bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of inclusion of maize silage in a diet based on grass silage on the intake, apparent digestibility and nitrogen retention in wether sheep
Authors: Knežević Mladen , Vranić Marina , Bošnjak Krešimir , Grbeša Darko , Perčulija Goran , Leto Josip , Kutnjak Hrvoje
Published: November 2007

The objective of this experiment was to study the effects of interactions between grass silage (GS) dominated by orchardgrass (Dactylis glomerata L.) and maize silage (MS) (Zea mays L.) on ad libitum intake, digestibility and nitrogen retention in wether sheep. The GS in this experiment reflected the quality of GS produced on family farms in Croatia, while the MS used is frequently produced in seasons unfavourable for high quality MS production. The study consisted of four feeding treatments involving GS and MS alone, and GS and MS mixtures in ratios of 67 : 33 or 33 : 67 (DM basis), fed twice daily. Mean DM contents of GS and MS were 396 and 264 g/kg fresh weight, respectively. MS was much lower (P < 0.001) in crude protein (CP) (62 g/kg DM) than the GS (120 g/kg DM). GS contained larger (P < 0.001) quantities of neutral detergent fibre (NDF) and acid detergent fibre (ADF) than MS. In contrast, MS contained more (P < 0.001) non-structural carbohydrate than GS, as starch, which comprised 211 g/kg DM. Inclusion of MS in the diet (33% v. 67%) had positive linear effects on fresh matter voluntary intake (P < 0.05), CP and starch digestibility (P < 0.05), and N balance (P < 0.05). A positive associative effect of GS and MS was observed for DM, organic matter intake (quadratic, P < 0.05), N intake and N balance (quadratic, P < 0.01), while it was negative for ADF digestibility (quadratic, P < 0.05). It was concluded that positive interactions of GS and MS were due to a better balance of available energy and protein when the two forages were fed together. No positive associative responses were recorded for digestibility, probably due to higher passage rates of digesta with MS supplementation i.e. lower MS quality in terms of maize plant maturity at harvest.
The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum
Authors: Rogers Lindsay D. , Foster Leonard J.
Published: November 2007

Macrophages use phagocytosis to control the spread of pathogens in the body, to clear apoptotic cells, and to aid in tissue remodeling. The phagosomal membrane is traditionally thought to originate from the plasmalemma and then go through a series of maturation steps involving sequential fusion with endosomal compartments, leading to the formation of a phagolysosome. A recent model suggests that the endoplasmic reticulum (ER) is involved in the maturation as well. Here we use stable isotope labeling and multiple quantitative proteomic approaches to follow the dynamic composition of the maturing phagosome in RAW 264.7 macrophage cells to a greater depth and higher temporal resolution than was previously possible. Analysis of the results suggests that the traditional model of a linear sequence of fusion events with different compartments is more complex or variable than previously thought. By concomitantly measuring the degree to which each component is enriched on phagosomes, our data argue that the amount of ER involved in phagocytosis is much less than predicted by the model of ER-mediated phagocytosis.
Excitatory and suppressive receptive field subunits in awake monkey primary visual cortex (V1)
Authors: Chen Xiaodong , Han Feng , Poo Mu-ming , Dan Yang
Published: November 2007

An essential step in understanding visual processing is to characterize the neuronal receptive fields (RFs) at each stage of the visual pathway. However, RF characterization beyond simple cells in the primary visual cortex (V1) remains a major challenge. Recent application of spike-triggered covariance (STC) analysis has greatly facilitated characterization of complex cell RFs in anesthetized animals. Here we apply STC to RF characterization in awake monkey V1. We found up to nine subunits for each cell, including one or two dominant excitatory subunits as described by the standard model, along with additional excitatory and suppressive subunits with weaker contributions. Compared with the dominant subunits, the nondominant excitatory subunits prefer similar orientations and spatial frequencies but have larger spatial envelopes. They contribute to response invariance to small changes in stimulus orientation, position, and spatial frequency. In contrast, the suppressive subunits are tuned to orientations 45°–90° different from the excitatory subunits, which may underlie cross-orientation suppression. Together, the excitatory and suppressive subunits form a compact description of RFs in awake monkey V1, allowing prediction of the responses to arbitrary visual stimuli.
Vaginal epithelial dendritic cells renew from bone marrow precursors
Authors: Iijima Norifumi , Linehan Melissa M. , Saeland Sem , Iwasaki Akiko
Published: November 2007

Dendritic cells (DCs) represent key professional antigen-presenting cells capable of initiating primary immune responses. A specialized subset of DCs, the Langerhans cells (LCs), are located in the stratified squamous epithelial layer of the skin and within the mucosal epithelial lining of the vaginal and oral cavities. The vaginal mucosa undergoes cyclic changes under the control of sex hormones, and the renewal characteristics of the vaginal epithelial DCs (VEDCs) remain unknown. Here, we examined the origin of VEDCs. In contrast to the skin epidermal LCs, the DCs in the epithelium of the vagina were found to be repopulated mainly by nonmonocyte bone-marrow-derived precursors, with a half-life of 13 days under steady-state conditions. Upon infection with HSV-2, the Gr-1
hi
monocytes were found to give rise to VEDCs. Furthermore, flow cytometric analysis of the VEDCs revealed the presence of at least three distinct populations, namely, CD11b
+
F4/80
hi
, CD11b
+
F4/80
int
, and CD11b
−
F4/80
−
. Importantly, these VEDC populations expressed CD207 at low levels and had a constitutively more activated phenotype compared with the skin LCs. Collectively, our results revealed mucosa-specific features of the VEDCs with respect to their phenotype, activation status, and homeostatic renewal potential.
Personality and cognitive processes in life and death decision making: An exploration into the source of judgment errors by police special squads
Authors: Girodo Michel
Published: November 2007

