bluuebunny/crossref_metadata_2025 huggingface dataset:
Metagenes Associated with Survival in Non-Small Cell Lung Cancer
Authors: Urgard Egon , Vooder Tõnu , Võsa Urmo , Välk Kristjan , Liu Mingming , Luo Cheng , Hoti Fabian , Roosipuu Retlav , Annilo Tarmo , Laine Jukka , Frenz Christopher M. , Zhang Liqing , Metspalu Andres
Published: June 2011

NSCLC (non-small cell lung cancer) comprises about 80% of all lung cancer cases worldwide. Surgery is most effective treatment for patients with early-stage disease. However, 30%–55% of these patients develop recurrence within 5 years. Therefore, markers that can be used to accurately classify early-stage NSCLC patients into different prognostic groups may be helpful in selecting patients who should receive specific therapies.

A previously published dataset was used to evaluate gene expression profiles of different NSCLC subtypes. A moderated two-sample t-test was used to identify differentially expressed genes between all tumor samples and cancer-free control tissue, between SCC samples and AC/BC samples and between stage I tumor samples and all other tumor samples. Gene expression microarray measurements were validated using qRT-PCR.

Bayesian regression analysis and Kaplan-Meier survival analysis were performed to determine metagenes associated with survival. We identified 599 genes which were down-regulated and 402 genes which were up-regulated in NSCLC compared to the normal lung tissue and 112 genes which were up-regulated and 101 genes which were down-regulated in AC/BC compared to the SCC. Further, for stage Ib patients the metagenes potentially associated with survival were identified.

Genes that expressed differently between normal lung tissue and cancer showed enrichment in gene ontology terms which were associated with mitosis and proliferation. Bayesian regression and Kaplan-Meier analysis showed that gene-expression patterns and metagene profiles can be applied to predict the probability of different survival outcomes in NSCLC patients.
Structurama: Bayesian Inference of Population Structure
Authors: Huelsenbeck John P. , Andolfatto Peter , Huelsenbeck Edna T.
Published: June 2011

Structurama is a program for inferring population structure. Specifically, the program calculates the posterior probability of assigning individuals to different populations. The program takes as input a file containing the allelic information at some number of loci sampled from a collection of individuals. After reading a data file into computer memory, Structurama uses a Gibbs algorithm to sample assignments of individuals to populations. The program implements four different models: The number of populations can be considered fixed or a random variable with a Dirichlet process prior; moreover, the genotypes of the individuals in the analysis can be considered to come from a single population (no admixture) or as coming from several different populations (admixture). The output is a file of partitions of individuals to populations that were sampled by the Markov chain Monte Carlo algorithm. The partitions are sampled in proportion to their posterior probabilities. The program implements a number of ways to summarize the sampled partitions, including calculation of the ‘mean’ partition—a partition of the individuals to populations that minimizes the squared distance to the sampled partitions.
Educação do campo e diversidade
Authors: Machado Ilma Ferreira
Published: June 2011

Neste texto, discute-se que a educação do campo, historicamente desprezada pelas políticas públicas, é uma das dimensões da diversidade sociocultural de nosso país que não pode mais ser negada. Os programas emergenciais e as políticas compensatórias de outrora, pensadas por agentes externos, centradas no aspecto econômico-produtivo e referenciadas em um padrão de cultura urbana, retratam a perspectiva de tratamento utilitarista e discriminatório dado ao campo. Essas políticas tentaram, dessa forma, silenciar a diversidade sociocultural do campo e a potencialidade criadora de seus sujeitos. Contra essa prática, emergem os movimentos sociais, procurando evidenciar a importância do protagonismo e da autonomia dos sujeitos do campo na construção de projetos político-sociais e pedagógicos que contemplem as especi) cidades desse contexto, possibilitando articular, em uma dimensão de totalidade, saber local e saber universal e, aomesmo tempo, buscando superar a polarização campo-cidade.
Negros e educação no Brasil: uma entrevista com o coração de uma militante acadêmica
Authors: Oliveira Iolanda de
Published: June 2011

Entrevista.
A preocupação com a metodologia de pesquisa está fora de moda? Análise de trabalhos apresentados em um evento da área da Educação
Authors: Damiani Magda Floriana , Pires Fabiana Lasta Beck , Castro Rafael Fonseca de
Published: June 2011

Este artigo tem como objetivo apresentar os resultados de uma análise oriunda de uma amostra aleatória de trabalhos que constavam dos anais de um conceituado evento da área da Educação. A análise centrou-se na presença/ausência de elementos considerados, pelo grupo de pesquisadores, fundamentais em um relato de pesquisa. Esses elementos foram estabelecidos a partir de uma revisão de literatura sobre o tema. Cada trabalho foi analisado por dois examinadores que preencheram formulários com informações acerca dos seguintes aspectos previamente selecionados: omissão de objetivos; ausência de descrição dos sujeitos e do seu processo de seleção; ausência de descrição dos instrumentos de coleta e análise de dados; e não-inclusão de bibliogra$ a relativa à metodologia de pesquisa nas referências. A análise desses percentuais indicou a existência de lacunas relativas aos diferentes elementos analisados, sugerindo problemas de qualidade nesses relatórios, o que re& ete um provável descaso com a descrição detalhada dos métodos investigativos utilizados. Os resultados são preocupantes e alertam para a importância de uma ampla discussão sobre metodologia de pesquisa e sobre elaboração de relatórios, tanto entre pesquisadores quanto entre cursos de formação para a pesquisa.
Diversidade e diferenciação pela pesquisa universitária
Authors: Caregnato Célia Elizabete
Published: June 2011

