bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ablation of retinal ciliopathy protein RPGR results in altered photoreceptor ciliary composition
Authors: Rao Kollu N. , Li Linjing , Anand Manisha , Khanna Hemant 
Published: June 2015

AbstractCilia regulate several developmental and homeostatic pathways that are critical to survival. Sensory cilia of photoreceptors regulate phototransduction cascade for visual processing. Mutations in the ciliary protein RPGR (retinitis pigmentosa GTPase regulator) are a prominent cause of severe blindness disorders due to degeneration of mature photoreceptors. However, precise function of RPGR is still unclear. Here we studied the involvement of RPGR in ciliary trafficking by analyzing the composition of photoreceptor sensory cilia (PSC) in Rpgrko retina. Using tandem mass spectrometry analysis followed by immunoblotting, we detected few alterations in levels of proteins involved in proteasomal function and vesicular trafficking in Rpgrko PSC, prior to onset of degeneration. We also found alterations in the levels of high molecular weight soluble proteins in Rpgrko PSC. Our data indicate RPGR regulates entry or retention of soluble proteins in photoreceptor cilia but spares the trafficking of key structural and phototransduction-associated proteins. Given a frequent occurrence of RPGR mutations in severe photoreceptor degeneration due to ciliary disorders, our results provide insights into pathways resulting in altered mature cilia function in ciliopathies.
Comparative Assessment of Transmission-Blocking Vaccine Candidates against Plasmodium falciparum
Authors: Kapulu M. C. , Da D. F. , Miura K. , Li Y , Blagborough A. M. , Churcher T. S. , Nikolaeva D. , Williams A. R. , Goodman A. L. , Sangare I. , Turner A. V. , Cottingham M. G. , Nicosia A. , Straschil U. , Tsuboi T. , Gilbert S. C. , Long Carole A. , Sinden R. E. , Draper S. J. , Hill A. V. S. , Cohuet A. , Biswas S. 
Published: June 2015

AbstractMalaria transmission-blocking vaccines (TBVs) target the development of Plasmodium parasites within the mosquito, with the aim of preventing malaria transmission from one infected individual to another. Different vaccine platforms, mainly protein-in-adjuvant formulations delivering the leading candidate antigens, have been developed independently and have reported varied transmission-blocking activities (TBA). Here, recombinant chimpanzee adenovirus 63, ChAd63 and modified vaccinia virus Ankara, MVA, expressing AgAPN1, Pfs230-C, Pfs25 and Pfs48/45 were generated. Antibody responses primed individually against all antigens by ChAd63 immunization in BALB/c mice were boosted by the administration of MVA expressing the same antigen. These antibodies exhibited a hierarchy of inhibitory activity against the NF54 laboratory strain of P. falciparum in Anopheles stephensi mosquitoes using the standard membrane feeding assay (SMFA), with anti-Pfs230-C and anti-Pfs25 antibodies giving complete blockade. The observed rank order of inhibition was replicated against P. falciparum African field isolates in A. gambiae in direct membrane feeding assays (DMFA). TBA achieved was IgG concentration dependent. This study provides the first head-to-head comparative analysis of leading antigens using two different parasite sources in two different vector species and can be used to guide selection of TBVs for future clinical development using the viral-vectored delivery platform.
Estimating the anomalous diffusion exponent for single particle tracking data with measurement errors - An alternative approach
Authors: Burnecki Krzysztof , Kepten Eldad , Garini Yuval , Sikora Grzegorz , Weron Aleksander 
Published: June 2015

