Miracle-dz/UniFAR-FTUs huggingface dataset:
Best practices for making reliable inferences from citizen science data: case study using eBird to estimate species distributions

Abstract Citizen science data are valuable for addressing a wide range of ecological research questions, and there has been a rapid increase in the scope and volume of data available. However, data from large-scale citizen science projects typically present a number of challenges that can inhibit robust ecological inferences. These challenges include: species bias, spatial bias, variation in effort, and variation in observer skill. To demonstrate key challenges in analysing citizen science data, we use the example of estimating species distributions with data from eBird, a large semi-structured citizen science project. We estimate three widely applied metrics for describing species distributions: encounter rate, occupancy probability, and relative abundance. For each method, we outline approaches for data processing and modelling that are suitable for using citizen science data for estimating species distributions. Model performance improved when data processing and analytical methods addressed the challenges arising from citizen science data. The largest gains in model performance were achieved with two key processes 1) the use of complete checklists rather than presence-only data, and 2) the use of covariates describing variation in effort and detectability for each checklist. Including these covariates accounted for heterogeneity in detectability and reporting, and resulted in substantial differences in predicted distributions. The data processing and analytical steps we outlined led to improved model performance across a range of sample sizes. When using citizen science data it is imperative to carefully consider the appropriate data processing and analytical procedures required to address the bias and variation. Here, we describe the consequences and utility of applying our suggested approach to semi-structured citizen science data to estimate species distributions. The methods we have outlined are also likely to improve other forms of inference and will enable researchers to conduct robust analyses and harness the vast ecological knowledge that exists within citizen science data.
Analysis of CDKN1C in fetal growth restriction and pregnancy loss

Background: Cyclin-dependent kinase inhibitor 1C (CDKN1C) is a key negative regulator of cell growth encoded by a paternally imprinted/maternally expressed gene in humans. Loss-of-function variants in CDKN1C are associated with an overgrowth condition (Beckwith-Wiedemann Syndrome) whereas “gain-of-function” variants in CDKN1C that increase protein stability cause growth restriction as part of IMAGe syndrome ( Intrauterine growth restriction, Metaphyseal dysplasia, Adrenal hypoplasia and Genital anomalies). As three families have been reported with CDKN1C mutations who have fetal growth restriction (FGR)/Silver-Russell syndrome (SRS) without adrenal insufficiency, we investigated whether pathogenic variants in CDKN1C could be associated with isolated growth restriction or recurrent loss of pregnancy. Methods: Analysis of published literature was undertaken to review the localisation of variants in CDKN1C associated with IMAGe syndrome or fetal growth restriction. CDKN1C expression in different tissues was analysed in available RNA-Seq data (Human Protein Atlas). Targeted sequencing was used to investigate the critical region of CDKN1C for potential pathogenic variants in SRS (n=66), FGR (n=37), DNA from spontaneous loss of pregnancy (n= 22) and women with recurrent miscarriages (n=78) (total n=203). Results: All published single nucleotide variants associated with IMAGe syndrome are located in a highly-conserved “hot-spot” within the PCNA-binding domain of CDKN1C between codons 272-279. Variants associated with familial growth restriction but normal adrenal function currently affect codons 279 and 281. CDKN1C is highly expressed in the placenta compared to adult tissues, which may contribute to the FGR phenotype and supports a role in pregnancy maintenance. In the patient cohorts studied no pathogenic variants were identified in the PCNA-binding domain of CDKN1C. Conclusion: CDKN1C is a key negative regulator of growth. Variants in a very localised “hot-spot” cause growth restriction, with or without adrenal insufficiency. However, pathogenic variants in this region are not a common cause of isolated fetal growth restriction phenotypes or loss-of-pregnancy/recurrent miscarriages.
Development of Ga-68 radiolabeled DOTA functionalized and acetylated PAMAM dendrimer-coated iron oxide nanoparticles as PET/MR dual-modal imaging agent