Os sistemas nacionais de Ensino Superior são diversi! cados e complexos, o que cria condições para a produção de pesquisa e de conhecimento pelas instituições com variados graus de abrangência e de repercussão. O presente artigo registra a construção de um caminho para a análise da relação entre a diversidade institucional e a atividade de pesquisa. Ao se interpretar a diferenciação de características das instituições de mesma natureza, contribui-se para o conhecimento do sistema de Ensino Superior. Recorre-se à metodologia de análise weberiana do tipo-ideal, sem, portanto, proporem-se modelos para classi! car as instituições reais ou os modelos ideais a serem atingidos.
Public Sector Accounting and Accountability in Greece: A Discussion
Authors: Maggina Anastasia
Published: June 2011

Publiuc sector accounting and accountability have strong origins in Ancient Greece in the framework of the democracy of Athens and the foreign aid later on.The organs of public accounting-management are stereotyped but transparency is still an open question.After the recommendations made by International Organizations(IMF,OECD,etc.) and European Institutions(EU,ECB) many changes/innovations are on the way to restore confidence to citizens,the european partners and the international markets in an effort to get financing or restructure the terms of the very high national debt.
Logbook Language Characteristics and Recordation Requirement
Authors: Huang Gang , Shen Jiang
Published: June 2011

With a view of the deficiency irregular phenomena existing in logbook recordation among Chinese crewmembers, this paper analyzed the language characteristics and recording requirement of logbook, expounded how to employ accurate, concise and precise words to record logbook, listed out matters to be paid attention to in the process of recording the logbook and took examples to make an analysis, with expectation to bring advantages for Chinese crewmembers to improve their competency of recording the logbook.
The Teacher of English: Pedagogic Relevance in Saudi Arabia
Authors: Alam Khan Intakhab
Published: June 2011

The present paper attempts to explore the characteristics of an effective teacher of English. Some related factors such as qualification, attributes, roles, and professional ethics have also been dealt with. In Saudi Arabia, the teacher of English plays the most important role in the process of teaching/learning. There are so many factors such as L1 interference, parental attitude, home environment, schooling etc that are usually influential in the case of educational setting in general and English classes in particular. It is believed that if the teacher of English has undergone a pre-service teacher training it is better for the learners of Saudi Arabia. In the other case, those who have not attended pre-service teacher training, they should go for in-service professional development programs in order to equip them further for innovative teaching and educational output.
Professionalize Sudanese Teachers’ Conception of Work through Action Research
Authors: Bashir Ishraga
Published: June 2011

Teacher action research is in the emergent stages in Sudanese schools and needs to be well disseminated and actively supported from the Ministry of education. Although the teacher-as-researcher movement has been in existence for some twenty years, there is a reason to think that the majority if not all, of Sudanese class teachers remain uninvolved. What lies behind their reluctance? This paper looks at the complexities in the role of a teacher engaging in action research. This includes the need to explore further the principles and practice of action research. This study puts forward explanations in four main areas: teachers’ perception of action research; teachers' professional status, teachers' confidence, and teachers' difficulty engaging in action research. For this purpose a workshop was held and representatives from seven Universities and 25 school teachers participated in a thorough discussion and further investigation was carried out based on the workshop discussion. The data was analyzed statistically and the results showed that the Sudanese teachers have no idea about action research it is not part of their culture as well as the institutions culture. Teachers are reluctant to do an action research and that due to the lack of knowledge which was an important factor. Teachers are not certain about the adequacy of doing an action research. There are other factors such as time and the over load. Based on these findings recommendations are drawn, it is suggested that classroom teaching is an all-demanding and all-involving task which is excluding of an activity as exacting as research. However, it is argued that with appropriate support more teachers may become involved in an action research.
An Examination of the Metacognitive Reading Strategies Used by Native Speakers of Arabic When Reading in English and Arabic
Authors: O. Alsheikh Negmeldin , Mokhtari Kouider
Published: June 2011

This study examined the metacognitive awareness and reading comprehension strategies used by advanced proficiency ESL readers whose native language is Arabic. The study looked at the perceived use of reading strategies by Arabic native speakers in Arabic and English and their actual use of these strategies in reading academic texts in the two languages. The goal was to compare the reading strategy profiles of Arabic native speakers in English and Arabic through quantitative means using a self-report survey of strategy use (n=90), and qualitative means using a think-aloud protocol with a subset of the original sample (n=10). The topic and research questions are pertinent because they add to a relatively small database showing Arabic native speakers rely heavily on reading strategies in their L2 than when reading in their L1.
Impact of Self-Correction on Extrovert and Introvert Students in EFL Writing Progress
Authors: Hajimohammadi Reza , Mukundan Jayakaran
Published: June 2011

