Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple phytohormone signalling pathways modulate susceptibility of tomato plants to Alternaria alternata f. sp. lycopersici

Three phytohormone molecules – ethylene (ET), jasmonic acid (JA) and salicylic acid (SA) – play key roles in mediating disease response to necrotrophic fungal pathogens. This study investigated the roles of the ET, JA, and SA pathways as well as their crosstalk during the interaction between tomato (Solanum lycopersicum) plants and a necrotrophic fungal pathogen Alternaria alternata f. sp. lycopersici (AAL). Both the ET and JASMONIC ACID INSENSITIVE1 (JAI1) receptor-dependent JA signalling pathways are necessary for susceptibility, while SA response promotes resistance to AAL infection. In addition, the role of JA in susceptibility to AAL is partly dependent on ET biosynthesis and perception, while the SA pathway enhances resistance to AAL and antagonizes the ET response. Based on these results, it is proposed that ET, JA, and SA each on their own can influence the susceptibility of tomato to AAL. Furthermore, the functions of JA and SA in susceptibility to the pathogen are correlated with the enhanced or decreased action of ET, respectively. This study has revealed the functional relationship among the three key hormone pathways in tomato defence against AAL.
Regularization Parameter Estimation for Non-Negative Hyperspectral Image Deconvolution

This paper aims at studying a method to automatically estimate the regularization parameters of non-negative hyperspectral image deconvolution methods. The deconvolution problem is formulated as a multi-objective optimization problem and the properties of the corresponding response surface are studied. Based on these properties, the minimum distance criterion (MDC) and the maximum curvature criterion (MCC) are proposed to estimate regularization parameters especially for the non-negativity constrained deconvolution problem. MDC has good theoretical properties (convexity and uniqueness) but requires to choose a reference point. On the contrary, MCC does not need to choose any reference point but does not have interesting theoretical properties. A grid-search-based approach to minimize the computational cost of MDC and MCC is proposed. It results in fast approaches to estimate the regularization parameters. Based on simulated 2D images, the proposed approaches are compared with the state-of-the-art methods, confirming the effectiveness of the MDC and MCC for the non-negativity constrained image deconvolution problem. In the case of non-negative hyperpsectral image deconvolution, the fast MDC yields better performances than the fast MCC. An application to real-world hyperspectral fluorescence microscopy images is also provided; it confirms the superiority of MDC.
Inflation and output forecasts for South Africa: monetary transmission implications

South Africa’s recent adoption of inflation targeting increases the need for good forecasting models of inflation and models for understanding the monetary transmission mechanism. This paper presents multi-step models for inflation and output, four-quarters ahead. The inflation model has an equilibrium correction form, which clarifies medium- or longer-run influences on inflation, including opening the economy to foreign imports. The model confirms the importance of the output gap and the exchange rate for forecasting inflation; and the influence from recent changes in the current account surplus to GDP ratio, which is also sensitive to short-term interest rates. However, a rise in interest rates can also raise inflation in the short-run, via a rise in mortgage interest payments (a component of the consumer price index). The unfortunate policy implications for South Africa are discussed. The output model uses a stochastic trend to measure long-run changes in the capacity to produce. On the demand side there are important negative interest rate effects, though these have been altered by changes in the monetary policy regime. The trade surplus and government surplus to GDP ratios, which also respond to interest rate changes, and improvements in the terms-of-trade, all have a positive effect on future output.
NONCONCAVE PENALIZED M-ESTIMATION WITH A DIVERGING NUMBER OF PARAMETERS