AbstractAccurately characterizing the anomalous diffusion of a tracer particle has become a central issue in biophysics. However, measurement errors raise difficulty in the characterization of single trajectories, which is usually performed through the time-averaged mean square displacement (TAMSD). In this paper, we study a fractionally integrated moving average (FIMA) process as an appropriate model for anomalous diffusion data with measurement errors. We compare FIMA and traditional TAMSD estimators for the anomalous diffusion exponent. The ability of the FIMA framework to characterize dynamics in a wide range of anomalous exponents and noise levels through the simulation of a toy model (fractional Brownian motion disturbed by Gaussian white noise) is discussed. Comparison to the TAMSD technique, shows that FIMA estimation is superior in many scenarios. This is expected to enable new measurement regimes for single particle tracking (SPT) experiments even in the presence of high measurement errors.
Dual channel time‐to‐digital converter module with 10 ps resolution and 320 ns full scale range
Authors: Tamborini D. , Portaluppi D. , Villa F. , Zappa F. 
Published: June 2015

A dual‐channel time‐to‐digital converter (TDC) module designed to accurately measure time intervals with 10 ps resolution, about 21 ps root‐mean‐square (rms) precision and 125 fs rms differential nonlinearity, over a 320 ns full scale range and up to 4 Mconv/s per channel is presented. The module can also operate the two channels in parallel, as a single TDC converter, in order to improve timing performance to about 15.3 ps rms. A USB 2.0 interface provides the power supply and allows fast data transfer to a computer, where a dedicated software interface handles measurement data and plots. Because of the excellent timing performance, compact dimensions and low power consumption, the dual‐channel TDC module is suitable for advanced multi‐channel time measurements at the picosecond level.
Pulsed gate bias control of GaN HEMTs to improve pulse‐to‐pulse stability in radar applications
Authors: Delprato J. , Delias A. , Medrel P. , Barataud D. , Campovecchio M. , Neveux G. , Martin A. , Bouysse P. , Nebus J.M. , Tolant C. , Eudeline P. 
Published: June 2015

A significant improvement is demonstrated in the measured pulse‐to‐pulse stability of an S‐band 6 W GaN high electron mobility transistor (HEMT) power amplifier by generating an appropriate pulse of the gate bias and thus a warm‐up drain current just before each radio‐frequency (RF) pulse of a periodic and coherent radar burst. The amplitude and the width of this gate bias pulse preceding each periodic RF pulse of the burst are experimentally varied to investigate the trade‐off between the improvement of pulse‐to‐pulse stability and the total power‐added efficiency. Finally, this technique of synchronised warm‐up gate bias pulse demonstrated a 10 dB improvement of measured amplitude pulse‐to‐pulse stabilities to meet the critical stability requirement below −55 dB for the RF power amplifier.
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Authors: Simão Felipe A. , Waterhouse Robert M. , Ioannidis Panagiotis , Kriventseva Evgenia V. , Zdobnov Evgeny M. 
Published: June 2015

Abstract
Motivation: Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
Results: We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO.
Availability and implementation: Software implemented in Python and datasets available for download from http://busco.ezlab.org.
Contact: evgeny.zdobnov@unige.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya
Authors: Tuti Timothy , Bitok Michael , Paton Chris , Makone Boniface , Malla Lucas , Muinga Naomi , Gathara David , English Mike 
Published: June 2015

Abstract
Objective To share approaches and innovations adopted to deliver a relatively inexpensive clinical data management (CDM) framework within a low-income setting that aims to deliver quality pediatric data useful for supporting research, strengthening the information culture and informing improvement efforts in local clinical practice.
Materials and methods The authors implemented a CDM framework to support a Clinical Information Network (CIN) using Research Electronic Data Capture (REDCap), a noncommercial software solution designed for rapid development and deployment of electronic data capture tools. It was used for collection of standardized data from case records of multiple hospitals’ pediatric wards. R, an open-source statistical language, was used for data quality enhancement, analysis, and report generation for the hospitals.
Results In the first year of CIN, the authors have developed innovative solutions to support the implementation of a secure, rapid pediatric data collection system spanning 14 hospital sites with stringent data quality checks. Data have been collated on over 37 000 admission episodes, with considerable improvement in clinical documentation of admissions observed. Using meta-programming techniques in R, coupled with branching logic, randomization, data lookup, and Application Programming Interface (API) features offered by REDCap, CDM tasks were configured and automated to ensure quality data was delivered for clinical improvement and research use.
Conclusion A low-cost clinically focused but geographically dispersed quality CDM (Clinical Data Management) in a long-term, multi-site, and real world context can be achieved and sustained and challenges can be overcome through thoughtful design and implementation of open-source tools for handling data and supporting research.
Effects of Phacoemulsification Combined With Goniosynechialysis on Primary Angle-closure Glaucoma
Authors: Zhang Hengli , Tang Guangxian , Liu Jie 
Published: June 2015

