Precision education: A Bayesian nonparametric approach for handling item and examinee heterogeneity in assessment data

We propose a novel nonparametric Bayesian IRT model in this paper by introducing the clustering effect at question level and further assume heterogeneity at examinee level under each question cluster, characterized by the mixture of Binomial distributions. The main contribution of this work is threefold: (1) We demonstrate that the model is identifiable. (2) The clustering effect can be captured asymptotically and the parameters of interest that measure the proficiency of examinees in solving certain questions can be estimated at a root n rate (up to a log term). (3) We present a tractable sampling algorithm to obtain valid posterior samples from our proposed model. We evaluate our model via a series of simulations as well as apply it to an English assessment data. This data analysis example nicely illustrates how our model can be used by test makers to distinguish different types of students and aid in the design of future tests

Patterns in leaf traits of woody species and their environmental determinants in a humid karstic forest in southwest China

IntroductionLeaf functional traits constitute a crucial component of plant functionality, providing insights into plants’ adaptability to the environment and their regulatory capacity in complex habitats. The response of leaf traits to environmental factors at the community level has garnered significant attention. Nevertheless, an examination of the environmental factors determining the spatial distribution of leaf traits in the karst region of southwest China remains absent.MethodsIn this study, we established a 25 ha plot within a karst forest and collected leaf samples from 144 woody species. We measured 14 leaf traits, including leaf area (LA), leaf thicknes (LT), specific leaf area (SLA), leaf length to width ratio (LW), leaf tissue density (LTD), leaf carbon concentration (LC), leaf nitrogen concentration (LN), and leaf phosphorus concentration (LP), leaf potassium concentration (LK), leaf calcium concentration (LCa), leaf magnesium Concentration (LMg), leaf carbon to nitrogen ratio (C/N), leaf carbon to phosphorus ratio (C/P), and leaf nitrogen to phosphorus ratio (N/P), to investigate the spatial distribution of community-level leaf traits and the response of the leaf trait community-weighted mean (CWM) to topographic, soil, and spatial factors.ResultsResults showed that the CWM of leaf traits display different spatial patterns, first, the highest CWM values for LT, LTD, C/N, and C/P at hilltops, second, the highest CWM values for LA, SLA, LW, LC, LN, LP, and LK at depressions, and third, the highest CWM values for LCa, LMg, and N/P at slopes. The correlation analysis showed that topographic factors were more correlated with leaf trait CWM than soil factors, with elevation and slope being the strongest correlations. RDA analysis showed that topographic factors explained higher percentage of leaf trait CWM than soil factors, with the highest percentage of 19.96% being explained by elevation among topographic factors. Variance Partitioning Analysis showed that the spatial distribution of leaf traits is predominantly influenced by the combined effects of topography and spatial factors (37%-47% explained), followed by purely spatial factors (24%-36% explained).DiscussionThe results could improve our understanding of community functional traits and their influencing factors in the karst region, which will contribute to a deeper understanding of the mechanisms that shape plant communities

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions

Noninvasive Assessment of Antenatal Hydronephrosis in Mice Reveals a Critical Role for Robo2 in Maintaining Anti-Reflux Mechanism

Antenatal hydronephrosis and vesicoureteral reflux (VUR) are common renal tract birth defects. We recently showed that disruption of the Robo2 gene is associated with VUR in humans and antenatal hydronephrosis in knockout mice. However, the natural history, causal relationship and developmental origins of these clinical conditions remain largely unclear. Although the hydronephrosis phenotype in Robo2 knockout mice has been attributed to the coexistence of ureteral reflux and obstruction in the same mice, this hypothesis has not been tested experimentally. Here we used noninvasive high-resolution micro-ultrasonography and pathological analysis to follow the progression of antenatal hydronephrosis in individual Robo2-deficient mice from embryo to adulthood. We found that hydronephrosis progressed continuously after birth with no spontaneous resolution. With the use of a microbubble ultrasound contrast agent and ultrasound-guided percutaneous aspiration, we demonstrated that antenatal hydronephrosis in Robo2-deficient mice is caused by high-grade VUR resulting from a dilated and incompetent ureterovesical junction rather than ureteral obstruction. We further documented Robo2 expression around the developing ureterovesical junction and identified early dilatation of ureteral orifice structures as a potential fetal origin of antenatal hydronephrosis and VUR. Our results thus demonstrate that Robo2 is crucial for the formation of a normal ureteral orifice and for the maintenance of an effective anti-reflux mechanism. This study also establishes a reproducible genetic mouse model of progressive antenatal hydronephrosis and primary high-grade VUR

Analysis of the function of IL-10 in chickens using specific neutralising antibodies and a sensitive capture ELISA

AbstractIn mammals, the inducible cytokine interleukin 10 is a feedback negative regulator of inflammation. To determine the extent to which this function is conserved in birds, recombinant chicken IL-10 was expressed as a secreted human Ig Fc fusion protein (chIL-10-Fc) and used to immunise mice. Five monoclonal antibodies (mAb) which specifically recognise chicken IL-10 were generated and characterised. Two capture ELISA assays were developed which detected native chIL-10 secreted from chicken bone marrow-derived macrophages (chBMMs) stimulated with lipopolysaccharide (LPS). Three of the mAbs detected intracellular IL-10. This was detected in only a subset of the same LPS-stimulated chBMMs. The ELISA assay also detected massive increases in circulating IL-10 in chickens challenged with the coccidial parasite, Eimeria tenella. The same mAbs neutralised the bioactivity of recombinant chIL-10. The role of IL-10 in feedback control was tested in vitro. The neutralising antibodies prevented IL-10-induced inhibition of IFN-γ synthesis by mitogen-activated lymphocytes and increased nitric oxide production in LPS-stimulated chBMMs. The results confirm that IL-10 is an inducible feedback regulator of immune response in chickens, and could be the target for improved vaccine efficacy or breeding strategies

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Multi-Objective Gate Allocation Problem Based on Multi-Commodity Network Flow Model

Gate allocation has always been a fundamental but critical issue in the daily operation of airports, which is related to service quality and schedule efficiency. In order to obtain reasonable and efficient gate allocation results, in this paper, a multi-commodity network flow model is proposed to describe the gate allocation process in flight flow, based on which a multi-objective optimization model is constructed. It not only comprehensively considers the flight information of aircraft arrivals and departures, but also integrates the broader interests of passengers, airlines, and airports. To solve it, a linear weighting technique is applied. In addition, K-means cluster analysis is used to explore different weight combinations, and on this basis, the idle time of the gate is introduced as a performance evaluation index to guide the selection of the final weight. By analyzing the optimization results of actual operation data, the proposed model significantly balances the interests of multiple parties and the number of flights at each gate and has a relatively high gate-utilization rate. It can provide rich decision support and a reasonable allocation scheme for airport management to a certain extent