M-estimation is a widely used technique for robust statistical inference. In this paper, we investigate the asymptotic properties of a nonconcave penalized M-estimator in sparse, high-dimensional, linear regression models. Compared with classic M-estimation, the nonconcave penalized M-estimation method can perform parameter estimation and variable selection simultaneously. The proposed method is resistant to heavy-tailed errors or outliers in the response. We show that, un- der certain appropriate conditions, the nonconcave penalized M-estimator has the so-called "Oracle Property"; it is able to select variables consistently, and the esti- mators of nonzero coefficients have the same asymptotic distribution as they would if the zero coefficients were known in advance. We obtain consistency and asymp- totic normality of the estimators when the dimension pn of the predictors satisfies the conditions pn log n/n → 0 and p 2/n → 0, respectively, where n is the sample size. Based on the idea of sure independence screening (SIS) and rank correla- tion, a robust rank SIS (RSIS) is introduced to deal with ultra-high dimensional data. Simulation studies were carried out to assess the performance of the proposed method for finite-sample cases, and a dataset was analyzed for illustration.
Third-Degree Hindpaw Burn Injury Induced Apoptosis of Lumbar Spinal Cord Ventral Horn Motor Neurons and Sciatic Nerve and Muscle Atrophy in Rats

Background. Severe burns result in hypercatabolic state and concomitant muscle atrophy that persists for several months, thereby limiting patient recovery. However, the effects of burns on the corresponding spinal dermatome remain unknown. This study aimed to investigate whether burns induce apoptosis of spinal cord ventral horn motor neurons (VHMNs) and consequently cause skeletal muscle wasting. Methods. Third-degree hindpaw burn injury with 1% total body surface area (TBSA) rats were euthanized 4 and 8 weeks after burn injury. The apoptosis profiles in the ventral horns of the lumbar spinal cords, sciatic nerves, and gastrocnemius muscles were examined. The Schwann cells in the sciatic nerve were marked with S100. The gastrocnemius muscles were harvested to measure the denervation atrophy. Result. The VHMNs apoptosis in the spinal cord was observed after inducing third-degree burns in the hindpaw. The S100 and TUNEL double-positive cells in the sciatic nerve increased significantly after the burn injury. Gastrocnemius muscle apoptosis and denervation atrophy area increased significantly after the burn injury. Conclusion. Local hindpaw burn induces apoptosis in VHMNs and Schwann cells in sciatic nerve, which causes corresponding gastrocnemius muscle denervation atrophy. Our results provided an animal model to evaluate burn-induced muscle wasting, and elucidate the underlying mechanisms.
Abstract data types and the development of data structures

Abstract data types can play a significant role in the development of software that is reliable, efficient, and flexible. This paper presents and discusses the application of an algebraic technique for the specification of abstract data types. Among the examples presented is a top-down development of a symbol table for a block structured language; a discussion of the proof of its correctness is given. The paper also contains a brief discussion of the problems involved in constructing algebraic specifications that are both consistent and complete.
Changes in sea-level associated with modifications on the mass balance of the Greenland and Antartic ice sheets over the 21st century

Changes in runo from Greenland and Antarctica are often cited as one of the major concerns linked to anthropogenic changes in climate. The changes in mass balance, and associated changes in sea-level, of these two ice sheets are examined by comparing the predictions of the six possible combinations of two climate models and three methods for estimating melting and runo . All models are solved on 20 and 40 km grids respectively for Greenland and Antarctica. The two temperature based runo parameterizations give adequate results for Greenland, less so for Antarctica. The energy balance based approach, which relies on an explicit modelling of the temperature and density structure within the snow cover, gives similar results when coupled to either climate model. The Greenland ice sheet, for a reference climate scenario similar to the IPCC's IS92a, is not expected to contribute signi cantly to changes in the level of the ocean over the 21 century. The changes in mass balance in Antarctica are dominated by the increase in snowfall, leading to a decrease in sea-level of 4 cm by 2100. The range of uncertainty in these predictions is estimated by repeating the calculation with the simpler climate model for seven climate change scenarios. Greenland would increase the level of the oceans by 0 { 2 cm, while Antarctica would decrease it by 2.5 { 6.5 cm. The combined e ect of both ice sheets lowers the sea-level by 2.5 { 4.5 cm over the next 100 years, this represents a 25% reduction of the sea-level rise estimated from thermal expansion alone. This surprisingly small range of uncertainty is due
Variations in Soil Microbial Communities and Residues Along an Altitude Gradient on the Northern Slope of Changbai Mountain, China

