bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gaseous Diffusion Coefficients
Authors: Marrero T. R. , Mason E. A. 
Published: October 2009

Diffusion coefficients of binary mixtures of dilute gases are comprehensively compiled, critically evaluated, and correlated by new semi-empirical expressions. There are seventy-four systems for which the data are sufficiently extensive, consistent and accurate to allow diffusion coefficients to be recommended with confidence. Deviation plots are given for most of these systems. Almost every gaseous diffusion coefficient which was experimentally determined and reported prior to 1970 can be obtained from the annotated bibliography and table of gas pairs.
A detailed analysis of experimental methods is given, and intercomparison of their results helps establish reliability limits for the data, which depend strongly on temperature. Direct measurements are supplemented by calculations based on knowledge of intermolecular forces derived from independent sources—molecular beam scattering for high temperatures, and London dispersion constants for low temperatures. In addition, diffusion coefficients for several mixtures are obtained from experimental data on mixture viscosities and thermal diffusion factors. Combination of all these results gives diffusion coefficients over a very extensive temperature range, from very low temperatures to 10 000 K.
All data are corrected for composition dependence and for quantum effects. New semi-empirical equations are derived for making such corrections easily.
Atlas of the Observed Absorption Spectrum of Carbon Monoxide Between 1060 and 1900 Å
Authors: Tilford S. G. , Simmons J. D. 
Published: October 2009

This atlas summarizes the results of a recent investigation of the carbon monoxide absorption spectrum between 1060 and 1900 Å. Twelve electronic transitions are observed in this region; four electric dipole allowed electric transitions from the ground state X 1Σ+ to the A 1Π, B 1Σ+, C 1Σ+, and E 1Π states, and eight forbidden transitions to the a′ 3Σ+, e 3Σ-, a 3Π, D 1Δ, d 3Δi, I 1Σ-, j 3Σ+, and c 3Π states. The following items are presented in the atlas:
(1) A photograph of the spectrum with band assignments;
(2) a table of band head measurements and assignments arranged by wavelength;
(3) a summary of the spectroscopic constants and potential curve for each electronic state;
(4) a line list, arranged by wavelength, of the observed rotational lines of the allowed transitions.
Computational protein profile similarity screening for quantitative mass spectrometry experiments
Authors: Kirchner Marc , Renard Bernhard Y. , Köthe Ullrich , Pappin Darryl J. , Hamprecht Fred A. , Steen Hanno , Steen Judith A. J. 
Published: October 2009

AbstractMotivation: The qualitative and quantitative characterization of protein abundance profiles over a series of time points or a set of environmental conditions is becoming increasingly important. Using isobaric mass tagging experiments, mass spectrometry-based quantitative proteomics deliver accurate peptide abundance profiles for relative quantitation. Associated data analysis workflows need to provide tailored statistical treatment that (i) takes the correlation structure of the normalized peptide abundance profiles into account and (ii) allows inference of protein-level similarity. We introduce a suitable distance measure for relative abundance profiles, derive a statistical test for equality and propose a protein-level representation of peptide-level measurements. This yields a workflow that delivers a similarity ranking of protein abundance profiles with respect to a defined reference. All procedures have in common that they operate based on the true correlation structure that underlies the measurements. This optimizes power and delivers more intuitive and efficient results than existing methods that do not take these circumstances into account.Results: We use protein profile similarity screening to identify candidate proteins whose abundances are post-transcriptionally controlled by the Anaphase Promoting Complex/Cyclosome (APC/C), a specific E3 ubiquitin ligase that is a master regulator of the cell cycle. Results are compared with an established protein correlation profiling method. The proposed procedure yields a 50.9-fold enrichment of co-regulated protein candidates and a 2.5-fold improvement over the previous method.Availability: A MATLAB toolbox is available from http://hci.iwr.uni-heidelberg.de/mip/proteomics.Contact: hanno.steen@childrens.harvard.eduSupplementary information: Supplementary data are available at Bioinformatics online.
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
Authors: Clement Nathan L. , Snell Quinn , Clement Mark J. , Hollenhorst Peter C. , Purwar Jahnvi , Graves Barbara J. , Cairns Bradley R. , Johnson W. Evan 
Published: October 2009

