bluuebunny/crossref_metadata_2025_split huggingface dataset:
Looking back at the doctorate: A qualitative study of Jordanian graduates from PhD programs in the UK
Authors: Ali Zeilani Ruqayya S. , Al‐Nawafleh Ahmed H. , Evans Catrin 
Published: August 2011

AbstractMany countries develop their nursing capacity by sending nurses overseas to gain their doctorates. There is a lack of research on their subsequent experience and career development. Focusing on the Jordanian and UK contexts, this qualitative study explored the doctoral and postdoctoral experience. Interviews were held with 16 PhD nursing graduates in Jordan. The participants had studied in 12 different universities in the UK and now worked as faculty members in seven Jordanian universities. The data were analyzed thematically. The participants reported that the most difficult task (but also the most significant achievement) was the transition to autonomous scholarship. They also described a profound personal transformation as a result of living in another country. However, very few of them could cite examples of how they were using their skills now to influence their current practice within their faculty roles. This suggests a possible under‐use of the skills, new perspectives, and enthusiasm that new doctoral graduates bring back home with them. Future research should focus on identifying ways to support and develop doctoral nursing graduates to maximize their potential on their return home.
All‐Hex Mesh Generation via Volumetric PolyCube Deformation
Authors: Gregson James , Sheffer Alla , Zhang Eugene 
Published: August 2011

AbstractWhile hexahedral mesh elements are preferred by a variety of simulation techniques, constructing quality all‐hex meshes of general shapes remains a challenge. An attractive hex‐meshing approach, often referred to as sub‐mapping, uses a low distortion mapping between the input model and a PolyCube (a solid formed from a union of cubes), to transfer a regular hex grid from the PolyCube to the input model. Unfortunately, the construction of suitable PolyCubes and corresponding volumetric maps for arbitrary shapes remains an open problem. Our work introduces a new method for computing low‐distortion volumetric PolyCube deformations of general shapes and for subsequent all‐hex remeshing. For a given input model, our method simultaneously generates an appropriate PolyCube structure and mapping between the input model and the PolyCube. From these we automatically generate good quality all‐hex meshes of complex natural and man‐made shapes.
Skeleton computation of orthogonal polyhedra
Authors: Martinez J. , Vigo M. , Pla‐Garcia N. 
Published: August 2011

AbstractSkeletons are powerful geometric abstractions that provide useful representations for a number of geometric operations. The straight skeleton has a lower combinatorial complexity compared with the medial axis. Moreover, while the medial axis of a polyhedron is composed of quadric surfaces the straight skeleton just consist of planar faces. Although there exist several methods to compute the straight skeleton of a polygon, the straight skeleton of polyhedra has been paid much less attention. We require to compute the skeleton of very large datasets storing orthogonal polyhedra. Furthermore, we need to treat geometric degeneracies that usually arise when dealing with orthogonal polyhedra. We present a new approach so as to robustly compute the straight skeleton of orthogonal polyhedra. We follow a geometric technique that works directly with the boundary of an orthogonal polyhedron. Our approach is output sensitive with respect to the number of vertices of the skeleton and solves geometric degeneracies. Unlike the existing straight skeleton algorithms that shrink the object boundary to obtain the skeleton, our algorithm relies on the plane sweep paradigm. The resulting skeleton is only composed of axis‐aligned and 45° rotated planar faces and edges.
An Explicit Link between Gaussian Fields and Gaussian Markov Random Fields: The Stochastic Partial Differential Equation Approach
Authors: Lindgren Finn , Rue Håvard , Lindström Johan 
Published: August 2011