This study sought to understand judgment errors by special police units such as those documented after the assault by the Bureau of Alcohol, Tobacco and Firearms on the Branch Davidians near Waco, Texas. The study examined the relation between personality traits, the cognitive organization of safety and survival skills, and past deadly force encounters in 131 tactical and command officers of Violent Crimes and Fugitives Task Forces, and as they executed live high‐risk arrest warrants in an all‐inclusive decision‐making simulation environment. Logistic regressions showed that getting shot on the job was related to very low neuroticism and low sensation (experience) seeking among officers. Getting shot in a deadly force encounter during a simulated team entry was also related to low neuroticism and low experience seeking. Making safety and survival errors in a simulated entry was positively related to toughmindedness in Task Force tactical officers but negatively related to toughmindedness in Task Force leaders. Principle components factor analysis of 27 self‐reported safety and survival competencies showed that, generally, TF leaders reasoned with higher cognitive processes of analysis and deliberation while tactical personnel reasoned more in terms of reactive and procedural knowledge. Getting shot during a simulated dangerous encounter was more likely to occur when there was a mismatch between task demands and an officer's preference of one knowledge system over another. It was speculated that the poor judgment by command staff at Waco might have been related to their use of a procedural knowledge system when higher cognitive processes were needed. Greater experience with executing arrest warrants would have triggered the recognition of a serious anomaly, which would have primed the use of higher cognitive processes.
Writing Back? Jalal Al-e Ahmad's (1923–69) Reflections on Selected Periods of Iranian History
Authors: Pistor-Hatam Anja
Published: November 2007

As a collectively acting subject, the Pahlavi regime constituted itself through a functional memory by construing a particular past. In this way, the official or political memory served as the regime's key legitimizing factor. Both Pahlavi shahs attempted to appropriate the Iranian past as well as its future; that is, they legitimized their rule in retrospect and sought to immortalize themselves prospectively. In contrast to the official historiography, ‘counter-memories’ are often established. The motive in producing such a ‘counter-memory,’ whose founders are usually the conquered and oppressed, is to delegitimize the perceived oppressive balance of power. An outspoken critic of the Pahlavi regime, the Iranian teacher and writer Jalal Al-e Ahmad ‘wrote back,’ trying his hand at a ‘counter memory’.
In Search of a Kurdish Novel that Tells Us Who the Kurds Are
Authors: Ahmadzadeh Hashem
Published: November 2007

Despite the fact that during the 1930s some Kurdish novels were published in the former Soviet Union, it was only towards the end of the twentieth century that this literary genre became an established literary tradition among the Kurds. Due to various political factors, the Kurdish novel has not been identified with any nation-state. In fact, the concept of the Kurdish novel refers to all such literature written in Kurdish, regardless of different orthographies and dialects. Alongside the published novels in Kurdish, there have been some Kurdish writers who have written their novels in other languages. This article aims to look for a novel that contributes to the representation of the Kurds and their identity and political condition.
Iranian University Students' Politics in the Post-Reform Movement Era: A Discourse Analysis
Authors: Mohammadi Majid
Published: November 2007

Based on the discourse analysis of the statements of the university student organizations in the period between 1996–2006, this paper will address the pros and cons of five approaches to politics in the post-reform movement era based on five discourses among university students in the past decade of Iranian politics and their consequences for reshaping the Iranian polity. This article first discusses five socio-political processes, i.e., Islamicization, social differentiation, limited political competition, transformation of Shi'ite authority, and personalization of power, which led to four social and political schisms in Iranian society; inequality; political, social, and cultural discrimination; and secular/Islamist tension. Referring to these schisms, political discourses shape the ideologies and actions of Iranian student movements. These discourses are social justice, tradition, totalitarianism, pluralism, and Islamic democracy. Even if these discourses were no more than intellectual pronouncements by the university students, they have been powerful enough to extend to the Iranian political society.
Nationalism and the Local Church: The Source of Ecclesiastical Conflict in the Orthodox Commonwealth
Authors: Payne Daniel P.
Published: November 2007