Purpose:
To assess the effects of phacoemulsification, intraocular lens implantation, and goniosynechialysis on patients with primary angle-closure glaucoma and cataract.

Methods:
A total of 145 eyes of 133 consecutively recruited patients were randomly divided into Phaco group and Trab group. Ocular parameters were measured before and after surgery.

Results:
The mean follow-up period was 13.2±5.6 months. The visual acuity in the Phaco group was significantly improved, whereas no alternation was found in the Trab group after surgery. The intraocular pressure (IOP) had no notable difference in 2 groups before surgery. Compared with preoperative IOP, there was significant decrease after surgery. No remarkable change in the IOP was measured in the 2 groups after surgery for 12 months. The anterior chamber depth was markedly augmented in the Phaco group compared with the Trab group after surgery for 3 months. Compared with the the Trab group, no obvious change in coefficient of outflow facility was found in the Phaco group before and after surgery, whereas there was a significant increase relative to its preoperation. The angle closure decreased from (290±25) to (60±35) degrees after surgery for 12 months in the Phaco group and no significant alteration was observed in the Trab group. The reduction extent of peripheral anterior synechiae was in direct proportion to the decreasing level of angle closure in the 2 groups. The change in the corneal endothelial cell density had no significant difference between 2 groups before and after surgery.

Conclusions:
The treatment of phacoemulsification, intraocular lens implantation, and goniosynechialysis is safe and effective for patients with primary angle-closure glaucoma and cataract.
Impact of the International Nosocomial Infection Control Consortium (INICC) Multidimensional Hand Hygiene Approach During 3 Years in 6 Hospitals in 3 Mexican Cities
Authors: Miranda-Novales María Guadalupe , Sobreyra-Oropeza Martha , Rosenthal Víctor Daniel , Higuera Francisco , Armas-Ruiz Alberto , Pérez-Serrato Irma , Torres-Hernández Héctor , Zamudio-Lugo Irma , Flores-Ruiz Eric M. , Campuzano Roberto , Mena-Brito Jorge , Sánchez-López Martha , Chávez-Gómez Amalia , Rivera-Morales Jaime , Valero-Rodríguez Julián E. 
Published: June 2015

Objectives
To evaluate the impact of the International Nosocomial Infection Control Consortium (INICC) multidimensional hand hygiene (HH) approach in Mexico, and analyze predictors of poor HH compliance.

Methods
From June 2002 to April 2006, we conducted a prospective, observational, before-and-after study in 8 intensive care units (ICUs) from 6 hospitals in 3 cities of Mexico. The approach included administrative support, availability of supplies, education and training, reminders in the workplace, process surveillance, and performance feedback.

Results
A total of 13,201 observations for HH opportunities were done in each ICU, during randomly selected 30-minute periods. Overall, HH compliance increased from 45% to 79% (95% confidence interval [CI], 69.1–86.5; P = 0.01). Univariate and multivariate analyses showed that several variables were significantly associated with poor HH compliance: males versus females (61% versus 66%; 95% CI, 0.91–0.96; P = 0.0001), physicians versus nurses (62% versus 67%; 95% CI, 0.91–0.97; P = 0.0001), and adult versus neonatal ICUs (67% versus 54%; 95% CI, 0.79–0.84; P = 0.0001), among others.

