bluuebunny/crossref_metadata_2025 huggingface dataset:
An Upwind-Biased Conservative Transport Scheme for Multistage Temporal Integrations on Spherical Icosahedral Grids
Authors: Miura Hiroaki
Published: July 2013

A standard nominally third-order upwind-biased spatial discretization of the flux-divergence operator was extended to a spherical icosahedral grid. The method can be used with multistage time-stepping schemes such as the Runge–Kutta method to compute the transport of variables on both hexagonal–pentagonal and triangular meshes. Two algorithms can be used to determine mesh cell face values: 1) interpolation using a quadratic function reconstructed subject to an integral constraint, or 2) calculation of the weighted mean of two linearly interpolated and extrapolated values. The first approach was adopted for a triangular mesh because the second approach depends on the mesh having a hexagonal or pentagonal shape. Both approaches were tested on the hexagonal–pentagonal mesh.

These schemes were subjected to standard transport tests on a spherical icosahedral grid. A three-stage Runge–Kutta time stepping method was used, and if necessary a flux limiter was applied to maintain monotonicity. The two different methods produced very similar solutions on a hexagonal–pentagonal mesh. Their accuracy was very close to the accuracy of a preexisting method designed for a Voronoi mesh only. When compared to another method that uses a quadratic polynomial interpolation, the phase error of the solutions was reduced, and their accuracy was much improved. The accuracies of the solutions were comparable on triangular and hexagonal–pentagonal meshes.
A Competence Model for Environmental Education
Authors: Roczen Nina , Kaiser Florian G. , Bogner Franz X. , Wilson Mark
Published: July 2013

The goal of environmental education is ultimately to enable a person to strive for and to attain a more ecological way of life. In this article, we begin by distinguishing three forms of environmental knowledge and go on to predict that people’s attitude toward nature represents the force that drives their ecological behavioral engagement. Based on data from 1,907 students, we calibrated previously established instruments to measure ecological behavior, environmental knowledge, and attitude toward nature with Rasch-type models. Using path modeling, we corroborated our theoretically anticipated competence structure. While environmental knowledge revealed a modest behavioral effect, attitude toward nature turned out to be, as expected, the stronger determinant of behavior. Overall, we propose a competence model that has the potential to guide us into more evidence-based ways of promoting the overall ecological engagement of individuals.
Aarogyasri Scheme in Andhra Pradesh, India: Some Critical Reflections
Authors: Reddy Sunita , Mary Immaculate
Published: July 2013

Various models are being tried out under Public–Private Partnerships in health care. Community health insurance is one of the models for providing health security for the people Below Poverty Line (BPL). Various states are experimenting on community health insurance with largely state financing, private provisioning of health care, especially curative care. When the partnership is with the for-profit private/corporate sector, where the underlining principle is profit making, the core principal of partnerships of beneficence and equity is undermined. The Aarogyasri scheme started in 2007 as a political move is continuing and praised as one of the most effective ways of treating tertiary, curative, largely surgeries and therapies for BPL population and is completely sponsored by the state. This article critically analyses the procedures and the cost incurred in private and public hospitals and finds that Aarogyasri is skewed towards curative tertiary care and is a big drain on the state exchequer with questions of sustainability. Further, this kind of partnership undermines the existence of large public sector, which is underutilised. The way forward for sustainable and comprehensive health care for people of Andhra Pradesh to ensure ‘Arogyandhra’ is to promote and strengthen public sector.
Drugs and Vaccines in Health Care: Problems and Possibilities
Authors: Bhargava Pushpa M.
Published: July 2013

Drugs and vaccines have played a crucial role in increasing dramatically the average life span of humans all over the world since the beginning of the last century. However, there are problems—often, though not always—created by vested interests or by ignorance of their use. They range from the sale of sub-standard or obsolete formulations to unethical nexus between pharmaceutical companies at one level and commercial health care establishments on the other. This article lists some of these problems which get magnified in the prevailing circumstance of a burgeoning profit-driven private health sector and inadequate and ineffective regulatory framework.
Evidence-based Planning—A Myth or Reality: Use of Evidence by the Planning Commission on Public–Private Partnership (PPP)
Authors: Karpagam Sylvia , Roy Bijoya , Seethappa Vijaya Kumar , Qadeer Imrana
Published: July 2013

Public–private partnerships (PPP) are being touted as the way forward for health care in the country as demonstrated by the draft chapter of the 12th Five-year Plan for health. The planning commission refers to the Rajiv Gandhi Super Specialty Hospital, Raichur, as ‘evidence’ of ‘good’ PPP without mentioning the multiple problems identified in this model, as documented in an evaluation report by the Government of Karnataka. The concerns raised by the evaluation team and the failure of the Planning Commission to take cognizance of these concerns are discussed in some detail in this article. Some of the issues identified with the PPP model of health care in Raichur are the absence of third-party evaluation, poor utilisation rates, lack of measurable benefit to the BPL population and poor governance and accountability systems.
Universal Health Care: The Trojan Horse of Neoliberal Policies
Authors: Qadeer Imrana
Published: July 2013

