bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction of point vortex equilibria via Brownian ratchets
Authors: Newton Paul K , Chamoun George
Published: March 2007

A theory capable of producing equilibrium configurations of point vortices in the plane, along with a numerical scheme to compute them, is described. The theory is formulated as a problem in linear algebra where one must find solutions to the matrix equation

, where
A
is the (1/2)
N
(
N
−1)×
N
non-normal configuration matrix obtained by requiring that all intervortical distances remain fixed, and

are the
N
-vortex strengths. For existence of an equilibrium,
A
must have a non-trivial nullspace. We consider the singular values of
A
; when this has one or more zero singular values, the nullspace of
A
is non-empty and an equilibrium exists for some choice of

Γ

. New equilibrium configurations are found numerically by randomly depositing
N
points in the plane, which generically gives rise to a configuration matrix
A
with empty nullspace. Using the sum of squares of the
k
smallest singular values of
A
as a ‘ratchet’, we ‘thermally fluctuate’ the configuration, allowing each point to execute a random walk in the plane, retaining only those configurations which reduce this quantity at the next step. The configuration is thus driven to one with nullspace (
A
)=
k
>0. These converged states are not necessarily nearby their initial configurations, typically they are asymmetric, and often we can drive the same initial state to several different equilibria. A reverse-ratchet method is also described, which can produce initial conditions that would evolve to a specified equilibrium state. Once a converged final state is achieved, the full singular value decomposition of
A
is used to calculate an optimal basis set for the nullspace of
A
and thus all allowable

Γ

. The
distribution
of the singular values gives important information on the size of each equilibrium state (as measured by Frobenius norm), their distance from each other (spacing and density) and how far a randomly chosen system of
N
points in the plane is from the nearest equilibrium configuration with a specified rank, as well as its Shannon entropy.
Symmetry transformation matrices for structures
Authors: Pagitz Markus , James Jonathan
Published: March 2007

Many structures in nature and engineering are symmetric. Depending on the degree of symmetry, it is possible to simplify the computations considerably by block diagonalizing the stiffness matrices. Closed-form solutions of transformation matrices for such block diagonalizations can be derived using group theory for arbitrary symmetry groups. This paper presents closed-form solutions of transformation matrices based on an alternative derivation. It is shown that transformation matrices for
C

nv

and
D

nh

groups can be obtained from a finite Fourier series decomposition of load and displacement vectors. Furthermore, it is shown that structures with tetrahedral, octahedral and icosahedral symmetries can be block diagonalized in an elegant way using vector spherical harmonics.
Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba
Authors: García-Fraile Paula , Rivas Raúl , Willems Anne , Peix Alvaro , Martens Miet , Martínez-Molina Eustoquio , Mateos Pedro F. , Velázquez Encarna
Published: March 2007

During a study of polysaccharide-hydrolysing bacteria present in different plant sources, two strains were isolated from pulverized decaying wood of Populus alba and classified in the genus Rhizobium on basis of their almost complete 16S rRNA gene sequences. Their closest phylogenetic relatives were Rhizobium galegae USDA 4128T and Rhizobium huautlense S02T, with 98.2 and 98.1 % 16S rRNA gene sequence similarity, respectively. recA and atpD sequence analysis showed that these species have less than 88 and 92 % similarity, respectively, to the novel strains. In contrast to their closest phylogenetic relatives, the two strains showed strong cellulase activity on plates containing CM-cellulose as a carbon source. They were also distinguishable from these species on the basis of other phenotypic characteristics. The strains were able to induce ineffective nodules on Medicago sativa and the sequence of their nodD gene was phylogenetically close to that of Ensifer meliloti 1021 (99.6 % similarity). DNA–DNA hybridization values ranged from 10 to 22 % with respect to R. galegae USDA 4128T and 14 to 25 % with respect to R. huautlense S02T, showing that the strains from this study belong to a novel species, for which the name Rhizobium cellulosilyticum sp. nov. is proposed. The type strain is ALA10B2T (=LMG 23642T=DSM 18291T=CECT 7176T).
Lactobacillus secaliphilus sp. nov., isolated from type II sourdough fermentation
Authors: Ehrmann Matthias A. , Brandt Markus , Stolz Peter , Vogel Rudi F. , Korakli Maher
Published: March 2007

Two strains of Gram-positive, catalase-negative, lactic acid bacteria, strains TMW 1.1309T and TMW 1.1313, were isolated at an interval of several years from an industrial type II sourdough. They occurred at cell numbers of 8×108 c.f.u. g−1 and therefore were considered to be one of the dominant members of the microbiota in this type of fermentation. Cells of both strains grow exclusively on modified MRS containing trypsin-digested rye-bran extract. Both strains possessed identical 16S rRNA gene sequences, but could be discriminated by RAPD fingerprints. Comparative 16S rRNA and tuf gene sequence analyses positioned strain TMW 1.1309T as part of the Lactobacillus reuteri phylogenetic group within the genus Lactobacillus. The 16S rRNA gene sequence similarities to the closest related species, Lactobacillus coleohominis and Lactobacillus ingluviei were 97.1 and 95.4 %, respectively. The DNA G+C content of strain TMW 1.1309T was 48 mol%. Growth characteristics, biochemical features and DNA–DNA hybridization values below 70 % with all the nearest neighbours demonstrated that the isolates represent a novel Lactobacillus species. The name Lactobacillus secaliphilus sp. nov. is proposed for the novel isolates, with the type strain TMW 1.1309T (=DSM 17896T=CCUG 53218T).
In vitro cytotoxicity of nelarabine, clofarabine and flavopiridol in paediatric acute lymphoblastic leukaemia
Authors: Beesley Alex H. , Palmer Misty‐Lee , Ford Jette , Weller Renae E. , Cummings Aaron J. , Freitas Joseph R. , Firth Martin J. , Perera Kanchana U. , De Klerk Nicholas H. , Kees Ursula R.
Published: March 2007

