Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Concurrent multi-scale modeling of civil infrastructures for analyses on structural deterioration—Part I : Modeling methodology and strategy

This paper aims to develop the methodology and strategy for concurrent finite element modeling of civil infrastructures at the different scale levels for the purposes of analyses of structural deteriorating. The modeling strategy and method were investigated to develop the concurrent multi-scale model of structural behavior (CMSM-of-SB) in which the global structural behavior and nonlinear damage features of local details in a large complicated structure could be concurrently analyzed in order to meet the needs of structural-state evaluation as well as structural deteriorating. In the proposed method, the “large-scale” modeling is adopted for the global structure with linear responses between stress and strain and the “small-scale” modeling is available for nonlinear damage analyses of the local welded details. A longitudinal truss in steel bridge decks was selected as a case to study how a CMSM-of-SB was developed. The reduced-scale specimen of the longitudinal truss was studied in the laboratory to measure its dynamic and static behavior in global truss and local welded details, while the multi-scale models using constraint equations and substructuring were developed for numerical simulation. The comparison of dynamic and static response between the calculated results by different models indicated that the proposed multi-scale model was found to be the most efficient and accurate. The verification of the model with results from the tested truss under the specific loading showed that, responses at the material scale in the vicinity of local details as well as structural global behaviors could be obtained and fit well with the measured results. The proposed concurrent multi-scale modeling strategy and implementation procedures were applied to Runyang cable-stayed bridge (RYCB) and the CMSM-of-SB of the bridge deck system was accordingly constructed as a practical application.

Mathematical models for describing the shape of the in vitro unstretched human crystalline lens

We developed orthogonal least-squares techniques for fitting crystalline lens shapes, and used the bootstrap method to determine uncertainties associated with the estimated vertex radii of curvature and asphericities of five different models. Three existing models were investigated including one that uses two separate conics for the anterior and posterior surfaces, and two whole lens models based on a modulated hyperbolic cosine function and on a generalized conic function. Two new models were proposed including one that uses two interdependent conics and a polynomial based whole lens model. The models were used to describe the in vitro shape for a data set of twenty human lenses with ages 7–82 years. The two-conic-surface model (7 mm zone diameter) and the interdependent surfaces model had significantly lower merit functions than the other three models for the data set, indicating that most likely they can describe human lens shape over a wide age range better than the other models (although with the two-conic-surfaces model being unable to describe the lens equatorial region). Considerable differences were found between some models regarding estimates of radii of curvature and surface asphericities. The hyperbolic cosine model and the new polynomial based whole lens model had the best precision in determining the radii of curvature and surface asphericities across the five considered models. Most models found significant increase in anterior, but not posterior, radius of curvature with age. Most models found a wide scatter of asphericities, but with the asphericities usually being positive and not significantly related to age. As the interdependent surfaces model had lower merit function than three whole lens models, there is further scope to develop an accurate model of the complete shape of human lenses of all ages. The results highlight the continued difficulty in selecting an appropriate model for the crystalline lens shape.

In vivo confocal microscopy of the bulbar conjunctiva

Background: The aim of this work is to develop a more complete qualitative and quantitative understanding of the in vivo histology of the human bulbar conjunctiva. Methods: Laser scanning confocal microscopy (LSCM) was used to observe and measure morphological characteristics of the bulbar conjunctiva of 11 healthy human volunteer subjects. Results: The superficial epithelial layer of the bulbar conjunctiva is seen as a mass of small cell nuclei. Cell borders are sometimes visible. The light grey borders of basal epithelial cells are clearly visible, but nuclei can not be seen. The conjunctival stroma is comprised of a dense meshwork of white fibres, through which traverse blood vessels containing cellular elements. Orifices at the epithelial surface may represent goblet cells that have opened and expelled their contents. Goblet cells are also observed in the deeper epithelial layers, as well as conjunctival microcysts and mature forms of Langerhans cells. The bulbar conjunctiva has a mean thickness of 32.9 1.1 mm, and a superficial and basal epithelial cell density of 2212 782 and 2368 741 cells/ mm2, respectively. Overall goblet and mature Langerhans cell densities are 111 58 and 23 25 cells/mm2, respectively. Conclusions: LSCM is a powerful technique for studying the human bulbar conjunctiva in vivo and quantifying key aspects of cell morphology. The observations presented here may serve as a useful marker against which changes in conjunctival morphology due to disease, surgery, drug therapy or contact lens wear can be assessed.