Abstract
Motivation: The advent of next-generation sequencing technologies has increased the accuracy and quantity of sequence data, opening the door to greater opportunities in genomic research.
Results: In this article, we present GNUMAP (Genomic Next-generation Universal MAPper), a program capable of overcoming two major obstacles in the mapping of reads from next-generation sequencing runs. First, we have created an algorithm that probabilistically maps reads to repeat regions in the genome on a quantitative basis. Second, we have developed a probabilistic Needleman–Wunsch algorithm which utilizes _prb.txt and _int.txt files produced in the Solexa/Illumina pipeline to improve the mapping accuracy for lower quality reads and increase the amount of usable data produced in a given experiment.
Availability: The source code for the software can be downloaded from http://dna.cs.byu.edu/gnumap.
Contact: nathanlclement@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Exocytosis Precedes and Predicts the Increase in Growth in Oscillating Pollen Tubes
Authors: McKenna Sylvester T. , Kunkel Joseph G. , Bosch Maurice , Rounds Caleb M. , Vidali Luis , Winship Lawrence J. , Hepler Peter K. 
Published: October 2009

AbstractWe examined exocytosis during oscillatory growth in lily (Lilium formosanum and Lilium longiflorum) and tobacco (Nicotiana tabacum) pollen tubes using three markers: (1) changes in cell wall thickness by Nomarski differential interference contrast (DIC), (2) changes in apical cell wall fluorescence in cells stained with propidium iodide (PI), and (3) changes in apical wall fluorescence in cells expressing tobacco pectin methyl esterase fused to green fluorescent protein (PME-GFP). Using PI fluorescence, we quantified oscillatory changes in the amount of wall material from both lily and tobacco pollen tubes. Measurement of wall thickness by DIC was only possible with lily due to limitations of microscope resolution. PME-GFP, a direct marker for exocytosis, only provides information in tobacco because its expression in lily causes growth inhibition and cell death. We show that exocytosis in pollen tubes oscillates and leads the increase in growth rate; the mean phase difference between exocytosis and growth is –98° ± 3° in lily and –124° ± 4° in tobacco. Statistical analyses reveal that the anticipatory increase in wall material predicts, to a high degree, the rate and extent of the subsequent growth surge. Exocytosis emerges as a prime candidate for the initiation and regulation of oscillatory pollen tube growth.
WASP plays a novel role in regulating platelet responses dependent on αIIbβ3 integrin outside‐in signalling
Authors: Shcherbina Anna , Cooley Jessica , Lutskiy Maxim I. , Benarafa Charaf , Gilbert Gary E. , Remold‐O’Donnell Eileen 
Published: October 2009

SummaryThe most consistent feature of Wiskott Aldrich syndrome (WAS) is profound thrombocytopenia with small platelets. The responsible gene encodes WAS protein (WASP), which functions in leucocytes as an actin filament nucleating agent –yet– actin filament nucleation proceeds normally in patient platelets regarding shape change, filopodia and lamellipodia generation. Because WASP localizes in the platelet membrane skeleton and is mobilized by αIIbβ3 integrin outside‐in signalling, we questioned whether its function might be linked to integrin. Agonist‐induced αIIbβ3 activation (PAC‐1 binding) was normal for patient platelets, indicating normal integrin inside‐out signalling. Inside‐out signalling (fibrinogen, JON/A binding) was also normal for wasp‐deficient murine platelets. However, adherence/spreading on immobilized fibrinogen was decreased for patient platelets and wasp‐deficient murine platelets, indicating decreased integrin outside‐in responses. Another integrin outside‐in dependent response, fibrin clot retraction, involving contraction of the post‐aggregation actin cytoskeleton, was also decreased for patient platelets and wasp‐deficient murine platelets. Rebleeding from tail cuts was more frequent for wasp‐deficient mice, suggesting decreased stabilisation of the primary platelet plug. In contrast, phosphatidylserine exposure, a pro‐coagulant response, was enhanced for WASP‐deficient patient and murine platelets. The collective results reveal a novel function for WASP in regulating pro‐aggregatory and pro‐coagulant responses downstream of integrin outside‐in signalling.
Lipid compounds of human Wharton’s jelly and their alterations in preeclampsia
Authors: Romanowicz Lech , Bańkowski Edward 
Published: October 2009