This article locates health care and technology within the shifts in capitalist evolution from welfare to neoliberal development and examines why the concept of Comprehensive Primary health care has been distorted by the market to varying extents globally. Its focus is on India’s planning process where the thrust is to transform health services into commodities and tools of extraction of profit to which all levels of health care are subordinated. Since the 1990s, all Plans, official planning committees and legislations are meant to mould services in this direction. Instead of an integrated health service with primary health care getting support from the secondary and tertiary, the current thrust of the planning process has been to fragment health service into independent components—UHC, tertiary care and NRHM—in the name of providing rural and urban health services. In each of these strategies, public–private partnerships, commercialisation and appropriation of the public resources are the dominant trends. UHC thus no more remains the state-led integrated and inclusive service but a Trojan horse of the neoliberal strategy.
Book Review: The Politics of Protection: The Limits of Humanitarian Action
Authors: Mathur Hari Mohan
Published: July 2013

Elizabeth G. Ferris, The Politics of Protection: The Limits of Humanitarian Action, Washington, DC, The Brookings Institution, 2011.
Book Review: Rights of Adolescent Girls in India: A Critical Look at Laws and Policies
Authors: Patel Vibhuti
Published: July 2013

Saumya Uma, Rights of Adolescent Girls in India: A Critical Look at Laws and Policies, Mumbai: Vacha Publications, 2012.
Vision-based place recognition: how low can you go?
Authors: Milford Michael
Published: July 2013

In this paper we use the algorithm SeqSLAM to address the question, how little and what quality of visual information is needed to localize along a familiar route? We conduct a comprehensive investigation of place recognition performance on seven datasets while varying image resolution (primarily 1 to 512 pixel images), pixel bit depth, field of view, motion blur, image compression and matching sequence length. Results confirm that place recognition using single images or short image sequences is poor, but improves to match or exceed current benchmarks as the matching sequence length increases. We then present place recognition results from two experiments where low-quality imagery is directly caused by sensor limitations; in one, place recognition is achieved along an unlit mountain road by using noisy, long-exposure blurred images, and in the other, two single pixel light sensors are used to localize in an indoor environment. We also show failure modes caused by pose variance and sequence aliasing, and discuss ways in which they may be overcome. By showing how place recognition along a route is feasible even with severely degraded image sequences, we hope to provoke a re-examination of how we develop and test future localization and mapping systems.
Neurovascular Anatomic Relationships to Arthroscopic Posterior and Transseptal Portals in Different Knee Positions
Authors: Makridis Konstantinos G. , Wajsfisz Anthony , Agrawal Nikhil , Basdekis Georgios , Djian Patrick
Published: July 2013

Background:

No study exists that directly measures the distances between posterior portals and the popliteal artery under arthroscopic conditions.

Purpose:

To define the anatomic relationship between the neural structures and standard posterior arthroscopic portals and between the popliteal artery and posterior as well as transseptal portals in different knee positions.

Study Design:

Descriptive laboratory study.

Methods:

Seventeen fresh-frozen cadaveric knees were used. The posterolateral, posteromedial, and transseptal portals were established at 90° of knee flexion. The popliteal artery was revealed using a shaver placed through the posteromedial portal. The distance from those portals to the popliteal artery was measured using a precision caliper. After the measurements were made, each specimen was dissected. The distance from a needle, blade, and cannula in each portal site to the adjacent neural structures was successively measured at 30°, 90°, and 120° of knee flexion.

Results:

The mean distance (in millimeters) from the posterolateral, posteromedial, and transseptal portals to the popliteal artery was significantly smaller at 30° (32.1 ± 4.6, 36.5 ± 4.9, and 9.0 ± 3.9, respectively) than at 90° (40.7 ± 5.1, 41.0 ± 3.8, and 18.0 ± 3.8, respectively) and 120° (38.4 ± 4.8, 38.7 ± 6.0, and 21.0 ± 4.0, respectively) of knee flexion. The mean distance from the posterolateral portal to the common peroneal nerve at 90° of flexion (needle, 26.6 ± 9.5; blade, 24.7 ± 6.9; cannula, 22.1 ± 6.9) was significantly greater than the distance at 30° (needle, 23.4 ± 6.5; blade, 21.4 ± 6.4; cannula, 18.4 ± 6.3) and 120° (needle, 21.8 ± 6.6; blade, 19.1 ± 6.3; cannula, 17.4 ± 6.7) of knee flexion. The mean distance between the posteromedial portal and the inferior infrapatellar branch of the saphenous nerve at 30° (needle, 18.6 ± 4.3; blade, 15.5 ± 3.3; cannula, 13.7 ± 5.8) of flexion was smaller than at 90° (needle, 20.1 ± 6.1; blade, 16.5 ± 5.3; cannula, 14.3 ± 4.4) and 120° (needle, 21.1 ± 3.6; blade, 17.7 ± 4.9; cannula, 15.1 ± 5.9) of flexion, but there was no statistical significance. The mean distance from the posteromedial portal to the sartorial branch of the saphenous nerve at 30° (needle, 22.8 ± 6.1; blade, 19.8 ± 5.3; cannula, 17.7 ± 6.2) of flexion was significantly smaller than that at 90° (needle, 29.7 ± 3.6; blade, 26.3 ± 6.3; cannula, 23.1 ± 4.7) and 120° (needle, 31.5 ± 3.9; blade, 28.9 ± 4.1; cannula, 25.4 ± 5.1) of flexion.