Le infrastrutture viarie dismesse o declassate ed il progetto di paesaggio

Paesaggio ed infrastrutture viarie sono un binomio molto forte: il primo ha insito il concetto di accessibilità, in quanto non può esistere senza la presenza di un osservatore; la strada, invece, trova i fattori che la connotano nel suo rapporto con la morfologia su cui insiste. Le infrastrutture viarie sono elemento strutturale e strutturante non solo di un territorio, ma anche di un paesaggio. Le attuali esigenze di mobilità portano oggi a ripensare ed adeguare molte infrastrutture viarie: laddove è possibile si potenziano le strutture esistenti, in diversi casi si ricorre a nuovi tracciati o a varianti di percorso. Porsi il problema di conservare itinerari testimoni della cultura materiale ed economica di una società implica considerazioni articolate, che travalicano i limiti del sedime: una via è un organismo più complesso della semplice linea di trasporto in quanto implica tutta una serie di manufatti a supporto della mobilità e soprattutto il corridoio infrastrutturale che genera e caratterizza, ovvero una porzione variabile di territorio definita sia dal tracciato che dalla morfologia del contesto. L’evoluzione dei modelli produttivi ed economici, che oggi porta quote sempre maggiori di popolazione a passare un tempo sempre minore all’interno del proprio alloggio, rende la riflessione sulle infrastrutture viarie dismesse o declassate occasione per la progettazione di spazi per l’abitare collettivo inseriti in contesti paesaggistici, tanto urbani che rurali, tramite reti di percorsi pensate per assorbire tagli di mobilità specifici e peculiari. Partendo da queste riflessioni la Tesi si articola in: Individuazioni del contesto teorico e pratico: Lo studio mette in evidenza come la questione delle infrastrutture viarie e del loro rapporto con il paesaggio implichi riflessioni incrociate a diversi livelli e tramite diverse discipline. La definizione dello spazio fisico della strada passa infatti per la costruzione di un itinerario, un viaggio che si appoggia tanto ad elementi fisici quanto simbolici. La via è un organismo complesso che travalica il proprio sedime per coinvolgere una porzione ampia di territorio, un corridoio variabile ed articolato in funzione del paesaggio attraversato. Lo studio propone diverse chiavi di lettura, mettendo in luce le possibili declinazioni del tema, in funzione del taglio modale, del rapporto con il contesto, del regime giuridico, delle implicazioni urbanistiche e sociali. La mobilità dolce viene individuata quale possibile modalità di riuso, tutela e recupero, del patrimonio diffuso costituito dalle diversi reti di viabilità. Antologia di casi studio: Il corpo principale dello studio si basa sulla raccolta, analisi e studio dello stato dell’arte nel settore; gli esempi raccolti sono presentati in due sezioni: la prima dedicata alle esperienze più significative ed articolate, che affrontano il recupero delle infrastrutture viarie a più livelli ed in modo avanzato non concentrandosi solo sulla conversione del sedime, ma proponendo un progetto che coinvolga tutto il corridoio attraversato dall’infrastruttura; la seconda parte illustra la pratica corrente nelle diverse realtà nazionali, ponendo in evidenza similitudini e differenze tra i vari approcci.

L'Impatto delle Condizioni Interne ed Esterne sul Ruolo del Cda : un'Analisi Empirica sulle Grandi Imprese Italiane [The impact of internal and external contingencies on board tasks performance : an empirical investigation of Italian companies]

Il Consiglio di Amministrazione (CdA) è il principale organo di governo delle aziende. La letteratura gli attribuisce tre ruoli: controllo, indirizzo strategico e collegamento con l’ambiente (networking). Precedenti studi empirici hanno analizzato se un Consiglio di Amministrazione è attivo o meno in tutti e tre i ruoli in un dato momento. Nel presente lavoro, invece, si propone un approccio «contingente» e si analizzano i ruoli svolti dal CdA al variare delle condizioni interne (aziende in crisi o di successo) ed esterne (aziende in settori competitivi o regolamentati).. L’indagine empirica è stata condotta su un campione di 301 imprese italiane di grandi dimensioni. I risultati supportano la tesi iniziale secondo cui le condizioni interne ed esterne incidono sul ruolo svolto dal CdA. In particolare i risultati evidenziano che il CdA non svolge sempre tutti e tre i ruoli nello stesso momento, ma esso si concentra sul ruolo o sui ruoli che assumono grande importanza nella situazione in cui si trova l’azienda. Con riferimento alle condizioni interne, nelle imprese in crisi il CdA è attivo in tutti e tre i ruoli, mentre in quelle di successo prevale un orientamento verso la funzione strategica. Nelle aziende che operano in settori competitivi il ruolo di controllo è più pressante mentre nei settori regolamentati prevale una funzione di networking.