SummaryContinuously indexed Gaussian fields (GFs) are the most important ingredient in spatial statistical modelling and geostatistics. The specification through the covariance function gives an intuitive interpretation of the field properties. On the computational side, GFs are hampered with the big n problem, since the cost of factorizing dense matrices is cubic in the dimension. Although computational power today is at an all time high, this fact seems still to be a computational bottleneck in many applications. Along with GFs, there is the class of Gaussian Markov random fields (GMRFs) which are discretely indexed. The Markov property makes the precision matrix involved sparse, which enables the use of numerical algorithms for sparse matrices, that for fields in ℝ2 only use the square root of the time required by general algorithms. The specification of a GMRF is through its full conditional distributions but its marginal properties are not transparent in such a parameterization. We show that, using an approximate stochastic weak solution to (linear) stochastic partial differential equations, we can, for some GFs in the Matérn class, provide an explicit link, for any triangulation of ℝd, between GFs and GMRFs, formulated as a basis function representation. The consequence is that we can take the best from the two worlds and do the modelling by using GFs but do the computations by using GMRFs. Perhaps more importantly, our approach generalizes to other covariance functions generated by SPDEs, including oscillating and non-stationary GFs, as well as GFs on manifolds. We illustrate our approach by analysing global temperature data with a non-stationary model defined on a sphere.
Protein tyrosine phosphatase σ regulates the synapse number of zebrafish olfactory sensory neurons
Authors: Chen Xigui , Yoshida Tomoyuki , Sagara Hiroshi , Mikami Yoshinori , Mishina Masayoshi 
Published: August 2011

J. Neurochem. (2011) 119, 532–543.AbstractThe formation and refinement of synaptic connections are key steps of neural development to establish elaborate brain networks. To investigate the functional role of protein tyrosine phosphatase (PTP) σ, we employed an olfactory sensory neuron (OSN)‐specific gene manipulation system in combination with in vivo imaging of transparent zebrafish embryos. Knockdown of PTPσ enhanced the accumulation of synaptic vesicles in the axon terminals of OSNs. The exaggerated accumulation of synaptic vesicles was restored to the normal level by the OSN‐specific expression of PTPσ, indicating that presynaptic PTPσ is responsible for the regulation of synaptic vesicle accumulation. Consistently, transient expression of a dominant‐negative form of PTPσ in OSNs enhanced the accumulation of synaptic vesicles. The exaggerated accumulation of synaptic vesicles was reproduced in transgenic zebrafish lines carrying an OSN‐specific expression vector of the dominant‐negative PTPσ. By electron microscopic analysis of the transgenic line, we found the significant increase of the number of OSN‐mitral cell synapses in the central zone of the olfactory bulb. The density of docked vesicles at the active zone was also increased significantly. Our results suggest that presynaptic PTPσ controls the number of OSN‐mitral cell synapses by suppressing their excessive increase.
A decision support methodology for increasing school efficiency in Bolivia's low‐income communities
Authors: de Figueiredo João Neiva , Marca Barrientos Miguel Angel 
Published: August 2011

AbstractThis paper presents a data envelopment analysis (DEA)‐based decision‐support methodology that has been implemented and is being used by a not‐for‐profit organization, Fe y Alegría, which runs 439 Bolivian schools reaching over 160,000 disadvantaged students in that poverty‐stricken Latin American nation. Bolivia is a poor country with the highest percentage of indigenous population and the lowest per capita income in South America and as such its inhabitants are in dire need of effective educational resources to help them out of poverty. The DEA‐based methodology described in this paper has offered an objective way to compare network schools among themselves and with out‐of‐network schools, providing a deeper understanding of school efficiency levels in the face of scarce resources, and allowing for sharing of best practices across the network. The paper introduces the educational environment in Bolivia, presents the DEA model, describes the decision support methodology, and provides two examples of its use. The first example compares Fe y Alegría secondary schools with out‐of‐network secondary schools using publicly available data, and the second compares Fe y Alegría secondary schools among themselves using a proprietary database. The paper also comments on lessons learned and the need for broad consensus‐building and organization‐wide buy‐in for successful adoption and maximum impact.
EFFECTS OF FARMING PRACTICES ON THE QUALITY OF ULTRA‐FROZEN MANDARIN JUICE
Authors: NAVARRO P. , MELENDEZ‐MARTINEZ A.J. , HEREDIA F. , GABALDON J.A. , PEREZ‐LOPEZ A.J. 
Published: August 2011

