bluuebunny/crossref_metadata_2025 huggingface dataset:
CYBA Gene Polymorphisms and Adverse Outcomes in Acute Kidney Injury: A Prospective Cohort Study
Authors: Perianayagam Mary C. , Tighiouart Hocine , Nievergelt Caroline M. , O’Connor Daniel T. , Liangos Orfeas , Jaber Bertrand L.
Published: October 2011

Background: NADPH oxidase is an important enzyme involved in the generation of reactive oxygen species in acute kidney injury (AKI). Its key subunit, p22phox, is encoded by the highly polymorphic CYBA gene. Methods: We examined the associations of CYBA gene polymorphisms across the CYBA locus (rs8854, rs3794624, rs4673, rs4782390, and rs1049255) with dialysis requirement or in-hospital death in 256 hospitalized adults with AKI. Dominant and haplotype multivariable logistic regression analyses were performed, adjusted for sex, race, age, and severity of illness. Results: The baseline characteristics of the patients were not different among genotype groups with the exception of a lower prevalence of sepsis and shock in the CYBA rs8854 A-allele group; a higher prevalence of shock in the CYBA rs4782390 T-allele group, and a higher APACHE II score in the CYBA rs1049255 G-allele group. The CYBA rs8854 A-allele had an adjusted odds ratio (OR) of 0.41 (95% confidence interval, CI, 0.18–0.96) for the outcome of dialysis requirement or in-hospital death. The CYBA rs4673 T-allele and rs1049255 G-allele had unadjusted ORs of 1.69 (95% CI 1.03–2.79) and 1.66 (95% CI 1.01–2.73) for the composite outcome, respectively, which became non-significant after multivariable adjustment. The remaining 2 polymorphisms were not associated with the outcomes of interest. Finally, the presence of the CYBA A-A-G-G haplotype (generated from rs4782390, rs4673, rs3794624, and rs8854, all in Hardy-Weinberg equilibrium) was associated with an elevated OR of 1.81 (95% CI 1.07–3.08) for dialysis requirement or in-hospital death, which was attenuated after multivariable adjustment (OR 1.80; 95% CI 0.99–3.29). Conclusion: This study identifies several polymorphisms spanning the entire CYBA gene locus and a common haplotype as risk markers for dialysis requirement or in-hospital death in patients with AKI. Additional studies are needed to validate these findings.
Virtues of SIN
Authors: Åslund Olof , Johansson Per
Published: October 2011

The labor market integration of immigrants is a top political priority throughout the Organization for Economic Cooperation and Development (OECD) countries. Social and fiscal gains, as well as sustained future labor supply make governments search for effective policies to increase employment among the mostly disadvantaged. The author studies SIN, a Swedish pilot workplace introduction program targeting these groups, using very detailed individual data and allowing for effects through several channels. The results show increased transitions from unemployment to work experience schemes and improved future employment probabilities for those who entered these schemes. A rough calculation suggests that each job year created cost about Euro 30,000.
Trust as a moderator of the relationship between organizational learning and marketing capabilities: Evidence from Spanish SMEs
Authors: Sanzo María J. , Santos Maria L. , García Nuria , Trespalacios Juan A.
Published: October 2011

In the current environment of technological change and increased competition, it is more important than ever for small- and medium-sized enterprises to develop competitive advantages that enable them to consolidate their market position. This research analyses the links among organizational learning (OL), operational marketing capability, and performance in such organizations. In particular, interpersonal trust may moderate the positive impact of OL on the development of marketing capabilities. This study is based on a nationwide survey of 163 small- and medium-sized Spanish industrial firms. The results confirm the existence of the moderating effect, as well as the positive influence of OL on performance.
Digital preservation strategies
Authors: Gbaje Ezra Shiloba
Published: October 2011

This study examines digital preservation strategies in national information centres in Nigeria. Specifically the study tried to find out the digital preservation strategies and structures put in place for the implementation of the strategies adopted. The population of the study consists of the National Library of Nigeria, the National Archives of Nigeria and the National Bureau of Statistics. A case study and qualitative methodology approaches were adopted for the study. A semi-structured questionnaire was designed and administered to a focused group of five staff of the digital preservation/digitization unit of the population. The study discovered, among others, that migration is the most popular digital preservation strategy adopted and no structure to assess digital objects for preservation action is put in place. The study recommended that a National Centre for Digital Preservation, responsible for monitoring and conducting research in digital preservation activities, should be established.
Synergizing the collections of libraries archives and museums for better user services
Authors: Prasad Neelam
Published: October 2011

The digital age has brought about new ways of information storage and information and communication technology has brought the stored information closer to its seekers. This has changed user behaviour in accessing information. This paper attempts to introduce a model of building a consortium involving libraries, archives and museums in India so that users can find information at a click of their mouse or mobile phone.
Rereading Winnicott's ‘Primary maternal preoccupation’
Authors: Hollway Wendy
Published: October 2011

