved independently in each of the major clades of Elaphoglossum, and in sect. Squamipedia it has evolved at least three times. Keys, illustrations, nomenclatural data, specimens examined, dot-distribution maps, and spore images are given for all species of sect. Squamipedia with short-creeping rhizomes. Conclusions. Three out of four members of sect. Squamipedia with short-creeping rhizomes have short-petiolate leaves forming a basket that traps organic matter falling from above. The only exception is E. tonduzii, which has longer petioles and leaves not forming a basket. The nest-forming habit is likely an adaptation to the epiphytic environment, being also known from other plant families.
Construct Validity of Assessing Interest in STEM Content Scale

The purpose of this research was to validate the assessing interest in STEM content scale. The sample in this research was 552 students in upper secondary school at Fangchanupathum School, Chiang Mai, Thailand, who validated the assessing interest in STEM content scale, which used a rating scale of four factors consisting of (1) science, (2) mathematics, (3) laboratorial skills, and (4) technology and 20 items. Confirmatory factor analysis was used to confirm the construct validity of the assessing interest in STEM content scale adapted from the study by Tyler-Wood, Knezek, and Christensen. The results confirmed that the construct validity of this assessing interest in STEM content scale had an excellent fit. They showed that the fitness index of validating the assessing interest in STEM content scale was X2 statistic of 163.679 (degree of freedom = 141, P value = 0.0928) and the X2/df ratio having a value of 1.160 indicating a good fit. The comparative fit index (CFI) was 0.991, and Tucker–Lewis coefficient (TLI) was 0.988. The root mean square error approximation (RMSEA) was 0.017. The standardized root mean residual (SRMR) was 0.047. All the indicators indicated that there was a good fit between the empirical data and the hypothetical measurement model.
The Relative Strength of Abiotic and Biotic Controls on Species Range Limits

Study of the determinants of species’ geographic distributions has a rich tradition in ecology and evolution, and understanding these determinants is becoming increasingly important in the face of climate change. While we know many range limits are set by abiotic stress, species interactions can also be important drivers of range limits. However, we lack any well-tested predictive framework for when and where each of these two broad classes of factors will most commonly set range limits. A long-standing, but still nearly untested, hypothesis suggests that abiotic stress most often sets range limits in seemingly stressful areas, such as arctic, high-alpine, or arid systems, with species interactions having more influence in apparently benign environments, such as the tropics, low-elevation, or mesic places. In my dissertation, I experimentally tested a fundamental assumption of this hypothesis: namely, that the relative importance of species interactions and abiotic stress for population performance varies systematically with abiotic stress. I tested the relative importance of abiotic stress vs. three species interactions (herbivory, neighbors, and pollinators) for population dynamics of a model plant species in central Kenya, Hibiscus meyeri, across a sharp aridity gradient. I find broad-scale support for Darwin’s hypothesis, with stronger effects of herbivores, neighbors, and pollinators on population growth rate in mesic areas v. arid areas. Interestingly, I find universal competitive effects of neighbors (rather than the switch from facilitative to competitive with increasing rainfall predicted by recent theoretical and empirical work). This work suggests that species interactions might be critical drivers of range limits only in unstressful regions of a species range. This work also has implications for projecting shifts in species’ distributions. While in some cases, leaving biotic interactions out of species’ distribution models reduces accuracy, the vast majority of projections of shifts in distributions with climate change do not include such interactions. This work suggests that species distribution modelers should include species interactions in their predictions only in abiotically benign portions of a species range.
Forecasting Stock Market Index Based on Pattern-Driven Long Short-Term Memory

Stock trend prediction is an important area of study for researchers and practitioners. In recent years, along with traditional statistical prediction models, machine learning and deep learning techniques have been increasingly adopted in various financial studies. Long Short-Term Memory (LSTM) is one of the deep learning models for predicting time-series data. In the case of vanilla LSTM, shared weights are learned based on all available data; hence, it is difficult to accurately learn patterns and predict the future value from a subset of data. In this paper, a pattern-driven hybrid model that combines an LSTM with an unsupervised learning algorithm is proposed for precise prediction of stock prices. The performance of the hybrid model is evaluated using Korea stock index data. The results demonstrate that the proposed model outperforms traditional recurrent neural network (RNN) and LSTM models.
ssdm: An r package to predict distribution of species richness and composition based on stacked species distribution models