Abstract Gallium-68 radiolabeled DOTA- acetyl-PAMAM coated iron oxide nanoparticles (NPs) were developed as dual-modality agents for PET-MR imaging. The increase in the chelator content, acetylation step, and radiolabeling condition had distinctive effects on the physical, biological, and radiochemical properties of NPs. The r2 relaxivity coefficient value of the NPs was 96.7 mM−1s−1. High accumulation of candidate NPs was in the liver and spleen and about 3.4% ID/g uptake (tissue sampling), and a distinctive uptake (PET-CT image) were observed in the tumor site. These NPs could be used as the dual-modality agent for the diagnosis of the tumors via PET-MR imaging. Graphical Abstract
School social segregation and social inequalities in political engagement among 16 to 20 year olds in fourteen countries

ABSTRACT This paper assesses the explanatory power of a perspective arguing that school social segregation enhances social inequalities in political engagement because of the distinct effects that concentrations of adolescents of disadvantaged backgrounds in educational settings generate. It tests this argument with data of the 2000 Civic Education Study among Upper Secondary students and uses intentions to participate and political competences as outcomes to represent political engagement. Social inequalities in political competences turn out to be greater in states with the most segregated systems, but social disparities in intentions to participate are unrelated to the level of segregation. The paper argues that policy makers should consider creating a more integrated school system if they seek to reduce social inequalities in informed political participation.
Phylogeography of Miniopterus fuliginosus (Chiroptera) with special reference to Jeju Island, South Korea

Abstract To better understand the genetic relatedness of the eastern bent-wing bat Miniopterus fuliginosus across East Asia, mitochondrial D-loop sequences were analyzed from 39 M. fuliginosus individuals living on Jeju Island, South Korea. Seven different haplotypes were identified. Neighbor-joining analysis was performed and divergence time was calculated in combination with available online data on D-loop and ND2 sequences of M. fuliginosus in East Asia, respectively. Results suggest that M. fuliginosus populations living on Jeju Island and in Japan originated from China in the past 20,000 years.
The Effects of Rhodobacter sphaeroides on the Composition of Gut Microbiota and Short-chain Fatty Acids in Mice

This study aims to determine the effects of Rhodobacter sphaeroides 8513 on the physiological and biochemical indicators, short-chain fatty acids, and gut microbiota of healthy BALB/c mice. Mice were divided into the control group and R. sphaeroides group (5×108 CFU/mL). After 28 days of continuous gavage, fecal samples were collected for high-throughput sequencing, then mice were sacrificed and the serum was taken for biochemical analysis. Liver, kidney, and spleen were obtained for organ coefficient calculation, and cecum contents were collected for short-chain fatty acid analysis by gas chromatography. The results showed that there was no significant difference in body weight gain, alanine aminotransferase (ALT) and urea nitrogen (BUN) levels between the control group and R. sphaeroides group, while R. sphaeroides significantly decreased the aspartate aminotransferase (AST) and creatinine (CRE) level. No side effect of R. sphaeroides treatment on the basic physiological health of mice was observed. R. sphaeroides significantly increased the content of acetic acids in the gut of mice, while there were no significant changes in the concentration of butyric and propionic acid. High-throughput sequencing analysis indicated that there was a significant difference in α-diversity between these 2 groups, while there was no significant difference in β-diversity between them. R. sphaeroides not only increased the abundance of anaerobic bacteria of Rhodospirillaceae, Desulfovibrionaceae, and Helicobacter in the gut of mice, but also increased the abundance of the predominant microflora in the gut such as Bacteroidaceae (Bacteroides), Prevotellaceae, Clostridiales_vadinBB60_group (Closporaceae). These results suggested that R. sphaeroides 8513 could modulate the microbial ecology in the gut of mice.
Irrigation Requirements and Yields of Maize Crop Under Future Climate in Some Cities of Northern Cameroon