Altitudinally-defined climate conditions provide specific vegetation types and soil environments that could influence soil microbial communities, which in turn may affect microbial residues. However, the knowledge is limited in terms of the degree to which microbial communities and residues present and differ along altitude. In this study, we examined the soil microbial communities and residues along the northern slope of Changbai Mountain, China using phospholipid fatty acid (PLFA) and amino sugar analysis, respectively. Soil samples were taken from five different vegetation belts defined by climates. Principal component analysis (PCA) revealed substantial differences in soil microbial community composition among study sites, appeared to be driven primarily by soil pH and C/N ratio on the first principal component (PC1) which accounted for 50.7% of the total sample variance. The alpine tundra was separated from forest sites on the second principal component (PC2) by a signifiscantly higher amount of fungal PLFA (18:2ω6,9). Soil pH and C/N ratio were also correlated with the ratios of Gram-positive to Gram-negative bacteria (Gm+/Gm−), glucosamine to galactosamine (GluN/GalN), and glucosamine to muramic acid (GluN/MurA). Both total PLFAs and amino sugars were positively correlated with soil organic carbon, inorganic nitrogen, available phosphorus and potassium. We concluded that soil pH and C/N ratio were the most important drivers for microbial community structure and amino sugar pattern, while substrate availability was of great importance in determining the concentrations of microbial communities and residues. These findings could be used to facilitate interpretation of soil microbial community and amino sugar data derived from measurements in latitude or managed forests.
Neurotrophin-Dependent Dendritic Filopodial Motility: A Convergence on PI3K Signaling

Synapse formation requires contact between dendrites and axons. Although this process is often viewed as axon mediated, dendritic filopodia may be actively involved in mediating synaptogenic contact. Although the signaling cues underlying dendritic filopodial motility are mostly unknown, brain-derived neurotrophic factor (BDNF) increases the density of dendritic filopodia and conditional deletion of tyrosine receptor kinase B (TrkB) reduces synapse number in vivo. Here, we report that TrkB associates with dendritic growth cones and filopodia, mediates filopodial motility, and does so via the phosphoinositide 3 kinase (PI3K) pathway. We used genetic and pharmacological manipulations of mouse hippocampal neurons to assess signaling downstream of TrkB. Conditional knock-out of two downstream negative regulators of TrkB signaling, Pten (phosphatase with tensin homolog) and Nf1 (neurofibromatosis type 1), enhanced filopodial motility. This effect was PI3K-dependent and correlated with synaptic density. Phosphatidylinositol 3,4,5-trisphosphate (PIP3) was preferentially localized in filopodia and this distribution was enhanced by BDNF application. Thus, intracellular control of filopodial dynamics converged on PI3K activation and PIP3 accumulation, a cellular paradigm conserved for chemotaxis in other cell types. Our results suggest that filopodial movement is not random, but responsive to synaptic guidance molecules.
Probabilistic Models of Cross-Lingual Semantic Similarity in Context Based on Latent Cross-Lingual Concepts Induced from Comparable Data

We propose the first probabilistic approach to modeling cross-lingual semantic similarity (CLSS) in context which requires only comparable data. The approach relies on an idea of projecting words and sets of words into a shared latent semantic space spanned by language-pair independent latent semantic concepts (e.g., crosslingual topics obtained by a multilingual topic model). These latent cross-lingual concepts are induced from a comparable corpus without any additional lexical resources. Word meaning is represented as a probability distribution over the latent concepts, and a change in meaning is represented as a change in the distribution over these latent concepts. We present new models that modulate the isolated out-ofcontext word representations with contextual knowledge. Results on the task of suggesting word translations in context for 3 language pairs reveal the utility of the proposed contextualized models of crosslingual semantic similarity.
The Effects of a Portable Computer Algebra System (CAS) on Pre-university Students’ Attitudes towards CAS