There is growing interest among conservationists in biodiversity mapping based on stacked species distribution models (SSDMs), a method that combines multiple individual species distribution models to produce a community‐level model. However, no user‐friendly interface specifically designed to provide the basic tools needed to fit such models was available until now. The “ssdm” package is a computer platform implemented in r providing a range of methodological approaches and parameterisation at each step in building the SSDM: e.g. pseudo‐absence selection, variable contribution and model accuracy assessment, inter‐model consensus forecasting, species assembly design, and calculation of weighted endemism. The object‐oriented design of the package is such that: users can modify existing methods, extend the framework by implementing new methods, and share them to be reproduced by others. The package includes a graphical user interface to extend the use of SSDMs to a wide range of conservation scientists and practitioners.
Enhancement of lipid productivity of Chlorella protothecoides cultivated in secondary wastewater under nitrogen starvation through optimization of environmental factors

ABSTRACT A lab scale externally illuminated photobioreactor was used to evaluate the lipid productivity (LP) of microalga Chlorella protothecoides (SAG-211-10C) cultivated in municipal secondary waste water supplemented with CO2. Experiments were conducted in two stages: growth phase (GP) and nitrogen starvation phase (NSP). The influence of five environmental factors (light intensity [LI], photoperiod, temperature, concentration of CO2, pH) on LP of Chlorella protothecoides under both phases was studied and the parameters were individually optimized. Under optimum operating conditions in GP (LI 6 klux, photoperiod 12 h:12 h, temperature 25°C, 6% concentration of CO2), the total nitrogen was completely consumed after 8 days of operation and highest LP of 64.7 mg/(L.day) was obtained. This value was further enhanced to 106.65 mg/(L.day) by operating the photobioreactor in NSP under its optimum conditions (LI of 4 klux, photoperiod of 16 h:8 h, temperature 25°C, pH 8, 4% concentration of CO2). Under optimum operating conditions, removal efficiency of total phosphorous and Chemical Oxygen Demand were 100 and 70.19%, respectively, and highest carbon fixation rate of 549.16 mg CO2/(L.day) was observed.
Young adults’ stigmatization of people who misuse prescription opioids: an exploratory study

ABSTRACT Based on the Social Cognitive Theory (SCT), this study used a survey to examine personal, behavioral, and environmental factors affecting young adults’ stigmatic views toward people misusing prescription opioid drugs (POD). Results indicated that stigmatic perception was negatively related to exposure to news coverage while positively associated with anti-opioid abuse messages. People with more stigmatic views toward POD misusers assigned more blame to these misusers than to pharmaceutical companies. POD misuse was negatively related to stigmatic views; the correlation coefficient was greater among people with high self-efficacy compared to those with low self-efficacy. The results provide an interesting glimpse and add to the overall knowledge of POD-related stigmatic views among young adults. It provides initial yet compelling evidence for the potential influence of various types of media content, self-efficacy, and POD misuse behavior on the stigmatic view. The findings may also help policymakers and the public to counter the opioid crisis in America more effectively.
Aluminum Nitride Nanofilms by Atomic Layer Deposition Using Alternative Precursors Hydrazinium Chloride and Triisobutylaluminum

The aim of this study is motivated by the pursuit to investigate the performance of new and as yet untested precursors such as hydrazinium chloride (N2H5Cl) and triisobutylaluminum Al(C4H9)3 in the AlN atomic layer deposition (ALD) process as well as to study effects of successive annealing on the quality of the resulting layer. Both precursors are significantly cheaper than their conventional counterparts while also being widely available and can boast easy handling. Furthermore, Al(C4H9)3 being a rather large molecule might promote steric hindrance and prevent formation of undesired hydrogen bonds. Chemical analysis is provided by X-ray photoelectron spectroscopy (XPS) and secondary-ion mass spectrometry (SIMS) techniques; surface morphology was studied using atomic force microscopy (AFM). Chlorine containing precursors such as AlCl3 are usually avoided in ALD process due to the risk of chamber contamination. However, experimental data of this study demonstrated that the use of N2H5Cl does not result in chlorine contamination due to the fact that temperature needed for HCl molecules to become reactive cannot be reached within the AlN ALD window (200–350 °C). No amount of chlorine was detected even by the most sensitive techniques such as SIMS, meaning it is fully removed out of the chamber during purge stages. A part of the obtained samples was subjected to annealing (1350 °C) to study effects of high-temperature processing in nitrogen atmosphere, the comparisons with unprocessed samples are provided.
INFLAMMATION AND INSULIN DYSREGULATION IN THE HORSE