The in vitro efficacies of three new drugs – clofarabine (CLOF), nelarabine (NEL) and flavopiridol (FP) – were assessed in a panel of acute lymphoblastic leukaemia (ALL) cell lines. The 50% inhibitory concentration (IC50) for CLOF across all lines was 188‐fold lower than that of NEL. B‐lineage, but not T‐lineage lines, were >7‐fold more sensitive to CLOF than cytosine arabinoside (ARAC). NEL IC50 was 25‐fold and 113‐fold higher than ARAC in T‐ and B‐lineage, respectively. T‐ALL cells were eightfold more sensitive to NEL than B‐lineage but there was considerable overlap. FP was more potent in vitro than glucocorticoids and thiopurines and at doses that recent phase I experience predicts will translate into clinical efficacy. Potential cross‐resistance of CLOF, NEL and FP was observed with many front‐line ALL therapeutics but not methotrexate or thiopurines. Methotrexate sensitivity was inversely related to that of NEL and FP. Whilst NEL was particularly effective in T‐ALL, a subset of patients with B‐lineage ALL might also be sensitive. CLOF appeared to be marginally more effective in B‐lineage than T‐ALL and has a distinct resistance profile that may prove useful in combination with other compounds. FP should be widely effective in ALL if sufficient plasma levels can be achieved clinically.
Paediatric SpRs' experiences of breaking bad news
Authors: Horwitz N. , Ellis J.
Published: March 2007

Aims  To ascertain the level of support and training available to paediatric specialist registrars (SpRs) in breaking bad news and their self‐reported confidence in this task.

Study design  A questionnaire‐based survey.

Participants  Paediatric SpRs working in North Thames region.

Methods  Specialist registrars (n = 206) were sent a questionnaire relating to the level of support and training available to them in breaking bad news and their attitudes to this task. A repeat questionnaire was sent out 2 weeks later.

Results  The response rate was 54.9%. The study sample included 78 females and 34 males. The median year of qualification was 1995 [interquartile range (IQR) 1993–1997] and the median year of Calman training was Year 3 (IQR 2–4). Only 15.9% of participants had guidelines where they worked and 91.2% had received training in breaking bad news. Median self‐perceived confidence in breaking bad news was rated as 4 out of 5. Only 21.2% of all respondents had both disclosed a diagnosis of Down syndrome and received feedback on their performance from their seniors. Few SpRs were able to adhere to all evidence‐based recommendations for breaking bad news.

Discussion  Most SpRs had received training in breaking bad news and self‐reported confidence in this skill was high, although their hands‐on experience was limited. Recent research shows, however, that parental dissatisfaction with the way in which bad news is broken remains high. The potential discrepancy between self‐reported confidence and actual competence casts doubt on the value of self‐evaluation.
Metabolic syndrome increases all‐cause and vascular mortality: the Hong Kong Cardiovascular Risk Factor Study
Authors: Thomas G. Neil , Schooling C. Mary , McGhee Sarah M. , Ho Sai‐Yin , Cheung Bernard M. Y. , Wat Nelson M. S. , Janus Edward D. , Lam Karen S. L. , Lam Tai Hing ,   for the Hong Kong Cardiovascular Risk Factor Prevalence Study Steering Committee
Published: March 2007

Objective  The metabolic syndrome has been associated with increased mortality in some Caucasian populations, but data in Asian populations are not available. We present data describing the association of the metabolic syndrome with mortality.

Methods  The impact of the US National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III) metabolic syndrome guidelines definition (using Asian central obesity criteria) on mortality was examined using Cox regression analyses in a population‐based cohort (n = 2863) of Chinese subjects.

Results   The cohort was followed up for a mean duration of 8·45 years, a total of 24 101 person‐years, with 89 deaths (33·7% of vascular origin). Compared to those without any component of the metabolic syndrome, following adjustment for age, socioeconomic status and a range of lifestyle habits, those with the metabolic syndrome had increased risk of both all‐cause [hazard ratio (HR) 2·02, 95% confidence interval (CI) 1·02–4·00, P for trend = 0·037] and vascular disease (HR 6·39, 95% CI 1·40–29·2, P < 0·05, P for trend = 0·002) mortality. When those with 0–2 components were compared to those with the metabolic syndrome, the HRs were 1·49 (95% CI 0·95–2·33, P = 0·084) and 3·36 (95% CI 1·57–7·19, P = 0·002), respectively.

Conclusion   This study shows that the metabolic syndrome is associated with increased mortality risk in an Asian population. The high prevalence of the metabolic syndrome, particularly in the elderly, forewarns of a rapidly increasing problem in mainland China, and other Asian populations, which could have overwhelming public health ramifications.
Chromosomal mosaicism mitigates stigmata and cardiovascular risk factors in Turner syndrome
Authors: El‐Mansoury Mostafa , Barrenäs Marie‐Louise , Bryman Inger , Hanson Charles , Larsson Christina , Wilhelmsen Lars , Landin‐Wilhelmsen Kerstin
Published: March 2007

Objective  To study genotype–phenotype correlations in Turner syndrome (TS) regarding body composition, cardiovascular risk factors, stigmata and age at diagnosis vs. degree of mosaicism estimated as the percentage of 45,X and 46,XX cells.