Conclusion/Clinical Relevance:

The position of 90° of knee flexion is safe to establish posterior and transseptal arthroscopic portals. The position of 120° of knee flexion is practically safe to establish posteromedial and transseptal portals, but it is unsafe to create a posterolateral portal because the risk of damaging the common peroneal nerve is high. The position of 30° of knee flexion is not recommended to establish posterior arthroscopic portals.
In the Zeal to Synthesize
Authors: Florczak Kristine L.
Published: July 2013

In this column, the author provides a clear explanation of the nature of meta-analysis, systematic reviews, integrative reviews, meta-synthesis, and metasummary along with a discussion of the paradigms that support each. Also the appropriateness of these methods of synthesis and a recommendation as to their use is discussed in terms of the utility of research.
Feeling at Home
Authors: Doucet Thomas J.
Published: July 2013

In this article, the author reports a Parse research study on the experience of feeling at home with 10 participants living in community. The central finding of the study is the structure: Feeling at home is quietude amid potential adversity, as uplifting certitude arises with the penetrable reverence of cherished affiliations. The findings are discussed in relation to the humanbecoming school of thought and extant literature.
A Comparison of the Prenatal Health Behaviors of Women from Four Cultural Groups in Turkey
Authors: Taşçı-Duran Emel , Sevil Umran
Published: July 2013

This research was conducted to uncover women’s health behaviors during prenatal periods using a transcultural approach. The qualitative ethnonursing method was used, and the research was conducted at the family health center in Bornova District in Izmir. The data were collected between November 2007 and August 2008 using the purposive sampling method. Eighteen pregnant women were included in the study and in-depth face-to-face semi-structured interviews were recorded on an audio recording device. A thematic analysis revealed four main themes: family, social learning-tradition transfer, perceptions, and behavioral changes.
Strengthening a Praxis of Suffering
Authors: Johnston Nancy Elizabeth
Published: July 2013

Suffering involves the loss of acceptable meaning and nourishing connection. How nurses are present to those who suffer makes a significant difference. In a context where sustained engagement with the sufferer is crucial but often neglected, important questions for educators arise. These include how to cultivate moral courage and compassion among our students and how to select philosophical and pedagogical approaches that can guide teaching and learning. This article presents the challenges raised in a graduate-level nursing course aimed at advancing a praxis of suffering as well as our experience integrating interpretive phenomenological and narrative-based approaches.
Social Determinants of Health in Nursing Education, Research, and Health Policy
Authors: Mahony Deborah , Jones Emily J.
Published: July 2013

The adoption of the Patient Protection and Affordable Care Act and the recent Institute of Medicine report, The Future of Nursing: Leading Change, Advancing Health, have brought about a resurgence of interest in the social determinants of health as the basis for healthcare decisions in nursing education, research, and health policy. Nurses are positioned to be at the forefront of crucial healthcare reform to affect health outcomes and reduce health disparities profoundly. However, for nurses of the 21st century to improve the health of U.S. citizens and promote health equity effectively, we must first intently address the social determinants of health in our current nursing educational models, research agendas, and public health policies.
Contesting imagined communities: Politics of script and Tai cosmopolitanism in upland Vietnam
Authors: Mukdawijitra Yukti
Published: July 2013

Based on ethnographic and historical research, this article characterizes the politics of Tai script as an instance of cosmopolitanism. The Tai, Vietnam’s third largest ethnic group, reside in the northwestern highlands. Because of their spatial formation in the past, the Tai have maintained their heterogeneous politics of space and identity even under the socialist and post-socialist regime. This study of Tai orthography politics indicates that political space constructed by literacy politics has long been contested. As opposed to the more commonly known littoral cosmopolitanism, this study of the Tai script expands the understanding of Southeast Asian cosmopolitanism from a mountain mainland’s perspective.
Cosmopolitanism without empire? Tense and tender ties in Don Lee’s Country of Origin
Authors: Wang Chih-ming
Published: July 2013

This article approaches the question of “lived cosmopolitanism” through the eyes of transnational mixed-race adoptees. In recent years, adoption has been understood as a paradox evolving in the tension of humanitarian benevolence on the one hand and as a biopolitical scheme of Western imperialism on the other. Mixed-race adoptees are at once viewed as cosmopolitan figures that transcend race and nation and as abject, displaced figures that are produced and orphaned at the borders of kinship, nation, and culture. This article looks at the adoptees’ stories to pry into the underside of cosmopolitanism and to consider how America’s imperial outreach is tied up with Asia’s modernity in the creation of adoptees. This approach promises to recast cosmopolitanism as a “reflexive project” by foregrounding our own embeddedness in the intimacies of nation and empire. The adoptees’ life stories embody the modern/colonial beginnings and becomings of Asia.
Creole Hadramis in the Malay world in the 1800s: Fragments of biographies and connected histories
Authors: Mandal Sumit K
Published: July 2013

This article explores cultural geographies at the conjunction of transregional and local histories by examining creole Hadrami biographies in the Malay world. It focuses on Abdullah al-Misri and Abdullah Munsyi and a few biographical fragments from their writings. Efforts to create national canons have led to the anachronistic application of national and ethnic categories to these nineteenth-century writers. Through biographical fragments, this article demonstrates the connected histories of creole Hadramis in the Malay world, and presents cultural geographies that bring to the fore the multi-scalar and shared histories of the citizens of contemporary nation-states. It makes a historically grounded argument for a cosmopolitan Malay world.
Pristane-induced lupus as a model of human lupus arthritis: evolvement of autoantibodies, internal organ and joint inflammation
Authors: Leiss H , Niederreiter B , Bandur T , Schwarzecker B , Blüml S , Steiner G , Ulrich W , Smolen JS , Stummvoll GH
Published: July 2013

Objective

Arthritis is frequently seen in human lupus, but rarely in lupus models. Pristane-induced lupus (PIL) can be induced in various mouse strains such as BALB/c and C57BL/6. We herein characterize clinical and histological features of arthritis in the context of systemic lupus and provide a prudent comparison with models of rheumatoid arthritis (RA).