OF DISSERTATION INFLAMMATION AND INSULIN DYSREGULATION IN THE HORSE Insulin dysregulation (ID) in the horse is receiving increasing attention as a serious health concern, in particular due to its association with the potentially career or life ending condition, laminitis. The role of inflammation and the immune system in ID as well as its associated health concerns has also been raised. However, the involvement of inflammation in and mechanisms behind ID in the horse remain unclear. Therefore, our overall hypothesis was that due in part to changes in their gut microbiota and plasma lipidome, horses with ID have changes in circulating proinflammatory markers, in particular in response to glycemic challenge, that further drive metabolic dysfunction. This work focuses on 7 potential associations between ID and inflammation to test this hypothesis; (H1) horses with ID will have an abnormal inflammatory response to glycemic challenge, (H2) ID horses will have differences in their gut microbiota compared to metabolically normal controls, (H3) these horses will likewise have differences in their plasma lipidome, (H4) response to routine vaccination will be reduced in horses with ID compared to metabolically normal controls, (H5) circulating endotoxin concentrations will be elevated in horses with ID, in particular in response to glycemic challenge, and their inflammatory and metabolic responses will be improved following supplementation with a gut modulating mannan rich fraction of the yeast cell wall, (H6) whole blood stimulation with endotoxin will induce TLR4 mediated inflammatory gene expression, and (H7) changing circulating lipid concentrations will improve both glycemic and inflammatory parameters in ID horses. Overall this work provides insight into contributing factors to ID in the horse, in particularly as they relate to inflammation.
Permittivity of 3D-Printed Nylon Substrates with Different Infill Patterns and Densities for Design of Microwave Components

Printed circuit boards, chemical etching, and computer numerical control milling currently dominate industrial processes for manufacturing microwave components. However, these manufacturing methods do not provide the flexibility for customization possible with additive manufacturing. Additive manufacturing (AM) has the potential to fabricate microwave components for desired frequency ranges with less effort in prototyping and fabrication. Relative permittivity (εr) of materials is a critical parameter in microwave component design, yet the value changes during the AM process. This article investigates how relative permittivity for nylon substrates, created with AM, changes with different infill densities and infill patterns. The measurement method and procedure can be used to design AM microwave components like antennas or dielectric-filled waveguides with desired characteristics. The two-microstrip-line method was used and improved for the accurate and convenient measurement of the relative permittivity of AM nylon substrates. Several nylon substrates with different infill patterns, including rectangular, hexagonal, triangular, and solid, were fabricated with AM to demonstrate how the relative permittivity value changes as the infill density increases. A linear relationship between the infill density of the rectangular pattern and the substrate permittivity was found. The permittivity data were applied to the design of a rectangular patch antenna for use in the 2.5-GHz WiMAX band. The fabricated antenna with AM, which was tested using a vector network analyzer, showed good agreement with simulation results. The method and procedure of permittivity measurements are specially designed to be applied in the design of microwave components with AM dielectric substrates.
ERASMUS UNIVERSITY ROTTERDAM Erasmus School of Economics Master Thesis: Econometrics and Management Science (Quantitative Finance) Optimization in an uncertain world The impact of uncertainty on portfolio allocation

In this paper, we investigate the impact of uncertainty on portfolio allocation and how incorporating stochasticity in the investment strategy improves performance. We use both stochastic programming and robust optimization to maximize return with constrained risk measured by Conditional Value-at-Risk (CVaR), using scenarios generated via Filtered Historical Simulation (FHS). We compare the results based on return, risk, stability of the weights over time, and a newly introduced dispersion measure. We find that incorporating uncertainty only slightly enhances performance. In an expanding window estimation, the effect of incorporating uncertainty in returns disappears and the inclusion of parameter uncertainty has a negative impact. Also, managerial and legislative restrictions have much influence on the optimization outcomes and induce the stochasticity in the risk constraint to have little impact. When we exclude these supplementary restrictions, incorporating uncertainty becomes more effective.