Methods  One hundred and twenty‐six TS women, mean age 31 years, were examined by three specialists, who reported stigmata independent of each other. Dual energy X‐ray absorptiometry (DXA) was used to measure bone mineral density (BMD). The karyotype was blinded. Fluorescence in situ hybridization (FISH) was performed on buccal cells. A random population sample served as controls.

Results  Forty‐four per cent exhibited a 45,X karyotype and 56% a second‐cell line, while 27% of all had a 45,X/46,XX mosaicism. Five 45,X cases with a conventional karyotype were 45,X/46,XX mosaic according to FISH. At diagnosis, 45,X cases were younger (P < 0·05) and had more stigmata per person (P < 0·01) than the mosaics. TS with marker chromosome X or Y, iso or ring, did not differ from 45,X in this aspect. The mosaics had higher BMD and SHBG and lower total cholesterol and FSH than TS with 45,X and did not differ compared with controls in terms of body mass index (BMI), waist/hip ratio, BMD, blood pressure, cholesterol, triglycerides, SHBG, diabetes or osteoporosis. The number of stigmata correlated positively to BMI, waist/hip ratio, cholesterol and %45,X and inversely to height and %46,XX according to FISH.

Conclusions  Mosaicism seems to mitigate the TS phenotype and the cardiovascular risk factor profile. Mosaics were diagnosed 8 years later than 45,X cases. This emphasizes the necessity for a stricter genotype categorization not only in the clinic but also in research on TS than previously adopted.
Incidence and cytological features of pulmonary hamartomas indeterminate on CT scan
Authors: Saqi A. , Shaham D. , Scognamiglio T. , Murray M. P. , Henschke C. I. , Yankelevitz D. , Vazquez M. F.
Published: March 2007

Objective:  Pulmonary hamartomas have a characteristic heterogeneous radiological appearance. However, when composed predominantly of undifferentiated mesenchymal fibromyxoid component, their homogeneous appearance on computed tomography is indeterminate for malignancy. Rendering an accurate preoperative diagnosis in these cases can alter management. The aim of this study was to determine the incidence and accuracy of cytodiagnosis for hamartomas ‘indeterminate’ by imaging.

Methods:  We retrospectively reviewed records for hamartomas diagnosed by transthoracic fine needle aspiration (FNA) including immediate impressions and final diagnoses. Cytological features evaluated included the presence of fibromyxoid stroma, bronchioloalveolar cell hyperplasia, fibroadipose tissue, cartilage and smooth muscle.

Results:  Eighteen (1.3%) hamartomas were identified from 1355 transthoracic FNAs. The immediate impression was hamartoma in 13 (72%), carcinoid in one (6%), mucinous bronchioloalveolar carcinoma in two (11%) and non‐diagnostic in two (11%). The final diagnosis of hamartoma in cases diagnosed as carcinoid, mucinous bronchioloalaveolar carcinoma and non‐diagnostic on immediate impression was rendered following assessment of all cytological material.

Conclusion:  Overall, FNAs are highly reliable for diagnosing hamartomas even when composed principally of undifferentiated mesenchymal fibromyxoid stroma, especially with the aid of all available preparations including Diff‐Quik smears, Papanicolaou smears, ThinPreps and cell block material.
Determination of the fate of13C labelled maize and wheat exudates in an agricultural soil during a short‐term incubation
Authors: Marx M. , Buegger F. , Gattinger A. , Zsolnay Á. , Munch J. C.
Published: March 2007

A broader knowledge of the contribution of carbon (C) released by plant roots (exudates) to soil is a prerequisite for optimizing the management of organic matter in arable soils. This is the first study to show the contribution of constantly applied13C‐labelled maize and wheat exudates to water extractable organic carbon (WEOC), microbial biomass‐C (MB‐C), and CO2‐C evolution during a 25‐day incubation of agricultural soil material. The CO2‐C evolution and respective δ13C values were measured daily. The WEOC and MB‐C contents were determined weekly and a newly developed method for determining δ13C values in soil extracts was applied. Around 36% of exudate‐C of both plants was recovered after the incubation, in the order WEOC < MB‐C < CO2‐C for maize and MB‐C < WEOC < CO2‐C for wheat. Around 64% of added exudate‐C was not retrieved with the methods used here. Our results suggest that great amounts of exudates became stabilized in non‐water extractable organic fractions. The amounts of MB‐C stayed relatively constant over time despite a continuous exudate‐C supply, which is the prerequisite for a growing microbial population. A lack of mineral nutrients might have limited microbial growth. The CO2‐C mineralization rate declined during the incubation and this was probably caused by a shift in the microbial community structure. Consequently, incoming WEOC was left in the soil solution leading to rising WEOC amounts over time. In the exudate‐treated soil additional amounts of soil‐derived WEOC (up to 110 μg g−1) and MB‐C (up to 60 μg g−1) relative to the control were determined. We suggest therefore that positive priming effects (i.e. accelerated turnover of soil organic matter due to the addition of organic substrates) can be explained by exchange processes between charged, soluble C‐components and the soil matrix. As a result of this exchange, soil‐derived WEOC becomes available for mineralization.
Climate change effects on upland stream macroinvertebrates over a 25‐year period
Authors: DURANCE ISABELLE , ORMEROD S. J.
Published: March 2007