SummaryWharton’s jelly is a myxomatous substance which surrounds the umbilical cord vessels protecting them against extension, bending, twisting and compression. Very low number of cells in this tissue produce high amounts of extracellular matrix; collagen, hyaluronate and proteoglycans which bind large quantities of peptide growth factors (PGFs). Preeclampsia (the most common pregnancy‐associated syndrome) is accompanied by a significant reduction in hyaluronate and a concomitant increase in sulphated glycosaminoglycans/proteoglycans content in Wharton’s jelly. Such a phenomenon corresponds to an ‘early ageing’ of this tissue. We have evaluated the lipid composition of Wharton’s jelly and its alteration in preeclampsia. Thin layer chromatography and high‐performance liquid chromatography were employed. It was found that Wharton’s jelly contains free fatty acids (FFA), mono‐, di‐ and triacylglycerols, free cholesterol and its esters. The characteristic feature is the presence of relatively high amounts of unsaturated fatty acids, including those (C18:2 and C18:3) which are nutritionally essential. Preeclampsia is associated with a slight increase in the total fatty acid content in Wharton’s jelly and with marked changes in the proportional relationships between various lipids. A distinct decrease in the amounts of FFA was observed with a concomitant increase in monoacylglycerols and cholesterol esters. At least in some cases the effects exerted by PGFs are mediated by the lipid second messengers. Thus it is possible that alterations in lipid compounds of Wharton’s jelly may participate in the deregulation of various cell functions, including overproduction of sulphated glycosaminoglycans or down‐regulation of enzymes which participate in their degradation.
Phylogeography and phylogeny of the epineritic cosmopolitan bonitos of the genus Sarda (Cuvier): inferred patterns of intra‐ and inter‐oceanic connectivity derived from nuclear and mitochondrial DNA data
Authors: Viñas Jordi , Alvarado Bremer Jaime R. , Pla Carles 
Published: October 2009

AbstractAim  To reconstruct the phylogenetic relationships of the four species of the genus Sarda (Sarda sarda, Sarda orientalis, Sarda australis and Sarda chilensis) and their phylogeographic history in the context of historical and ecological biogeography. Also, to reconstruct within‐species phylogenetic relationships to test whether the North Atlantic and Mediterranean populations of Atlantic bonito (S. sarda) warrant subspecies status, and the validity of the allopatric northern and southern populations of eastern Pacific bonito (S. chiliensis), recognized as S. chiliensis lineolata and S. chiliensis chiliensis.Location  Representative samples of all four Sarda species collected world‐wide were analysed.Methods  Phylogenetic inference was carried out with neighbour‐joining, maximum parsimony and maximum likelihood, employing nucleotide sequences of the mitochondrial DNA (mtDNA) control region I (CR‐I) and of the single‐copy nuclear DNA (nDNA) Tmo‐4c4 gene. Analysis of molecular variance was used on the mtDNA data to estimate the extent of geographic population structuring.Results  Gene trees derived from mtDNA and nDNA data yielded concordant phylogenies that support the monophyly of the genus Sarda. The following sibling pairs received strong statistical support: striped bonito (S. orientalis) with Australian bonito (S. australis), and Atlantic bonito (S. sarda) with eastern Pacific bonito (S. chiliensis). Furthermore, the origin of S. sarda mtDNA is paraphyletic with respect to S. chiliensis, and these results are indicative of introgression. The analysis of Tmo‐4c4 sequences corroborates the ancestral hybridization between these allopatric species. Comparisons of north‐west Atlantic and Mediterranean populations of S. sarda using mtDNA CR‐I data revealed substantial genetic differentiation. By contrast, no differences between the putative northern and southern allopatric subspecies of S. chiliensis were detected.Main conclusions  The monophyly of the genus Sarda as indicated by morphology is corroborated using both molecular markers. However, molecular phylogenies depicted a paraphyletic relationship between S. sarda and S. chiliensis. This phylogeographical relationship is better explained by an ancestral introgression facilitated by trans‐Arctic contact during the Pleistocene. The pronounced genetic differentiation between S. sarda samples from the north‐west Atlantic and the Mediterranean is consistent with the differentiation of these two regions, but not with the amphi‐Atlantic speciation hypothesis. Finally, the S. chiliensis lineolata and S. chiliensis chiliensis subspecies status is not supported by the molecular data.
Measuring the importance of competition: a new formulation of the problem
Authors: Damgaard Christian , Fayolle Adeline 
Published: October 2009