Using data examples, I re-approach Donald Winnicott's idea of primary maternal preoccupation (1984[1956]) through Bracha Ettinger's matrixial concept of transsubjectivity. I argue that Winnicott recognises the radical difference between the mental state that women will have occupied formerly and the state that the prenatal and postnatal infant will claim, if the mother is available to it. With the benefit of a matrixial perspective it is possible to see how this description need not pathologise women, nor reproduce misogynistic discourses. On the contrary it begins to do justice to the enormity of women's transition as they become mothers: enormity because it threatens to pitch them beyond the experience of being a self-contained autonomous individual, a position which is normalised in what Ettinger calls phallic logic. Feminists risk reproducing phallic logic if we dismiss on ideological grounds, and thereby pathologise, this radically other state characteristic of the peri-natal period that many women experience when they become mothers.
Observational data for comparative effectiveness research: An emulation of randomised trials of statins and primary prevention of coronary heart disease
Authors: Danaei Goodarz , Rodríguez Luis A García , Cantero Oscar Fernández , Logan Roger , Hernán Miguel A
Published: October 2011

This article reviews methods for comparative effectiveness research using observational data. The basic idea is using an observational study to emulate a hypothetical randomised trial by comparing initiators versus non-initiators of treatment. After adjustment for measured baseline confounders, one can then conduct the observational analogue of an intention-to-treat analysis. We also explain two approaches to conduct the analogues of per-protocol and as-treated analyses after further adjusting for measured time-varying confounding and selection bias using inverse-probability weighting. As an example, we implemented these methods to estimate the effect of statins for primary prevention of coronary heart disease (CHD) using data from electronic medical records in the UK. Despite strong confounding by indication, our approach detected a potential benefit of statin therapy. The analogue of the intention-to-treat hazard ratio (HR) of CHD was 0.89 (0.73, 1.09) for statin initiators versus non-initiators. The HR of CHD was 0.84 (0.54, 1.30) in the per-protocol analysis and 0.79 (0.41, 1.41) in the as-treated analysis for 2 years of use versus no use. In contrast, a conventional comparison of current users versus never users of statin therapy resulted in a HR of 1.31 (1.04, 1.66). We provide a flexible and annotated SAS program to implement the proposed analyses.
Securitization, sectors and functional differentiation
Authors: Albert Mathias , Buzan Barry
Published: October 2011

So far, securitization analysis has proceeded on the basis of an assumption that there are sectoral differences between securitization dynamics. However, sectors in this context were primarily seen as analytical ‘lenses’, as complexity-reducing cuts through a complex social reality. In this article, we first reflect on the ontological status of ‘sectors’. Do they represent functionally differentiated realms of world politics or world society, or do sectors and functional realms need to be separated from one another clearly? After giving a short introduction to the notion of ‘functional differentiation’ in international relations and briefly reflecting on the ontological/analytical distinction, we scrutinize the relation between sectors and functionally differentiated realms of society. Although sectors hang together with functional differentiation, much depends on the version of functional differentiation theory used. In the communication theoretical version, securitization would be firmly located within the political system. References to functionally specific sectors would then – contra Waltz – point not only towards functional differentiation between the political and other functionally defined realms of (international) society, but also towards ongoing functional differentiation within the (international) political system.
Can securitization theory be used in normative analysis? Towards a just securitization theory
Authors: Floyd Rita
Published: October 2011

While securitization studies have paid considerable attention to the moral value of desecuritization, they have paid almost no attention to the morality of securitization. In this article, I attempt to rectify that situation by proposing a revision of securitization theory that specifies three criteria that – if fulfilled at the same time – would render a securitization morally right. The criteria are: (1) that there is an objective existential threat; (2) that the referent object of security is morally legitimate; and (3) that the security response is appropriate to the threat in question. Although what is suggested here is considerably removed from the Copenhagen School’s original securitization theory, it is akin to that framework insofar as it retains the functional distinction between the security analyst and the securitizing actor. Indeed, the development of criteria that determine the moral rightness of securitization is analogous to the Copenhagen School’s devising criteria that determine both the existence and the success of securitization.
Resisting the ‘protest business’: Bureaucracy, post-bureaucracy and active membership in social movement organizations
Authors: Hensby Alexander , Sibthorpe Joanne , Driver Stephen
Published: October 2011

Over the past few decades, the legitimacy of membership-based social movement organizations (SMOs) has been called into question (Bosso, 2005; Jordan and Maloney, 1997, 2007; Putnam, 2000). As professionally-run institutions, SMOs have been accused of a preoccupation with maintaining income through membership marketing at the expense of fostering active participation among their members. In a nutshell, SMOs are seen to be self-serving ‘protest businesses’ which contribute little to social movement activism, and civic engagement in general. Our research into student members of a leading SMO takes issue with this assertion. Whilst organizationally SMOs can appear bureaucratic and impersonal in their marketing strategies, it cannot be assumed that this approach is only capable of attracting passive ‘chequebook activists’. Our findings suggest that younger members feel a sense of loyalty and trust towards the SMO as an effective ‘brand leader’ in its field, though this is by no means unrelenting. As reflexive consumers of activism, members have also grown more accustomed to the flexibilities of emerging post-bureaucratic ‘DIY’ activist groups. In sum, SMOs would benefit from a stronger and more consistent ‘feedback loop’ between the organization and its younger and more active members, as this will help provide scope for greater innovation whilst resisting tendencies towards self-serving ‘bureaucratized activism’.
The use of Buddhist mindfulness meditation in psychotherapy: A case report from Sri Lanka
Authors: de Zoysa Piyanjali
Published: October 2011