To investigate the impact of self-correction method as an alternative to the traditional teacher-correction method, on the one side, and to evaluate the impact of personality traits of Extroversion/Introversion, on the other side, on the writing progress of the pre-intermediate learners three null-hypotheses were proposed. In spite of students absolutely different personalities some teachers probably expect all the students to react to their incompetent feedback in an indistinguishable way. To put it in other words, these teachers pay no attention to the fact that each student is completely a different human being with his/her exclusive personality. These instructors pursue the traditional correction method and correct every error and even do not agonize to present work for different correction methods let alone thinking of making learners engage in their own learning. Therefore, 120 pre-intermediate Iranian female EFL students were selected through employing of Nelson English Language Test (NELT) and the Eysenck Personality Questionnaire (EPQ). They were assigned to four different groups-two groups include extroverts and two groups include introverts. Subsequently, they were given five expository topics to write about in a five-week period. While two groups, one extroverted and one introverted enjoyed self-correction, the teacher corrected the writings of the other two groups. The obtained results showed that personality type had no significant effect on learners' progress in writing. Nevertheless, self-correction method showed to be significantly effective at 0.5.
From Face-to-Face to Paired Oral Proficiency Interviews: The Nut is Yet to be Cracked
Authors: Birjandi Parviz , Bagherkazemi Marzieh
Published: June 2011

The pressing need for English oral communication skills in multifarious contexts today is compelling impetus behind the large number of studies done on oral proficiency interviewing. Moreover, given the recently articulated concerns with the fairness and social dimension of such interviews, parallel concerns have been raised as to how most fairly to assess the oral communication skills of examinees, and what factors contribute to more skilled performance. This article sketches theory and practice on two rather competing formats of oral proficiency interviewing: face-to-face and paired. In the first place, it reviews the related literature on the alleged disadvantages of the individual format. Then, the pros and cons of the paired format are enumerated. It is discussed that the paired format has indeed met some of the criticisms leveled at individual oral proficiency interviewing. However, exploitation of the paired format as an undisputable alternative to the face-to-face format begs the question.
Check This One out: Analyzing Slang Usage among Iranian Male and Female Teenagers
Authors: Shahraki Sara Hashemi , Rasekh Abbass Eslami
Published: June 2011

Slang usage in modern age Iran is a popular phenomenon among most male and female teenagers. How pervasive this variation of language use is among various age and sex groups in Iran has been a question of debate given the significance of religion in a theological system of social structure. The work presented in this study aims to investigate the effect of age and sex on variability of slang usage. Sixty Iranian participants were selected, and then were divided into three age groups (i.e. primary school, high school, and senior university students) each group consisting of ten males and ten females. A self-made questionnaire in the form of Discourse Completion Test (DCT) describing nine situations of friendly conversations was given to the participants. They were asked to make their choice on the responses, which ranged from formal to very informal style (common teenage slang expressions), or to write down what they wish to say under each circumstance. The results of the chi–square tests indicated that slang usage among high school students is more frequent as compared with other age groups. Unlike the popular belief suggesting that slang is used by boys rather than girls, the findings suggested that young Iranians both male and female use slang as a badge of identity showing their attachment to the social group they wish to be identified with.
The Role of Audiovisual Mass Media News in Language Learning
Authors: CaoBahrani Taher , Sim Tam Shu
Published: June 2011

The present paper focuses on the role of audio/visual mass media news in language learning. In this regard, the two important issues regarding the selection and preparation of TV news for language learning are the content of the news and the linguistic difficulty. Content is described as whether the news is specialized or universal. Universal contexts are likely to be more comprehensible than specialized contexts. As for the linguistic difficulty, it consists of acoustic, lexical/syntactic and text-type difficulties. Accordingly, audiovisual texts with greater iconic combinations are likely to be more comprehensible for language learning. Moreover, the present paper provides empirical evidence of the role of exposure to news from mass media on speaking fluency.
Surface modification of POSS‐nanocomposite biomaterials using reactive oxygen plasma treatment for cardiovascular surgical implant applications
Authors: Solouk Atefeh , Cousins Brian G. , Mirzadeh Hamid , Solati‐Hashtjin Mehran , Najarian Siamak , Seifalian Alexander M.
Published: June 2011

In this study, central composite design (CCD) was used to develop predictive models to optimize operating conditions of plasma surface modification. It was concluded that out of the two process variables, power and duration of plasma exposure, the latter was significantly affecting the surface energy (γs), chemistry, and topography of polyhedral oligomeric silsesquioxane–poly(carbonate‐urea)urethane (POSS‐PCU) films. On the basis of experimental data, CCD was used to model the γs using a quadratic modeling of the process variables to achieve optimum surface energy to improve the interaction between endothelial cells (ECs). It was found that optimal water θ for EC adhesion and retention, which was reported 55° from supporting literature (equivalent to γs = 51 mN/m), was easily achievable using the following experimental conditions: (1) power output at 30 W for 75 Sec, (2) 90 W for 40 Sec, and (3) 90 W for 55 Sec in oxygen. In vitro cell culture and metabolic activity studies on optimized films [as in (1)] demonstrate increased adhesion, coverage, and growth of human umbilical vein endothelial cells that were confluent over a shorter time period (<24 H) than controls. Such materials enhanced the EC response and promoted endothelialization on optimized films, thus demonstrating their use as bypass graft materials.
Myocardial Perfusion Defect in Patients With Coronary Artery Disease Demonstrated by 64‐Multidetector Computed Tomography at Rest
Authors: Iwasaki Kohichiro , Matsumoto Takeshi
Published: June 2011