Climate change effects on some ecosystems are still poorly known, particularly where they interact with other climatic phenomena or stressors. We used data spanning 25 years (1981–2005) from temperate headwaters at Llyn Brianne (UK) to test three hypotheses: (1) stream macroinvertebrates vary with winter climate; (2) ecological effects attributable to directional climate change and the North Atlantic Oscillation (NAO) are distinguishable and (3) climatic effects on macroinvertebrates depend on whether streams are impacted by acidification. Positive (i.e. warmer, wetter) NAO phases were accompanied by reduced interannual stability (=similarity) in macroinvertebrate assemblage in all streams, but associated variations in composition occurred only in acid moorland. The NAO and directional climate change together explained 70% of interannual variation in temperature, but forest and moorland streams warmed respectively by 1.4 and 1.7°C (P<0.001) between 1981 and 2005 after accounting for NAO effects. Significant responses among macroinvertebrates were confined to circumneutral streams, where future thermal projections (+1, +2, +3°C) suggested considerable change. Spring macroinvertebrate abundance might decline by 21% for every 1°C rise. Although many core species could persist if temperature gain reached 3°C, 4–10 mostly scarce taxa (5–12% of the species pool) would risk local extinction. Temperature increase in Wales approaches this magnitude by the 2050s under the Hadley HadCM3 scenarios.

These results support all three hypotheses and illustrate how headwater stream ecosystems are sensitive to climate change. Altered composition and abundance could affect conservation and ecological function, with the NAO compounding climate change effects during positive phases. We suggest that acidification, in impacted streams, overrides climatic effects on macroinvertebrates by simplifying assemblages and reducing richness. Climatic processes might, nevertheless, exacerbate acidification or offset biological recovery.
Complete coding sequence of a new HLA‐A allele, HLA‐A*0326†
Authors: Balas A. , García‐Sánchez F. , Vicario J. L.
Published: March 2007

A novel human leukocyte antigen‐A allele, officially named A*0326, was found in a bone marrow donor when sequencing based typing was carried out. A*0326 differs from A*030101 in a point mutation at codon 268 (AAG→GAG), generating an amino acid substitution of K to E.
Molecular aspects of a novel HLA‐A*02 allele (A*0297): the first HLA class I allele mutated at codon 232†
Authors: Garino E. , Miertus J. , Berrino M. , Bertinetto F. , Caropreso P. , Gay V. , Mazzola G. , Tondat F. , Frecer V. , Miertus S. , Amoroso A.
Published: March 2007

We describe a new HLA‐A*02 allele, identified in a cord blood unit and in her mother. Nucleotide sequence analysis showed the presence of a new HLA‐A*02 allele identical to HLA‐A*02010101 except for a non‐synonymous nucleotide exchange in exon 4 modifying codon 232 from GAG (Glu) to GAC (Asp). No other human leucocyte antigen class I allele sequenced so far shows this triplet at codon 232. The amino acid exchange affects a position that is part of the membrane proximal domain of class I major histocompatibility complex (MHC), designated alpha 3, and involved in the interaction with CD8 molecule. Using molecular modelling approach, the interactions between different subunits of the native and mutated forms of MHC‐I resulted in relevant changes.
SURGEONS’ ATTITUDES TOWARDS AND USAGE OF EVIDENCE‐BASED MEDICINE IN SURGICAL PRACTICE: A PILOT STUDY
Authors: Kitto Simon , Villanueva Elmer V. , Chesters Janice , Petrovic Ana , Waxman Bruce P. , Smith Julian A.
Published: March 2007

Background:  Within surgery the debate about the place of evidence‐based medicine (EBM) has focused on the nature and compatibility of EBM with surgical practice with an inevitable polarization of opinion. However, EBM techniques are being embedded into undergraduate medical curricula and surgical training programs across Australia. The Monash University Department of Surgery at Monash Medical Centre implemented a pilot study to explore current knowledge, attitudes and behaviours of practising surgeons towards EBM techniques.

Methods:  Descriptive survey of surgeons based in a tertiary care environment.

Results:  The results from the surgeons surveyed suggest that (i) they believe that EBM marginalizes patient involvement in decision‐making; (ii) they believe that EBM‐generated knowledge is useful and is commonly used in daily clinical decision‐making – however, not using EBM does not adversely affect their daily clinical decision‐making; (iii) they have high confidence in their own judgement compared with low confidence in clinical practice guidelines and other sources of evidence; and (iv) journal summaries of the latest research related to a subject are the most useful resources in clinical practice above clinical practice guidelines.

Conclusion:  The importance of incorporating concepts of the ‘culture’ of surgery as an important factor in understanding and developing new ways to mobilize Australian surgeons to adopt EBM into their practice is discussed.
REDUCING TIME TO URGENT SURGERY BY TRANSPORTING RESOURCES TO THE TRAUMA PATIENT
Authors: McMonagle Morgan P. , Flabouris Arthas , Parr Michael J. A. , Sugrue Michael
Published: March 2007

Background:  Time to definitive trauma care directly influences patient survival. Patient transport (retrieval) services are essential for the transportation of remotely located trauma patients to a major trauma centre. Trauma surgical expertise can potentially be combined with the usual retrieval response (surgically supported response) and delivered to the patient before patient transportation. We identified the frequency and circumstances of such surgically supported retrievals.