Buddhist practices have been increasingly influencing psychotherapy. For over 20 centuries, Buddhism has been the religion of a majority of Sri Lankans. However, there is little documentation of the use of Buddhist practices in psychotherapy in Sri Lanka. This paper presents a case study in which Theravadan Buddhist mindfulness meditation and cognitive therapy practices were used in the treatment of a client with depressive disorder. The paper also summarizes the influence of Buddhist concepts and mindfulness meditation on psychotherapy and illustrate how Buddhist doctrine and practices can be considered a psychotherapeutic method.
Distancing: A traditional mechanism of dealing with suicide among the Baganda, Uganda
Authors: Mugisha James , Hjelmeland Heidi , Kinyanda Eugene , Knizek Birthe Loa
Published: October 2011

This qualitative study investigated attitudes and cultural responses to suicide among the Baganda in Uganda using both focus group discussions and key-informant interviews. Interviews indicate that suicide is perceived as dangerous to the whole family and the entire community. Communities and family members adopt various ritual practices to distance themselves both symbolically and socially from the suicide. These rituals are characterized by broad themes: the regulation of affect and the attempt to secure future generations.
Energy Consumption Behaviour of an Urban Residential Sector in the Northern Province of Madhya Pradesh (India)
Authors: Verma Anita , Jaiswal Y. K. , Wani Khurshreed Ahmad
Published: October 2011

Energy crises represent a bottleneck in the progress of the Indian economy. In the present scenario, high energy consumption is more noticeable with the development of the economy of the country, due to changes in the lifestyle of the consumers in the residential sector. The current challenge is to seek sustainable development, maintaining activities, transformation and progress levels while adopting more efficient use of existing resources and achieving energy conservation. An assessment of the energy consumption of the residential sector of the Gwalior city, Madhya Pradesh (India) has been carried out in the present investigation. Structured questionnaires were distributed among the 500 households during the present investigation. The survey has indicated that the majority of households are using modern high energy appliances leading to overuse of the valuable energy resources. The present investigation demonstrates that most of the buildings were not climate responsive, and were consuming high levels of energy to achieve thermal comfort for residents. The western region of the country is the largest consumer of the total energy. There is a dire need to go for an energy-efficient operation with public participation that may greatly reduce the energy consumption and ultimately reduce burden on fossil fuels.
Transportation and Risk Analysis of Influenza Indoor and Outdoor Transportation and Exposure Risk Analysis of Influenza Aerosol
Authors: Liu Wei , You Xue-Yi
Published: October 2011

With the frequent outbreak of influenza virus in urban areas, the ecological security of high-density housing is becoming increasingly prominent. An Eulerian-Lagrangian pollutant diffusion model based on Large Eddy Simulation (LES) is established to simulate the transport of airborne virus. After the reliability of the numerical model is validated by the indoor experiment, the indoor and outdoor dispersion of microbial aerosol are simulated. The exposure risk is further studied based on the space-time concentration of pathogenic microorganisms of numerical simulation. The outcome can provide evidences for building plan optimization, environmental risk analysis and safety withdrawal planning.
Towards practical application of electrical resistance change measurement for damage monitoring using an addressable conducting network
Authors: Takahashi Kosuke , Hahn H Thomas
Published: October 2011

This article considers the practical use of electrical resistance change method (ERCM) for damage detection in graphite/polymer composites. ERCM utilizes the high electrical conductivity of graphite fibers in the composites and can detect damage by change in electrical resistance. Since the effectiveness of ERCM has been shown extensively in the literature, it is now necessary to consider how to apply ERCM into existing structures. For practical use of ERCM, a new concept of an addressable conducting network (ACN) has been proposed, which consists of two sets of conducting lines normal to each other. One set of lines resides on the top surface of the laminate and the other resides on the bottom surface. Damage can be detected by monitoring resistance change between two lines across the laminate thickness. In this article, composite panels with several sets of conducting lines are locally loaded by a static indentation test and examined to monitor the distribution of electrical resistance changes. Monitoring the changes in resistance successfully indicated the damage occurrence, but it is sometimes difficult to pinpoint the damage location due to the resistance changes caused by compressive deformation. To improve the sensitivity of ACN to damage, the relationship between damage location and electrical conductivity was investigated using a design of experiments. The changes in resistance with various damage locations and electrical conductivities were acquired from finite element analysis, and the results suggested several ways to optimize damage detection. Depending on the damage tolerance of target structure, spacing of conducting lines and the electrical conductivities can be preferably selected toward practical application of ACN.
Accelerated climate aging of building materials and their characterization by Fourier transform infrared radiation analysis
Authors: Jelle Bjørn Petter , Nilsen Tom-Nils , Hovde Per Jostein , Gustavsen Arild
Published: October 2011

Building materials and their durability and aging are essential to the performance of buildings and their building physical aspects over time. Accelerated climate aging investigations are carried out in order to study the durability of various building materials in a substantial shorter time span than natural weather aging would have allowed. Climate parameters such as temperature that includes freezing/thawing cycles, relative air humidity, water spray amount, solar and/or ultraviolet (UV) radiation and exposure duration are controlled in different climate aging apparatuses. Various aging processes in building materials, aging both by natural and accelerated climate exposure, may be studied in an attenuated total reflectance (ATR) Fourier transform infrared (FTIR) radiation analysis following the decomposition and/or formation of chemical bonds in these building materials and products.

