rCUR: an R package for CUR matrix decomposition

BACKGROUND: Many methods for dimensionality reduction of large data sets such as those generated in microarray studies boil down to the Singular Value Decomposition (SVD). Although singular vectors associated with the largest singular values have strong optimality properties and can often be quite useful as a tool to summarize the data, they are linear combinations of up to all of the data points, and thus it is typically quite hard to interpret those vectors in terms of the application domain from which the data are drawn. Recently, an alternative dimensionality reduction paradigm, CUR matrix decompositions, has been proposed to address this problem and has been applied to genetic and internet data. CUR decompositions are low-rank matrix decompositions that are explicitly expressed in terms of a small number of actual columns and/or actual rows of the data matrix. Since they are constructed from actual data elements, CUR decompositions are interpretable by practitioners of the field from which the data are drawn. RESULTS: We present an implementation to perform CUR matrix decompositions, in the form of a freely available, open source R-package called rCUR. This package will help users to perform CUR-based analysis on large-scale data, such as those obtained from different high-throughput technologies, in an interactive and exploratory manner. We show two examples that illustrate how CUR-based techniques make it possible to reduce significantly the number of probes, while at the same time maintaining major trends in data and keeping the same classification accuracy. CONCLUSIONS: The package rCUR provides functions for the users to perform CUR-based matrix decompositions in the R environment. In gene expression studies, it gives an additional way of analysis of differential expression and discriminant gene selection based on the use of statistical leverage scores. These scores, which have been used historically in diagnostic regression analysis to identify outliers, can be used by rCUR to identify the most informative data points with respect to which to express the remaining data points

A Study of the Interactions Between the Double Bonds in Unsaturated Ketones

The interactions between C=C and C=O double bonds in several unsaturated ketones have been studied by comparing MIND0/2 caloulations wiith ionisation potentials determined by photoelectron spectroscopy (PES). With one exception (norbornadienone) the direct through-space interactions in conjugated .ketones appear to be negligible, the double bonds couple hyperoonjugatively via the intervening a bonds. This kind of approach should prove useful for studying other long range interactions

Analysis of persistence and current account divergence in the European economies by panel methods

Visok spoljnotrgovinski deficit predstavlja najveći izazov za eksternu ravnotežu. Velik broj zemalja se suočava sa rastućom divergencijom trgovinskih tokova i uravnotežen tekući bilans se pre može smatrati kao retkost, nego kao pravilo u ekonomskoj praksi. Nakon izbijanja globalne finansijske i ekonomske krize, nejednakosti zemalja u pogledu kretanja tekućeg računa su postale sve intenzivnije. Jedna od značajnijih implikacija datih trendova jeste perzistentna eksterna neravnoteža koja varira u zavisnosti od meĎunarodne pozicije zemlje, trgovinske otvorenosti, unutrašnjih performansi i sposobnosti da se apsorbuju različiti eksterni šokovi. U tom smislu, predmet istraživanja doktorske disertacije odnosi se na analizu perzistentnosti i ispitivanje divergentnih trendova tekućeg računa u članicama Evropske unije u periodu 1995-2015. godine. Ideja je da se primenom panel tehnika ispita uticaj pojedinačnih faktora na trgovinsku neravnotežu i, konačno, oceni stepen perzistentnosti tekućeg računa. Prevashodno, upotrebljeni su dinamički modeli panela kako bi se ocenio uticaj odabranih determinanti na kretanje tekućeg računa u zemalja članicama Evropske unije u periodu 1995-2015. godine, sa ciljem provere prve hipoteze koja podrazumeva ispitivanje stepena perzistentnosti tekućeg računa. Nakon toga, imajući u vidu značaj održivosti tekućeg računa u dugom roku, prilikom analize determinanti tekućeg računa izvršena je podela na strukturne i ciklične komponente, što je značajno sa aspekta sagledavanja prirode eksterne neravnoteže. Za potrebe analize uticaja strukturnih faktora na dinamiku tekućeg računa u srednjem roku formirani su petogodišnji proseci podataka, dok je ocena cikličnih determinanti sprovedena na podacima koji predstavljaju jednogodišnja odstupanja od petogodišnjih proseka. Rezultati primene uopštenog metoda momenata i metoda kvazi maksimalne verodostojnosti ukazali su da su saldo bilansa tekućih transakcija u zemljama Evropske unije u velikoj meri odredili sledeći faktori: kretanje tekućeg računa iz prethodnog perioda, fiskalni bilans, stopa rasta GDP-a, stepen trgovinske otvorenosti, strane direktne investicije i odnosi razmene iz grupe makroekonomskih faktora, odnosno stopa rasta populacije, stopa zavisnosti stanovništva prema godinama starosti, odobreni krediti privatnom sektoru i pokazatelj efikasnosti vlade iz kategorija demografskih, finansijskih i institucionalnih komponenti.The high current account deficit is the biggest challenge for the external balance. A large number of countries are facing with a growing current account divergence and a balanced current account is considered more as a rarity than as a rule in economic practice. After the outbreak of the global financial and economic crisis, inequality between countries in terms of the current account developments has become more intense. One of the major implications of this trends is persistent external imbalance, which varies depending on the international position of the country, trade openness, internal performance and the ability of the country to absorb various external shocks. To this end, the purpose of a doctoral dissertation is related to the analysis of the persistence and divergent trends in the current account in the Member States of the European Union during the period 1995-2015. The idea is to examine the impact of individual factors on the trade imbalance by using panel data econometric methods, as well as to estimate the degree of persistence of the current account. Primarily, dynamic panel models are used in order to assess the impact of selected determinants on the current account movement in the Member States of the European Union during the period 1995-2015, with the aim of testing the first hypothesis which involves the examination of the degree of the current account persistence. After that, given the importance of current account sustainability in the long run, current account determinants are divided into structural and cyclic components, which is important in terms of assessing the nature of external imbalances. Five-year averages of data are formed for the analysis of the impact of structural factors on the dynamics of the current account in the medium term, while the estimation of impact of cyclical determinants was carried out on data which represent annual deviations from the five-year averages. Estimation results of dynamic panel data models obtained by generalized method of moments and the method of quasi maximum likelihood pointed out that main determinants of current account balance in the European Union were as follows: movement of the current account from the previous period, fiscal balance, GDP growth rate, degree of trade openness, foreign direct investment and terms of trade from the group of macroeconomic factors, and population growth rate, age dependency ratio, approved loans to the private sector and indicator of government effectiveness from the category of demographic, financial and institutional components