Methods

A total of 57 BALB/c mice received pristane (PIL group) and were analyzed for serum autoantibodies (anti-chromatin-, -histone, -Sm, -dsDNA), as well as for clinical features and histopathology of joints, lungs and kidneys. Joint pathology was quantified by image analysis and tissue cytometry. Ten C57BL/6 mice (Bl/6-PIL) and historical groups of two different RA models were analyzed accordingly.

Results

In BALB/c PIL, clinical arthritis started at three months, occurred finally in 79% of PIL (but not in controls, p < 0.001) and correlated with areas of inflammation, erosion, cartilage damage, osteoclast numbers and total severity score (for all: r > 0.7, p < 0.001). After eight months, 58% of PIL (but no controls, p < 0.001) had mild-erosive arthritis. In contrast to RA, the most frequent inflammatory cell type of the pannus was granulocytes (17.7%), PIL had lower numbers of osteoclasts, erosions rarely affected both layers of the cortical bone and there was no progression to complete joint destruction (even after one year of observation). Serum autoantibodies (auto-abs) preceded arthritis and became significantly elevated in all PIL; affected joints showed increased deposits of IgG (and IgM) within the inflammatory tissue, indicative of an ab-mediated process. PIL mice with arthritis also showed signs of pulmonary (100%) and renal (46%) lupus. In contrast to BALB/c, Bl/6-PIL mice did not develop any signs of arthritis.

Conclusion

PIL in BALB/c mice is characterized by severe organ involvement, typical autoabs and by a mild-erosive arthritis with similarities to, but also with distinct differences from, RA. PIL may help to study arthritis along with other key features of systemic lupus erythematosus after therapeutic interventions or in knock-out models based on a BALB/c but not on a C57BL/6 background.
Peer Support for Carers
Authors: Greenwood Nan , Habibi Ruth , Mackenzie Ann , Drennan Vari , Easton Nicky
Published: July 2013

Being a carer of someone with dementia can be rewarding and also challenging. Volunteer peer support schemes for carers are being introduced, little is known about either their impact on carers and volunteers or about volunteers' and carers' experiences. This study investigated peer volunteer and carer recipient experiences of a peer support service. Thematic analysis of 13 in-depth interviews with 9 carers and 4 peer volunteers revealed that peer support helped both carers and peer volunteers through the realization that they were “not alone” in their experiences and emotions. Additional carer benefits included opportunities to talk freely about difficult experiences and learning how others cope. Volunteers found their role rewarding, describing satisfaction from putting their own experiences to good use. These findings highlight the isolation and exclusion experienced by current and former carers of people with dementia and draw attention to the benefits of peer support for both the groups.
Physical Activity and Memory Complaints in Middle-Age Americans
Authors: Lee Pai-Lin , Hsiao Ching-Hsiang , Wang Chiao-Li
Published: July 2013

Work-related physical activity (PA; WRPA), household PA (HPA), and leisure-time PA(LTPA) are the 3 important PA domains for most people, but their relationships with cognition functions have not been thoroughly examined, especially the subjective memory complaints (SMCs). We used a data set from the 2005 midlife development in the United States (MIDUS) survey for community-dwelling adults aged 35 to 64 years (mean age = 51.01) to examine the relationship between these 3 PA domains (and 3 levels under the domains) with SMCs (N = 1044). The moderate levels of HPA and LTPA are significantly but oppositely linked to SMCs, with the adjusted odds ratios and 95% confidence intervals of .864 and .764-.978 for HPA and 1.130 and 1.010-1.264 for LTPA, respectively. Neither vigorous or low PA level nor domains of WRPA link to SMCs. The interaction terms were not found to be associated with sex and age. Future works and limitations were also discussed.
Brain Metabolic Dysfunction in Capgras Delusion During Alzheimer’s Disease
Authors: Jedidi H. , Daury N. , Capa R. , Bahri M. A. , Collette F. , Feyers D. , Bastin C. , Maquet P. , Salmon E.
Published: July 2013

Capgras delusion is characterized by the misidentification of people and by the delusional belief that the misidentified persons have been replaced by impostors, generally perceived as persecutors. Since little is known regarding the neural correlates of Capgras syndrome, the cerebral metabolic pattern of a patient with probable Alzheimer’s disease (AD) and Capgras syndrome was compared with those of 24-healthy elderly participants and 26 patients with AD without delusional syndrome. Comparing the healthy group with the AD group, the patient with AD had significant hypometabolism in frontal and posterior midline structures. In the light of current neural models of face perception, our patients with Capgras syndrome may be related to impaired recognition of a familiar face, subserved by the posterior cingulate/precuneus cortex, and impaired reflection about personally relevant knowledge related to a face, subserved by the dorsomedial prefrontal cortex.
Identification of human immunodeficiency virus type 1 (HIV-1) gp120-binding sites on scavenger receptor cysteine rich 1 (SRCR1) domain of gp340
Authors: Chu Ying , Li Jiahuang , Wu Xilin , Hua Zichun , Wu Zhiwei
Published: July 2013

Background

gp340, a member of scavenger receptor cysteine rich family encoded by Deleted in Malignant Brain Tumors 1 (DMBT1), is an important component in innate immune defense. The first scavenger receptor cysteine rich domain (SRCR1) of gp340 has been shown to inhibit HIV-1 infection through binding to the N-terminal flank of the V3 loop of HIV-1 gp120.