Methods:  Retrospective review of trauma patients transported by the NRMA CareFlight, New South Wales Medical Retrieval Service, Australia, from 1999 to 2003, identifying patients who had a surgically supported retrieval response and an urgent surgical procedure carried out before patient transportation to an major trauma centre.

Results:  Seven hundred and forty‐nine trauma interhospital patient transfers were identified of which 511 (68%) were categorized as urgent and 64% of which were rural based. Three (0.4%) patients had a surgically supported retrieval response and had an urgent surgical procedure carried out before patient transportation. All patients benefited from that early surgical intervention.

Conclusion:  A surgically supported retrieval response allows for the more timely delivery of urgent surgical care. Patients can potentially benefit from such a response. There are, however, important operational considerations in providing a surgically supported retrieval response.
Medical thoracoscopy in an Australian regional hospital
Authors: Simpson G
Published: March 2007

Medical thoracoscopy is not widely available in Australia. A medical thoracoscopy service has been set up in a regional hospital using no specialized equipment and at minimal cost. Of the first 100 procedures carried out, 89 were for investigation of pleural effusion, 6 for pneumothorax and 6 for empyema. Of the 89 pleural effusions, 73 were diagnosed as malignant (43 carcinoma, 24 mesothelioma, 3 lymphoma, 2 melanoma and 1 sarcoma). The sensitivity for a malignant diagnosis was 94.5%, with 100% specificity. Four patients had unsuspected tuberculous effusions. Pleurodesis was carried out with instillation of dry sterile talc in 67 cases. In 92.5% of these, no further drainage procedure was needed. There was one fatality caused by pre‐existing sepsis in a debilitated patient with disseminated carcinoma. Medical thoracoscopy is a simple, safe and cost‐effective technique for diagnosing and treating pleural effusions and provides a useful service in the setting of a regional hospital.
The Rhizobium etli opt operon is required for symbiosis and stress resistance
Authors: Vos K. , Braeken K. , Fauvart M. , Ndayizeye M. , Verhaert J. , Zachurzok S. , Lambrichts I. , Michiels J.
Published: March 2007

Rhizobium etli is a Gram‐negative root‐colonizing soil bacterium capable of fixing nitrogen while living in symbiosis with its leguminous host Phaseolus vulgaris. A genome‐wide screening for R. etli symbiotic mutants revealed a R. etli operon encoding an oligopeptide ABC‐transporter (Opt), two redA homologous genes and one redB gene. Expression analysis showed this opt operon to be transcribed both under free‐living and symbiotic conditions and expression levels were demonstrated to be growth‐phase‐dependent. Plants nodulated by R. etli opt mutants showed a reduced symbiotic nitrogen fixation activity (approximately 50% reduction). Growth experiments with opt mutants in the presence of oligopeptides as the sole nitrogen source confirmed the involvement of the opt genes in oligopeptide uptake. Further phenotypic analysis of the opt mutants revealed them to display an enhanced resistance to the oligopeptide antibiotic bacitracin, an increased susceptibility to the β‐lactam antibiotic ampicillin and a decreased osmotolerance. In conclusion, our results demonstrate that the opt operon plays a crucial role during symbiosis and stress resistance.
Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus
Authors: Weigele Peter R. , Pope Welkin H. , Pedulla Marisa L. , Houtz Jennifer M. , Smith Alexis L. , Conway James F. , King Jonathan , Hatfull Graham F. , Lawrence Jeffrey G. , Hendrix Roger W.
Published: March 2007

Cyanobacteriophage Syn9 is a large, contractile‐tailed bacteriophage infecting the widespread, numerically dominant marine cyanobacteria of the genera Prochlorococcus and Synechococcus. Its 177 300 bp genome sequence encodes 226 putative proteins and six tRNAs. Experimental and computational analyses identified genes likely involved in virion formation, nucleotide synthesis, and DNA replication and repair. Syn9 shows significant mosaicism when compared with related cyanophages S‐PM2, P‐SSM2 and P‐SSM4, although shared genes show strong purifying selection and evidence for large population sizes relative to other phages. Related to coliphage T4 – which shares 19% of Syn9's genes – Syn9 shows evidence for different patterns of DNA replication and uses homologous proteins to assemble capsids with a different overall structure that shares topology with phage SPO1 and herpes virus. Noteworthy bacteria‐related sequences in the Syn9 genome potentially encode subunits of the photosynthetic reaction centre, electron transport proteins, three pentose pathway enzymes and two tryptophan halogenases. These genes suggest that Syn9 is well adapted to the physiology of its photosynthetic hosts and may affect the evolution of these sequences within marine cyanobacteria.
The 2004 elections in Indonesia: Political reform and democratisation
Authors: Dagg Christopher J.
Published: March 2007

Abstract:  The 2004 elections in Indonesia were incredibly complex logistically, resulted in reshaped representative institutions, and allowed presidential elections by direct vote for the first time. This paper analyses the reform processes that surrounded these elections, including reforms to the representative institutions, and the legislative and presidential elections. The different strategies of the main political personalities are analysed, and the results of the legislative elections, and both the first and second presidential election rounds, are evaluated. The paper demonstrates that the elections hold several important messages for Indonesian politicians regarding electoral expectations, and how these are changing rapidly in the post‐Suharto era. Accountability, good governance and social development are among the key factors that are seen to have been important in swaying political votes, rather than traditional voting loyalties.
From Sabang to Merauke: Nationalist secession movements in Indonesia
Authors: Webster David
Published: March 2007