Conclusions
Hand hygiene programs should focus on variables found to be predictors of poor HH compliance.
Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap
Authors: Sovic Ivan , Sikic Mile , Wilm Andreas , Fenlon Shannon Nicole , Chen Swaine , Nagarajan Niranjan 
Published: June 2015

AbstractExploiting the power of nanopore sequencing requires the development of new bioinformatics approaches to deal with its specific error characteristics. We present the first nanopore read mapper (GraphMap) that uses a read-funneling paradigm to robustly handle variable error rates and fast graph traversal to align long reads with speed and very high precision (>95%). Evaluation on MinION sequencing datasets against short and long-read mappers indicates that GraphMap increases mapping sensitivity by at least 15-80%. GraphMap alignments are the first to demonstrate consensus calling with <1 error in 100,000 bases, variant calling on the human genome with 76% improvement in sensitivity over the next best mapper (BWA-MEM), precise detection of structural variants from 100bp to 4kbp in length and species and strain-specific identification of pathogens using MinION reads. GraphMap is available open source under the MIT license athttps://github.com/isovic/graphmap.
The role of uniqueness in destination branding: the case of historical Portsmouth harbor
Authors: Apostolakis Alexandros , Jaffry Shabbar , Sizeland Faye , Cox Adam 
Published: June 2015

Purpose
– The purpose of this paper is to examine the potential for utilizing a unique resource, such as the Historic Portsmouth Harbor, in order to differentiate the local brand.

Design/methodology/approach
– The objective of the paper is to examine the role of unique local resources and attractions as a source of competitive advantage through destination branding.

Findings
– The main findings of the paper indicate that policy makers and destination managers should more proactively utilize the unique elements of the Historic Portsmouth Harbor “brand,” as opposed to the commonplace “waterfront city” brand. This could be achieved by staging events of international significance or through a bid for gaining world heritage status. In addition to that, the paper argues that in order for this branding initiative to have a higher impact, a prominent high profile individual should be appointed. This individual could act as a leader or “brand ambassador” in order to attract stakeholder interest and participation.

Originality/value
– The paper could be of value to destination managers and marketing organizations in a local, sub-regional and regional level.
Unsteady convective heat and mass transfer of a nanofluid in Howarth’s stagnation point by Buongiorno’s model
Authors: Dinarvand Saeed , Hosseini Reza , Pop Ioan 
Published: June 2015

Purpose
– The purpose of this paper is to do a comprehensive study on the unsteady general three-dimensional stagnation-point flow and heat transfer of a nanofluid by Buongiorno’s model.

Design/methodology/approach
– In this study, the convective transport equations include the effects of Brownian motion and thermophoresis. By introducing new similarity transformations for velocity, temperature and nanoparticle volume fraction, the basic equations governing the flow, heat and mass transfer are reduced into highly non-linear ordinary differential equations. The resulting non-linear system has been solved both analytically and numerically.

Findings
– The analysis shows that velocity, temperature and nanoparticle concentration profiles in the respective boundary layers depend on five parameters, namely unsteadiness parameter A, Brownian motion parameter Nb, thermophoresis parameter Nt, Prandtl number Pr and Lewis number Le. It is found that the thermal boundary layer thickens with a rise in both of the Brownian motion and the thermophoresis effects. Therefore, similar to the earlier reported results, the Nusselt number decreases as the Brownian motion and thermophoresis effects become stronger. A correlation for the Nusselt number has been developed based on a regression analysis of the data. This correlation predicts the numerical results with a maximum error of 9 percent for a usual domain of the physical parameters.