Results

Through homology modeling and docking analysis of SRCR1 to a gp120-CD4-X5 antibody complex, we identified three loop regions containing polar or acidic residues that directly interacted with gp120. To confirm the docking prediction, a series of over-lapping peptides covering the SRCR1 sequence were synthesized and analyzed by gp120-peptide binding assay. Five peptides coincide with three loop regions showed the relative high binding index. An alanine substitution scan revealed that Asp34, Asp35, Asn96 and Glu101 in two peptides with the highest binding index are the critical residues in SRCR1 interaction with gp120.

Conclusion

We pinpointed the vital gp120-binding regions in SRCR1 and narrowed down the amino acids which play critical roles in contacting with gp120.
Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions
Authors: Jaiswal Varun , Chanumolu Sree Krishna , Gupta Ankit , Chauhan Rajinder S , Rout Chittaranjan
Published: July 2013

Background

Subunit vaccines based on recombinant proteins have been effective in preventing infectious diseases and are expected to meet the demands of future vaccine development. Computational approach, especially reverse vaccinology (RV) method has enormous potential for identification of protein vaccine candidates (PVCs) from a proteome. The existing protective antigen prediction software and web servers have low prediction accuracy leading to limited applications for vaccine development. Besides machine learning techniques, those software and web servers have considered only protein’s adhesin-likeliness as criterion for identification of PVCs. Several non-adhesin functional classes of proteins involved in host-pathogen interactions and pathogenesis are known to provide protection against bacterial infections. Therefore, knowledge of bacterial pathogenesis has potential to identify PVCs.

Results

A web server, Jenner-Predict, has been developed for prediction of PVCs from proteomes of bacterial pathogens. The web server targets host-pathogen interactions and pathogenesis by considering known functional domains from protein classes such as adhesin, virulence, invasin, porin, flagellin, colonization, toxin, choline-binding, penicillin-binding, transferring-binding, fibronectin-binding and solute-binding. It predicts non-cytosolic proteins containing above domains as PVCs. It also provides vaccine potential of PVCs in terms of their possible immunogenicity by comparing with experimentally known IEDB epitopes, absence of autoimmunity and conservation in different strains. Predicted PVCs are prioritized so that only few prospective PVCs could be validated experimentally. The performance of web server was evaluated against known protective antigens from diverse classes of bacteria reported in Protegen database and datasets used for VaxiJen server development. The web server efficiently predicted known vaccine candidates reported from Streptococcus pneumoniae and Escherichia coli proteomes. The Jenner-Predict server outperformed NERVE, Vaxign and VaxiJen methods. It has sensitivity of 0.774 and 0.711 for Protegen and VaxiJen dataset, respectively while specificity of 0.940 has been obtained for the latter dataset.

Conclusions

Better prediction accuracy of Jenner-Predict web server signifies that domains involved in host-pathogen interactions and pathogenesis are better criteria for prediction of PVCs. The web server has successfully predicted maximum known PVCs belonging to different functional classes. Jenner-Predict server is freely accessible at http://117.211.115.67/vaccine/home.html
Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
Authors: Xu Xiao , Zhang Yuanhao , Williams Jennie , Antoniou Eric , McCombie W Richard , Wu Song , Zhu Wei , Davidson Nicholas O , Denoya Paula , Li Ellen
Published: July 2013

Background

High throughput parallel sequencing, RNA-Seq, has recently emerged as an appealing alternative to microarray in identifying differentially expressed genes (DEG) between biological groups. However, there still exists considerable discrepancy on gene expression measurements and DEG results between the two platforms. The objective of this study was to compare parallel paired-end RNA-Seq and microarray data generated on 5-azadeoxy-cytidine (5-Aza) treated HT-29 colon cancer cells with an additional simulation study.

Methods

We first performed general correlation analysis comparing gene expression profiles on both platforms. An Errors-In-Variables (EIV) regression model was subsequently applied to assess proportional and fixed biases between the two technologies. Then several existing algorithms, designed for DEG identification in RNA-Seq and microarray data, were applied to compare the cross-platform overlaps with respect to DEG lists, which were further validated using qRT-PCR assays on selected genes. Functional analyses were subsequently conducted using Ingenuity Pathway Analysis (IPA).

Results

Pearson and Spearman correlation coefficients between the RNA-Seq and microarray data each exceeded 0.80, with 66%~68% overlap of genes on both platforms. The EIV regression model indicated the existence of both fixed and proportional biases between the two platforms. The DESeq and baySeq algorithms (RNA-Seq) and the SAM and eBayes algorithms (microarray) achieved the highest cross-platform overlap rate in DEG results from both experimental and simulated datasets. DESeq method exhibited a better control on the false discovery rate than baySeq on the simulated dataset although it performed slightly inferior to baySeq in the sensitivity test. RNA-Seq and qRT-PCR, but not microarray data, confirmed the expected reversal ofSPARCgene suppression after treating HT-29 cells with 5-Aza. Thirty-three IPA canonical pathways were identified by both microarray and RNA-Seq data, 152 pathways by RNA-Seq data only, and none by microarray data only.