Background:

The first‐pass imaging of 64‐multidetector computed tomography (MDCT) using pharmacological stress has been used to assess myocardial perfusion. However, detection of myocardial ischemia at rest using MDCT has yet to be elucidated. We studied the incidence of myocardial perfusion defect (MPD) by 64‐MDCT at rest and the effect of coronary revascularization therapy on MPD in patients with coronary artery disease.

Hypothesis:

MPD by 64‐MDCT at rest indicates myocardial ischemia.

Methods:

We studied 76 patients with coronary artery disease who underwent 64‐MDCT before and after revascularization therapy and 55 patients who did not undergo revascularization therapy. According to percent diameter stenosis, we defined group A, B, C, and D to have stenosis between 70% and 90%, 50% and 69%, 30% and 49%, and 10% and 29%, respectively. We evaluated regional myocardial contrast enhancement by long and short axis planes. MPD was defined as hypoenhancement area of some extent with CT value <50 HU during diastole.

Results:

MPD was found in 60.0% and 32.4% of group A and B patients, respectively (P = 0.0176). The incidence was 4.8% and 0% in group C and D patients, respectively (P<0.0001 compared with group A and B). All patients in group A and B and 2 patients with MPD in group C underwent coronary revascularization therapy. MPD disappeared after revascularization therapy in all but 3 group A patients. No patients showed new MPD after revascularization therapy.

Conclusions:

Our results demonstrate that a significant percentage of patients with significant coronary artery stenosis show MPD by 64‐MDCT at rest, and these MPDs may represent myocardial ischemia. © 2011 Wiley Periodicals, Inc.

The authors have no funding, financial relationships, or conflicts of interest to disclose.
Canonical notch pathway protects hepatocytes from ischemia/reperfusion injury in mice by repressing reactive oxygen species production through JAK2/STAT3 signaling
Authors: Yu Heng-Chao , Qin Hong-Yan , He Fei , Wang Lin , Fu Wei , Liu Dong , Guo Feng-Cheng , Liang Liang , Dou Ke-Feng , Han Hua
Published: June 2011

Hepatic ischemia/reperfusion (I/R) injury is initiated by reactive oxygen species (ROS) accumulated during the early reperfusion phase after ischemia, but cellular mechanisms controlling ROS production and scavenging have not been fully understood. In this study, we show that blocking Notch signal by knockout of the transcription factor RBP-J or a pharmacological inhibitor led to aggravated hepatic I/R injury, as manifested by deteriorated liver function and increased apoptosis, necrosis, and inflammation, both

in vitro

and

in vivo.

Interruption of Notch signaling resulted in increased intracellular ROS in hepatocytes, and a ROS scavenger cured exacerbated hepatic I/R injury after Notch signaling blockade, suggesting that Notch signal deficiency aggravated I/R injury through increased ROS levels. Notch signal blockade resulted in down-regulation of Hes5, leading to reduced formation of the Hes5-STAT3 complex and hypophosphorylation of STAT3, which further attenuated manganese superoxide dismutase (MnSOD) expression and increased ROS and apoptosis. Indeed, overexpression of a constitutively active STAT3 rescued MnSOD expression and I/R injury–induced apoptosis in the absence of Notch signaling. Finally, forced Notch activation by ligand stimulation or Hes5 overexpression reduced intracellular ROS and protected hepatocytes from apoptosis after I/R injury through the activation of STAT3 and MnSOD expression. Notch signal protects hepatocytes from I/R injury by Hes5-dependent activation of STAT3, which activates the expression of MnSOD, leading to the scavenging of ROS. (HEPATOLOGY 2011;).
Simultaneous analysis of foodborne pathogenic bacteria by an oligonucleotide microarray assay
Authors: Hu Yushan , Liu Junhua , Xia Dan , Chen Shouyi
Published: June 2011

A rapid and accurate method for simultaneous identification of foodborne infectious pathogens was developed based on oligonucleotide microarray technology. The proposed identification method is based on PCR amplification of the target region of the groEL genes with degenerate primers, followed by the PCR products hybridization with oligonucleotide probes specific for species. The groEL gene amplification products of seventeen species of pathogenic bacteria were hybridized to the oligonucleotide array. Hybridization results were analyzed with digoxigenin‐linked enzyme reaction. Results indicated that fifteen species of pathogenic bacteria showed high sensitivity and specificity for the oligonucleotide array, while two other species gave cross‐reaction with the E. coli. Our results suggested that microarray analysis of foodborne infectious pathogens might be very useful for simultaneous identification of bacterial pathogens. The oligonucleotide array can also be applied to samples collected in clinical settings of foodborne infections. The superiority of oligonucleotide array over other tests lies on its rapidity, accuracy and efficiency in the diagnosis, treatment and control of foodborne infections. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification of volatiles from pineapple (Ananas comosus L.) pulp by comprehensive two‐dimensional gas chromatography and gas chromatography/mass spectrometry
Authors: Pedroso Marcio P. , Ferreira Ernesto C. , Hantao Leandro W. , Bogusz Stanislau , Augusto Fabio
Published: June 2011