Much of the social science literature pertaining to the development of civil society in post-communist Eastern Europe focuses on the issue of religious pluralism, especially the relationship of religious minorities and new religious movements (NRMs) to the state and their established Orthodox churches. Their findings suggest that the equation of ethno-religious nationalism, cultural identity, and the state becomes a hindrance to religious pluralism and the development of civil society in these nation-states. As a result, social scientists depict these national churches, and in most cases rightly so, as being the caretakers and fomenters of ethno-religious nationalism in their particular states. A factor in this debate that is often overlooked, however, is the role of the local church in intra-ecclesial relations. Is the concept of the “local church,” which developed in the time of the Roman and Byzantine Empires, to be identified with the modern national church? If this is the case, these churches may be guilty of the sin of ethno-phyletism, which the Council of Constantinople condemned in 1872 in regards to the Bulgarian schism. Additionally, while the development of religious pluralism in post-communist society with the proliferation of Protestant Christian sects and NRMs challenges the religious hegemony of the national churches, even more problematic has been the issue of inter-territorial Orthodox churches in Eastern Europe. The existence of a plurality of national Orthodox churches in the same territory violates the ecclesiological principle of the “local church” as well as perpetuates the sin of ethno-phyletism. While some social scientists may laud the development of a multiplication of churches in the same territory, from an ecclesiastical standpoint such a multiplication denies the unity and identity of the Orthodox Church as the one, holy, catholic and apostolic Church, which it confesses to be. What social scientists have failed to discuss is this important self-understanding of the Orthodox churches, especially as it pertains to inter-Orthodox ecclesial relations. Only with this self-understanding of the church blended with the issue of ethno-nationalism can the problems pertaining to the relations and development of ethno-national churches be properly understood.
Effect of the Angiotensin Receptor Blocker Valsartan on Coronary Microvascular Flow Reserve in Moderately Hypertensive Patients with Stable Coronary Artery Disease
Authors: Higuchi Takahiro , Abletshauser Claudia , Nekolla Stephan G. , Schwaiger Markus , Bengel Frank M.
Published: November 2007

Aims:To noninvasively investigate the effects of the angiotensin receptor blocker (ARB) Valsartan, on myocardial microcirculation in moderately hypertensive patients with stable coronary artery disease (CAD).

Methods and Results:In this prospective open‐label study, patients with mild stable CAD and moderate systolic and/or diastolic hypertension were treated with 160 mg Valsartan daily. Myocardial blood flow was quantified noninvasively using positron emission tomography (PET) with N‐13 ammonia at baseline, after one week and after 16 weeks. Mean blood pressure at rest improved significantly from baseline to week 16 (105 ± 10 vs. 98 ± 9 mm Hg; p = 0.017, n = 12), but no significant change was observed after one week (103 ± 11 vs. 100 ± 11, p = 0.43, n = 13). PET analysis revealed that flow increase during endothelial‐dependent, sympathetic stimulation by cold pressor testing (CPT) and in response to pharmacologic vasodilation with adenosine improved from baseline after 1 week (CPT: 1.10 ± 0.3 vs. 1.37 ± 0.3; p = 0.017, adenosine: 2.34 ± 0.52 vs. 2.91 ± 0.81; p = 0.048) and at week 16 (CPT: 1.15 ± 0.4 vs 1.39 ± 0.2; p = 0.10, adenosine: 2.34 ± 0.52 vs 2.81 ± 0.91; p = 0.039).

Conclusions:In patients with stable coronary disease, ARB results in improved PET‐determined microvascular flow reserve. Improvements in microcirculation preceded the reduction of blood pressure, suggesting direct beneficial effects on microvascular function.
An In‐Vivo Analysis of Capillary Stasis and Endothelial Apoptosis in a Model of Hypertension
Authors: Tran Edward D. , Schmid‐Schönbein Geert W.
Published: November 2007

Objective: Recent evidence suggests endothelial apoptosis may be a mechanism for capillary rarefaction in hypertensives. The objective of this study was to examine the early phase of endothelial apoptosis and capillary blood flow in the spontaneously hypertensive rat (SHR) and the normotensive Wistar‐Kyoto (WKY) rat.

Methods: Since hypertension in SHR is dependent on glucocorticoids, the animals were treated with dexamethasone (DEX), by intraperitoneal injection and then by superfusion on exposed mesentery. Selected capillaries were continuously observed. Annexin V and propidium iodide were used to detect apoptosis.

Results: Without central pressure reduction, permanent capillary stasis was initiated by the entrapment of leukocytes at the location of an endothelial cell that had platelets attached to it. Apoptosis of the endothelial cell was followed by apoptosis in other endothelial cells of the obstructed capillary. The incidence of stasis and total cell death in WKY+DEX were higher than WKY, whereas there were no differences between SHR+DEX and SHR. Blockade of the lectin domain of L‐selectin or a platelet membrane adhesion molecule (glycoprotein IIb/IIIa) blocked the development of stasis.

Conclusions: Glucocorticoid facilitates cell death and microvessel stasis. Immobilized platelets and leukocytes play a central role in capillary stasis, which leads to progression of endothelial apoptosis.
Saved by structure? The course of psychosis within a prison population
Authors: Blaauw Eric , Roozen Hendrik G. , Van Marle Hjalmar G. C.
Published: November 2007

About 4% of all prisoners can be diagnosed with a psychotic disorder, but it is largely unknown how these prisoners function during imprisonment. The present study aimed to describe symptoms of psychotic prisoners during imprisonment and incidents caused by them as well as care provided to these prisoners. A total of 61 prisoners were observed for a maximum of 12 weeks. Results show that poverty of speech and blunted affect significantly decreased over time. The largest group of psychotic prisoners either did not suffer from positive psychotic symptoms or the encountered positive psychotic symptoms exhibited a steady or decreasing pattern during their imprisonment. Reasons for these findings still remain unclear.
Genome-wide co-expression based prediction of differential expressions
Authors: Lai Yinglei
Published: November 2007

Motivation: Microarrays have been widely used for medical studies to detect novel disease-related genes. They enable us to study differential gene expressions at a genomic level. They also provide us with informative genome-wide co-expressions. Although many statistical methods have been proposed for identifying differentially expressed genes, genome-wide co-expressions have not been well considered for this issue. Incorporating genome-wide co-expression information in the differential expression analysis may improve the detection of disease-related genes.

