Crystal structure and infrared analysis of a new trinuclear platinum(II) complex with L-cysteine

A new trinuclear platinum(II) complex with cysteine of composition [Pt(C3H6NO2S)Cl](3)center dot(C2H6SO)(3) was obtained and structurally characterized by X-ray diffraction and infrared analysis. The compound crystallizes in the trigonal system, space group R3, and is described in a hexagonal cell with a=17.739(1), c=9.531(1) and Z=3. Cysteine is coordinated to Pt(II) through the nitrogen and sulphur atoms. Each cysteine sulphur bridges between two metal atoms. A square planar coordination sphere of platinum is completed by a chlorine atom. The complex is soluble in dimethyl sulfoxide.

Analysis of inteins in the Candida parapsilosis complex for simple and accurate species identification

Inteins are coding sequences that are transcribed and translated with flanking sequences and then are excised by an autocatalytic process. There are two types of inteins in fungi, mini-inteins and full-length inteins, both of which present a splicing domain containing well-conserved amino acid sequences. Full-length inteins also present a homing endonuclease domain that makes the intein a mobile genetic element. These parasitic genetic elements are located in highly conserved genes and may allow for the differentiation of closely related species of the Candida parapsilosis (psilosis) complex. The correct identification of the three psilosis complex species C. parapsilosis, Candida metapsilosis, and Candida orthopsilosis is very important in the clinical setting for improving antifungal therapy and patient care. In this work, we analyzed inteins that are present in the vacuolar ATPase gene VMA and in the threonyl-tRNA synthetase gene ThrRS in 85 strains of the Candida psilosis complex (46 C. parapsilosis, 17 C. metapsilosis, and 22 C. orthopsilosis). Here, we describe an accessible and accurate technique based on a single PCR that is able to differentiate the psilosis complex based on the VMA intein. Although the ThrRS intein does not distinguish the three species of the psilosis complex by PCR product size, it can differentiate them by sequencing and phylogenetic analysis. Furthermore, this intein is unusually present as both mini- and full-length forms in C. orthopsilosis. Additional population studies should be performed to address whether this represents a common intraspecific variability or the presence of subspecies within C. orthopsilosis. Copyright © 2013, American Society for Microbiology. All Rights Reserved.

Analysis of evening and morning transitions in complex terrain: MATERHORN campaign 2013

A field study of thermal circulation over very gentle slope is described for a specific day characterised by weak synoptic conditions. The emphasis was on morning and evening transitions, but measurements cover the entire day; therefore a brief analysis is performed to represent the general thermal circulation pattern. Both transition periods are characterised by complex dynamic behaviours. During evening transition, the upslope flow has got through a stagnation condition characterised by wind velocity U<0:5 m=s. Only when the stagnating air has become negative buoyant, the flow is allowed to pour downslope like a slab. Some features of front formation has been found during the transition development, such as delay time of downslope flow start up along the slope, and the presence of positive turbulent kinetic energy at the onset of the motion. Eventually the observed evening transition has followed a mixed mechanisms, with features from different models. Therefore the Rayleigh number seems not to be a good criterion by which parametrise evening transition itself. Morning transition is characterised by destruction of nocturnal temperature inversion and the onset of upslope flow. Inversion destruction can be described in terms of CBL growth at surface and inversion decent from the top of the layer. KH has found to be a good indicator of inversion breakup, if used as parameter to study the inversion breakup in terms of temperature reversal. After the inversion breakup, buoyancy and mechanical productions supply the flow with the necessary energy to start the upslope wind. More quantitative analysis are provided by the study of stability parameters and turbulent kinetic energy budgets. Gradient Richardson number has been used in this terms, finding that a mixed SBL-CBL behaviour dominates the most of the observed layers. Tke budget has shown high turbulent behaviour during morning transition while the evening transition has developed entirely in laminar condition, apart from short intermittent turbulent events.

Comparison of density functional theory predictions of gas-phase deprotonation data

The SVWN, BVWN, BP86, BLYP, BPW91, B3P86, B3LYP, B3PW91, B1LYP, mPW1PW, and PBE1PBE density functionals, as implemented in Gaussian 98 and Gaussian 03, were used to calculate ΔG0 and ΔH0 values for 17 deprotonation reactions where the experimental values are accurately known. The PBE1PBE and B3P86 functionals are shown to compute results with accuracy comparable to more computationally intensive compound model chemistries. A rationale for the relative performance of various functionals is explored.