Combining qualitative data from the chromatographic structure of 2‐D gas chromatography with flame ionization detection (GC×GC‐FID) and that from gas chromatography‐mass spectrometry (GC/MS) should result in a more accurate assignment of the peak identities than the simple analysis by GC/MS, where coelution of analytes is unavoidable in highly complex samples (rendering spectra unsuitable for qualitative purposes) or for compounds in very low concentrations. Using data from GC×GC‐FID combined with GC/MS can reveal coelutions that were not detected by mass spectra deconvolution software. In addition, some compounds can be identified according to the structure of the GC×GC‐FID chromatogram. In this article, the volatile fractions of fresh and dehydrated pineapple pulp were evaluated. The extraction of the volatiles was performed by dynamic headspace extraction coupled to solid‐phase microextraction (DHS‐SPME), a technique appropriate for slurries or solid matrices. Extracted analytes were then analyzed by GC×GC‐FID and GC/MS. The results obtained using both techniques were combined to improve compound identifications.
Gamete membrane microdomains and their associated molecules in fertilization signaling
Authors: Hasan A.K.M. Mahbub , Fukami Yasuo , Sato Ken‐ichi
Published: June 2011

Fertilization is the fundamental system of biological reproduction in many organisms, including animals, plants, and algae. A growing body of knowledge has emerged to explain how fertilization and activation of development are accomplished. Studies on the molecular mechanisms of fertilization are in progress for a wide variety of multicellular organisms. In this review, we summarize recent findings and debates about the long‐standing questions concerning fertilization: how egg and sperm become competent for their interaction with each other, how the binding and fusion of these gamete cells are made possible, and how the fertilized eggs initiate development to a newborn. We will focus on the structure and function of the membrane microdomains (MDs) of egg and sperm that may serve as a platform or signaling center for the aforementioned cellular functions. In particular, we provide evidence that MDs of eggs from the African clawed frog, Xenopus laevis, play a pivotal role in receiving extracellular signals from fertilizing sperm and then transmitting them to the egg cytoplasm, where the tyrosine kinase Src is present and responsible for the subsequent signaling events collectively called egg activation. The presence of a new signaling axis involving uroplakin III, an MD‐associated transmembrane protein, and Src in this system will be highlighted and discussed. Mol. Reprod. Dev. 78:814–830, 2011. © 2011 Wiley Periodicals, Inc.
Cows are not mice: The role of cyclic AMP, phosphodiesterases, and adenosine monophosphate‐activated protein kinase in the maintenance of meiotic arrest in bovine oocytes
Authors: Bilodeau‐Goeseels Sylvie
Published: June 2011

Meiotic maturation in mammalian oocytes is initiated during fetal development, and is then arrested at the dictyate stage – possibly for several years. Oocyte meiosis resumes in preovulatory follicles in response to the lutenizing hormone (LH) surge or spontaneously when competent oocytes are removed from follicles and cultured. The mechanisms involved in meiotic arrest and resumption in bovine oocytes are not fully understood, and several studies point to important differences between oocytes from rodent and livestock species. This paper reviews earlier and contemporary studies on the effects of cAMP‐elevating agents and phosphodiesterase (PDE) enzyme inhibitors on the maintenance of meiotic arrest in bovine oocytes in vitro. Contrary to results obtained with mouse oocytes, bovine oocyte meiosis is inhibited by activators of the energy sensor adenosine monophosphate‐activated protein kinase (AMPK, mammalian gene PRKA), which is activated by AMP, the degradation product of cAMP. It is not clear whether or not the effects were due to AMPK activation, and they may depend on culture conditions. Evidence suggests that other signaling pathways (for example, the cGMP/nitric oxide pathway) are involved in bovine oocyte meiotic arrest, but further studies are needed to understand the interactions between the signaling pathways that lead to maturation promoting factor (MPF) being inactive or active. An improved understanding of the mechanisms involved in the control of bovine oocyte meiosis will facilitate better control of the process in vitro, resulting in increased developmental competence and increased efficiency of in vitro embryo production procedures. Mol. Reprod. Dev. 78:734–743, 2011. © 2011 Wiley Periodicals, Inc.
Always, never, or sometimes: Examining variation in condom‐use decision making among black adolescent mothers
Authors: Nelson LaRon E. , Morrison‐Beedy Dianne , Kearney Margaret H. , Dozier Ann
Published: June 2011

Our purpose in this study was to describe Black adolescent mothers' decisions regarding condom use and non‐use with their male sex partners, including their children's fathers. Research on partner type and condom use has been insufficiently focused on understanding the specific influence that the biological father of the baby has on condom use among adolescent mothers. We conducted five focus groups and three interviews with 31 predominantly African‐American mothers. We found that their decisions to use condoms always, never, or sometimes were based on partner type and on emotional and relationship factors. The “baby daddy” was the only partner with whom they never used condoms. HIV/STI prevention interventions for adolescent mothers must address risk taking with their children's biological fathers. © 2011 Wiley Periodicals, Inc. Res Nurs Health 34:270–281, 2011
Quantification of proteins using data‐independent analysis (MSE) in simple andcomplex samples: A systematic evaluation
Authors: Levin Yishai , Hradetzky Eva , Bahn Sabine
Published: June 2011