Raman spectroscopic study of a hydroxy-arsenate mineral containing bismuth-atelestite Bi2O(OH)(AsO4)

The Raman spectrum of atelestite Bi2O(OH)(AsO4), a hydroxy-arsenate mineral containing bismuth, has been studied in terms of spectra-structure relations. The studied spectrum is compared with the Raman spectrum of atelestite downloaded from the RRUFF database. The sharp intense band at 834 cm-1 is assigned to the 1 AsO43- (A1) symmetric stretching mode and the three bands at 767, 782 and 802 cm-1 to the 3 AsO43- antisymmetric stretching modes. The bands at 310, 324, 353, 370, 395, 450, 480 and 623 cm-1 are assigned to the corresponding ν4 and ν2 bending modes and Bi-O-Bi (vibration of bridging oxygen) and Bi-O (vibration of non-bridging oxygen) stretching vibrations. Lattice modes are observed at 172, 199 and 218 cm-1. A broad low intensity band at 3095 cm-1 is attributed to the hydrogen bonded OH units in the atelestite structure. A weak band at 1082 cm-1 is assigned to  (Bi-OH) vibration.

Order and disorder in the structures of two crystal polymorphs of the adduct bis(quinolinium-2-carboxylate) DL-malic acid

The structures of two polymorphs of the anhydrous cocrystal adduct of bis(quinolinium-2-carboxylate) DL-malic acid, one triclinic the other monoclinic and disordered, have been determined at 200 K. Crystals of the triclinic polymorph 1 have space group P-1, with Z = 1 in a cell with dimensions a = 4.4854(4), b = 9.8914(7), c = 12.4670(8)Å, α = 79.671(5), β = 83.094(6), γ = 88.745(6)deg. Crystals of the monoclinic polymorph 2 have space group P21/c, with Z = 2 in a cell with dimensions a = 13.3640(4), b = 4.4237(12), c = 18.4182(5)Å, β = 100.782(3)deg. Both structures comprise centrosymmetric cyclic hydrogen-bonded quinolinic acid zwitterion dimers [graph set R2/2(10)] and 50% disordered malic acid molecules which lie across crystallographic inversion centres. However, the oxygen atoms of the malic acid carboxylic groups in 2 are 50% rotationally disordered whereas in 1 these are ordered. There are similar primary malic acid carboxyl O-H...quinaldic acid hydrogen-bonding chain interactions in each polymorph, extended into two-dimensional structures but in l this involves centrosymmetric cyclic head-to-head malic acid hydroxyl-carboxyl O-H...O interactions [graph set R2/2(10)] whereas in 2 the links are through single hydroxy-carboxyl hydrogen bonds.

Highly discriminatory single-nucleotide polymorphism interrogation of Escherichia coli by use of allele-specific real-time PCR and eBURST analysis

In total, 782 Escherichia coli strains originating from various host sources have been analyzed in this study by using a highly discriminatory single-nucleotide polymorphism (SNP) approach. A set of eight SNPs, with a discrimination value (Simpson's index of diversity [D]) of 0.96, was determined using the Minimum SNPs software, based on sequences of housekeeping genes from the E. coli multilocus sequence typing (MLST) database. Allele-specific real-time PCR was used to screen 114 E. coli isolates from various fecal sources in Southeast Queensland (SEQ). The combined analysis of both the MLST database and SEQ E. coli isolates using eight high-D SNPs resolved the isolates into 74 SNP profiles. The data obtained suggest that SNP typing is a promising approach for the discrimination of host-specific groups and allows for the identification of human-specific E. coli in environmental samples. However, a more diverse E. coli collection is required to determine animal- and environment-specific E. coli SNP profiles due to the abundance of human E. coli strains (56%) in the MLST database.

As trajetorias de carreiras tradicionais estao dando passegem as proteanas? Um estudo com gereentes no setor public Australiano com foco em diferencas quanto ao genero ( Have traditional career paths given way to protean ones?: Evidence from senior managers in the Australian public sector)

Purpose – This mixed-method study aims to determine the extent to which the career paths of senior managers conform with the traditional versus protean elements described in the careers literature and whether these paths vary by gender. Design/methodology/approach – A total of 15 senior managers (seven women and eight men) in a large public sector agency in Australia were interviewed about their career trajectories to date. Data were coded according to four major areas which characterise and distinguish between traditional and protean careers: development, orientation of the employee, definition of success, and organisational environment. A total of 81 managers (34 women and 47 men) from the same organisation were also surveyed. Variables of interest were those that could be triangulated with qualitative data such as the availability of career opportunities. Findings – Results suggest that, contrary to much existing literature which proposes that all careers have been fundamentally altered, the traditional career which relies on length of service, geographic mobility and a steady climb up the corporate ladder, is still the dominant model in some organisations. However, the trend towards protean careers is evident and is more pronounced for women than for men. Research limitations/implications – The specific nature of the organisation (large, male-dominated, public sector) may limit the generalisability of results. Practical implications – The framework used to explore career paths according to traditional/ protean elements in this study may assist human resource practitioners to develop appropriate strategies which maximise the professional development of employees. Originality/value – The results of this research challenge the universality of change in the nature of careers, particularly in public sector environments.