: The main objective of this study was to investigate the effects of a portable computer algebra system (CAS) on students’ attitudes towards CAS. An intact class of second year pre-university (Year 12) students in Singapore participated in this study. The participating students were each given access to a CAS calculator for approximately six months and underwent a CAS Intervention Programme (CASIP). The CAS Attitude Scale (CASAS) was administered on three separate occasions to the participating class to measure students’ attitudes towards CAS. The CASAS comprises four subscales of 10 items to measure students’ sense of Anxiety, Confidence, Liking and Usefulness in regard to the CAS. Based on paired-sample t-tests, even though the second and third surveys indicated improvement in all four subscales and the overall scale, with the exception of the liking subscale in the first comparison, the results were not statistically significant.
A Drosophila LexA Enhancer-Trap Resource for Developmental Biology and Neuroendocrine Research

Novel binary gene expression tools like the LexA-LexAop system could powerfully enhance studies of metabolism, development, and neurobiology in Drosophila. However, specific LexA drivers for neuroendocrine cells and many other developmentally relevant systems remain limited. In a unique high school biology course, we generated a LexA-based enhancer trap collection by transposon mobilization. The initial collection provides a source of novel LexA-based elements that permit targeted gene expression in the corpora cardiaca, cells central for metabolic homeostasis, and other neuroendocrine cell types. The collection further contains specific LexA drivers for stem cells and other enteric cells in the gut, and other developmentally relevant tissue types. We provide detailed analysis of nearly 100 new LexA lines, including molecular mapping of insertions, description of enhancer-driven reporter expression in larval tissues, and adult neuroendocrine cells, comparison with established enhancer trap collections and tissue specific RNAseq. Generation of this open-resource LexA collection facilitates neuroendocrine and developmental biology investigations, and shows how empowering secondary school science can achieve research and educational goals.
The Role of Nitric Oxide in Development of Topographic Precision in the Retinotectal Projection of Chick

The axonal projection from the retina to the tectum exhibits a precise topographic order in the mature chick such that neighboring ganglion cells send axons to neighboring termination zones in the contralateral tectum. The initial pattern formed during development is much less organized and is refined to the adult pattern during a discrete period of development. Refinement includes elimination of radically aberrant projections, such as those from the temporal side of the retina to posterior regions of the tectum, as well as a more subtle improvement in the topographic precision of the projection. The enzyme that synthesizes nitric oxide is expressed at high levels in the tectum during the developmental period in which the topography improves. Pharmacological blockade of nitric oxide synthesis during this period prevented elimination of topographically inappropriate retinotectal projections in a dose-dependent manner. This effect could not be duplicated by treatment of embryos with a vasoconstrictor, indicating that vascular changes were not a factor. These results show that nitric oxide is involved in refinement of the topography of the retinotectal projection as well as in other aspects of refinement of this projection in developing chick.
Dollarization and the multiple currency phenomenon in Lao PDR: Costs, benefits and policy options

The multiple currency phenomenon (MCP) in Lao PDR takes the form of the use of foreign currencies such as dollars and baht in the presence of a domestically issued currency. The MCP has both costs and benefits. The costs include the social loss associated with seigniorage, the inability to conduct an independent monetary policy and the relative ineffectiveness of the exchange rate as an adjustment mechanism. The benefits of the MCP include the discipline imposed on the government by limiting its capacity to finance spending through inflation tax, and the stability and certainty induced by an effectively fixed exchange rate. Since the costs appear to exceed the benefits, how should the Government of Lao PDR respond? Enforcing the use of the kip is not the answer, and may well be counter-productive. This is because the MCP is not the problem, but is merely a symptom. The problem is a lack of confidence in the kip, whilst the symptom is the use of another currency such as the dollar or baht. The causes of the problem emanate from an underdeveloped monetary system, macroeconomic instability, and weak legal and institutional systems. These are the problems that need to be addressed directly. When these problems are addressed, then the symptom, which is the MCP, will also cease to be a constraint.
Glycaemic index and glycaemic load values of commercially available products in the UK