ABSTRACTThe effects of the farming type (organic or conventional) and cyclodextrin addition on the quality (loss of ascorbic acid, carotenoids composition, color and antioxidant activity) of freshly squeezed, nonpasteurized, ultra‐frozen mandarin juices were studied during a shelf life of 145 days. The vitamin C content was reduced from 540 and 470 mg/L to 515 and 447 mg/L in organic and conventional juices, respectively. Carotenoids were stable during the storage time (decreases being in the range 5–10%), with β‐cryptoxanthin (7.21 ± 0.31 mg/L) being the most abundant compound, followed by lutein and zeaxanthin. The juices color was not affected by thermal treatment and these data were provided by both instrumental Commission internationale de l'éclairage L*, a*, b* data and the sensory studies conducted. The antioxidant activity was 0.04 and 0.06 mMT/mL, at day 0, for the organic and conventional juices; the losses during the storage were below 18%. The addition of cyclodextrins did not have any significant effect on the parameters under study. This study showed that the nutritional and organoleptic quality of ultra‐frozen juices is quite stable during the storage period.PRACTICAL APPLICATIONSThe application of cyclodextrins in the food industry is very important as solubilizing agents, stabilizers and emulsifiers. The molecular encapsulation of lipophilic food ingredients with cyclodextrin improves the stability of flavors, vitamins, colorants and unsaturated fats, etc., both in physical and chemical sense leading to extended product shelf life, accelerated and long‐term storage stability.
Depth Cues Versus the Simplicity Principle in 3D Shape Perception
Authors: Li Yunfeng , Pizlo Zygmunt 
Published: August 2011

AbstractTwo experiments were performed to explore the mechanisms of human 3D shape perception. In Experiment 1, the subjects’ performance in a shape constancy task in the presence of several cues (edges, binocular disparity, shading and texture) was tested. The results show that edges and binocular disparity, but not shading or texture, are important in 3D shape perception. Experiment 2 tested the effect of several simplicity constraints, such as symmetry and planarity on subjects’ performance in a shape constancy task. The 3D shapes were represented by edges or vertices only. The results show that performance with or without binocular disparity is at chance level, unless the 3D shape is symmetric and/or its faces are planar. In both experiments, there was a correlation between the subjects’ performance with and without binocular disparity. Our study suggests that simplicity constraints, not depth cues, play the primary role in both monocular and binocular 3D shape perception. These results are consistent with our computational model of 3D shape recovery.
Statistical software for microcomputers: News and reviews
Authors: LOVIE PAT 
Published: August 2011

A press release about a new package called SOLO from the BMDP people got me quite excited recently. It promised all manner of statistical goodies and interactive graphics. Actually, SOLO is just a rebadged version of the NCSS package which was reviewed in the November 1988 issue. The sterling equivalent price quoted by Statistical Software Ltd (Cork Technology Park, Model Farm Road, Cork, Ireland) is considerably more than it would cost to import NCSS directly. But I suppose that having support closer to hand than Utah may be worth the extra to some users. By the way, I am expecting, momentarily, an upgrade to NCSS which promises macros and much more. A report should find its way into a later issue.By the time you read this, the current version of Minitab is almost certain to be Release 7. So, just in case you are wondering why the review which follows is of Release 6, the sorry tale involves a last minute copy of the beta test version of Release 7, scrambled floppy diskettes (they were probably X‐rayed or something similar in Customs) and no time to get replacements. There was nothing for it except to go back to Release 6.In fact, I doubt very much that Release 7 alters any existing facilities to an extent that would seriously compromise my review. Information gleaned from the documentation suggests that the most important changes are the new features, notably, a data editor, a general linear model command and statistical process control charts. I hope to report on these in the next issue.For my first review, however, I take a look at Microstat‐II. This is a completely revamped version of the original Microstat package which first saw the light of day over ten years ago.
Imbalance of Th17 Cells and Regulatory T Cells in Tuberculous Pleural Effusion
Authors: Ye Zhi-Jian , Zhou Qiong , Du Rong-Hui , Li Xiao , Huang Bo , Shi Huan-Zhong 
Published: August 2011