Abstract:  Popular movements in Aceh and Papua seeking separation from Indonesia must be understood in the context of earlier nationalist movements in history, including Indonesia's own movement for independence from the Netherlands. Movements in Aceh and Papua have built a sense of identity, considering themselves to be ‘notion‐states’ even if they are not yet nation‐states. This process parallels Indonesian identity formation in the early twentieth century. Aceh originally combined local, Indonesian and Islamic identities, but intrusion by central government institutions sparked a defensive nationalist reaction, which was stimulated further by uneven economic development and by repressive tactics by the centre. Papua was incorporated into Indonesia by means that led local people to believe they had been denied their right to self‐determination, spurring a historical sense of grievance and a collective identity of shared suffering much like that in Aceh. By the end of Sukarno's Guided Democracy and Suharto's New Order, both territories had passed a point of no return in their nationalism. Repressive tactics have failed to contain aspirations for independence; a new approach based on dialogue is needed.
Fragile But Real: Children's Capacity to Use Newly Acquired Words to Convey Preverbal Memories
Authors: Morris Gwynn , Baker‐Ward Lynne
Published: March 2007

There is ongoing debate about children's ability to use subsequently acquired language to describe preverbal experiences. This issue was addressed experimentally in this investigation using a novel paradigm. Two‐year‐old children who lacked color words were individually taught to activate a bubble machine by selecting a particular color of bubble solution. The children then participated in weekly, experimenter‐provided activities that fostered their acquisition of the color labels. After 2 months, their ability to apply the newly acquired words in reporting the original event was assessed. A significant proportion of the children demonstrated verbal recall when prompted in the presence of physical reminders of the event. These findings indicate that some early, preverbal memories are translated into words at a later time.
Origins of Individual Differences in Imitation: Links With Language, Pretend Play, and Socially Insightful Behavior in Two‐Year‐Old Twins
Authors: McEwen Fiona , Happé Francesca , Bolton Patrick , Rijsdijk Fruhling , Ronald Angelica , Dworzynski Katharina , Plomin Robert
Published: March 2007

Imitation, vocabulary, pretend play, and socially insightful behavior were investigated in 5,206 same‐ and opposite‐sex 2‐year‐old twin pairs in the United Kingdom. Individual differences in imitative ability were due to modest heritability (30%), while environmental factors shared between twins (42%) and unique to each twin (28%) also made significant contributions to the variance. Imitation correlated significantly, although modestly, with vocabulary, pretend play, and socially insightful behavior, and the strongest relationship was with vocabulary. A model that represented the covariance between the variables as being due to correlated latent genetic and environmental factors fitted the data well, with shared environmental factors influencing most of the covariance. Parents who encourage imitation may also tend to foster the development of language, pretence, and socially insightful behavior.
Infants' Use of Shared Linguistic Information to Clarify Ambiguous Requests
Authors: Ganea Patricia A. , Saylor Megan M.
Published: March 2007

Do infants use past linguistic information to interpret an ambiguous request for an object? When infants in this research were shown 2 objects, and asked for 1 with an indefinite request (e.g., “Can you get it for me?”), both 15‐ and 18‐month‐olds used the speaker's previous reference to an absent object to interpret the request. The 18‐month‐olds did so even when the request was made after a 2.5‐min delay. When the request was made by a person who did not participate in the conversation, the infants did not use the previous verbal information. These results demonstrate infants' ability to use language as a source of information in ambiguous contexts and indicate an early appreciation of the shared nature of conversation.
Accurate Depth of Field Simulation in Real Time
Authors: Zhou Tianshu , Chen Jim X. , Pullen Mark
Published: March 2007

We present a new post processing method of simulating depth of field based on accurate calculations of circles of confusion. Compared to previous work, our method derives actual scene depth information directly from the existing depth buffer, requires no specialized rendering passes, and allows easy integration into existing rendering applications. Our implementation uses an adaptive, two‐pass filter, producing a high quality depth of field effect that can be executed entirely on the GPU, taking advantage of the parallelism of modern graphics cards and permitting real time performance when applied to large numbers of pixels.
A New Kind of Creative Energy: Yadé Kara's Selam Berlin and Fatih Akin's Kurz und Schmerzlos and Gegen die Wand
Authors: Fachinger Petra
Published: March 2007

ABSTRACT

This article argues that recent Turkish‐German writing and film reflect a new self‐understanding and present a new perspective on things Turkish within mainstream German society. A comparative/contrastive analysis of Akif Pirinçci's Tränen sind immer das Ende (1980), the first Turkish‐German novel by a second‐generation writer, and Yadé Kara's Selam Berlin (2003) demonstrates how the Turkish‐German self‐representation has changed over the last two decades. In Selam Berlin the portrayal of the young Turkish‐German male's identity crisis not only takes on a different shape – while Pirinçci's Akif remains entrenched in the Turkish/German divide, Kara's Hasan is not burdened by his dual cultural heritage – but the novel also participates in a new literary discourse that is closely associated with the rise of the Berlin Republic. Like Selam Berlin, Fatih Akin's films Kurz und schmerzlos (1997) and Gegen die Wand (2004) are imbued with a new energy that manifests itself in a new Turkish‐German self‐definition. The article shows how Akin rewrites the strategies and objectives of the New German Cinema, particularly those of Rainer Werner Fassbinder, by playfully undermining persisting stereotypes of Turks as well as of what ‘ethnic’ filmmaking is supposed to be about, by reversing character roles, using space subversively, and undercutting audience expectations and genre conventions. Ultimately, both Kara and Akin offer a complex representation of things Turkish in Germany by demonstrating that there are more than two different value systems, one Turkish and one German, set against each other.
Thalami and corona radiata in juvenile NCL (CLN3): a voxel‐based morphometric study
Authors: Autti T. , Hämäläinen J. , Åberg L. , Lauronen L. , Tyynelä J. , Van Leemput K.
Published: March 2007