Results: In this study, we proposed a statistical method for predicting differential expressions through the local regression between differential expression and co-expression measures. The smoother span parameter was determined by optimizing the rank correlation between the observed and predicted differential expression measures. A mixture normal quantile-based method was used to transform data. We used the gene-specific permutation procedure to evaluate the significance of a prediction. Two published microarray data sets were analyzed for applications. For the data set collected for a prostate cancer study, the proposed method identified many genes with weak differential expressions. Several of these genes have been shown in literature to be associated with the disease. For the data set collected for a type 2 diabetes study, no significant genes could be identified by the traditional methods. However, the proposed method identified many genes with significantly low false discovery rates.

Availability: The R codes are freely available at http://home.gwu.edu/~ylai/research/CoDiff, where the gene lists ranked by our method are also provided as the Supplementary Material.

Contact:  ylai@gwu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Gene Set Expression Comparison kit for BRB-ArrayTools
Authors: Xu Xiaojiang , Zhao Yingdong , Simon Richard
Published: November 2007

Summary: A Gene Set Expression Comparison kit is developed as a module of BRB-ArrayTools for discovering biologically meaningful patterns in gene expression data. The kit consists of gene sets of transcription factor (TF) targets, gene sets containing genes whose protein products share the same protein domain and gene sets of microRNA targets. Using this module of BRB-ArrayTools, researchers can efficiently analyze pre-defined sets of gene whose expression is correlated with a categorical quantitative phenotype or patient survival.

Availability: Gene Set Expression Comparison kit is freely available as a module of BRB-ArrayTools for non-commercial users. BRB-ArrayTools is available at http://linus.nci.nih.gov/BRB-ArrayTools.html.

Contact:  rsimon@mail.nih.gov

Supplementary information: Supplementary data are available at Bioinformatics online.
Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories
Authors: Yang Da , Li Yanhui , Xiao Hui , Liu Qing , Zhang Min , Zhu Jing , Ma Wencai , Yao Chen , Wang Jing , Wang Dong , Guo Zheng , Yang Baofeng
Published: November 2007

Motivation: In microarray studies, numerous tools are available for functional enrichment analysis based on GO categories. Most of these tools, due to their requirement of a prior threshold for designating genes as differentially expressed genes (DEGs), are categorized as threshold-dependent methods that often suffer from a major criticism on their changing results with different thresholds.

Results: In the present article, by considering the inherent correlation structure of the GO categories, a continuous measure based on semantic similarity of GO categories is proposed to investigate the functional consistence (or stability) of threshold-dependent methods. The results from several datasets show when simply counting overlapping categories between two groups, the significant category groups selected under different DEG thresholds are seemingly very different. However, based on the semantic similarity measure proposed in this article, the results are rather functionally consistent for a wide range of DEG thresholds. Moreover, we find that the functional consistence of gene lists ranked by SAM metric behaves relatively robust against changing DEG thresholds.

Availability: Source code in R is available on request from the authors.

Contact: guoz@ems.hrbmu.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.
Using multinomial models to analyse data from Iberian sardine egg incubation experiments: a comparison with traditional techniques
Authors: Bernal Miguel , Ibaibarriaga Leire , Lago de Lanzós Ana , Lonergan Mike E. , Hernández Carmen , Franco Concha , Rasines Inmaculada , Valdés Luis , Borchers David L.
Published: November 2007

Bernal, M., Ibaibarriaga, L., Lago de Lanzós, A., Lonergan, M. E., Hernández, C., Franco, C., Rasines, I., Valdés, L., and Borchers, D. L. 2008. Using multinomial models to analyse data from Iberian sardine egg incubation experiments: a comparison with traditional techniques. – ICES Journal of Marine Science, 65: 51–59. Multinomial rather than traditional models were applied to improve data analysis of incubation experiments for Iberian sardine (Sardina pilchardus) eggs. Incubation experiments were carried out in 2002 in the Gulf of Cádiz, southwestern Spain, and data were taken from the literature for the Cantabrian Sea area. Rigorous review of the traditional models revealed shortcomings in the statistical framework for modelling the developmental progression of egg stages as well as a lack of transparency of the inherent assumptions. Multinomial model results show that egg stage duration varies for all stages, with stages 3 and 4 having the shortest duration. Comparison of the results between multinomial and traditional models shows that multinomial models provide improved insight into developmental mechanisms than that can be achieved using traditional models.
Bovine milk fat enriched in conjugated linoleic and vaccenic acids attenuates allergic airway disease in mice
Authors: Kanwar R. K. , MacGibbon A. K. , Black P. N. , Kanwar J. R. , Rowan A. , Vale M. , Krissansen G. W.
Published: November 2007

Background
It has been argued that a reduction in the Western diet of anti‐inflammatory unsaturated lipids, such as n‐3 polyunsaturated fatty acids, has contributed to the increase in the frequency and severity of allergic diseases.