ABSTRACTBoth T helper interleukin 17 (IL-17)-producing cells (Th17 cells) and regulatory T cells (Tregs) have been found to be increased in human tuberculous pleural effusion (TPE); however, the possible interaction between Th17 cells and Tregs in TPE remains to be elucidated. The objective of the present study was to investigate the distribution of Th17 cells in relation to Tregs, as well as the mechanism of Tregs in regulating generation and differentiation of Th17 cells in TPE. In the present study, the numbers of Th17 cells and Tregs in TPE and blood were determined by flow cytometry. The regulation and mechanism of CD39+Tregs on generation and differentiation of Th17 cells were explored. Our data demonstrated that the numbers of Th17 cells and CD39+Tregs were both increased in TPE compared with blood. Th17 cell numbers were correlated negatively with Tregs in TPE but not in blood. When naïve CD4+T cells were cultured with CD39+Tregs, Th17 cell numbers decreased as CD39+Treg numbers increased, and the addition of the anti-latency-associated peptide monoclonal antibody to the coculture reversed the inhibitory effect exerted by CD39+Tregs. This study shows that Th17/Treg imbalance exists in TPE and that pleural CD39+Tregs inhibit generation and differentiation of Th17 cells via a latency-associated peptide-dependent mechanism.
Rous Sarcoma Virus Gag Has No Specific Requirement for Phosphatidylinositol-(4,5)-Bisphosphate for Plasma Membrane Association
In Vivo
or for Liposome Interaction
In Vitro
Authors: Chan Jany , Dick Robert A. , Vogt Volker M. 
Published: August 2011

ABSTRACT

The MA domain of the retroviral Gag protein mediates interactions with the plasma membrane, which is the site of productive virus release. HIV-1 MA has a phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P
2
] binding pocket; depletion of this phospholipid from the plasma membrane compromises Gag membrane association and virus budding. We used multiple methods to examine the possible role of PI(4,5)P
2
in Gag-membrane interaction of the alpharetrovirus Rous sarcoma virus (RSV). In contrast to HIV-1, which was tested in parallel, neither membrane localization of RSV Gag-GFP nor release of virus-like particles was affected by phosphatase-mediated depletion of PI(4,5)P
2
in transfected avian cells. In liposome flotation experiments, RSV Gag required acidic lipids for binding but showed no specificity for PI(4,5)P
2
. Mono-, di-, and triphosphorylated phosphatidylinositol phosphate (PIP) species as well as high concentrations of phosphatidylserine (PS) supported similar levels of flotation. A mutation that increases the overall charge of RSV MA also enhanced Gag membrane binding. Contrary to previous reports, we found that high concentrations of PS, in the absence of PIPs, also strongly promoted HIV-1 Gag flotation. Taken together, we interpret these results to mean that RSV Gag membrane association is driven by electrostatic interactions and not by any specific association with PI(4,5)P
2
.
Major Histocompatibility Complex Class II Transactivator CIITA Is a Viral Restriction Factor That Targets Human T-Cell Lymphotropic Virus Type 1 Tax-1 Function and Inhibits Viral Replication
Authors: Tosi Giovanna , Forlani Greta , Andresen Vibeke , Turci Marco , Bertazzoni Umberto , Franchini Genoveffa , Poli Guido , Accolla Roberto S. 
Published: August 2011

ABSTRACT

Human T-cell lymphotropic virus type 1 (HTLV-1) is the causative agent of an aggressive malignancy of CD4
+
T lymphocytes. Since the viral transactivator Tax-1 is a major player in T-cell transformation, targeting Tax-1 protein is regarded as a possible strategy to arrest viral replication and to counteract neoplastic transformation. We demonstrate that CIITA, the master regulator of major histocompatibility complex class II gene transcription, inhibits HTLV-1 replication by blocking the transactivating function of Tax-1 both when exogenously transfected in 293T cells and when endogenously expressed by a subset of U937 promonocytic cells. Tax-1 and CIITA physically interact
in vivo
via the first 108 amino acids of Tax-1 and two CIITA adjacent regions (amino acids 1 to 252 and 253 to 410). Interestingly, only CIITA 1-252 mediated Tax-1 inhibition, in agreement with the fact that CIITA residues from positions 64 to 124 were required to block Tax-1 transactivation. CIITA inhibitory action on Tax-1 correlated with the nuclear localization of CIITA and was independent of the transcription factor NF-YB, previously involved in CIITA-mediated inhibition of Tax-2 of HTLV-2. Instead, CIITA severely impaired the physical and functional interaction of Tax-1 with the cellular coactivators p300/CBP-associated factor (PCAF), cyclic AMP-responsive element binding protein (CREB), and activating transcription factor 1 (ATF1), which are required for the optimal activation of HTLV-1 promoter. Accordingly, the overexpression of PCAF, CREB, and ATF1 restored Tax-1-dependent transactivation of the viral long-terminal-repeat promoter inhibited by CIITA. These findings strongly support our original observation that CIITA, beside increasing the antigen-presenting function for pathogen antigens, acts as an endogenous restriction factor against human retroviruses by blocking virus replication and spreading.
Targeted Bacterial Immunity Buffers Phage Diversity
Authors: Haerter Jan O. , Trusina Ala , Sneppen Kim 
Published: August 2011