The objective of this paper is to provide glycaemic index (GI) and glycaemic load (GL) values for a variety of foods that are commercially available in the UK and to compare these with previously published values. Fasted subjects were given isoglucidic (50 or 25 g carbohydrate) servings of a glucose reference at least two to three times, and test foods once, on separate occasions. For each test food, tests were repeated in at least eight subjects. Capillary blood glucose was measured via finger-prick samples in fasting subjects (0 min) and at 15, 30, 45, 60, 90 and 120 min after the consumption of each test food. The GI of each test food was calculated geometrically by expressing the incremental area under the blood glucose response curve (IAUC) of each test food as a percentage of each subject's average IAUC for the reference food. GL was calculated as the product of the test food's GI and the amount of available carbohydrate in a reference serving size. The majority of GI values of foods tested in the current study compare well with previously published values. More importantly, our data set provides GI values of several foods previously untested and presents values for foods produced commercially in the UK.
UvA-DARE ( Digital Academic Repository ) MonetDB : Two Decades of Research in Column-oriented Database Architectures

MonetDB is a state-of-the-art open-source column-store database management system targeting applications in need for analytics over large collections of data. MonetDB is actively used nowadays in health care, in telecommunications as well as in scientific databases and in data management research, accumulating on average more than 10,000 downloads on a monthly basis. This paper gives a brief overview of the MonetDB technology as it developed over the past two decades and the main research highlights which drive the current MonetDB design and form the basis for its future evolution.
Designing Household Survey Questionnaires for Developing Countries: Lessons from 15 Years of the Living Standards Measurement Study, Volume 3

The objective of this book is to provide detailed advice on how to design multi-topic household surveys based on the experience of past household surveys. The book will help identify define objectives, identify data needed to analyze objectives, and draft questionnaires to collect such data. Much of the book is based on the experience of the World Bank's Living Standard's Measurement Study (LSMS) program, established in 1980 to explore ways the accuracy, timeliness, and policy relevance of household survey data collected in developing countries. It is part of an attempt to extend the range of policy issues that can be analyzed with LSMS data; to increase the reliability and accuracy of the surveys; and to make it easier to implement LSMS surveys. The books first discuss the "big picture" concerning the overall design of surveys, modules to be used, and procedures for combining modules into questionnaires and questionnaires into surveys. Individual modules are discussed in depth as well as major policy issues. The process of manipulating modules to form a better 'fit' in the case of a specific survey is examined. Specific modules include: consumption, education, health employment, anthropometry, non-labor income, housing, price data, environmental issues, fertility, household income, savings, household enterprises, and time use. The third volume provides draft questionnaires, referenced in the prior chapters.
An Informant Questionnaire for Detecting Alzheimer's Disease: Are Some Items Better Than Others?

Abstract A decline in everyday cognitive functioning is important for diagnosing dementia. Informant questionnaires, such as the informant questionnaire on cognitive decline in the elderly (IQCODE), are used to measure this. Previously, conflicting results on the IQCODEs ability to discriminate between Alzheimer's disease (AD), mild cognitive impairment (MCI), and cognitively healthy elderly were found. We aim to investigate whether specific groups of items are more useful than others in discriminating between these patient groups. Informants of 180 AD, 59 MCI, and 89 patients with subjective memory complaints (SMC) completed the IQCODE. To investigate the grouping of questionnaire items, we used a two-dimensional graded response model (GRM). The association between IQCODE, age, gender, education, and diagnosis was modeled using structural equation modeling. The GRM with two groups of items fitted better than the unidimensional model. However, the high correlation between the dimensions (r=.90) suggested unidimensionality. The structural model showed that the IQCODE was able to differentiate between all patient groups. The IQCODE can be considered as unidimensional and as a useful addition to diagnostic screening in a memory clinic setting, as it was able to distinguish between AD, MCI, and SMC and was not influenced by gender or education. (JINS, 2011, 17, 674–681)