Objective
We investigated whether feeding milk fat enriched in conjugated linoleic acid and vaccenic acids (VAs) (‘enriched’ milk fat), produced by supplementing the diet of pasture‐fed cows with fish and sunflower oil, will prevent development of allergic airway responses.

Methods
C57BL/6 mice were fed a control diet containing soybean oil and diets supplemented with milk lipids. They were sensitized by intraperitoneal injection of ovalbumin (OVA) on days 14 and 28, and challenged intranasally with OVA on day 42. Bronchoalveolar lavage fluid, lung tissues and serum samples were collected 6 days after the intranasal challenge.

Results
Feeding of enriched milk fat led to marked suppression of airway inflammation as evidenced by reductions in eosinophilia and lymphocytosis in the airways, compared with feeding of normal milk fat and control diet. Enriched milk fat significantly reduced circulating allergen‐specific IgE and IgG1 levels, together with reductions in bronchoalveolar lavage fluid of IL‐5 and CCL11. Treatment significantly inhibited changes in the airway including airway epithelial cell hypertrophy, goblet cell metaplasia and mucus hypersecretion. The two major components of enriched milk fat, cis‐9, trans‐11 conjugated linoleic acid and VA, inhibited airway inflammation when fed together to mice, whereas alone they were not effective.

Conclusion
Milk fat enriched in conjugated linoleic and VAs suppresses inflammation and changes to the airways in an animal model of allergic airway disease.
Recommendations for reporting economic evaluations of haemophilia prophylaxis: a nominal groups consensus statement on behalf of the Economics Expert Working Group of The International Prophylaxis Study Group
Authors: NICHOLSON A. , BERGER K. , BOHN R. , CARCAO M. , FISCHER K. , GRINGERI A. , HOOTS K. , MANTOVANI L. , SCHRAMM W. , VAN HOUT B. A. , WILLAN A. R. , FELDMAN B. M.
Published: November 2007

Summary.  Background: The need for clearly reported studies evaluating the cost of prophylaxis and its overall outcomes has been recommended from previous literature. Objectives: To establish minimal ‘‘core standards’’ that can be followed when conducting and reporting economic evaluations of hemophilia prophylaxis. Methods: Ten members of the IPSG Economic Analysis Working Group participated in a consensus process using the Nominal Groups Technique (NGT). The following topics relating to the economic analysis of prophylaxis studies were addressed; Whose perspective should be taken? Which is the best methodological approach? Is micro‐ or macro‐costing the best costing strategy? What information must be presented about costs and outcomes in order to facilitate local and international interpretation? Results: The group suggests studies on the economic impact of prophylaxis should be viewed from a societal perspective and be reported using a Cost Utility Analysis (CUA) (with consideration of also reporting Cost Benefit Analysis [CBA]). All costs that exceed $500 should be used to measure the costs of prophylaxis (macro strategy) including items such as clotting factor costs, hospitalizations, surgical procedures, productivity loss and number of days lost from school or work. Generic and disease specific quality of lífe and utility measures should be used to report the outcomes of the study. Conclusions: The IPSG has suggested minimal core standards to be applied to the reporting of economic evaluations of hemophilia prophylaxis. Standardized reporting will facilitate the comparison of studies and will allow for more rational policy decisions and treatment choices.
Staunch protections: the ethics of haemophilia gene transfer research
Authors: KIMMELMAN J.
Published: November 2007

Summary.  Haemophilia has long been considered an ideal system for validating human gene transfer (GT). However, haemophilia GT trials present a particular ethical challenge because they involve subjects whose medical condition is stabilized by standard therapies. Below, I review the ethics and risks of haemophilia GT clinical research. I propose several conditions and practices that strengthen the ethical basis for such trials. These include consultation with haemophilia advocacy organizations as trials are designed and executed, high standards of supporting evidence before trials are initiated, pretrial publication of this evidence, and the offer of indemnification for participants. I further argue against the conduct of paediatric haemophilia GT studies at this time, and raise questions about the fairness of recruiting economically disadvantaged subjects into studies that are primarily directed towards the health needs of persons in the developed world.
Seven novel point mutations in the F11 gene in Iranian FXI‐deficient patients
Authors: FARD‐ESFAHANI P. , LARI G. R. , RAVANBOD S. , MIRKHANI F. , ALLAHYARI M. , RASSOULZADEGAN M. , ALA F.
Published: November 2007

Summary.  Factor XI (FXI) deficiency disorder is caused by defects in the F11 gene. The affected patients may suffer unexpected and major bleeding after trauma. Hence, the aim of this study was to identify the mutations underlying FXI deficiency in Iranian patients. The genetic basis of FXI deficiency was investigated in nine Iranian patients from unrelated families using conformation‐sensitive gel electrophoresis (CSGE) and direct sequencing. Nine different mutations were detected among which seven changes were not previously reported. Among the novel mutations, one was a point mutation that interfered with normal splicing of the mRNA; the other six changes were missense mutations that resulted in amino acid substitutions. Five mutations out of nine were heterozygous and were found in moderately affected patients, whereas the other four changes were homozygous among severely affected patients.
Agile requirements engineering practices and challenges: an empirical study
Authors: Ramesh Balasubramaniam , Cao Lan , Baskerville Richard
Published: November 2007