ABSTRACTBacteria have evolved diverse defense mechanisms that allow them to fight viral attacks. One such mechanism, the clustered, regularly interspaced, short palindromic repeat (CRISPR) system, is an adaptive immune system consisting of genetic loci that can take up genetic material from invasive elements (viruses and plasmids) and later use them to reject the returning invaders. It remains an open question how, despite the ongoing evolution of attack and defense mechanisms, bacteria and viral phages manage to coexist. Using a simple mathematical model and a two-dimensional numerical simulation, we found that CRISPR adaptive immunity allows for robust phage-bacterium coexistence even when the number of virus species far exceeds the capacity of CRISPR-encoded genetic memory. Coexistence is predicted to be a consequence of the presence of many interdependent species that stress but do not overrun the bacterial defense system.
Chlamydia trachomatisserovars in community-based HIV-positive and HIV-negative men who have sex with men in Sydney, Australia
Authors: Templeton D J , Twin J , Jin F , Grulich A E , Garland S M , Tabrizi S N 
Published: August 2011

ObjectivesThere are few data on the distribution of specificChlamydia trachomatisserovars among men who have sex with men (MSM) outside clinical settings. To investigate these patterns, serovar determination was performed on chlamydia-positive samples from two community-based cohort studies of HIV-positive and HIV-negative MSM in Sydney, Australia.MethodsFrom January 2005 to June 2007 all positiveC trachomatispharyngeal, urine and anal samples were evaluated. The serovar of eachC trachomatisinfection was determined byomp1gene sequencing with confirmatory quantitative PCR screening. Symptom data were routinely reported by study participants at the time of testing.ResultsSerovar determination was possible for 54 samples among 52 participants. Seven samples were not able to be typed. Site-specific symptoms were reported by fewer than 10% of participants diagnosed with pharyngeal and anogenital chlamydia. The most commonly identified serovars were serovar D (n=32, 59.3%, 95% CI 45.0 to 72.4), followed by serovar G (n=11, 20.4%, 95% CI 10.6 to 33.5) and serovar J (n=5, 9.3%, 95% CI 3.1 to 20.3). Only one lymphogranuloma venereum serovar was identified (L2b).ConclusionsThis community-based study found a similar distribution of chlamydia serovars to that observed among Australian community-based MSM several years ago, and serovar distribution recently observed among predominantly symptomatic MSM at a Sydney clinic. These findings suggest little change inC trachomatisserovar distribution in Australian MSM over the past decade and a lack of correlation of specific chlamydia serovars with anogenital symptoms among MSM.
A Quasi-Three-Dimensional Variably Saturated Groundwater Flow Model for Climate Modeling
Authors: Xie Zhenghui , Di Zhenhua , Luo Zhendong , Ma Qian 
Published: August 2011

AbstractIn this study, a quasi-three-dimensional, variably saturated groundwater flow model was developed by approximately dividing the three-dimensional soil water and groundwater flow into an unsaturated vertical soil water flow and a horizontal groundwater flow to simulate the interactions among soil water, groundwater, and vegetation. The developed model consists of a one-dimensional unsaturated soil water flow model with the water table as the moving boundary using an adaptive grid structure for a vertical soil column formed based on discrete grid cells in a horizontal domain, a two-dimensional groundwater flow model for the horizontal domain, and an interface model connecting the two components for the horizontal grid cells in the domain. Synthetic experiments by the model were conducted to test the sensitivities of the model parameters of river elevation, ground surface hydraulic conductivity, and surface flux, and the results from the experiments showed the robustness of the proposed model under different conditions. Comparison of the simulation by the model and that by a full three-dimensional scheme showed its feasibility and efficiency. A case of stream water conveyance in the lower reaches of the Tarim River was then applied to validate the developed model for simulation of the water table elevations at the Yingsu section. Finally, a numerical experiment by the model for the Tarim River basin was conducted to discuss the groundwater latent flow for large-scale high-relief topography with stream water conveyance. The results show that the model can simulate the water table reasonably well.