Convergent evolution of marine mammals is associated with distinct substitutions in common genes

Phenotypic convergence is thought to be driven by parallel substitutions coupled with natural selection at the sequence level. Multiple independent evolutionary transitions of mammals to an aquatic environment offer an opportunity to test this thesis. Here, whole genome alignment of coding sequences identified widespread parallel amino acid substitutions in marine mammals; however, the majority of these changes were not unique to these animals. Conversely, we report that candidate aquatic adaptation genes, identified by signatures of likelihood convergence and/or elevated ratio of nonsynonymous to synonymous nucleotide substitution rate, are characterized by very few parallel substitutions and exhibit distinct sequence changes in each group. Moreover, no significant positive correlation was found between likelihood convergence and positive selection in all three marine lineages. These results suggest that convergence in protein coding genes associated with aquatic lifestyle is mainly characterized by independent substitutions and relaxed negative selection.

A comparative study of the energetics, structures, and mechanisms of the HCN H HNC and LiCN <-> LiNC isomerizations

The potential energy surfaces of the HCN<->HNC and LiCN<->LiNC isomerization processes were determined by ab initio theory using fully optimized triple-zeta double polarization types of basis sets. Both the MP2 corrections and the QCISD level of calculations were performed to correct for the electron correlation. Results show that electron correlation has a considerable influence on the energetics and structures. Analysis of the intramolecular bond rearrangement processes reveals that, in both cases, H (or Li+) migrates in an almost elliptic path in the plane of the molecule. In HCN<->HNC, the migrating hydrogen interacts with the in-plane pi,pi* orbitals of CN, leading to a decrease in the C-N bond order. In LiCN<->LiNC, Li+ does not interact with the corresponding pi,pi* orbitals of CN.

A comparative Raman study of the interaction of electron donor and acceptor molecules with graphene prepared by different methods

Interaction of tetrathiafulvalene (TTF) and tetracyanoethylene (TCNE) with few-layer graphene samples prepared by the exfoliation of graphite oxide (EG), conversion of nanodiamond (DG) and arc-evaporation of graphite in hydrogen (HG) has been investigated by Raman spectroscopy to understand the role of the graphene surface. The position and full-width at half maximum of the Raman G-band are affected on interaction with TTF and TCNE and the effect is highest with EG and least with HG. The effect of TTF and TCNE on the 2D-band is also maximum with EG. The magnitude of interaction between the donor/acceptor molecules varies in the same order as the surface areas of the graphenes. (C) 2009 Published by Elsevier B. V.

Structure of nonactin-calcium perchlorate, C40H64O12.Ca(ClO4)2, and a comparative study of metal-nonactin complexes

M r= 975.9, orthorhombic, Pnna, a = 20.262 (3), b= 15.717 (2), c= 15.038 (1)A, V= 4788.97 A 3, z = 4, D x = 1.35 Mg m -3, Cu Kct radiation, 2 = 1.5418 A, /t = 2.79 mm -1, F(000) -= 2072, T = 293 K, R = 0.08, 3335 observed reflections. The molecular structure and the crystal packing are similar to those observed in the nonactin complexes of sodium thiocyanate and potassium thiocyanate. The eight metal-O distances are nearly the same in the potassium complex whereas the four distances involving carbonyl O atoms are shorter than the remaining four involving the tetrahydrofuran-ring O atoms in the Na and the Ca complexes. This observation can be explained in terms of the small ionic radii of Na + and Ca 2+, and leads to a plausible structural rationale for the stronger affinity of nonactin for K + than for the other two metal ions.

Comparative proteomics of uropathogenic Escherichia coli during growth in human urine identify UCA-like (UCL) fimbriae as an adherence factor involved in biofilm formation and binding to uroepithelial cells

Uropathogenic Escherichia coli (UPEC) are the primary cause of urinary tract infection (UTI) in humans. For the successful colonisation of the human urinary tract, UPEC employ a diverse collection of secreted or surface-exposed virulence factors including toxins, iron acquisition systems and adhesins. In this study, a comparative proteomic approach was utilised to define the UPEC pan and core surface proteome following growth in pooled human urine. Identified proteins were investigated for subcellular origin, prevalence and homology to characterised virulence factors. Fourteen core surface proteins were identified, as well as eleven iron uptake receptor proteins and four distinct fimbrial types, including type 1, P, F1C/S and a previously uncharacterised fimbrial type, designated UCA-like (UCL) fimbriae in this study. These pathogenicity island (PAI)-associated fimbriae are related to UCA fimbriae of Proteus mirabilis, associated with UPEC and exclusively found in members of the E. coli B2 and D phylogroup. We further demonstrated that UCL fimbriae promote significant biofilm formation on abiotic surfaces and mediate specific attachment to exfoliated human uroepithelial cells. Combined, this study has defined the surface proteomic profiles and core surface proteome of UPEC during growth in human urine and identified a new type of fimbriae that may contribute to UTI.