ATR-FTIR analysis of different building material samples exhibit various levels of experimental difficulties. In this investigation we have studied the FTIR spectra of climate-weathered wood, wood rot, mold fungus on wood, mold fungus on plasterboard, and plastic degradation by UV radiation. Both qualitative and quantitative results may be obtained by an ATR-FTIR analysis. In order to determine the aging progress and assess the effective lifetime of materials, components, or products, FTIR spectra should be recorded before, during, and after the climate aging. Hence, FTIR may be developed as an important tool to track the condition of various materials, components, and products during the lifetime of a building, and thereby applied as a tool for condition assessment, selection of maintenance intervals, and service life prediction of buildings.
High-Ability Students’ Time Spent Outside the Classroom
Authors: Makel Matthew C. , Li Yan , Putallaz Martha , Wai Jonathan
Published: October 2011

This study considered how three groups of academically talented high school students—those who attended an academic summer program (TIP), those who qualified for the program but chose not to attend (QNA), and those who did not qualify (DNQ)—spent time outside the classroom. These groupings differentiated students by ability (QNA vs. DNQ) and attendance (TIP vs. QNA). Male–female comparisons were also conducted. By comparing participation rates across a variety of activities and by sex, the current study helps explain the lives of high-ability students outside the arena by which they are defined: their academic ability. Results reveal numerous group and sex differences based on how high-ability students spend their time outside the classroom. Females tended to participate more than males in activities that were generally positively associated with academic achievement, while also participating in more types of activities. Males, however, reported watching more TV and were less likely to participate in any activity. QNA students reported spending more time on academic-related activities, such as homework and academic clubs, than did DNQ students, indicating a generally higher interest in academic endeavors. However, the QNA and TIP groups differed only in their service club participation rates, indicating that attending a summer program is not associated with spending time outside the classroom differently during the school year. This research underscores the heterogeneity of different groups of high-ability students and suggests some caution when generalizing from research findings based only on program participants. Knowing how students spend their time can help parents, educators, and researchers understand and foster adolescent development.
A Reliability Generalization of the Overexcitability Questionnaire–Two
Authors: Warne Russell T.
Published: October 2011

Reliability generalization (RG) is a meta-analysis that combines and synthesizes reliability coefficients from different studies to ascertain the average observed reliability across studies. An RG study was conducted on previously reported data from 16 samples of the Overexcitability Questionnaire–Two (OEQII) with a combined N of 5,275. Cronbach’s alpha was found to be consistently higher on all OEQII subscales when scale variance was high and the sample consisted of adults. Sample size, gender composition of the sample, number of items from the subscale used, and location of sample (United States or a different county) had varying effects on observed alpha levels for each subscale. Suggestions are proposed for substantive research using the OEQII and for future psychometric research on the instrument.
Measuring Teacher Effectiveness in Gifted Education
Authors: Welsh Megan E.
Published: October 2011

States and districts are under increasing pressure to evaluate the effectiveness of their teachers and to ensure that all students receive high-quality instruction. This article describes some of the challenges associated with current effectiveness approaches, including paper-and-pencil tests of pedagogical content knowledge, classroom observation systems, and value-added models. It proposes development of a new teacher evaluation system using a virtual reality environment and describes how innovations in educational measurement and technology can be used to develop an improved teacher effectiveness measure.
Selecting a single model or combining multiple models for microarray-based classifier development? – A comparative analysis based on large and diverse datasets generated from the MAQC-II project
Authors: Chen Minjun , Shi Leming , Kelly Reagan , Perkins Roger , Fang Hong , Tong Weida
Published: October 2011

Background

Genomic biomarkers play an increasing role in both preclinical and clinical application. Development of genomic biomarkers with microarrays is an area of intensive investigation. However, despite sustained and continuing effort, developing microarray-based predictive models (i.e., genomics biomarkers) capable of reliable prediction for an observed or measured outcome (i.e., endpoint) of unknown samples in preclinical and clinical practice remains a considerable challenge. No straightforward guidelines exist for selecting a single model that will perform best when presented with unknown samples. In the second phase of the MicroArray Quality Control (MAQC-II) project, 36 analysis teams produced a large number of models for 13 preclinical and clinical endpoints. Before external validation was performed, each team nominated one model per endpoint (referred to here as 'nominated models') from which MAQC-II experts selected 13 'candidate models' to represent the best model for each endpoint. Both the nominated and candidate models from MAQC-II provide benchmarks to assess other methodologies for developing microarray-based predictive models.