A MS‐based method for the quantification of proteins termed data‐independent analysis (or MSE) has been introduced recently. Although this method has been applied to the analysis of various types of biological samples, a thorough evaluation to assess the performance of this approach has yet to be conducted. Presented here is the first systematic and comprehensive study investigating the MSE approach for quantitative analysis of low‐, medium‐, and high‐complexity samples. We demonstrate that this method has a linear dynamic range spanning three orders of magnitude with a limit of quantification of 61 amol/uL in low‐complexity samples and 488 amol/uL in high‐complexity samples. In addition, comprehensive sequence coverage was obtained and accurate quantification achieved for expression ratios ranging from 1:1.5 to 1:6. However, underestimation of ratios was detected independent of sample type, consistent with other quantitative proteomic methods. The present study provides validation of the MSE approach for accurate quantitative proteomic analysis of biological samples while, at the same time, proving high sequence coverage of target proteins.
Selective area growth of GaN rod structures by MOVPE: Dependence on growth conditions
Authors: Li Shunfeng , Fündling Sönke , Wang Xue , Erenburg Milena , Al‐Suleiman Mohamed Aid Mansur , Wei Jiandong , Bergbauer Werner , Strassburg Martin , Wehmann Hergo‐Heinrich , Waag Andreas
Published: June 2011

Selective area growth of GaN nanorods by metalorganic vapor phase epitaxy is highly demanding for novel applications in nano‐optoelectronic and nanophotonics. Recently, we report the successful selective area growth of GaN nanorods in a continuous‐flow mode. In this work, as examples, we show the morphology dependence of GaN rods with µm or sub‐µm in diameters on growth conditions. Firstly, we found that the nitridation time is critical for the growth, with an optimum from 90 to 180 seconds. This leads to more homogeneous N‐polar GaN rods growth. A higher temperature during GaN rod growth tends to increase the aspect ratio of the GaN rods. This is due to the enhanced surface diffusion of growth species. The V/III ratio is also an important parameter for the GaN rod growth. Its increase causes reduction of the aspect ratio of GaN rods, which could be explained by the relatively lower growth rate on (000‐1) N‐polar top surface than it on {1‐100} m‐planes by supplying more NH3 (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Virtualized HPC: a contradiction in terms?
Authors: Birkenheuer Georg , Brinkmann André , Kaiser Jürgen , Keller Axel , Keller Matthias , Kleineweber Christoph , Konersmann Christoph , Niehörster Oliver , Schäfer Thorsten , Simon Jens , Wilhelm Maximilian
Published: June 2011

System virtualization has become the enabling technology to manage the increasing number of different applications inside data centers. The abstraction from the underlying hardware and the provision of multiple virtual machines (VM) on a single physical server have led to a consolidation and more efficient usage of physical servers. The abstraction from the hardware also eases the provision of applications on different data centers, as applied in several cloud computing environments. In this case, the application need not adapt to the environment of the cloud computing provider, but can travel around with its own VM image, including its own operating system and libraries. System virtualization and cloud computing could also be very attractive in the context of high‐performance computing (HPC). Today, HPC centers have to cope with both, the management of the infrastructure and also the applications. Virtualization technology would enable these centers to focus on the infrastructure, while the users, collaborating inside their virtual organizations (VOs), would be able to provide the software. Nevertheless, there seems to be a contradiction between HPC and cloud computing, as there are very few successful approaches to virtualize HPC centers. This work discusses the underlying reasons, including the management and performance, and presents solutions to overcome the contradiction, including a set of new libraries. The viability of the presented approach is shown based on evaluating a selected parallel, scientific application in a virtualized HPC environment. Copyright © 2011 John Wiley & Sons, Ltd.
CONSANGUINEOUS MARRIAGES IN AFGHANISTAN
Authors: SAIFY KHYBER , SAADAT MOSTAFA
Published: June 2011

The present cross-sectional study was done in order to illustrate the prevalence and types of consanguineous marriages among Afghanistan populations. Data on types of marriages were collected using a simple questionnaire. The total number of couples in the study was 7140 from the following provinces: Badakhshan, Baghlan, Balkh, Bamyan, Kabul, Kunduz, Samangan and Takhar. Consanguineous marriages were classified by the degree of relationship between couples: double first cousins, first cousins, first cousins once removed, second cousins and beyond second cousins. The coefficient of inbreeding (F) was calculated for each couple and the mean coefficient of inbreeding (α) estimated for each population. The proportion of consanguineous marriages in the country was 46.2%, ranging from 38.2% in Kabul province to 51.2% in Bamyan province. The equivalent mean inbreeding coefficient (α) was 0.0277, and ranged from 0.0221 to 0.0293 in these two regions. There were significant differences between provinces for frequencies of different types of marriages (p<0.001). First cousin marriages (27.8%) were the most common type of consanguineous marriages, followed by double first cousin (6.9%), second cousin (5.8%), beyond second cousin (3.9%) and first cousin once removed (1.8%). There were significant differences between ethnic groups for the types of marriages (χ2=177.6, df=25, p<0.001). Tajiks (Soni) and Turkmens (also Pashtuns) showed the lowest (α=0.0250) and highest (α=0.0297) mean inbreeding coefficients, respectively, among the ethnic groups in Afghanistan. The study shows that Afghanistan's populations, like other Islamic populations, have a high level of consanguinity.
Numerical solution of nonlinear electron kinetic equation in self-similar variables
Authors: POTAPENKO I. F. , KRASHENINNIKOV S. I.
Published: June 2011