Conclusions

These results suggest that RNA-Seq has advantages over microarray in identification of DEGs with the most consistent results generated from DESeq and SAM methods. The EIV regression model reveals both fixed and proportional biases between RNA-Seq and microarray. This may explain in part the lower cross-platform overlap in DEG lists compared to those in detectable genes.
Splice variants and promoter methylation status of the Bovine Vasa Homology (Bvh) gene may be involved in bull spermatogenesis
Authors: Luo Hua , Zhou Yang , Li Yingxia , Li Qifa
Published: July 2013

Background

Vasa is a member of the DEAD-box protein family that plays an indispensable role in mammalian spermatogenesis, particularly during meiosis. Bovine vasa homology (Bvh) ofBos taurushas been reported, however, its function in bovine testicular tissue remains obscure. This study aimed to reveal the functions ofBvhand to determine whetherBvhis a candidate gene in the regulation of spermatogenesis in bovine, and to illustrate whether its transcription is regulated by alternative splicing and DNA methylation.

Results

Here we report the molecular characterization, alternative splicing pattern, expression and promoter methylation status ofBvh. The full-length coding region ofBvhwas 2190 bp, which encodes a 729 amino acid (aa) protein containing nine consensus regions of the DEAD box protein family.Bvhis expressed only in the ovary and testis of adult cattle. Two splice variants were identified and termedBvh-V4(2112 bp and 703 aa) andBvh-V45(2040 bp and 679 aa). In male cattle, full-lengthBvh(Bvh-FL),Bvh-V4andBvh-V45are exclusively expressed in the testes in the ratio of 2.2:1.6:1, respectively. Real-time PCR revealed significantly reduced mRNA expression ofBvh-FL,Bvh-V4andBvh-V45in testes of cattle-yak hybrids, with meiotic arrest compared with cattle and yaks with normal spermatogenesis (P < 0.01). The promoter methylation level ofBvhin the testes of cattle-yak hybrids was significantly greater than in cattle and yaks (P < 0.01).

Conclusion

In the present study,Bvhwas isolated and characterized. These data suggest that Bvh functions in bovine spermatogenesis, and that transcription of the gene in testes were regulated by alternative splice and promoter methylation.
Cis-2-dodecenoic acid quorum sensing system modulates N-acyl homoserine lactone production through RpfR and cyclic di-GMP turnover in Burkholderia cenocepacia
Authors: Deng Yinyue , Lim Amy , Wang Jing , Zhou Tielin , Chen Shaohua , Lee Jasmine , Dong Yi-Hu , Zhang Lian-Hui
Published: July 2013

Background

Burkholderia cenocepaciaemploys both N-Acyl homoserine lactone (AHL) andcis-2-dodecenoic acid (BDSF) quorum sensing (QS) systems in regulation of bacterial virulence. It was shown recently that disruption of BDSF synthase RpfFBccaused a reduction of AHL signal production inB. cenocepacia. However, how BDSF system influences AHL system is still not clear.

Results

We show here that BDSF system controls AHL system through a novel signaling mechanism. Null mutation of either the BDSF synthase, RpfFBc, or the BDSF receptor, RpfR, caused a substantial down-regulation of AHL signal production inB. cenocepaciastrain H111. Genetic and biochemical analyses showed that BDSF system controls AHL signal production through the transcriptional regulation of the AHL synthase genecepIby modulating the intracellular level of second messenger cyclic di-GMP (c-di-GMP). Furthermore, we show that BDSF and AHL systems have a cumulative role in the regulation of various biological functions, including swarming motility, biofilm formation and virulence factor production, and exogenous addition of either BDSF or AHL signal molecules could only partially rescue the changed phenotypes of the double deletion mutant defective in BDSF and AHL signal production.

Conclusions

These results, together with our previous findings, thus depict a molecular mechanism with which BDSF regulates AHL signal production and bacterial virulence through modulating the phosphodiesterase activity of its receptor RpfR to influence the intracellular level of c-di-GMP.
The Arabidopsis LRR-RLK, PXC1, is a regulator of secondary wall formation correlated with the TDIF-PXY/TDR-WOX4 signaling pathway
Authors: Wang Jiehua , Kucukoglu Melis , Zhang Linbin , Chen Peng , Decker Daniel , Nilsson Ove , Jones Brian , Sandberg Göran , Zheng Bo
Published: July 2013

Background

Although a number of leucine-rich repeat receptor-like kinase-encoding genes (LRR-RLKs) have been identified in plants, a functional role has been determined for only a few. Recent studies have demonstrated that an LRR-RLK, PXY/TDR, is important for the process of secondary vascular development. Other studies have indicated that PXY/TDR is unlikely to be the sole LRR-RLK involved in this complex process.

Results

In this study, in silico analyses led to the identification of three Arabidopsis LRR-RLK genes (PXY-correlated; PXC1, 2, 3) with transcript accumulation profiles that correlated strongly with several key regulators of vascular development, including PXY/TDR, HB-8, REV, and CLE41. Expression profiling using qPCR and promoter:reporter lines indicated that all three PXC genes are associated with the vasculature. One in particular, PXC1 (At2g36570), had a strong correlation with PXY/TDR. Shifting pxc1 mutants from long-days to short-days showed that loss of the gene led to a dramatic reduction in secondary wall formation in xylem fibers. Transcript analysis of mutants for a variety of secondary cell wall-associated genes, including PXY/TDR indicated that the pathways mediated by PXC1 connect with those mediated by the TDIF-PXY/TDR-WOX4 system.