Summary 1. Currently, there is a debate among plant ecologists on the concepts of the intensity of competition and the importance of competition, which is central to many issues of modern plant population ecology and plant community ecology. 2. It is problematic that the current measures of intensity and importance of competition, typically, are reported as dimensionless indices because they hide the fact that both indices are functions of plant density and the level of the environmental gradient. 3. Here, a new formulation of the concepts is suggested, which explicitly highlights the functional dependencies on plant density and the level of the environmental gradient. The new measures are a generalization of the previous indices and correspond to the previous indices in the case of a simple experimental design. 4. The suggested measures of the intensity and importance of competition are exemplified using data from a response surface competition experiment between Agrostis capillaris and Festuca ovina along a herbicide gradient, where the expected clear effect of plant density was demonstrated. 5. Synthesis. As the suggested measures of the intensity and importance of competition explicitly highlight the functional dependencies on plant density and the level of the environmental gradient, we think that they will help to ensure a closer connection between experimental plant ecology and the attempts to model plant populations and communities.
An idealized model for tree–grass coexistence in savannas: the role of life stage structure and fire disturbances
Authors: Baudena Mara , D’Andrea Fabio , Provenzale A. 
Published: October 2009

Summary 1. We discuss a simple implicit‐space model for the competition of trees and grasses in an idealized savanna environment. The model represents patch occupancy dynamics within the habitat and introduces life stage structure in the tree population, namely adults and seedlings. A tree can be out‐competed by grasses only as long as it is a seedling. 2. The model is able to predict grassland, forest, savanna and bistability between forest and grassland, depending on the different characteristics of the ecosystem, represented by the model’s parameters. 3. The inclusion of stochastic fire disturbances significantly widens the parameter range where coexistence of trees and grasses is found. At the same time, grass‐fire feedback can induce bistability between forest and grassland. 4. Synthesis. These results suggest that tree–grass coexistence in savannas can be either deterministically stable or stabilized by random disturbances, depending on prevailing environmental conditions and on the types of plant species present in the ecosystem.
Direct trade‐off between cyanogenesis and resistance to a fungal pathogen in lima bean (Phaseolus lunatus L.)
Authors: Ballhorn Daniel J. , Pietrowski Andrea , Lieberei Reinhard 
Published: October 2009

Summary 1. Plants are simultaneously attacked by multiple herbivores and pathogens. While some plant defences act synergistically, others trade‐off against each other. Such trade‐offs among resistances to herbivores and pathogens are usually explained by the costs of resistance, i.e. resource limitations compromising a plant’s overall defence. 2. Here, we demonstrate that trade‐offs can also result from direct negative interactions among defensive traits. We studied cyanogenesis (release of HCN) of lima bean (Fabaceae: Phaseolus lunatus) and effects of this efficient anti‐herbivore defence on resistance to a fungal pathogen (Melanconiaceae: Colletotrichum gloeosporioides). 3. Leaf tissue destruction by fungal growth was significantly higher on high cyanogenic (HC) lima bean accessions than on low cyanogenic (LC) plants. The susceptibility of HC accessions to the fungal pathogen was strongly correlated to reduced activity of resistance‐associated polyphenol oxidases (PPOs) in leaves of these plants. LC accessions, in contrast, showed high PPO activity, which was correlated with distinct resistance to C. gloeosporioides. 4. Experimentally applied, gaseous HCN reduced PPO activity and significantly increased the size of lesions caused by C. gloeosporioides in LC leaves. 5. Field observations of a wild lima bean population in Mexico revealed a higher infection rate of HC compared to LC plant individuals. The types of lesions observed on the different cyanogenic plants in nature were similar to those observed on HC and LC plants in the laboratory. 6. Synthesis. We suggest that cyanogenesis of lima bean directly trades off with plant defence against fungal pathogens and that the causal mechanism is the inhibition of PPOs by HCN. Our findings provide a functional explanation for the observed phenomenon of the low resistance of HC lima beans in nature.
The effects of sleep and sleep deprivation on task‐switching performance
Authors: COUYOUMDJIAN ALESSANDRO , SDOIA STEFANO , TEMPESTA DANIELA , CURCIO GIUSEPPE , RASTELLINI ELISABETTA , DE GENNARO LUIGI , FERRARA MICHELE 
Published: October 2009