We present numerical solution of a fully nonlinear electron kinetic equation in self-similar variables, which on the one hand has all features of a ‘standard’ hydrodynamics (ratios of the electron mean free path to the scale length γ ≡ λC/L 1), and on the other hand has no restriction on the smallness of the parameter γ. The self-similar variable approach reduces dimensionality of the space-dependent kinetic equation, thereby providing numerical analysis of the electron heat transport in the velocity space. The electron distribution structure and its super thermal power-law tail are examined.

PACS number(s): 52.25.Dg, 52.65.Ff, 52.50.-b
An Evaluation of a CBT Group for Women with Low Self-Esteem
Authors: Morton Liza , Roach Louise , Reid Helen , Stewart Scott Hallam
Published: June 2011

Background: Self-esteem is an important factor in the development and maintenance of good psychological health. Low self-esteem can be a consequence of mental health disorders (such as depression, anxiety and panic) or it can be a vulnerability factor for the development of such problems. Aims and method: The current study reports pilot findings from a Cognitive Behavioural Therapy (CBT) group intervention for 37 adult women with low self-esteem, based on Fennell's Overcoming Low Self-Esteem Self-Help Course. Results: Findings suggest that the group is (statistically and clinically) effective at increasing levels of self-esteem and at reducing levels of depression and anxiety. Conclusions: Together, results suggest that the group provides an efficient and therapeutically beneficial service. However, since these findings are limited by the lack of control or follow-up data, they warrant further investigation.
Influence of radio frequency power on thermal diffusivity of plasma enhanced chemical vapor deposition-grown hydrogenated amorphous carbon thin-films
Authors: Young Kim Yun , Adli Alwi Hasan , Awang Rozidawati , Krishnaswamy Sridhar
Published: June 2011

Thermal diffusivity (α) of hydrogenated amorphous carbon (a-C:H) thin-films was characterized using the picosecond thermoreflectance measurement technique in the present study. The samples were fabricated in a plasma enhanced chemical vapor deposition system with varying radio frequency (RF) discharge powers from 15 to 70 W. Chemical bonding properties of the a-C:H films were determined from the Fourier transform infrared spectra and Raman spectroscopy. Results show that α is enhanced from 0.07 to 0.20 mm2 s−1 as the RF power increases. It attributes to the dehydrogenation of film resulting from the bombardment of high-energy ion species that breaks C–H bonds at the lower power regime. Particularly at the highest RF power, however, the increase of α is more influenced by the restructuring of bonding configuration associated with the breaking up of sp2 clusters into smaller ones.
The provision of fishery information by ICES–WGFTFB to assessment working groups: use of information and lessons learned
Authors: Rihan Dominic , Graham Norman , Reid Dave G. , Lordan Colm
Published: June 2011

Rihan, D., Graham, N., Reid, D. G., and Lordan, C. 2011. The provision of fishery information by ICES–WGFTFB to assessment working groups: use of information and lessons learned. – ICES Journal of Marine Science, 68: 1809–1814. ICES is now asked to provide advice that is more holistic in nature, including information on the influence and effects of human activities on the marine ecosystem. From a fishing-technology perspective, this includes information on how fishers respond and adapt to changes in regulatory frameworks, the impact of technology creep, ecosystem impacts, and changes in fleet dynamics. Recognizing the importance of this, in 2005, the ICES–Food and Agriculture Organization (FAO) Working Group on Fish Technology and Fish Behaviour (WGFTFB) began to collect data and information to support scientific advice on fisheries and ecosystem issues through a questionnaire circulated to its members. The information from the questionnaires was collated by the WGFTFB and submitted in the form of summary documents to various ICES assessment working groups. This paper describes the background to this initiative, the questionnaire structure, the type of information provided, and its utility.
Web‐enabled registry of inherited bleeding disorders in Portugal: conditions and perception of the patients
Authors: TEIXEIRA L. , FERREIRA C. , SANTOS B. S. , SAAVEDRA V.
Published: June 2011