Methods

We developed a simple ensemble method by taking a number of the top performing models from cross-validation and developing an ensemble model for each of the MAQC-II endpoints. We compared the ensemble models with both nominated and candidate models from MAQC-II using blinded external validation.

Results

For 10 of the 13 MAQC-II endpoints originally analyzed by the MAQC-II data analysis team from the National Center for Toxicological Research (NCTR), the ensemble models achieved equal or better predictive performance than the NCTR nominated models. Additionally, the ensemble models had performance comparable to the MAQC-II candidate models. Most ensemble models also had better performance than the nominated models generated by five other MAQC-II data analysis teams that analyzed all 13 endpoints.

Conclusions

Our findings suggest that an ensemble method can often attain a higher average predictive performance in an external validation set than a corresponding “optimized” model method. Using an ensemble method to determine a final model is a potentially important supplement to the good modeling practices recommended by the MAQC-II project for developing microarray-based genomic biomarkers.
Applications of graph theory in protein structure identification
Authors: Yan Yan , Zhang Shenggui , Wu Fang-Xiang
Published: October 2011

There is a growing interest in the identification of proteins on the proteome wide scale. Among different kinds of protein structure identification methods, graph-theoretic methods are very sharp ones. Due to their lower costs, higher effectiveness and many other advantages, they have drawn more and more researchers’ attention nowadays. Specifically, graph-theoretic methods have been widely used in homology identification, side-chain cluster identification, peptide sequencing and so on. This paper reviews several methods in solving protein structure identification problems using graph theory. We mainly introduce classical methods and mathematical models including homology modeling based on clique finding, identification of side-chain clusters in protein structures upon graph spectrum, and de novo peptide sequencing via tandem mass spectrometry using the spectrum graph model. In addition, concluding remarks and future priorities of each method are given.
Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks
Authors: Meng Jia , Zhang Jianqiu , Chen Yidong , Huang Yufei
Published: October 2011

Background

Transcriptional regulation by transcription factor (TF) controls the time and abundance of mRNA transcription. Due to the limitation of current proteomics technologies, large scale measurements of protein level activities of TFs is usually infeasible, making computational reconstruction of transcriptional regulatory network a difficult task.

Results

We proposed here a novel Bayesian non-negative factor model for TF mediated regulatory networks. Particularly, the non-negative TF activities and sample clustering effect are modeled as the factors from a Dirichlet process mixture of rectified Gaussian distributions, and the sparse regulatory coefficients are modeled as the loadings from a sparse distribution that constrains its sparsity using knowledge from database; meantime, a Gibbs sampling solution was developed to infer the underlying network structure and the unknown TF activities simultaneously. The developed approach has been applied to simulated system and breast cancer gene expression data. Result shows that, the proposed method was able to systematically uncover TF mediated transcriptional regulatory network structure, the regulatory coefficients, the TF protein level activities and the sample clustering effect. The regulation target prediction result is highly coordinated with the prior knowledge, and sample clustering result shows superior performance over previous molecular based clustering method.

Conclusions

The results demonstrated the validity and effectiveness of the proposed approach in reconstructing transcriptional networks mediated by TFs through simulated systems and real data.
Determination of HCV genotypes and viral loads in chronic HCV infected patients of Hazara Pakistan
Authors: Ali Amjad , Nisar Muhammad , Ahmad Habib , Saif Nausheen , Idrees Muhammad , Bajwa Mohammad A
Published: October 2011

Hepatitis C Virus (HCV) genotype and viral load are two significant predictive variables knowledge of which might persuade treatment decisions. The objective of the present study was to identify the distribution of different HCV genotypes circulating in the study area and to estimate viral load in chronically HCV infected patients. Out of total 305 HCV positive patients, 177 (58%) were males and 128 (42%) were females. Frequency breakup of the HCV positive patients was 169, 69, 38 and 29 from Abbottabad, Mansehra, Haripur and Battagram districts respectively. Out of the total 305 tested serum samples, 255 (83.06%) were successfully genotyped whereas 50 (16.4%) samples were found with unclassified genotypes. Among typable genotypes, 1a accounted for 21 (6.8%) 1b for 14 (4.6%), 2a for 4 (1.31%) 3a for 166 (54.42%) and genotype 3b for (8.19%). Twenty five (8.19%) patients were infected with mixed HCV genotypes. Viral load distribution was classified into three categories based on its viral load levels such as low (< 60, 0000 IU/mL), intermediate (60,0000-80,0000 IU/mL) and high (> 80,0000 IU/mL). The baseline HCV RNA Viral load in HCV genotype 3 infected patients was 50 (26.17%), 46 (24.08%) and 95 (49.73%) for low, intermediate and high categories respectively. For genotypes other than 3, these values for low, intermediate and high viral load categories were 50 (43.85), 35 (30.70) and 29 (25.43) respectively. Pre-treatment viral load in patients with untypable genotype was 19 (38.00%), 5 (20.00%) and 11 (44.00%) for low, intermediate and high viral load categories. Viral load distribution was also categorized sex wise; for males it was 58 (32.76%), 26 (14.68%) and 93 (52.54%) whereas for females it was 40 (31.25%), 34 (26.56%) and 54 (42.18%) for low, intermediate and high viral load respectively. In conclusion HCV genotype 3a is the most prevalent genotype circulating in Hazara Division like other parts of pakistan. Pre-treatment viral load is significantly high (p 0.014) in patients infected with HCV genotype 3 as compared to other genotypes.
Effect of herbal extract granules combined with probiotic mixture on irritable bowel syndrome with diarrhea: study protocol for a randomized controlled trial
Authors: Ko Seok-Jae , Ryu Bongha , Kim Jinsung , Hong Beom-Gi , Yeo Inkwon , Lee Beom-Joon , Lee Jin-Moo , Park Jae-Woo
Published: October 2011