Ampelometric evaluation of wild grape (Vitis vinifera L. ssp. sylvestris (C.C. Gmel.) Hegi) accessions in the germplasm collection of FEM-IASMA, Italy

In this paper, 45 wild grapevine accessions collected during two consecutive years were compared for 36 ampelometric traits using digital image analysis. The sample set contained male and female individuals from different geographic regions: Germany, North Italy, Central Italy, South Italy, Sardinia and Turkey. The leaf morphological data from the collected samples suggest that geographic origin, gender and vintage could have an effect on ampelometric traits in this species

Impacts of Nickel Nanoparticles on Mineral Carbonation

This work presents experimental results regarding the use of pure nickel nanoparticles (NiNP) as a mineral carbonation additive. The aim was to confirm if the catalytic effect of NiNP, which has been reported to increase the dissolution of CO2 and the dissociation of carbonic acid in water, is capable of accelerating mineral carbonation processes. The impacts of NiNP on the CO2 mineralization by four alkaline materials (pure CaO and MgO, and AOD and CC steelmaking slags), on the product mineralogy, on the particle size distribution, and on the morphology of resulting materials were investigated. NiNP-containing solution was found to reach more acidic pH values upon CO2 bubbling, confirming a higher quantity of bicarbonate ions.This effect resulted in acceleration of mineral carbonation in the first fifteen minutes of reaction time when NiNP was present. After this initial stage, however, no benefit of NiNP addition was seen, resulting in very similar carbonation extents after one hour of reaction time. It was also found that increasing solids content decreased the benefit of NiNP, even in the early stages. These results suggest that NiNP has little contribution to mineral carbonation processes when the dissolution of alkaline earth metals is rate limiting

SCF MO Calculations for 1,3-Thiazole and 2-Phenyl-1,3- thiazole and Rotational Barriers in 2-Phenyl-1,3-thiazole and Its Protonated Form

SCF MO calculations show that 2-phenyl-1,3-thiazole exists in planar configuration, while protonated 2-phenyl-1,3-thiazole tends to stabilize in a non-planar form

Stability of Ampelometric Characteristics of Vitis vinifera L. cv. ‘Syrah’ and ‘Sauvignon blanc’ Leaves: Impact of Within-vineyard Variability and Pruning Method/Bud Load