This paper describes empirical research into agile requirements engineering (RE) practices. Based on an analysis of data collected in 16 US software development organizations, we identify six agile practices. We also identify seven challenges that are created by the use of these practices. We further analyse how this collection of practices helps mitigate some, while exacerbating other risks in RE. We provide a framework for evaluating the impact and appropriateness of agile RE practices by relating them to RE risks. Two risks that are intractable by agile RE practices emerge from the analysis. First, problems with customer inability and a lack of concurrence among customers significantly impact agile development. Second, risks associated with the neglecting non‐functional requirements such as security and scalability are a serious concern. Developers should carefully evaluate the risk factors in their project environment to understand whether the benefits of agile RE practices outweigh the costs imposed by the challenges.
Colonization of Pacific islands by parasites of low dispersal ability: phylogeography of two monogenean species parasitizing butterflyfishes in the South Pacific Ocean
Authors: Plaisance Laetitia , Rousset Vincent , Morand Serge , Littlewood D. Timothy J.
Published: November 2007

Aim  To investigate the phylogeographical patterns of two poorly dispersing but widely distributed monogenean species, Haliotrema aurigae and Euryhaliotrematoides grandis, gill parasites of coral reef fishes from the family Chaetodontidae.

Location  South Pacific Ocean (SPO).

Methods  Sequence data from the mitochondrial cytochrome oxidase subunit I (COI) gene were obtained from samples from five localities of the SPO (Heron Island, Lizard Island, Moorea, Palau and Wallis) for the two parasite species. Phylogenetic and genetic diversity analyses were used to reconstruct phylogeographical patterns, and dates of cladogenetic events were estimated.

Results  Overall, 50 individuals of 17 Haliotrema aurigae and 33 of Euryhaliotrematoides grandis were sequenced from five localities of the SPO for COI mtDNA (798 bp). Our results revealed a deep phylogeographical structure in the species Euryhaliotrematoides grandis. The molecular divergence between individuals from Moorea and individuals from the remaining localities (7.7%) may be related to Pleistocene sea‐level fluctuations. In contrast, Haliotrema aurigae shows no phylogeographical patterns with the presence of most of the mitochondrial haplotypes in every locality sampled.

Main conclusions  Our study shows contrasting phylogeographical patterns of the two monogenean parasite species studied, despite many shared characteristics. Both parasites are found on the same host family, share the same geographical range and ecology, and are phylogenetically close. We propose two hypotheses that may help explain the diparity: the hypotheses involve differences in the evolutionary age of the parasite species and their dispersal capabilities. Additionally, the lack of phylogeographical structure in Haliotrema aurigae contrasts with its apparently restricted dispersion, which is likely to occur during the egg stage of the life cycle, inducing a passive dispersal mechanism in butterflyfish monogeneans.
Mitochondrial phylogeographic structure of the white‐browed piculet (Sasia ochracea): cryptic genetic differentiation and endemism in Indochina
Authors: Fuchs Jérôme , Ericson Per G.P. , Pasquet Eric
Published: November 2007

Aim  Our understanding of the geographic patterns of gene flow between populations of birds in the Indo‐Malayan faunal region is surprisingly poor compared with that in other parts of the world. A thorough knowledge of general patterns of phylogeographic structure is, however, of utmost importance for conservation purposes. Species with poor dispersal capabilities could serve as indicators of endemism and genetic isolation in the Indochinese subregion. From their morphology (tiny size, short tail, short and rounded wings), piculets of the genus Sasia are inferred to have poor dispersal capabilities, and thus form a suitable focal species. This study analysed the pattern of genetic variation within the White‐browed Piculet (Sasia ochracea).

Location  Southeast Asia, north of the Isthmus of Kra.

Methods  We sampled 43 individuals throughout the breeding range of S. ochracea. DNA was extracted both from fresh tissues (n = 15) and from toe pads from ancient museum skins (n = 28). We amplified a 801‐bp fragment of the mitochondrial ND2 gene to reconstruct the phylogeographic history of the White‐browed Piculet. The sequence data were analysed using Bayesian inference, statistical parsimony, and population genetics methods (analysis of molecular variance, mismatch distributions). We estimated the amount of ongoing gene flow between populations using the coalescent‐based method implemented in Mdiv.

Results  The analysis of molecular variance indicated that the current taxonomy does not adequately reflect the amount of genetic variation within S. ochracea, as the great majority of genetic variation was nested within the nominal subspecies, which is distributed from Nepal to southern Vietnam. Bayesian inference analyses and haplotype networks suggested the occurrence of five main lineages that are strongly correlated with geography. Our coalescent‐based analyses indicated a very limited amount of ongoing gene flow between these five lineages. Our dating analyses suggested that the genetic structuring probably occurred during the last 400,000 years.