Background

Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder characterized by abdominal pain and change of bowel habits without organic disease. Many patients seek alternative IBS treatments because of the limitations of conventional treatments. Gwakhyangjeonggisan (GJS), a herbal formula, has long been used for alleviating diarrhea-predominant IBS (D-IBS) in traditional medicine. Duolac7S, which comprises 7 bacterial species as probiotics, has been frequently used for D-IBS. Although GJS and Duolac7S have been administered simultaneously in many D-IBS patients, no study has investigated the effects of GJS and Duolac7S combination therapy on D-IBS.

Methods/Design

The current trial is a randomized, double-blinded, placebo-controlled, 4-arm study. After a 2-week run-in period, 60 patients with D-IBS will be randomly assigned to one of the 4 combination groups consisting of GJS (water extract granules, 3 g/pack, 3 times a day) with Duolac7S (powder form, 1 capsule, 2 times a day) or their placebos and followed up for 2 weeks. The assigned treatments will last for 8 weeks. The primary outcomes are adequate relief of IBS pain and discomfort and the proportion of responders (on a weekly basis). The secondary outcomes are visual analog scale for IBS symptoms (on a daily basis), quality of life (at 0, 8, and 10 weeks), intestinal permeability, and composition of intestinal microbiota (at 0 and 8 weeks).

Discussion

The present study is designed to examine the safety and efficacy of GJS and Duolac7S combination therapy on D-IBS. Our study provides the clinical evidence of a new therapeutic strategy for D-IBS.

Trial registration

ClinicalTrials.gov NCT01342718.
Maize microarray annotation database
Authors: Coetzer Nanette , Myburg Alexander A , Berger Dave K
Published: October 2011

Background

Microarray technology has matured over the past fifteen years into a cost-effective solution with established data analysis protocols for global gene expression profiling. The Agilent-016047 maize 44 K microarray was custom-designed from EST sequences, but only reporter sequences with EST accession numbers are publicly available. The following information is lacking: (a) reporter - gene model match, (b) number of reporters per gene model, (c) potential for cross hybridization, (d) sense/antisense orientation of reporters, (e) position of reporter on B73 genome sequence (for eQTL studies), and (f) functional annotations of genes represented by reporters. To address this, we developed a strategy to annotate the Agilent-016047 maize microarray, and built a publicly accessible annotation database.

Description

Genomic annotation of the 42,034 reporters on the Agilent-016047 maize microarray was based on BLASTN results of the 60-mer reporter sequences and their corresponding ESTs against the maize B73 RefGen v2 "Working Gene Set" (WGS) predicted transcripts and the genome sequence. The agreement between the EST, WGS transcript and gDNA BLASTN results were used to assign the reporters into six genomic annotation groups. These annotation groups were: (i) "annotation by sense gene model" (23,668 reporters), (ii) "annotation by antisense gene model" (4,330); (iii) "annotation by gDNA" without a WGS transcript hit (1,549); (iv) "annotation by EST", in which case the EST from which the reporter was designed, but not the reporter itself, has a WGS transcript hit (3,390); (v) "ambiguous annotation" (2,608); and (vi) "inconclusive annotation" (6,489). Functional annotations of reporters were obtained by BLASTX and Blast2GO analysis of corresponding WGS transcripts against GenBank.

The annotations are available in the Maize Microarray Annotation Databasehttp://MaizeArrayAnnot.bi.up.ac.za/, as well as through a GBrowse annotation file that can be uploaded to the MaizeGDB genome browser as a custom track.

The database was used to re-annotate lists of differentially expressed genes reported in case studies of published work using the Agilent-016047 maize microarray. Up to 85% of reporters in each list could be annotated with confidence by a single gene model, however up to 10% of reporters had ambiguous annotations. Overall, more than 57% of reporters gave a measurable signal in tissues as diverse as anthers and leaves.