Conclusions

The data indicate that the LRR-RLK, PXC1 is involved in secondary cell wall formation in xylem fibers. Whereas further study is needed to identify the ligands and mode of action of the PXC1 protein, it is clear from this work that similarly to the shoot apical meristem (SAM), secondary vascular development requires contributions from a number of LRR-RLKs.
Care managers’ confidence in managing home-based end-of-life care: a cross-sectional study
Authors: Watanabe Maiko , Yamamoto-Mitani Noriko , Nishigaki Masakazu , Okamoto Yuko , Igarashi Ayumi , Suzuki Miho
Published: July 2013

Background

There are increasing occasions for care managers (CMs) to manage end-of-life (EOL) situations for older persons at home, in Japan. However, many CMs report anxiety, difficulties and low confidence in managing such care, although confidence is considered a significant determinant of professional performance. This study examined the confidence of CMs at managing home-based EOL situations and its factors.

Methods

Participants of this cross-sectional study were CMs from 1,200 homecare agencies in Japan, which were systematically sampled from a national database. Participants were asked about their overall confidence in managing home-based EOL situations, as well as their demographic, professional and agency characteristics. Multiple logistic regression analysis was conducted to examine the factors associated with CM confidence levels.

Results

Valid responses were obtained from 458 participants (response rate, 39.4%). Among the respondents, 81.0% (n = 371) were female; mean age 49.2 years old (standard deviation = 8.8). Their professional backgrounds included nurses (28.2%), care workers (49.8%), social workers (10.9%), and home attendants (6.1%). Approximately 70% of CMs expressed some level of confidence in managing home-based EOL situations. Multiple logistic regression analysis showed that being confident was significantly associated with having a nursing license (OR: 2.71, 95% CI: 1.26–6.19) and having an additional work responsibility other than being a CM, such as working as a homecare nurse or a home attendant (OR: 2.78, 95% CI: 1.06–4.74). Higher confidence levels were more frequently reported among those who had multiple experiences with EOL situations, compared with those who had none, or only one experience: OR=2.60 (95% CI 1.26–5.50) for those with 2-3 cases; OR=7.12 (3.21–16.56) for those with 4-10 cases; OR = 33.67 (8.14–235.19) for those with 11 cases and over.

Conclusions

These results suggest that CMs with direct, hands-on experience with EOL care, or who have managed multiple EOL cases, tended to be confident at managing home-based EOL situations. Given that the number of nurses working as CMs is decreasing, further research is needed to explore what support CMs need to increase their confidence, especially when the CMs do not have nursing licenses and/or experience with EOL situations.
The incidence and aetiology of hospitalised community-acquired pneumonia among Vietnamese adults: a prospective surveillance in Central Vietnam
Authors: Takahashi Kensuke , Suzuki Motoi , Minh Le Nhat , Anh Nguyen Hien , Huong Luu Thi Minh , Son Tran Vo Vinh , Long Phan The , Ai Nguyen Thi Thuy , Tho Le Huu , Morimoto Konosuke , Kilgore Paul E , Anh Dang Duc , Ariyoshi Koya , Yoshida Lay Myint
Published: July 2013

Background

Lower respiratory tract infection (LRTI) including Community-acquired pneumonia (CAP) is a common infectious disease that is associated with significant morbidity and mortality. The patterns of aetiological pathogens differ by region and country. Special attention must be paid to CAP in Southeast Asia (SEA), a region facing rapid demographic transition. Estimates burden and aetiological patterns of CAP are essential for the clinical and public health management. The purposes of the study are to determine the incidence, aetiological pathogens, clinical pictures and risk factors of community-acquired pneumonia (CAP) in the Vietnamese adult population.

Methods

A prospective surveillance for hospitalised adult CAP was conducted in Khanh Hoa Province, Central Vietnam. All adults aged ≥15 years with lower respiratory tract infections (LRTI) admitted to a provincial hospital from September 2009 to August 2010 were enrolled in the study. Patients were classified into CAP and non-pneumonic LRTI (NPLRTI) according to the radiological findings. Bacterial pathogens were identified from sputum samples by the conventional culture and polymerase chain reaction (PCR) for Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis; 13 respiratory viruses were identified from nasopharyngeal specimens by PCR.

Results

Of all 367 LRTI episodes examined, 174 (47%) were CAP. Older age, the presence of underlying respiratory conditions, and higher index score of smoking were associated with CAP. The one-year estimated incidence of hospitalised adult CAP in our study population was 0.81 per 1,000 person years. The incidence increased considerably with age and was highest among the elderly. The case fatality proportion of hospitalised CAP patients was 9.8%. Among 286 sputum samples tested for bacterial PCR, 79 (28%) were positive for H. influenzae, and 65 (23%) were positive for S. pneumoniae. Among 357 samples tested for viral PCR, 73 (21%) were positive for respiratory viruses; influenza A (n = 32, 9%) was the most common.