Juvenile neuronal ceroid lipofuscinosis (CLN3) is characterized by progressive cerebral atrophy. The purpose of this study was to re‐evaluate the three‐dimensional magnetic resonance (3D‐MR) images of patients with CLN3 using voxel‐based morphometry (VBM) to achieve a detailed understanding of the affected brain regions. T1‐weighted 3D‐MR images of 15 patients with CLN3 (age range: 12–25 years, mean age 17.6 years) and 15 age‐ and sex‐matched controls were analyzed using VBM. VBM showed strikingly focal alterations in the brains of CLN3 patients: the gray matter volume was significantly decreased in the dorsomedial part of the thalami of CLN3 patients. In addition, the volume of the white matter was significantly decreased in the corona radiata, containing cortical efferents and afferents in the transition between the internal capsule and the subcortical white matter. These data suggest that the dorsomedial part of the thalamus and the corona radiata may have a central, previously unrecognized role in the pathogenesis of CLN3.
Genetic variants in the IMPA2 gene do not confer increased risk of febrile seizures in Caucasian patients
Authors: Blair M. A. , Ma S. , Abou‐Khalil B. , Hedera P.
Published: March 2007

Pathogenesis of febrile seizures (FS), causing the most common of types of seizures in children, remains unknown. Genetic factors appear to play a pivotal role and FS can be inherited as a monogenic or genetically complex disorder. Several risks factors have been proposed but many of the previously reported genetic associations were not replicated. Non‐coding polymorphisms in the myo‐inositol monophosphatase 2 gene (IMPA2) have been suggested as a susceptibility factor for FS in Japanese patients. It is unknown whether genetic variants in the same gene constitute a risk factor for FS in other ethnic groups because the frequency of FS is significantly higher in Japanese children than in Caucasian patients. We investigated the role of the IMPA2 gene in a cohort of 96 unrelated Caucasian subjects with a history of FS. We did not identify any significant differences in genotypes of cases and matched controls; no mutations or non‐synonymous polymorphisms were detected in these individuals. Our data suggest that the genetic variants in the IMPA2 gene are not associated with a risk of FS in Caucasian patients and patients from various genetic groups are likely to have different genetic causes of FS.
Rationality and the Shoulds
Authors: DRYDEN WINDY , STILL ARTHUR
Published: March 2007

This paper is about rational and irrational uses of deontological words, such as “should”, “ought”, and “must”, referred to as “the shoulds”. Rationality is taken as a mutual relationship between conceptual schemes and human agency. These are expressed in what Bakhtin referred to as authoritative discourse and internally persuasive discourse respectively. When the conceptual scheme is in place and its authority transparent, and there is interplay between authoritative discourse and internally persuasive discourse, then the shoulds are perceived as rational. When the interplay is disrupted or suppressed the shoulds are seen as irrational. Breakdown occurs in two main ways. First, when the effective conceptual schemes are hidden, and the origin of the shoulds obscured. We describe some instances of the latter, from philosophy, psychotherapy, and experimental studies of rationality. Second, in technology and science the mutual relationship sometimes breaks down because authoritative discourse is too powerful, and inhibits the interplay in order to maintain itself. After describing these pathologies, we turn to William James, who drew attention to a repair kit for rationality in his detection of the psychologist's fallacy. Describing the work of Dewey and Husserl as elaborations of this, we distinguished two essential aspects of rationality, disciplinary expressed in authoritative discourse, and emancipatory expressed in internally persuasive discourse.
Africa’s Initial Encounter with Texas: The Significance of Afro‐Tejanos in Colonial Tejas, 1528–1821*
Authors: RICHMOND DOUGLAS. W.
Published: March 2007

The topic of African slavery and the role of Afro‐Tejanos in Texas during the period of Spanish colonial rule has been totally neglected. Primary sources used in this study discuss Afro‐Tejano family life, economic activities, military duties, and their experiences both as slaves and as individuals who gained their freedom. Hispanic treatment of Africans gradually became more enlightened by the eighteenth century to the point that Afro‐Tejanos suffered a decline in their overall standard of living after Texas became an independent republic in 1836. The relationship of Afro‐Tejanos to Mexico’s current total of 500,000 Afro‐Mexicans is an issue of contemporary relevance because of recent efforts in Mexico to highlight its African heritage.
How to deal with multiple treatment or dose groups in randomized clinical trials? Another approach
Authors: Boissel Jean‐Pierre
Published: March 2007

The multiple test issue is a tricky one. There is no entirely correct solution. It is better to avoid it by careful thinking prior to beginning the experiment. In fundamental and clinical pharmacology, there are several established concepts that allow researchers to minimize the cases where the issue arises.
What Do Confidence Items Measure in the Physical Activity Domain?1
Authors: Rhodes Ryan E. , Blanchard Chris M.
Published: March 2007