Main conclusions  Our analyses revealed that S. ochracea is composed of at least five lineages: south Vietnam (South Annam and ‘Cochinchina’), India and Nepal, Myanmar and India, the remainder of Indochina, and probably southern Myanmar (Tenasserim). We strongly recommend that studies aiming to understand the phylogeographic structure within Indo‐Malayan species sample these areas.
A review of children’s decision‐making competence in health care
Authors: Mårtenson Eva K , Fägerskiöld Astrid M
Published: November 2007

Aims and objectives.  The purpose of this literature review was to search for and review, systematically, children’s decision‐making competence in health care in the scientific literature. Findings of both quantitative and qualitative studies were analysed thematically.

Background.  Most previous research in children’s decision‐making competence in health care concerns adults’ care in the best interests of the child. It is important to consider decision‐making competence from the child’s perspective because of children’s own human rights.

Methods.  Systematic review including database search, manual selection, supplementary searching, management and acquisition of relevant literature, quality appraisal, literature review saturation and thematic review.

Results.  Six themes emerged: measurable issues, values and beliefs, power, parent‐related communication, trust and self‐determination. Measurable issues were age, reading ability and memory. Values and beliefs as well as power and parent‐related communication were associated with healthcare professionals. Children showed trust and expressed a wish to use self‐determination.

Conclusions.  Age appropriate information and participation were prerequisites for allowing children to have possibilities of making competent decisions about their own care. Children’s decision‐making competence is dependent on others, such as parents and healthcare professionals, attitudes and not only on their own capacity. Lack of competence, however, does not exclude children from the human right to have a say. It should be noted that it is a decision to leave the determination to a parent or healthcare professional.

Relevance to clinical practice.  Future research from the viewpoint of children is important to reach optimal levels of participation, through respecting their integrity and to develop them into potential competent decision makers.
‘Good’ and ‘bad’ stories: decisive moments, ‘shock and awe’ and being moral
Authors: Carter Bernie
Published: November 2007

Aim.  Within this paper I explore some of the issues related to eliciting, interpreting, choosing and re‐telling stories gathered within narrative inquiry.

Background.  Most of the literature focusing on narrative inquiry and narratives makes little mention of what makes a story intrinsically ‘good’ or ‘bad’ although it is generally acknowledged that stories have moral lessons embedded within them and have a teaching/learning function. However, many of the moral issues associated with gathering, interpreting and re‐telling stories are not really addressed.

Method.  Adopting a reflexive stance, I draw on Cartier‐Bresson's notion of decisive moments and link this to narratives as a way of exploring what makes a story ‘good’/compelling as well as potentially ‘bad’/morally problematic. I develop the idea that narrative researchers may act as ‘horror magnets’ attracting ‘bad news’ stories and may be overlooking some of the more ‘neutral’ and ‘good’/‘good news’ stories.

Conclusion.  Narrative researchers may be adopting a ‘shock and awe’ approach to their stories without fully considering the potential impact. I propose that narrative researchers should engage in a morally proficient manner with participants/stories and conclude that a relational ethical approach can help us to ‘act well’ with people's stories.

Relevance to clinical practice.  Narrative inquiry and a storied approach to practice has much to offer researchers, practitioners and patients/families. Stories can get to the heart of patients’ experiences. Stories provide practitioners with one means of ‘acting well’ and in a relational way with their patients.
Factors affecting exclusive breastfeeding of healthy babies aged zero to four months: a community‐based study of Turkish women
Authors: Karaçam Zekiye
Published: November 2007

Aim.  The purpose of this study was to determine the factors that affect exclusive breastfeeding of healthy babies aged 0–4 months.

Background.  Both the World Health Organization (WHO) and UNICEF recommend feeding babies of 0–6 months exclusively with breast milk and starting complementary foods after the sixth month. In Turkey, however, a vast majority of babies 1–5 months of age (89·4%) are given complementary foods.

Methods.  This cross‐sectional study was conducted in central Ankara province, with a sampling of 514 individuals who were selected using the convenience sampling method.

Results.  Of the 514 mothers who participated in my research, 260 (50·6%) were found to be feeding their babies exclusively with breast milk; 77 (15·0%), with breast milk + water; 87 (16·9%), with breast milk + baby formula; 70 (13·6%), with breast milk + baby formula + other foods; and 20 (3·9%), baby formula + other foods. Based on multivariate logistic regression analysis results, the mother's employment [odds ratio (OR) = 0·488; 95% confidence interval (CI) = 0·288–0·827) considerably reduced the incidence of complementary foods, while frequent crying of the baby (OR = 1·687; 95% CI = 1·125–2·530) significantly increased the use of supplementary foods in infant nutrition.

Conclusion.  This study concluded that frequent crying of the baby increases the likelihood of giving the baby complementary foods. Midwives and nurses can encourage exclusive breastfeeding behaviour by providing individual education and counselling to women whose babies cry frequently.