Conclusions

The current adult CAP incidence in Vietnam was relatively low; this result was mainly attributed to the young age of our study population.
Natural ventilation reduces high TB transmission risk in traditional homes in rural KwaZulu-Natal, South Africa
Authors: Lygizos Melissa , Shenoi Sheela V , Brooks Ralph P , Bhushan Ambika , Brust James CM , Zelterman Daniel , Deng Yanhong , Northrup Veronika , Moll Anthony P , Friedland Gerald H
Published: July 2013

Background

Transmission of drug susceptible and drug resistant TB occurs in health care facilities, and community and households settings, particularly in highly prevalent TB and HIV areas. There is a paucity of data regarding factors that may affect TB transmission risk in household settings. We evaluated air exchange and the impact of natural ventilation on estimated TB transmission risk in traditional Zulu homes in rural South Africa.

Methods

We utilized a carbon dioxide decay technique to measure ventilation in air changes per hour (ACH). We evaluated predominant home types to determine factors affecting ACH and used the Wells-Riley equation to estimate TB transmission risk.

Results

Two hundred eighteen ventilation measurements were taken in 24 traditional homes. All had low ventilation at baseline when windows were closed (mean ACH = 3, SD = 3.0), with estimated TB transmission risk of 55.4% over a ten hour period of exposure to an infectious TB patient. There was significant improvement with opening windows and door, reaching a mean ACH of 20 (SD = 13.1, p < 0.0001) resulting in significant decrease in estimated TB transmission risk to 9.6% (p < 0.0001). Multivariate analysis identified factors predicting ACH, including ventilation conditions (windows/doors open) and window to volume ratio. Expanding ventilation increased the odds of achieving ≥12 ACH by 60-fold.

Conclusions

There is high estimated risk of TB transmission in traditional homes of infectious TB patients in rural South Africa. Improving natural ventilation may decrease household TB transmission risk and, combined with other strategies, may enhance TB control efforts.
Impact of a tenofovir disoproxil fumarate plus ritonavir-boosted protease inhibitor-based regimen on renal function in HIV-infected individuals: a prospective, multicenter study
Authors: Cao Ying , Han Yang , Xie Jing , Cui Qu , Zhang Lixia , Li Yijia , Li Yanling , Song Xiaojing , Zhu Ting , Li Taisheng
Published: July 2013

Background

The aim of this study was to investigate the impact of a tenofovir disoproxil fumarate (TDF) plus ritonavir-boosted protease inhibitor (PI/r) regimen on renal function in Chinese HIV-infected patients.

Methods

Seventy-five HIV-1 infected patients failing first-line antiretroviral therapy (ART) comprised the TDF+PI/r group. Seventy-five HIV-1 infected patients matched for gender, age, and renal function made up the control. All subjects completed follow-up visits over 48 weeks. CD4 cell count, plasma HIV-1 viral load, and urine protein level were assessed at the trial start (baseline, week 0) and at week 48. The serum creatinine and estimated glomerular filtration rate (eGFR) were monitored at each follow-up point. Change in eGFR from baseline to week 48 was also compared.

Results

Compared to control, the TDF+PI/r group exhibited higher levels of serum creatinine (79 vs. 69.7 μmol/L, P<0.001) and a lower rate of eGFR (93.0 vs. 101.6 ml/min/1.73m2, P=0.009) at the end of week 48. Patients treated with TDF+PI/r showed greater decline in eGFR than control (−8.8 vs. 6.4ml/min/1.73m2, P<0.001). Compared to baseline renal function of the control group, the TDF+PI/r group exhibited a greater median decline in eGFR at the end of week 48 (P<0.001).

Conclusions

We found that a TDF+PI/r based ART regimen resulted in greater renal function decline over 48 weeks. Therefore, renal function should be monitored especially when TDF is used in combination with PI/r.

Trial registration

ClinicalTrials.gov identifier: NCT00872417
Cross-reactivities between human IgMs and the four serotypes of dengue virus as probed with artificial homodimers of domain-III from the envelope proteins
Authors: Zidane Nora , Dussart Philippe , Bremand Laetitia , Bedouelle Hugues
Published: July 2013

Background

Dengue fever is the most important vector-borne viral disease. Four serotypes of dengue virus, DENV1 to DENV4, coexist. Infection by one serotype elicits long-lasting immunity to that serotype but not the other three. Subsequent infection by a different serotype is a risk factor for severe dengue. Domain III (ED3) of the viral envelope protein interacts with cell receptors and contains epitopes recognized by neutralizing antibodies. We determined the serotype specificity and cross-reactivity of human IgMs directed against ED3 by using a well-characterized collection of 90 DENV-infected and 89 DENV-uninfected human serums.

Methods

The recognitions between the four serotypes of ED3 and the serums were assayed with an IgM antibody-capture ELISA (MAC-ELISA) and artificial homodimeric antigens. The results were analyzed with Receiving Operator Characteristic (ROC) curves.

Results

The DENV-infected serums contained IgMs that reacted with one or several ED3 serotypes. The discrimination by ED3 between serums infected by the homotypic DENV and uninfected serums varied with the serotype in the decreasing order DENV1 > DENV2 > DENV3 > DENV4. The ED3 domain of DENV1 gave the highest discrimination between DENV-infected and DENV-uninfected serums, whatever the infecting serotype, and thus behaved like a universal ED3 domain for the detection of IgMs against DENV. Some ED3 serotypes discriminated between IgMs directed against the homotypic and heterotypic DENVs. The patterns of cross-reactivities and discriminations varied with the serotype.

Conclusions

The results should help better understand the IgM immune response and protection against DENV since ED3 is widely used as an antigen in diagnostic assays and an immunogen in vaccine candidates.