Using meteorological data obtained from Regional Model (REMO), maize yields from the years 2020 to 2099 were simulated by AquaCrop Model in Maroua, Garoua and Kaélé. These future yields are almost nil for the three cities. In view to determine the minimum quantities of water needed to improve them, the hypothesis of no water moisture stress was considered. For the four periods of 20 consecutive years (2020-2039, 2040-2059, 2060-2079 and 2080-2099), average yields of 5.21, 5.11, 4.97, and 4.73 ton/ha are obtained in Garoua, 5.05, 4.97, 4.64, and 3.87 ton/ha in Maroua and 4.91, 4.82, 4.51 and 3.69 t/ha in Kaélé. The average quantities of water irrigation (also obtained with AquaCrop) for the same periods are 13, 19, 46 and 78 mm for Garoua; 34, 48, 84 and 147 mm for Maroua and 57, 68, 111 and 171 mm for Kaélé. The yields by considering these irrigation water quantities are improved and the following values are obtained for the four periods indicated above: 5.20, 5.10, 4.99 and 4.82 ton/ha for Garoua; 5.10, 5.00, 4.78 and 4.35 ton/ha for Maroua and 4.99, 4.91, 4.75 and 4.50 ton/ha for Kaélé.
Overvoltages and Transients Identification In On-line Bushing Monitoring

Overvoltages and transients are sometimes recognized as the cause of bushings’ rapid failure. This fact is confirmed by the studies published at the 2018 CIGRE session. They can also initiate dangerous resonance phenomena in transformer windings. The identification of very fast overvoltages characterized by high dynamics of voltage changes, so-called "transients", is difficult due to the limited frequency response of station voltage transformers. However, the bushing monitoring systems, based on the so-called "voltage method" can be used for this purpose successfully. There are several running bushing monitoring systems based on this method in Poland. The transients’ events are registered together with their oscillographs in Transformer Monitoring Systems (TMS). The overvoltage statistics are also performed to support service procedures. The TMS are integrated with station systems, which greatly increases the possibility of overvoltages’ phenomena analyzing.
Washable Colorimetric Nanofiber Nonwoven for Ammonia Gas Detection

The colorimetric sensor is a facile, cost-effective, and non-power-operated green energy material for gas detection. In this study, the colorimetric sensing property of a meta-aramid/dye 3 nanofiber sensor for ammonia (NH3) gas detection was investigated. This colorimetric sensor was prepared using various dye 3 concentrations via electrospinning. Morphological, thermal, structural, and mechanical analyses of the sensor were carried out by field-emission scanning electron microscopy, thermogravimetric analysis, Fourier-transform infrared spectroscopy, and a universal testing machine, respectively. A homemade computer color matching machine connected with a gas flow device characterized the response of the meta-aramid/dye 3 nanofiber colorimetric sensor to various exposure levels of NH3 gas. From the results, we confirmed that this colorimetric green energy sensor could detect ammonia gas in the concentration of 1–10 ppm with a sensing response time of 10 s at room temperature. After washing with laundry detergent for 30 min, the colorimetric sensors still exhibited sensing property and reversibility.
Myelin Oligodendrocyte Glycoprotein (MOG) Antibody Positive Patients in a Multi-Ethnic Canadian Cohort

Introduction: Myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease is a recently described central nervous system (CNS) inflammatory disorder with phenotypic overlap with Neuromyelitis Optica Spectrum Disorder (NMOSD). NMOSD seronegative patients, and those with limited forms of the disorder, become suspects for MOG antibody-associated disease. We describe a multi-ethnic population with MOG antibody seropositivity from the University of British Columbia MS/NMO clinic. Methods: AQP4-antibody seronegative patients presenting 2005–2016 with CNS inflammatory disease suspicious for NMOSD, as well as 20 MS controls, were retrospectively tested for MOG-IgG1 antibodies by live cell-based assay at Oxford Autoimmune Neurology Diagnostic Laboratory (UK) and by a commercial fixed cell-based assay at MitogenDx (Calgary, Canada). Additional MOG seropositive cases were identified through routine clinical interaction (2016–2018) using one of these laboratories. Clinical data was reviewed retrospectively. Results: Retrospective testing identified 21 MOG seropositives (14 by live assay only, 3 by fixed assay only and 4 by both) representing 14% of the “NMOSD suspects” cohort. One multiple sclerosis (MS) control serum was MOG seropositive. Twenty additional MOG positive cases were identified prospectively. Of 42 patients (27 female), median disease onset age was 29 years (range 3–62; 9 pediatric cases), 20 (47%) were non-Caucasian, and 3 (7%) had comorbid autoimmune disease. Most common onset phenotypes were optic neuritis (23, 55%; 8 bilateral) and myelitis (9, 21%; 6 longitudinally extensive) Three of the patients in our cohort experienced cortical encephalitis; two presented with seizures. Onset was moderate-severe in 64%, but 74% had good response to initial steroid therapy. Cumulative relapse probability for the MOG positive group at 1 year was 0.428 and at 4 years was 0.628. Most had abnormal brain imaging, including cortical encephalitis and poorly demarcated subcortical and infratentorial lesions. Few “classic MS” lesions were seen. Optic nerve lesions (frequently bilateral) were long and predominantly anterior, but 5 extended to the chiasm. Spinal cord lesions were long and short, with involvement of multiple spinal regions simultaneously, including the conus medullaris. Conclusions: Our MOG seropositive patients display phenotypes similar to previous descriptions, including cortical lesions with seizures and conus medullaris involvement. Many patients relapsed, predominantly in a different CNS location from onset. Serologic data from two different cell-based antibody assays highlight the discrepancies between live and fixed testing for MOG antibodies.
Cephalopods of Australia and Sub-Antarctic Territories