Comparative analysis of the uropathogenic Escherichia coli surface proteome by tandem mass-spectrometry of artificially induced outer membrane vesicles

Uropathogenic Escherichia coli (UPEC) are the major cause of urinary tract infections. For successful colonisation of the urinary tract, UPEC employ multiple surface-exposed or secreted virulence factors, including adhesins and iron uptake systems. Whilst individual UPEC strains and their virulence factors have been the focus of extensive research, there have been no outer membrane (OM) proteomic studies based on large clinical UPEC collections, primarily due to limitations of traditional methods. In this study, a high-throughput method based on tandem mass-spectrometry of EDTA heat-induced outer membrane vesicles (OMVs) was developed for the characterisation of the UPEC surface-associated proteome. The method was applied to compare the OM proteome of fifty-four UPEC isolates, resulting in the identification of 8789 proteins, consisting of 619 unique proteins, which were subsequently interrogated for their subcellular origin, prevalence and homology to characterised virulence factors. Multiple distinct virulence-associated proteins were identified, including two novel putative iron uptake proteins, an uncharacterised type of chaperone-usher fimbriae and various highly prevalent hypothetical proteins. Our results give fundamental insight into the physiology of UPEC and provide a framework for understanding the composition of the UPEC OM proteome.

A comparative study of multiple attribute tree and inverted file structures for large bibliographic files

A variety of data structures such as inverted file, multi-lists, quad tree, k-d tree, range tree, polygon tree, quintary tree, multidimensional tries, segment tree, doubly chained tree, the grid file, d-fold tree. super B-tree, Multiple Attribute Tree (MAT), etc. have been studied for multidimensional searching and related problems. Physical data base organization, which is an important application of multidimensional searching, is traditionally and mostly handled by employing inverted file. This study proposes MAT data structure for bibliographic file systems, by illustrating the superiority of MAT data structure over inverted file. Both the methods are compared in terms of preprocessing, storage and query costs. Worst-case complexity analysis of both the methods, for a partial match query, is carried out in two cases: (a) when directory resides in main memory, (b) when directory resides in secondary memory. In both cases, MAT data structure is shown to be more efficient than the inverted file method. Arguments are given to illustrate the superiority of MAT data structure in an average case also. An efficient adaptation of MAT data structure, that exploits the special features of MAT structure and bibliographic files, is proposed for bibliographic file systems. In this adaptation, suitable techniques for fixing and ranking of the attributes for MAT data structure are proposed. Conclusions and proposals for future research are presented.

A comparative study of side-band Fresnel holograms recorded with self-imaging and general objects

This paper deals with new results obtained in regard to the reconstruction properties of side-band Fresnel holograms (SBFH) of self-imaging type objects (for example, gratings) as compared with those of general objects. The major finding is that a distribution I2, which appears on the real-image plane along with the conventional real-image I1, remains a 2Z distribution (where 2Z is the axial distance between the object and its self-imaging plane) under a variety of situations, while its nature and focusing properties differ from one situation to another. It is demonstrated that the two distributions I1 and I2 can be used in the development of a novel technique for image subtraction.

Comparative analysis of traffic state estimation ─ Cumulative counts-based and trajectory-based methods

The Macroscopic Fundamental Diagram (MFD) relates space-mean density and flow. Since the MFD represents the area-wide network traffic performance, studies on perimeter control strategies and network-wide traffic state estimation utilising the MFD concept have been reported. Most previous works have utilised data from fixed sensors, such as inductive loops, to estimate the MFD, which can cause biased estimation in urban networks due to queue spillovers at intersections. To overcome the limitation, recent literature reports the use of trajectory data obtained from probe vehicles. However, these studies have been conducted using simulated datasets; limited works have discussed the limitations of real datasets and their impact on the variable estimation. This study compares two methods for estimating traffic state variables of signalised arterial sections: a method based on cumulative vehicle counts (CUPRITE), and one based on vehicles’ trajectory from taxi Global Positioning System (GPS) log. The comparisons reveal some characteristics of taxi trajectory data available in Brisbane, Australia. The current trajectory data have limitations in quantity (i.e., the penetration rate), due to which the traffic state variables tend to be underestimated. Nevertheless, the trajectory-based method successfully captures the features of traffic states, which suggests that the trajectories from taxis can be a good estimator for the network-wide traffic states.