Conclusions

The Maize Microarray Annotation Database will assist users of the Agilent-016047 maize microarray in (i) refining gene lists for global expression analysis, and (ii) confirming the annotation of candidate genes before functional studies.
A new chapter: hematopoietic stem cells are direct players in immunity
Authors: Zheng Junke , Song Chun , Zhang Cheng Cheng
Published: October 2011

Several lines of evidence support the hypothesis that hematopoietic stem cells (HSCs) directly interact with the immune system and have potential for immune privilege. Although the microenvironment or niche provides protection for HSCs from immune attack, HSCs are also capable of interacting with the immune system as signal "providers" and signal "receivers". On the one hand, HSCs display surface immune inhibitory molecules to evade the attack from the innate and adaptive immune systems; on the other hand, HSCs are capable of directly sensing the signals from the immune system through their surface receptors. Thus, HSCs are important direct players in the immune system.
Visual hallucinations in dementia with Lewy bodies: transcranial magnetic stimulation study
Authors: Taylor John-Paul , Firbank Michael , Barnett Nicola , Pearce Sarah , Livingstone Anthea , Mosimann Urs , Eyre Janet , McKeith Ian G. , O'Brien John T.
Published: October 2011

Background

The aetiology of visual hallucinations is poorly understood in dementia with Lewy bodies. Pathological alterations in visual cortical excitability may be one contributory mechanism.

Aims

To determine visual cortical excitability in people with dementia with Lewy bodies compared with aged-matched controls and also the relationship between visual cortical excitability and visual hallucinations in dementia with Lewy bodies.

Method

Visual cortical excitability was determined by using transcranial magnetic stimulation (TMS) applied to the occiput to elicit phosphenes (transient subjective visual responses) in 21 patients with dementia with Lewy bodies and 19 age-matched controls.

Results

Phosphene parameters were similar between both groups. However, in the patients with dementia with Lewy bodies, TMS measures of visual cortical excitability correlated strongly with the severity of visual hallucinations (P = 0.005). Six patients with dementia with Lewy bodies experienced visual hallucination-like phosphenes (for example, seeing people or figures on stimulation) compared with none of the controls (P = 0.02).

Conclusions

Increased visual cortical excitability in dementia with Lewy bodies does not appear to explain visual hallucinations but it may be a marker for their severity.
Shear Wave Velocity- and Geology-Based Seismic Microzonation of Port-au-Prince, Haiti
Authors: Cox Brady R. , Bachhuber Jeff , Rathje Ellen , Wood Clinton M. , Dulberg Ranon , Kottke Albert , Green Russell A. , Olson Scott M.
Published: October 2011

A seismic site classification microzonation for the city of Port-au-Prince is presented herein. The microzonation is based on 35 shear wave velocity ( VS) profiles collected throughout the city and a new geologic map of the region. The VS profiles were obtained using the multichannel analysis of surface waves (MASW) method, while the geologic map was developed from a combination of field mapping and geomorphic interpretation of a digital elevation model (DEM). Relationships between mean shear wave velocity over the upper 30 m of the subsurface ( VS30) and surficial geologic unit have been developed, permitting code-based seismic site classification throughout the city. A site classification map for the National Earthquake Hazards Reduction Program/International Building Code (NEHRP/IBC) classification scheme is provided herein. Much of the city is founded on deposits that classify as either NEHRP Site Class C or D, based on VS30. Areas of the city requiring additional subsurface information for accurate site classification are noted.
Massive Damage Assessment Program and Repair and Reconstruction Strategy in the Aftermath of the 2010 Haiti Earthquake
Authors: Miyamoto H. Kit , Gilani Amir S. J. , Wong Ken
Published: October 2011

The January 2010 Haiti earthquake resulted in over 230,000 deaths, affected 3 million people, and damaged or collapsed over 200,000 structures. An unprecedented earthquake damage assessment project by a joint operation of the Haitian Ministry of Public Works, the United Nations Office of Project Services, the Pan American Development Foundation, and the authors was undertaken with three strategic goals: (1) rapid damage assessment, (2) reconstruction database development, and (3) upgrade the technical capabilities of Haitian engineers. A modified version of the Applied Technology Council's ATC-20 technical platform, accounting for Haitian building design, was developed. As part of this program, PDA-based data collection techniques and quality-assurance programs were implemented, and approximately 600 Haitian engineers were trained. As of March 2011, approximately 400,000 buildings had been inspected. This database was used to develop: (1) repair strategies for yellow-tagged structures, and (2) reparability, reconstruction, and demolition assessments or red-tagged structures. This program could also be extended as a platform for a seismic damage evaluation and reconstruction strategies in other parts of the world.
Recipe for Disaster: Construction Methods, Materials, and Building Performance in the January 2010 Haiti Earthquake
Authors: Marshall Justin D. , Lang Anna F. , Baldridge Steven M. , Popp Daniel R.
Published: October 2011