The study's purpose was to examine the measurement domain of confidence items used in physical activity research. We hypothesized that confidence items, including a phrase to hold motivation constant, would differ from standard confidence items. Participants (N = 248 students) completed confidence items, a thought‐listing procedure, and a 2‐week self‐report of physical activity. Results showed that confidence items with motivation held constant loaded exclusively on one factor, but standard confidence items were factor complex with intention. Correlations with physical activity intention and behavior were larger for confidence items than confidence items with motivation held constant. Finally, the thought‐listing procedure identified that 3 of the 7 reasons for answering confidence items were outside the intended measurement domain of self‐efficacy.
Childhood Experiences of Parenting and Causal Attributions for Criminal Behavior Among Young Offenders and Non‐Offenders
Authors: Palmer Emma J. , Gough Kirsty
Published: March 2007

This study examined the relationships between childhood experiences of parenting and causal attributions for criminal behavior among offenders against the person, property offenders, and non‐offenders. Analysis showed that non‐offenders perceived their fathers to be warmer and more overprotecting than did person offenders. Person offenders perceived their mothers to be less warm than did property offenders and non‐offenders, and less overprotecting than non‐offenders. Mothers were perceived to be more overprotecting and warmer than fathers by all 3 groups. All 3 samples viewed a range of explanations to be important in explaining criminal behavior. No significant associations were revealed between perceptions of parenting and causal attributions for crime. Group membership was predicted by home area crime level and perceived parental emotional warmth.
Temperature influence on the fish assemblage structure in a large lowland river, the lower Oder River, Germany
Authors: Wolter C.
Published: March 2007

Abstract –  Water temperatures were expected to structure river fish assemblages by promoting: (i) offspring's growth and densities in warm years, (ii) spring spawning fish when temperatures increase early and (iii) improved growth and overwintering condition from elongated vegetation periods. Favourable temperature conditions in their first year should improve growth and survival in consecutive years. In the lower Oder River, Germany, fish have been sampled annually, 0+ in July since 1997, and older fish in November since 1998. This data set was analysed to test the hypotheses mentioned above. The water temperature ranged between −0.4 and 25.1 °C during the study period, resulting in substantial variations of the 29 temperature metrics derived from daily means. Cumulative degree‐days until catch, in spring and during March, as well as minimum and mean temperatures in March and spring explained 63% of the variability observed. The mean total length of the most frequent 0+ fish differed significantly between years related to temperature. Increased length growth at higher temperatures was a general tendency. Total length and density of 0+ fish were significantly inversely correlated, but the potential influence of temperature on species densities was not significant. The mean fish densities varied not significantly between years. No indication was found that higher total length in the first year of life resulted in an improved growth in subsequent years.

For future research and management it has to be expected that temperature impacts become increasingly significant in regulated river systems. With decreasing hydrodynamics the significance of temperature effects will increase.
CONSUMER AND TRAINED PANEL EVALUATION OF HIGH PRESSURE THERMALLY TREATED SCRAMBLED EGG PATTIES
Authors: JULIANO P. , CLARK S. , KOUTCHMA T. , OUATTARA M. , MATHEWS J.W. , DUNNE C.P. , BARBOSA‐CÁNOVAS G.V.
Published: March 2007

Consumer acceptability of three commercial scrambled egg patty formulations were evaluated before and after high pressure high temperature (HPHT) processing at 700 MPa/105C and 700 MPa/121C, and a selected formulation was also in‐pouch retort treated to an F0 of 5.6 min. A 40‐member consumer panel and a six‐member trained sensory panel (29 attributes judged) evaluated treated and untreated patties. Samples were also stored at 37C for 3 and 6 months for shelf‐life testing. Egg patty with added processed cheese was the most accepted formulation after treatment at 700 MPa/105C, maintaining most quality parameters after pressurization. Egg patty formulation with added xanthan gum gave similar acceptability scores at 700 MPa/105C and at 700 MPa/121C. After 6‐month incubation, HPHT‐treated products did not produce gas or decompose, while control patties degraded after 1 week storage at 37C. Thermal pressurization processing proved promising for the development of novel shelf‐stable egg‐based products.
Challenges in community health nursing of old migrant patients in Norway – an exploratory study
Authors: Thyli Bente , Athlin Elsy , Hedelin Birgitta
Published: March 2007

Old people of non‐western minority backgrounds are an invisible group in Norway in several ways: in the national debate about the ageing population, in geriatric health care services, and in the general picture of ethnic minorities. There is a lack of knowledge about health and care amongst old migrants. This study aimed at exploring nurse managers’ perceptions of the content of community health nursing care of older people from non‐western countries of origin, and the challenges associated with caring for this group of patients. The study took place in a medium‐sized Norwegian community, a mostly urban area with surrounding rural areas. The community health nursing system was organized in six districts with nurses in management positions, covering nursing homes, special housing and home‐based care. Data were collected by a questionnaire with structured and open‐ended questions answered by 18 nurse managers. The data provided scarce information, but indicated a lack of systematic cultural care assessments. Community health nursing of old non‐western migrant patients was described as deficient and a demanding burden. The challenges were captured in four themes: language barriers, family involvement in care, deficiencies in cultural competency and the need for development. Increased competency, action and local responsibility were identified as propositions to manage the challenges. The lack of awareness and knowledge concerning cultural issues found in this study highlights the need for further development and research on this topic.