« Le roman est agréablement traduit » : Étude comparative sur la visibilité des traductions et des traducteurs en Finlande et en France à travers des critiques des livres

Pro gradu -työssä tutkitaan ja vertaillaan käännöskirjallisuuden arvosteluja Ranskassa ja Suomessa. Empiirinen aineisto koostuu kaikista Helsingin Sanomien ja Le Monden vuonna 2003 julkaisemista arvosteluista. Lehdissä oli yhteensä 2691 arvosteltua kirjaa, joista 845 oli käännöksiä. Päätavoite on ollut selvittää näiden valtasanomalehtien kritiikkejä tutkimalla, kummassa maassa kääntäjän ja käännöksen asema on näkyvämpi ja minkälaisia julkaistut käännöskritiikit ovat. Lisäksi tavoitteena on ollut tutkia, kumpi lehdistä on avoimempi vieraskielisiä kirjoja ja käännöksiä kohtaan. Kirja-arvostelujen lähemmälle tutkimiselle luodaan pohjaa perehtymällä kääntäjän ja käännöksen näkyvyyteen liittyviin seikkoihin. Tässä käytetään hyväksi Koskisen (2000) tutkimusta. Tutkimuksessa tarkastellaan myös, millainen on hyvä käännös eri kääntäjien ja tutkijoiden mielestä, sekä muita saman aihepiirin tutkimuksia ja aiheesta vallalla ollutta keskustelua. Lisäksi selvitetään, miksi laadukkaat käännösarvostelut ovat harvinaisia ja mistä tämä johtuu. Analyysivaiheen kvantitatiivisessa osassa perehdytään käännösten määrälliseen osuuteen sekä aineistossa että Ranskan ja Suomen kokonaisjulkaisumäärissä. Aineiston käännösarvostelut luokitellaan niiden sisällön mukaan. Tässä on käytetty soveltuvin osin Gullinin (1998) kehittelemää mallia. Käännösarvostelujen sisältöanalyysissa kiinnitetään huomiota niiden käännöstä ja kääntäjää koskeviin kommentteihin. Arvostelujen laadun ja kriitikkojen käyttämien arvosteluperusteiden pohdinta nojautuu aiheesta aikaisemmin tehtyihin teoreettisiin sekä empiirisiin tutkimuksiin. Pro gradu -työ sisältää myös erillisen katsauksen käännettyjen lastenkirjojen arvosteluihin sekä arvostelujen ulkopuolisiin kääntäjiin ja kääntämiseen liittyviin artikkeleihin. Koko tutkimuksen ajan lähestymistapa on vertaileva Le Monden ja Helsingin Sanomien välillä. Tutkimuksesta selviää, että Le Monde julkaisee huomattavasti enemmän kirja-arvosteluja. Molemmat lehdet sisältävät kuitenkin suhteellisesti yhtä paljon arvosteluja käännöskirjoista. Helsingin Sanomissa on enemmän vieraskielisten teosten arvosteluja, ja käännösten ja kääntäjän asema on huomattavasti näkyvämpi lehden kritiikeissä. Suurin osa Le Monden käännösarvosteluista sisältää vain kääntäjän nimen bibliografisissa tiedoissa. Helsingin Sanomissa vain alle puolet käännöskirjoista on arvosteltu tällä tavoin. Myös kritiikit, joissa kääntäjän nimeä ei mainita ollenkaan, ovat yleisempiä ranskalaislehdessä. Suhteellisen pieni osa käännösarvosteluista arvioi käännöksen laatua. Näille arvioille on ominaista perustelujen ja analyysin puuttuminen ja ne ovat usein lyhyitä. Arviot ovat sävyltään enimmäkseen positiivisia tai neutraaleja. Hyvin yleistä on myös se, että kriitikko sekoittaa kaksi eri asiaa: kääntäjän ja kirjailijan tyylin. Yleisin kriitikkojen käyttämä arviointikriteeri on tutkia käännöksen ja kohdekielen tai käännöksen ja lähtötekstin suhdetta. Monesti arviointikriteeri jää täysin epäselväksi. Helsingin Sanomien kritiikeissä kääntäjiin viitataan huomattavasti useammin myös itse arvostelutekstissä. Lehti tuo näkyvästi esille kääntäjiä muissakin kuin kirja-arvosteluartikkeleissaan. Sen sijaan Le Mondessa ei ole pelkästään kääntäjiä käsitteleviä tekstejä.

Virtual versus classroom language teaching : A comparative study of the learning outcomes and student responses between two English reading comprehension groups