The earthquake that shook Hispaniola on 12 January 2010 devastated Haiti. The damage was widespread due to uncontrolled construction, poor material quality, and lack of rigorous engineering design. Post-event reconnaissance has brought to light serious deficiencies in these areas. Residential buildings in Haiti are typically constructed by their owners, who may or may not have the skills or resources to build a structure that is earthquake-safe. Few structures are designed by engineering professionals or are inspected for quality of construction. The two most common construction materials are masonry block and reinforced concrete. Masonry blocks, concrete cylinders, and reinforcing steel were taken from Haiti and tested in the United States. The concrete and masonry were shown to be of low strength and quality. The steel samples show expected strength properties with some specimens having reduced ductility due to bending. Building performance is demonstrated by reconnaissance photographs and case studies of the structures inspected by reconnaissance team members.
Damage Patterns in Port-au-Prince during the 2010 Haiti Earthquake
Authors: Rathje Ellen M. , Bachhuber Jeff , Dulberg Ranon , Cox Brady R. , Kottke Albert , Wood Clinton , Green Russell A. , Olson Scott , Wells Donald , Rix Glenn
Published: October 2011

The 2010 Haiti earthquake represents one of the most devastating earthquakes in history. Damage to structures was widespread across the city of Port-au-Prince, but its intensity varied considerably from neighborhood to neighborhood. This paper integrates damage statistics with geologic data, shear wave velocity measurements, and topographic information to investigate the influence of these conditions on the damage patterns in the city. The results indicate that the most heavily damaged areas in downtown Port-au-Prince are underlain by Holocene alluvium with shear wave velocities that average about 350 m/s over the top 30 m. The remainder of Port-au-Prince is underlain mostly by older geologic units with higher shear wave velocities. Damage was also concentrated on hillsides around Port-au-Prince. These pockets of damage appear to have been caused by a combination of factors, including topographic amplification, soil amplification, and failure of weakly cemented, steep hillsides.
Novel three-dimensional long-term bone marrow culture system using polymer particles with grafted epoxy-polymer-chains supports the proliferation and differentiation of hematopoietic stem cells
Authors: Hirabayashi Yukio , Hatta Yoshihiro , Takeuchi Jin , Tsuboi Isao , Harada Tomonori , Ono Kentaro , Glomm Wilhelm Robert , Yasuda Masahiro , Aizawa Shin
Published: October 2011

Hematopoiesis occurs in the bone marrow, where primitive hematopoietic cells proliferate and differentiate in close association with a three-dimensional (3D) hematopoietic microenvironment composed of stromal cells. We examined the hematopoietic supportive ability of stromal cells in a 3D culture system using polymer particles with grafted epoxy polymer chains. Umbilical cord blood-derived CD34+ cells were co-cultivated with MS-5 stromal cells. They formed a 3D structure in the culture dish in the presence of particles, and the total numbers of cells and the numbers of hematopoietic progenitor cells, including colony-forming unit (CFU)-Mix, CFU-granulocyte-macrophage, CFU-megakaryocyte and burst-forming unit-erythroid, were measured every seven days. The hematopoietic supportive activity of the 3D culture containing polymer particles and stromal cells was superior to that of 2D culture, and allowed the expansion and maintenance of hematopoietic progenitor cells for more than 12 weeks. Various types of hematopoietic cells, including granulocytes, macrophages and megakaryocytes at different maturation stages, appeared in the 3D culture, suggesting that the CD34+ cells were able to differentiate into a range of blood cell types. Morphological examination showed that MS-5 stromal cells grew on the surface of the particles and bridged the gaps between them to form a 3D structure. Hematopoietic cells slipped into the 3D layer and proliferated within it, relying on the presence of the MS-5 cells. These results suggest that this 3D culture system using polymer particles reproduced the hematopoietic phenomenon in vitro, and might thus provide a new tool for investigating hematopoietic stem cell–stromal cell interactions.
Preventive effect of urinary trypsin inhibitor on the development of liver fibrosis in mice
Authors: Kono Toru , Kashiwade Yurino , Asama Toshiyuki , Chisato Naoyuki , Ebisawa Yoshiaki , Yoneda Masashi , Kasai Shinichi
Published: October 2011

Urinary trypsin inhibitor (UTI) is a serine protease inhibitor produced in the liver that inhibits the production and activation of various cytokines, notably transforming growth factor- β (TGF- β), which are associated with the progression of liver fibrosis. However, the various roles of endogenous UTI in liver fibrosis have not been examined. This study, therefore, examined the long-term effects of UTI deficiency during both steady-state conditions and thioacetamide (TA)-induced liver fibrosis. Furthermore, the effects of continuous exogenous UTI administration were examined. Analyses of liver fibrosis marker, hyaluronic acid (HA), TGF- β concentrations and histological findings at 30 weeks of age showed that homozygous UTI-knockout (KO) mice had higher HA and TGF- β concentrations than did heterozygous UTI-KO mice and wild-type mice, although there was no histological evidence of liver fibrosis in these mice. TA treatment for 20 weeks also resulted in greater HA and TGF- β levels in homozygous mice than in heterozygous and wild-type mice. Furthermore, homozygous mice had more severe liver fibrosis based on histological analyses. HA and TGF- β levels were lower in homozygous UTI-KO mice that were continuously administered UTI versus those given distilled water. These findings indicate that UTI deficiency leads to the production of HA and hepatic TGF- β and that administering exogenous UTI can ameliorate these changes. We conclude that endogenous UTI is produced in the liver to suppress the production and activation of TGF- β and that administering exogenous UTI may be therapeutically beneficial for preventing liver fibrosis.