Australian waters contain the highest diversity of cephalopods (squid, cuttlefish and octopus) found anywhere in the world. They are highly significant ecologically, both as top-level predators and as prey for numerous vertebrates, including fishes, seals, cetaceans and seabirds. Cephalopods of Australia and Sub-Antarctic Territories is a comprehensive guide covering 226 species, which represent over a quarter of the world’s cephalopod fauna. With an emphasis on identification, this book includes keys, species descriptions, full-colour illustrations and distribution maps, as well as a summary of the biology and behaviour of cephalopods and fisheries information. This is an invaluable tool for researchers and fisheries experts as well as amateur naturalists, fishers and divers.
The complete chloroplast genome sequence of Dendrobium densiflorum and its phylogenetic implications

Abstract Dendrobium is one of the largest genera in Orchidaceae with approximately 1500 species. Many of them have been used as Traditional Chinese Medicine (TCM) for hundreds of years. Here, the first complete chloroplast genome sequence of D. densiflorum was reported and characterized. The complete cpDNA of D. densiflorum is a circular molecule of 153,122 bp, which contains 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Our phylogenetic analysis indicated that the newly sequenced cpDNA of D. densiflorum could be used for the phylogenetic study of Dendrobium species.
Dust Suppression Analysis of a New Spiral Hopper Using CFD-DEM Simulations and Experiments

A new dust suppression hopper with a spiral guide plate embedded in the conventional hopper is proposed for the dust suppression of hopper transfer processes in this article. The Computational Fluid Dynamics-Discrete Element Method (CFD-DEM) coupling numerical method is used to investigate the particle motion and flow field distribution of the hopper transfer process. The experiment is undertaken to determine dust suppression performance. The results show that the maximum particle velocity for the spiral hopper is dropped by 1.6 m/s compared to the conventional hopper, which means the collision of the particles and the spiral hopper is weakened. The axial airflow velocity of the spiral is reduced. In addition, the maximum dust concentration of the spiral hopper inlet is reduced by 56.9% due to the impact velocity of particles is small, and the secondary fugitive dust is controlled inside a semi-closed space formed by the spiral guide plate. It is thus concluded that the spiral hopper provides an effective way in dust control.
Energy-Efficient UAV Crowdsensing with Multiple Charging Stations by Deep Learning

Different from using human-centric mobile devices like smartphones, unmanned aerial vehicles (UAVs) can be utilized to form a new UAV crowdsensing paradigm, where UAVs are equipped with build-in high-precision sensors, to provide data collection services especially for emergency situations like earthquakes or flooding. In this paper, we aim to propose a new deep learning based framework to tackle the problem that a group of UAVs energy-efficiently and cooperatively collect data from low-level sensors, while charging the battery from multiple randomly deployed charging stations. Specifically, we propose a new deep model called "j-PPO+ConvNTM" which contains a novel spatiotemporal module "Convolution Neural Turing Machine" (ConvNTM) to better model long-sequence spatiotemporal data, and a deep reinforcement learning (DRL) model called "j-PPO", where it has the capability to make continuous (i.e., route planing) and discrete (i.e., either to collect data or go for charging) action decisions simultaneously for all UAVs. Finally, we perform extensive simulation to show its illustrative movement trajectories, hyperparameter tuning, ablation study, and compare with four other baselines.
The Misfolding Pathway of SOD1: Implications for Drug Design in ALS