A 26-hour English reading comprehension course was taught to two groups of second year Finnish Pharmacy students: a virtual group (33 students) and a teacher-taught group (25 students). The aims of the teaching experiment were to find out: 1.What has to be taken into account when teaching English reading comprehension to students of pharmacy via the Internet and using TopClass? 2. How will the learning outcomes of the virtual group and the control group differ? 3. How will the students and the Department of Pharmacy respond to the different and new method, i.e. the virtual teaching method? 4. Will it be possible to test English reading comprehension learning material using the groupware tool TopClass? The virtual exercises were written within the Internet authoring environment, TopClass. The virtual group was given the reading material and grammar booklet on paper, but they did the reading comprehension tasks (written by the teacher), autonomously via the Internet. The control group was taught by the same teacher in 12 2-hour sessions, while the virtual group could work independently within the given six weeks. Both groups studied the same material: ten pharmaceutical articles with reading comprehension tasks as well as grammar and vocabulary exercises. Both groups took the same final test. Students in both groups were asked to evaluate the course using a 1 to 5 rating scale and they were also asked to assess their respective courses verbally. A detailed analysis of the different aspects of the student evaluation is given. Conclusions: 1.The virtual students learned pharmaceutical English relatively well but not significantly better than the classroom students 2. The overall student satisfaction in the virtual pharmacy English reading comprehension group was found to be higher than that in the teacher-taught control group. 3. Virtual learning is easier for linguistically more able students; less able students need more time with the teacher. 4. The sample in this study is rather small, but it is a pioneering study. 5. The Department of Pharmacy in the University of Helsinki wishes to incorporate virtual English reading comprehension teaching in its curriculum. 6. The sophisticated and versatile TopClass system is relatively easy for a traditional teacher and quite easy for the students to learn. It can be used e.g. for automatic checking of routine answers and document transfer, which both lighten the workloads of both parties. It is especially convenient for teaching reading comprehension. Key words: English reading comprehension, teacher-taught class, virtual class, attitudes of students, learning outcomes

Comparative growth and pathogenicity of geographical isolates of Sclerotinia sclerotiorum on lentil genotypes

Isolates of Sclerotinia sclerotiorum were collected from infected lentil plants from 2 agro-ecological zones of Syria and used to study their comparative growth on culture media and pathogenicity on different lentil genotypes. The growth studies were carried out on Potato Dextrose Agar (PDA) growth media under laboratory conditions. Mycelial radial growth and sclerotial production were the parameters used to compare the isolates. Pathogenicity studies were carried out with selected isolates on 10 lentil genotypes, infected as detached shoots and as whole potted-plants in the plastic house. The isolates showed considerable variation in cultural characteristics through mycelial growth, mycelial pigmentation and sclerotial production in the media plates. There were significant differences in the growth and sclerotial production of most of the isolates, but no apparent correlation between mycelial growth and sclerotial production among the isolates. Genotype by isolate interactions was significant for the isolates tested for pathogenicity. These interactions, however, appeared to be caused by differences in virulence of the isolates and did not suggest the occurrence of distinct pathogenic races of the pathogen isolates.

Photosynthetic responses of subtidal seagrasses to a daily light cycle in Torres Strait: A comparative study

In this study, we examined the photosynthetic responses of five common seagrass species from a typical mixed meadow in Torres Strait at a depth of 5–7 m using pulse amplitude modulated (PAM) fluorometry. The photosynthetic response of each species was measured every 2 h throughout a single daily light cycle from dawn (6 am) to dusk (6 pm). PAM fluorometry was used to generate rapid light curves from which measures of electron transport rate (ETRmax), photosynthetic efficiency (α), saturating irradiance (Ek) and light-adapted quantum yield (ΔF/F′m) were derived for each species. The amount of light absorbed by leaves (absorption factor) was also determined for each species. Similar diurnal patterns were recorded among species with 3–4 fold increases in maximal electron rate from dawn to midday and a maintenance of ETRmax in the afternoon that would allow an optimal use of low light by all species. Differences in photosynthetic responses to changes in the daily light regime were also evident with Syringodium isoetifolium showing the highest photosynthetic rates and saturating irradiances suggesting a competitive advantage over other species under conditions of high light. In contrast Halophila ovalis, Halophila decipiens and Halophila spinulosa were characterised by comparatively low photosynthetic rates and minimum light requirements (i.e. low Ek) typical of shade adaptation. The structural makeup of each species may explain the observed differences with large, structurally complex species such as Syringodium isoetifolium and Cymodocea serrulata showing high photosynthetic effciciencies (α) and therefore high-light-adapted traits (e.g. high ETRmax and Ek) compared with the smaller Halophila species positioned lower in the canopy. For the smaller Halophila species these shade-adapted traits are features that optimise their survival during low-light conditions. Knowledge of these characteristics and responses improves our understanding of the underlying causes of changes in seagrass biomass, growth and survival that occur when modifications in light quantity and quality arise from anthropogenic and climatic disturbances that commonly occur in Torres Strait.

Male nursing students in training: A comparative analysis of hidden advantage and discrimination

Aim The aim of this study was to examine the lived experience of men training to be registered nurses within a regional New Zealand context. Design This study draws upon the key principles of descriptive phenomenology. Sample Five male students enrolled from the 1st and 3rd year of the BN programme. Findings - A Career with Prospects - Gender inequality by superiors; - Developing professional boundaries with female colleagues; - Being unique has its advantages.