Relevance to clinical practice.  Exclusive breastfeeding of babies aged 0–6 months is crucial for the development and growth of the baby and instrumental in reducing infant morbidities and mortalities. One factor that increases the likelihood of provision of complementary foods is frequent crying of the baby. Midwives and nurses can encourage exclusive breastfeeding behaviour by providing individual education and counselling to women whose babies cry frequently.
A comparison of some of the cardiovascular risk factors in vegetarian and omnivorous Turkish females
Authors: Karabudak E. , Kiziltan G. , Cigerim N.
Published: November 2007

Background  Elevated serum total homocysteine (tHcy) is associated with an increased risk of cardiovascular disease. Homocysteine levels may be influenced by dietary habits. The aim of the present study was to determine the effects of a vegetarian diet on some of the cardiovascular risk factors in Turkish females.

Method  The study was conducted on 26 vegetarian and 26 omnivore females. Serum tHcy, folate, vitamin B12 and lipids were determined and dietary data were assessed using a 4‐day food intake record at two time points.

Results  Compared with omnivores, vegetarians had higher plasma tHcy, 10.8 ± 3.72 versus 12.6 ± 5.97, (P < 0.05) and folate (P < 0.05) levels. The prevalence of hyperhomocysteinaemia was higher in vegetarians than in omnivores (34.6% versus 12.0%). In addition, serum vitamin B12 levels were lower in vegetarians than in omnivores (P < 0.05). In vegetarians, significant inverse correlation was found between tHcy and serum vitamin B12 levels (r = −0.969, P = 0.001).

Conclusion  The higher prevalence of mild hyperhomocysteinaemia in vegetarians indicated a diminished protective effect of vegetarian nutrition in cardiovascular disease prevention.
Evolution of serum biochemical indicators in anorexia nervosa patients: a 1‐year follow‐up study
Authors: Nova E. , Lopez‐Vidriero I. , Varela P. , Casas J. , Marcos A.
Published: November 2007

Background  Long‐term studies on the evolution of serum biochemical indicators in anorexia nervosa (AN) patients during treatment are lacking in the literature. Thus, a 1‐year follow‐up of serum biochemical parameters in a homogeneous group of AN patients was performed.

Methods  Fourteen restricting‐type AN patients were studied on admission to hospital, after 1 month of inpatient treatment and after 6 and 12 months after admission.

Results  Red blood cell count (RBC) and haemoglobin, serum glucose, total protein and the enzyme activities aspartate aminotransferase (AST), alkaline phosphatase (AlP), lactate dehydrogenase (LDH) and creatine kinase (CK) were significantly lower in patients on admission than in the control group. Total protein, high‐density lipoprotein cholesterol (HDL‐c), AST, AlP and CK showed significant changes among time points (anova, P < 0.05). Significant correlations were found between the change in RBC, haemoglobin, haematocrit, and the change in weight and body mass index (r = 0.74–0.86; P < 0.01). High cholesterol and amylase activity were found at all time points. While AST, LDH and CK reached control values within 6 months of treatment, AlP was always lower.

Conclusion  Serum AlP, hypercholesterolaemia and RBC seem to need longer periods of treatment with further weight gain to fully normalize. Therefore, these parameters should be monitored in AN patients long‐term follow‐up.
Identification and characterization of int (integrase), xis (excisionase) and chromosomal attachment sites of the integrative and conjugative element ICEBs1 of Bacillus subtilis
Authors: Lee Catherine A. , Auchtung Jennifer M. , Monson Rita E. , Grossman Alan D.
Published: November 2007

ICEBs1 is an integrative and conjugative element (conjugative transposon) integrated into trnS‐leu2 in Bacillus subtilis. In response to DNA damage or high concentrations of potential mating partners, ICEBs1 can excise and transfer to various recipients, including other species. We found that excision of ICEBs1 occurs by site‐specific recombination within 60 bp direct repeats that mark the junctions between ICEBs1 and chromosomal DNA. Excision required two ICEBs1 genes, int (integrase, ydcL), predicted to encode a tyrosine recombinase similar to that of phage lambda, and xis (excisionase, sacV). Ectopic expression of xis was sufficient to induce excision of ICEBs1, indicating that regulation of xis transcription by DNA damage and peptide signalling normally controls excision. Int, but not Xis, was needed for site‐specific integration. We found that in the absence of the primary bacterial attachment site (attB) in trnS‐leu2, ICEBs1 integrated in secondary attachment sites that are similar to a 17 bp sequence in attB. In the absence of int, ICEBs1 could recombine into the chromosome by RecA‐dependent homologous recombination, provided ICEBs1 contained a region of sequence identity to a chromosomal locus.
Detection of a novel papillomavirus in pigmented plaques of four pugs
Authors: Tobler K. , Lange C. , Carlotti D. N. , Ackermann M. , Favrot C.
Published: November 2007

Pugs are predisposed to the development of deeply pigmented, slightly elevated hyperkeratotic noncancerous plaques. Polymerase chain reaction amplification of a papillomavirus (PV)‐like DNA fragment from such lesions suggested that PV may be responsible for them, although the predicted virus has not yet been identified. The goal of the present study was to make use of pigmented plaques from four pugs to identify and sequence the predicted virus. Taking advantage of the circular nature of PV DNA, the entire viral genome was amplified by rolling circle amplification and restriction enzyme analysis disclosed the same pattern in all four cases. Sequencing of one of the amplificates revealed a novel canine PV, termed CPV4, related to the recently described CPV3 but clearly distinct from canine oral PV and CPV2. Thus, a novel canine PV and a method for its future diagnosis are described.