Historically, grapevine (Vitis vinifera L.) leaf characterisation has been a driving force in the identificationof cultivars. In this study, ampelometric (foliometric) analysis was done on leaf samples collected fromhand-pruned, mechanically pruned and minimally pruned ‘Sauvignon blanc’ and ‘Syrah’ vines to estimatethe impact of within-vineyard variability and a change in bud load on the stability of leaf properties.The results showed that within-vineyard variability of ampelometric characteristics was high within acultivar, irrespective of bud load. In terms of the O.I.V. coding system, zero to four class differences wereobserved between minimum and maximum values of each characteristic. The value of variability of eachcharacteristic was different between the three levels of bud load and the two cultivars. With respect to budload, the number of shoots per vine had a significant effect on the characteristics of the leaf laminae. Singleleaf area and lengths of veins changed significantly for both cultivars, irrespective of treatment, while anglebetween veins proved to be a stable characteristic. A large number of biometric data can be recorded on asingle leaf; the data measured on several leaves, however, are not necessarily unique for a specific cultivar.The leaf characteristics analysed in this study can be divided into two groups according to the response toa change in bud load, i.e. stable (angles between the veins, depths of sinuses) and variable (length of theveins, length of the petiole, single leaf area). The variable characteristics are not recommended to be usedin cultivar identification, unless the pruning method/bud load is known

Magnesium Chloride as a Leaching and Aragonite-promoting Self-regenerative Additive for the Mineral Carbonation of Calcium-rich Materials

Two approaches for the intensification of the mineral carbonation reaction are combined and studied in this work, namely: (i) the calcium leaching and aragonite promoting effects of magnesium chloride (MgCl2), and (ii) the passivating layer abrasion effect of sonication. The alkaline materials subjected to leaching and carbonation tests included lime, wollastonite, steel slags, and air pollution control (APC) residue. Batch leaching tests were conducted with varying concentrations of additives to determine extraction efficiency, and with varying solids-to-liquid ratios to determine solubility limitations. Aqueous mineral carbonation tests, with and without the use of ultrasound, were conducted applying varying concentrations of magnesium chloride and varying durations to assess CO2 uptake improvement and characterize the formed carbonate phases. The leaching of calcium from lime with the use of MgCl2 was found to be atomefficient (1 mol Ca extracted for every mole Mg added), but the extraction efficiency from slags and APC residue was limited to 26–35 % due to mineralogical and microstructural constraints. The addition of MgCl2 notably improved argon oxygen decarburization (AOD) slag carbonation extent under sonication, where higher additive dosage resulted in higher CO2 uptake. Without ultrasound, however, carbonation extent was reduced with MgCl2 addition. The benefit of MgCl2 under sonication can be linked to the preferential formation of aragonite (85 wt% of formed carbonates), which precipitates on the slag particles in the form of acicular crystals with low packing density, thus becoming more susceptible to the surface erosion effect of sonication, as evidenced by the significantly reduced carbonated slag particle size

Conservation value of the native Hungarian wild grape (Vitis sylvestris Gmel.) evaluated by microsatellite markers

Wild grape (Vitis sylvestris GMEL.) has became a highly threatened species in Europe because of habitat loss, competition with alien grape species and intensive forest exploitation. Twenty-three Vitis spp. samples were analysed at 8 microsatellite loci to estimate the genetic diversity of the natural Vitis sylvestris specimens. In order to analyse the morphological traits and to perform molecular analysis, 11 native individuals were sampled from 6 remnant Hungarian habitats of the wild grape. To compare the genetic relationships among the wild specimens, samples from Turkish habitats, as well as cultivars of Vitis vinifera, Vitis labrusca and Vitis riparia were also included. Genetic diversity was higher within the Hungarian wild grape locations, with a mean of He = 0.74, which was higher that of samples originating from a larger area of Turkey, He = 0.69. Most of the Hungarian samples formed a well-defined, separate branch on the NJ tree. Based on the morphological traits and molecular analysis on the territory of Szentendre Island, formerly considered to be one of the largest native locations of wild grape, interspecific hybrids of Vitis sylvestris and Vitis riparia were identified. It can be concluded from the results that most of the Hungarian habitats studied could be valuable for the conservation. This paper reports on Hungarian Vitis sylvestris habitats, providing the first genetic study on diversity and on the relationship of Vitis sylvestris to other Vitis specimens, wild or cultivated, in the central part of the Carpathian Basin