An analysis of the Galveston Hurricane using the 20CR data set

The Twentieth Century Reanalysis (20CR) is an atmospheric dataset consisting of 56 ensemble members, which covers the entire globe and reaches back to 1871. To assess the suitability of this dataset for studying past extremes, we analysed a prominent extreme event, namely the Galveston Hurricane, which made landfall in September 1900 in Texas, USA. The ensemble mean of 20CR shows a track of the pressure minimum with a small standard deviation among the 56 ensemble members in the area of the Gulf of Mexico. However, there are systematic differences between the assimilated “Best Track” from the International Best Track Archive for Climate Stewardship (IBTrACS) and the ensemble mean track in 20CR. East of the Strait of Florida, the tracks derived from 20CR are located systematically northeast of the assimilated track while in the Gulf of Mexico, the 20CR tracks are systematically shifted to the southwest compared to the IBTrACS position. The hurricane can also be observed in the wind field, which shows a cyclonic rotation and a relatively calm zone in the centre of the hurricane. The 20CR data reproduce the pressure gradient and cyclonic wind field. Regarding the amplitude of the wind speeds, the ensemble mean values from 20CR are significantly lower than the wind speeds known from measurements.

New methods for quantification and analysis of quantitative real-time polymerase chain reaction data

Quantitative real-time polymerase chain reaction (qPCR) is a sensitive gene quantitation method that has been widely used in the biological and biomedical fields. The currently used methods for PCR data analysis, including the threshold cycle (CT) method, linear and non-linear model fitting methods, all require subtracting background fluorescence. However, the removal of background fluorescence is usually inaccurate, and therefore can distort results. Here, we propose a new method, the taking-difference linear regression method, to overcome this limitation. Briefly, for each two consecutive PCR cycles, we subtracted the fluorescence in the former cycle from that in the later cycle, transforming the n cycle raw data into n-1 cycle data. Then linear regression was applied to the natural logarithm of the transformed data. Finally, amplification efficiencies and the initial DNA molecular numbers were calculated for each PCR run. To evaluate this new method, we compared it in terms of accuracy and precision with the original linear regression method with three background corrections, being the mean of cycles 1-3, the mean of cycles 3-7, and the minimum. Three criteria, including threshold identification, max R2, and max slope, were employed to search for target data points. Considering that PCR data are time series data, we also applied linear mixed models. Collectively, when the threshold identification criterion was applied and when the linear mixed model was adopted, the taking-difference linear regression method was superior as it gave an accurate estimation of initial DNA amount and a reasonable estimation of PCR amplification efficiencies. When the criteria of max R2 and max slope were used, the original linear regression method gave an accurate estimation of initial DNA amount. Overall, the taking-difference linear regression method avoids the error in subtracting an unknown background and thus it is theoretically more accurate and reliable. This method is easy to perform and the taking-difference strategy can be extended to all current methods for qPCR data analysis.^

Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO2-driven acidification during the initiation of calcification

The impact of ocean acidification (OA) on coral calcification, a subject of intense current interest, is poorly understood in part because of the presence of symbionts in adult corals. Early life history stages of Acropora spp. provide an opportunity to study the effects of elevated CO(2) on coral calcification without the complication of symbiont metabolism. Therefore, we used the Illumina RNAseq approach to study the effects of acute exposure to elevated CO(2) on gene expression in primary polyps of Acropora millepora, using as reference a novel comprehensive transcriptome assembly developed for this study. Gene ontology analysis of this whole transcriptome data set indicated that CO(2) -driven acidification strongly suppressed metabolism but enhanced extracellular organic matrix synthesis, whereas targeted analyses revealed complex effects on genes implicated in calcification. Unexpectedly, expression of most ion transport proteins was unaffected, while many membrane-associated or secreted carbonic anhydrases were expressed at lower levels. The most dramatic effect of CO(2) -driven acidification, however, was on genes encoding candidate and known components of the skeletal organic matrix that controls CaCO(3) deposition. The skeletal organic matrix effects included elevated expression of adult-type galaxins and some secreted acidic proteins, but down-regulation of other galaxins, secreted acidic proteins, SCRiPs and other coral-specific genes, suggesting specialized roles for the members of these protein families and complex impacts of OA on mineral deposition. This study is the first exhaustive exploration of the transcriptomic response of a scleractinian coral to acidification and provides an unbiased perspective on its effects during the early stages of calcification.