SummaryNeural systems of the prefrontal cortex (PFC) involved in executive functions are particularly vulnerable to sleep deprivation (SD). In this study, we investigated whether SD selectively affects specific components of the executive control processes involved in task‐switching performance. Two different tasks are performed in rapid and random succession in this procedure, so that the to‐be‐executed task may change from one trial to the next (switch trial), or may be repeated (repetition trial). Task‐switches are usually slower than task repetitions, giving way to the ‘switch cost’. One hundred and eight university students were assigned randomly to the sleep (S) or the SD group. Each of them was tested on a task‐switching paradigm before and after an experimental night (S or SD), and after one recovery night. SD impaired both task‐switching accuracy and speed. A higher proportion of errors and increased switch costs after SD have been observed, compared to normal sleep. Control analyses on switch and repetition trials showed that the SD group was significantly worse only on the switch trials. The effects of SD are reverted by one night of recovery sleep. It is concluded that the ability to adjust behaviour rapidly and flexibly to changing environmental demands, which relies on the functional integrity of the PFC, is impacted negatively by sleep loss.
Morphology of Testes from Transgenic Rabbits: Histological and Ultrastructural Aspects
Authors: Chrenek P. , Makarevich A. V. , Kubovičová E. , Pivko J. 
Published: October 2009

SummaryThe aim of this study was to compare morphological characteristics of testes from transgenic (the WAP‐hFVIII gene) and non‐transgenic rabbits with emphasis on the histological and ultrastructural aspects. Samples of testes from both groups were fixed and embedded into Durcupan ACM for transmission electron microscopy. For histological analysis, semi‐thin toluidine blue‐stained sections were evaluated under a Jenaval light microscope. Male fertility was tested based on egg fecundity and blastocyst yield; transgene transmission was proved using PCR assay. Spermatogenesis in rabbit testes had not been destroyed both in transgenic and non‐transgenic rabbits. No significant differences were found in the occurrence of individual cell organelles of the Sertoli cells in transgenic and non‐transgenic rabbits. The ultrastructure of Leydig cells in testes of transgenic and non‐transgenic rabbits was rather similar. No differences in the occurrence of individual organelles of Leydig cells between transgenic and non‐transgenic males were found. These results were in concert with fertilizing capacity of transgenic spermatozoa. The presented status of organelles in this study indicates functional activity of the analysed cells.
Apoptosis in the Myocardium of the Adult Dromedary Camel: Ultrastructural Characterization
Authors: Osman A.‐H. K. , Sato S. , Caceci T. , Pfeiffer D. C. 
Published: October 2009

SummaryApoptosis is a highly regulated mode of cell death that occurs in the absence of inflammation. Light microscopic (LM) examination of the myocardium of apparently healthy camel did not reveal evidence of apoptosis in any samples; however, evidence of apoptosis was apparent by transmission electron microscopy (TEM). The most common apoptotic features observed by TEM included (1) an intact sarcolemma with some bleb formation; (2) nuclear chromatin condensation and margination with nucleolar disruption; (3) mitochondrial swelling and disorganization, accompanied by degeneration or hypercondensation of cristae; and (4) an intercalated disc region with a higher‐than‐normal mitochondrion/myofibril ratio, or surrounded from both sides by asymmetrically contracted sarcomeres. Apoptotic alterations were also noted among the endothelial cells lining the microvasculature of the myocardium. These alterations included (1) marked nuclear chromatin condensation and margination; (2) villous blebs on the adluminal plasmalemma, which projected into the lumen; (3) cytoplasmic vacuolation; (4) presence of intraluminal membrane‐bounded vesicles; and (5) occasional pericapillary edema and accumulations of cellular debris. The results of this study indicate that myocardial apoptosis can occur in apparently healthy camels, in the absence of a clear‐cut etiology.