With the development of modern medicine, many diseases and maladies have been eradicated or rendered non-fatal. This has allowed human beings to live longer and more comfortably. As the average lifespan has increased, however, diseases that tend to occur late in life have become more prominent. Neurodegenerative diseases, such as Alzheimer’s disease and amyotrophic lateral sclerosis (ALS), affect the brain and nervous system, killing neuronal cells necessary for proper bodily function. In almost all cases, protein misfolding and the accumulation of aggregated material are involved in these toxic effects. In the case of ALS, protein misfolding and aggregation occur in motor neurons, causing them to die which leads to a progressive full-body paralysis and death by respiratory failure. In ~20% of ALS cases showing familial inheritance, over 180 mutations in the Cu, Zn superoxide dismutase protein (SOD1) have been recognized as causing the disease. These mutations do not have the common property of compromising the superoxide scavenging activity of this protein. Rather, mutations increase its propensity to adopt non-native conformations that acquire some
Jabberwocky: an ontology-aware toolkit for manipulating text

Unstructured textual data is underused, as extracting the key textual elements is complicated by a lack of structured terms, e.g., collecting the sentences from a corpus that are discussing a particular topic. To extract valuable text about a topic from a corpus, a user will need to gather a set of related terms. For example, when analysing clinical documents we can extract sentences by using specific clinicial terms. However this can miss additional valuable sentences where synonyms are used instead (e.g., physician notes that use shorthand). By considering terms and their synonyms we can extract more sentences from a corpus, making more data available for analysis. One way to do this and represent our knowledge of terms associated with a domain is to create an ontology. Ontologies allow us to formalise our knowledge of a domain in a condensed manner by using controlled terms, called classes (Hoehndorf, Schofield, & Gkoutos, 2015). Classes can be annotated with metadata, including synonyms. Ontologies can include relationships between terms, and annotations such as cross-references to other ontologies (Hoehndorf et al., 2015).
Lived Experiences of Asian and Latinx Online Doctoral Students

ABSTRACT Over the past two decades, Asian and Hispanic immigrants who have been living in the United States for ≥ 10 years has increased substantially. Yet, Asian and Latinx students are behind Caucasians in doctoral degree completion rates. Enhancing enrollment, time-to-completion rates, and decreasing attrition, are of national concern among promoters of higher educational for these groups. We conducted a phenomenological study to explore the lived experiences of seven Asian and 10 Latinx online doctoral students (N = 17). Participants were recruited using nonrandom purposive convenience sampling and snowball techniques. Data were collected by one of three members of the research team. The other two research team members independently coded and conducted the thematic analysis of the de-identified transcribed interviews and reached consensus for inter-rater reliability. The major findings were that both Asian and Latinx students experienced a sense of duty and rely on family to earn a doctoral degree. Asian students were typically not the first in their families to pursue a doctorate whereas Latinx students usually were. Asian students feel pressure to succeed in the “respectable professions” by their families. Latinx students rely on “cultural capital” to succeed. Language barriers were more of a challenge for Latinx students than for Asian students. Asian and Latinx students desire shorter timeframes for feedback. The research implications include that integrating a limited amount of synchronous teaching could improve their feeling of cohesiveness which coincides with collectivism. Also, shortening timeframes for feedback during the dissertation phase could impact time to completion and decrease attrition rates.
PHENIX results on J/ψ polarization in p+p collisions.

One of the big questions in quarkonia production is how heavy-quark pairs are produced in the initial hard scattering and hadronize into final quarkonia states. This question also affects the estimation of quarkonia breakup cross-sections and color screening in heavy ion collisions. Many existing models describe well general features of quarkonia production like cross-section and transverse momentum distributions. In order to differentiate between various models one has to study quarkonia production in more details. One of such tools is a study of angular distributions of decay leptons, usually called polarization. The PHENIX experiment has measured inclusive J/ψ polar and azimuthal angular decay coefficients in the mid (|y|<0.35) and forward (1.2<|y|<2.2) rapidity regions in p+p collisions at 200 GeV and 510 GeV. This talk will present the analysis strategy as well as the results in different polarization frames.