bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variance-Based Sensitivity Analysis: An Illustration on the Lorenz'63 Model
Authors: Marzban Caren 
Published: July 2013

Abstract
Sensitivity analysis (SA) generally refers to an assessment of the sensitivity of the output(s) of some complex model with respect to changes in the input(s). Examples of inputs or outputs include initial state variables, parameters of a numerical model, or state variables at some future time. Sensitivity analysis is useful for data assimilation, model tuning, calibration, and dimensionality reduction; and there exists a wide range of SA techniques for each. This paper discusses one special class of SA techniques, referred to as variance based. As a first step in demonstrating the utility of the method in understanding the relationship between forecasts and parameters of complex numerical models, here the method is applied to the Lorenz'63 model, and the results are compared with an adjoint-based approach to SA. The method has three major components: 1) analysis of variance, 2) emulation of computer data, and 3) experimental–sampling design. The role of these three topics in variance-based SA is addressed in generality. More specifically, the application to the Lorenz'63 model suggests that the Z state variable is most sensitive to the b and r parameters, and is mostly unaffected by the s parameter. There is also evidence for an interaction between the r and b parameters. It is shown that these conclusions are true for both simple random sampling and Latin hypercube sampling, although the latter leads to slightly more precise estimates for some of the sensitivity measures.
An Upwind-Biased Conservative Transport Scheme for Multistage Temporal Integrations on Spherical Icosahedral Grids
Authors: Miura Hiroaki 
Published: July 2013

Abstract
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.
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.
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.
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

Abstract

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

Abstract

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

AbstractBackgroundHigh 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.MethodsWe 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).ResultsPearson 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.ConclusionsThese 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

AbstractBackgroundVasa 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.ResultsHere 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).ConclusionIn 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

AbstractBackgroundBurkholderia 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.ResultsWe 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.ConclusionsThese 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

Abstract

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

Abstract

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.