Baby-friendly hospital accreditation, in-hospital care practices and breastfeeding : a population based survey

OBJECTIVES: To investigate the effect of Baby-Friendly Hospital Initiative (BFHI) accreditation and hospital care practices on breastfeeding rates at 1 and 4 months. METHODS: All women who birthed in Queensland, Australia, from February 1 to May 31, 2010, received a survey 4 months postpartum. Maternal, infant, and hospital characteristics; pregnancy and birth complications; and infant feeding outcomes were measured. RESULTS: Sample size was 6752 women. Breastfeeding initiation rates were high (96%) and similar in BFHI-accredited and nonaccredited hospitals. After adjustment for significant maternal, infant, clinical, and hospital variables, women who birthed in BFHI-accredited hospitals had significantly lower odds of breastfeeding at 1 month (adjusted odds ratio 0.72, 95% confidence interval 0.58–0.90) than those who birthed in non–BFHI-accredited hospitals. BFHI accreditation did not affect the odds of breastfeeding at 4 months or exclusive breastfeeding at 1 or 4 months. Four in-hospital practices (early skin-to-skin contact, attempted breastfeeding within the first hour, rooming-in, and no in-hospital supplementation) were experienced by 70% to 80% of mothers, with 50.3% experiencing all 4. Women who experienced all 4 hospital practices had higher odds of breastfeeding at 1 month (adjusted odds ratio 2.20, 95% confidence interval 1.78–2.71) and 4 months (adjusted odds ratio 2.93, 95% confidence interval 2.40–3.60) than women who experienced fewer than 4. CONCLUSIONS: When breastfeeding-initiation rates are high and evidence-based practices that support breastfeeding are common within the hospital environment, BFHI accreditation per se has little effect on both exclusive or any breastfeeding rates.C

Infrared and Raman spectroscopic characterization of the phosphate mineral kosnarite KZr2(PO4)3 in comparison with other pegmatitic phosphates

In this research, we have used vibrational spectroscopy to study the phosphate mineral kosnarite KZr2(PO4)3. Interest in this mineral rests with the ability of zirconium phosphates (ZP) to lock in radioactive elements. ZP have the capacity to concentrate and immobilize the actinide fraction of radioactive phases in homogeneous zirconium phosphate phases. The Raman spectrum of kosnarite is characterized by a very intense band at 1,026 cm−1 assigned to the symmetric stretching vibration of the PO4 3− ν1 symmetric stretching vibration. The series of bands at 561, 595 and 638 cm−1 are assigned to the ν4 out-of-plane bending modes of the PO4 3− units. The intense band at 437 cm−1 with other bands of lower wavenumber at 387, 405 and 421 cm−1 is assigned to the ν2 in-plane bending modes of the PO4 3− units. The number of bands in the antisymmetric stretching region supports the concept that the symmetry of the phosphate anion in the kosnarite structure is preserved. The width of the infrared spectral profile and its complexity in contrast to the well-resolved Raman spectrum show that the pegmatitic phosphates are better studied with Raman spectroscopy.

Oropharyngeal dysphagia in an elderly post-operative hip fracture population : a prospective cohort study

Background: normal ageing processes impact on oropharyngeal swallowing function placing older adults at risk of developing oropharyngeal dysphagia (OD). Anecdotal clinical experience has observed that older patients recovering from hip fracture surgery commonly develop OD post-operatively. Objective: to document the presence of OD following hip fracture surgery, and the factors associated with OD. Methods: one hundred and eighty-one patients with a mean age of 83 years (range: 65–103) admitted to a specialised orthogeriatric unit were assessed for OD post-surgery for hip fracture. Pre-admission, intra-operative and post-operative factors were examined to determine their relationship with the presence of OD. Results: OD was found to be present post-operatively in 34% (n = 61) of the current population. Multivariate logistic regression analyses revealed the presence of pre-existing neurological and respiratory medical co-morbidities, presence of post-operative delirium, age and living in a residential aged care facility prior to hospital admission to be associated with the post-operative OD. Conclusion: these results highlight that OD is present in a large number of the older hip fracture population. Early identification of OD has important implications for the provision of timely dysphagia management that may prevent secondary complications and potentially reduce the hospital length of stay.