Computer-based analysis of the binding steps in protein complex formation

Computer models were used to examine whether and under what conditions the multimeric protein complex is inhibited by high concentrations of one of its components—an effect analogous to the prozone phenomenon in precipitin tests. A series of idealized simple “ball-and-stick” structures representing small oligomeric complexes of protein molecules formed by reversible binding reactions were analyzed to determine the binding steps leading to each structure. The equilibrium state of each system was then determined over a range of starting concentrations and Kds and the steady-state concentration of structurally complete oligomer calculated for each situation. A strong inhibitory effect at high concentrations was shown by any protein molecule forming a bridge between two or more separable parts of the complex. By contrast, proteins linked to the outside of the complex by a single bond showed no inhibition whatsoever at any concentration. Nonbridging, multivalent proteins in the body of the complex could show an inhibitory effect or not depending on the structure of the complex and the strength of its bonds. On the basis of this study, we suggest that the prozone phenomenon will occur widely in living cells and that it could be a crucial factor in the regulation of protein complex formation.

Statistical analysis of shape of objects based on landmark data.

Two objects with homologous landmarks are said to be of the same shape if the configurations of landmarks of one object can be exactly matched with that of the other by translation, rotation/reflection, and scaling. The observations on an object are coordinates of its landmarks with reference to a set of orthogonal coordinate axes in an appropriate dimensional space. The origin, choice of units, and orientation of the coordinate axes with respect to an object may be different from object to object. In such a case, how do we quantify the shape of an object, find the mean and variation of shape in a population of objects, compare the mean shapes in two or more different populations, and discriminate between objects belonging to two or more different shape distributions. We develop some methods that are invariant to translation, rotation, and scaling of the observations on each object and thereby provide generalizations of multivariate methods for shape analysis.

Examining the impact of pre-k and kindergarten classroom alignment on school readiness outcomes

This study explored children’s experiences of instructional alignment from prekindergarten to kindergarten and analyzed the impact of those alignment experiences on children’s school readiness outcomes. The study answered the following overarching research question: Does the alignment of children’s learning experiences between prekindergarten and kindergarten impact school readiness outcomes? Three sub-questions drove the research design: (1) How do children’s prekindergarten and kindergarten learning experiences align; (2) To what extent does the alignment of early learning experiences predict children’s school readiness outcomes; and (3) Does the quality of prekindergarten classroom teacher interactions moderate the impact of any PK-K alignment effects? Using cluster analysis and hierarchical linear modeling (HLM) to analyze data from over 1,300 children in the 2009 Head Start Family and Child Experiences Survey (FACES), the study found that children have distinct and definable experiences of PK-K alignment. Results also indicated a disparity in children’s PK-K alignment experiences, with Hispanic/Latino children more likely to attend Head Start programs with poor systems transition practices followed by kindergartens with poor classroom structures. The study found that growth in the use of instructional activity centers from prekindergarten to kindergarten is predictive of better literacy and math outcomes. Findings further suggested that boys, minority students, and children from lower income households are predicted to score lower than girls, white classmates, and higher-income peers across school readiness measures. Findings support the need for equitable transition and alignment practices for children from all racial and ethnic groups. They also argue for an increase in child-directed activity centers in kindergarten. With one exception, the current findings did not support the hypothesis that prekindergarten teacher quality is a moderator of alignment effects on children’s school readiness outcomes. The study presents suggestions for further research.

The theory of functions of a complex variable. [Lectures] New York University, Institute for Mathematics and Mechanics.

"First edition 1948. Second printing 1952."

Statistical analysis of 102-inch wide intercity bus accident data. Final report.

National Highway Traffic Safety Administration, Washington, D.C.