Summary.  Local and national haemophilia registries are powerful instruments to support the healthcare and researchers and improve the communication between Comprehensive Haemophilia Diagnostic and Treatment Centres (HTCs) and patients. Hemo@care is an example of a Local Haemophilia Registry Systems (LHR_Sys) based on the Web, developed in collaboration with a HTC located in Portugal, to support the haemophilia treatments registry, collect and manage the clinical information and provide mechanisms to control the clotting factor concentrates (CFC) stock. To extend this solution (the hemo@care) to other Portuguese HTCs and consequently to meet the preconditions to create a National Haemophilia Registry Systems (NHR_Sys), a study based on a questionnaire was carried out at nationwide. This study aims to assess the conditions and motivations of people with haemophilia (PWH) geographically scattered throughout the country, to use a potential Web‐enabled registry with the purpose of replacing the traditional paper‐diaries, to understand their judgment about a potential NHR_Sys currently non‐existent in Portugal, and at the same time, to characterize demographically and pathologically those people at the nationwide. The results based on the analysis of 168 responses (response rate of 31%) confirmed the high prevalence of the disease in haemophilia A (75%) compared with haemophilia B (11.3%) and a large incidence in the severe levels, or the existence of people with mild severity without diagnosis and treatment. Furthermore, the results also revealed the need, conditions and motivation for using a registry system by PWH; thus it is deemed to justify the extension of the hemo@care to other HTCs in Portugal and consequently to create the NHR_Sys.
UKHCDO guidelines on the management of HCV in patients with hereditary bleeding disorders 2011
Authors: WILDE J. T. , MUTIMER D. , DOLAN G. , MILLAR C. , WATSON H. G. , YEE T. T. , MAKRIS M.
Published: June 2011

Summary.  Chronic HCV infection continues to be of significant clinical importance in patients with hereditary bleeding disorders. This guideline provides information on the recent advances in the investigation and treatment of HCV infection and gives GRADE system based recommendations on the management of the infection in this patient group.
The identification of risk factors for critically ill patients with acute fever and formulation of activation criteria to alert outpatient clinic doctors
Authors: Xiao Hongli , Qi Haiyu , Wang Jing , Li Xiaoli , Ma Suxia , Diao Zongli , Wang Yan , Sun Fangfang , Yin Chenghong
Published: June 2011

Rationale, aims and objectives  Acute fever is the most common early clinical symptom of many critical illnesses with a high mortality rate. It is necessary to identify patients with severe acute fever early and accurately. The aim of this study is to identify risk factors for critically ill outpatients with acute fever and formulate activation criteria of adult fever state score (AFSS) to alert outpatient clinic doctors.

Methods  Retrospectively, 357 adult patients with acute fever were divided into two groups: 180 patients with a severe state and 177 patients with a mild state. Logistic regression was used to determine risk factors for the severe state. Risk factors were weighted and an AFSS was formulated. A receiver operating characteristic (ROC) analysis of weighted cumulative scores was performed to evaluate the diagnostic accuracy of AFSS, and the kappa test was used to confirm diagnostic reliability. A χ2‐test for trend was applied to determine the relevance between AFSS and admission rate and in‐hospital mortality. A Kruskal–Wallis test was used to examine the relationship between AFSS and length of stay.

Results  Risk factors for state included: old age, long fever course, past medical history, abnormal temperature, abnormal respiratory rate, abnormal heart rate, abnormal mean arterial pressure and abnormal peripheral white blood cell count. The area under the ROC curve of AFSS was 0.964 and ≥8 points predicted severe state; the Kappa value was 0.801. With an increase in score, there was an increase in admission rate, mortality rate and length of stay. The forecast performance of AFSS was superior to the modified early warning score.

Conclusions  The AFSS has high diagnostic accuracy and reliability for the early identification of patients with severe acute fever.
Anaesthesia for endoscopic retrograde cholangiopancreatography
Authors: KAPOOR H.
Published: June 2011

Endoscopic Retrograde Cholangiopancreatography is used for both diagnostic and therapeutic purposes. It is relatively more complex than routine endoscopies and requires adequate patient sedation. Furthermore the patients often have co‐morbidities. This article provides an overview of various anaesthetic drugs and the type of anaesthesiological support.
The genome sequence of Desulfatibacillum alkenivorans AK‐01: a blueprint for anaerobic alkane oxidation
Authors: Callaghan A. V. , Morris B. E. L. , Pereira I. A. C. , McInerney M. J. , Austin R. N. , Groves J. T. , Kukor J. J. , Suflita J. M. , Young L. Y. , Zylstra G. J. , Wawrik B.
Published: June 2011

Desulfatibacillum alkenivorans AK‐01 serves as a model organism for anaerobic alkane biodegradation because of its distinctive biochemistry and metabolic versatility. The D. alkenivorans genome provides a blueprint for understanding the genetic systems involved in alkane metabolism including substrate activation, CoA ligation, carbon‐skeleton rearrangement and decarboxylation. Genomic analysis suggested a route to regenerate the fumarate needed for alkane activation via methylmalonyl‐CoA and predicted the capability for syntrophic alkane metabolism, which was experimentally verified. Pathways involved in the oxidation of alkanes, alcohols, organic acids and n‐saturated fatty acids coupled to sulfate reduction and the ability to grow chemolithoautotrophically were predicted. A complement of genes for motility and oxygen detoxification suggests that D. alkenivorans may be physiologically adapted to a wide range of environmental conditions. The D. alkenivorans genome serves as a platform for further study of anaerobic, hydrocarbon‐oxidizing microorganisms and their roles in bioremediation, energy recovery and global carbon cycling.