Originality/value
– The stagnation point flow toward a wavy cylinder (with nodal and saddle stagnation points) that a little attention has been given to it up to now. The examination of unsteadiness effect on the general three-dimensional stagnation-point flow. The application of an interesting and global model (Boungiorno’s model) for the nanofluid that incorporates the effects of Brownian motion and thermophoresis. The study of the effects of Brownian motion and thermophoresis on the nanofluid flow, heat and mass transfer characteristics. The prediction of correlation for the Nusselt number based on a regression analysis of the data. General speaking, we can tell the problem with this geometry, characteristics, the applied model, and comprehensive results, was Not studied and analyzed in literature up to now.
An improved turbulence model for predicting unsteady cavitating flows in centrifugal pump
Authors: Wang Jian , Wang Yong , Liu Houlin , Huang Haoqin , Jiang Linglin 
Published: June 2015

Purpose
– The purpose of this paper is to study the unsteady caivitating flows in centrifugal pump, especially for improving the turbulence model to obtain highly resolution results-capable of predicting the cavitation inception, shedding off and collapse procedures.

Design/methodology/approach
– Both numerical simulations and experimental visualizations were performed in the present paper. An improved RCD turbulence models was proposed by considering three corrected methods: the rotating corrected method, the compressible corrected method and the turbulent viscosity corrected method. Unsteady RANS computations were conducted to compare with the experiments.

Findings
– The comparison of pump cavitation performance showed that the RCD turbulence model obtained better performance both in non-cavitation and cavitation conditions. The visualization of the cavitation evolution was recorded to validate the unsteady simulations. Good agreement was noticed between calculations and visualizations. It is indicated the RCD model can successfully capture the bubbles detachment and collapse at the rear of the cavity region, since it effectively reduces the eddy viscosity in the multiphase region of liquid and vapor. Furthermore, the eddy viscosity, the instantaneous pressure and density distribution were investigated. The effectiveness of the compressibility was found. Meanwhile, the influence of the rotating corrected method on prediction was explored. It is found that the RCD model solved more unsteady flow characteristics.

Originality/value
– The current work presented a turbulence model which was much more suitable for predicting the cavitating flow in centrifugal pump.
Inequity in access to health services between migrants and natives of Chandigarh, India
Authors: Kaur Manmeet , Singh Sukhbir , Gupta Madhu , Bahuguna Pankaj , Rani Soma 
Published: June 2015

Purpose
– People often migrate from rural to urban areas within a country or from less developed to more developed countries for better life opportunities but may remain outside the range of health services. The purpose of this paper was to find out the socio-economic and health system factors that may affect the utilization of health services by the migrants.

Design/methodology/approach
– Five villages and three slums were randomly selected from 23 villages and 18 slums of Chandigarh, a northwest Indian city. Using stratified random sampling, 145 migrants and 63 native women, who were pregnant or had delivered a baby from April 1, 2009 to March 31, 2012 were interviewed using semi-structured interview schedule. χ2 was used for testing statistical significance of the differences, and logistic regression was utilized to evaluate the “independent effect” of migration on Maternal and Child Health (MCH) service utilization.

Findings
– The level of education was higher among migrants than the natives but their income was less than that of natives. Majority of the migrant women had registered themselves for antenatal care (ANC) in the first trimester of pregnancy (55 percent) compared to the natives (21 percent), but only few had availed more than three ANC check-ups (18 percent) as compared to the natives (44 percent). Knowledge about danger signs of childhood diarrhea and pneumonia was low among migrants compared to the natives (p
<
0.0001). Health workers interacted less often with migrants (29 percent) than the natives (67 percent). After controlling the effect of socio-economic and -demographic variables, utilization of MCH care services were significantly higher among natives than the migrants. Inadequate community support among migrants led to the lower utilization of MCH care.

Research limitations/implications
– Present study reflects early ANC registration among migrants but the number of ANC visits much less than the natives. This could be further be investigated using qualitative methods.

Practical implications
– Specific strategies are required to address the health needs of migrants such as formation of community-based support groups. Health services and health workers need to be oriented to support migrants to the special needs of migrants.

Social implications
– Reduction in inequality in accessing health between natives and migrants can be addressed with social support.

Originality/value
– The study supports the fact that migration is one of the social determinants of health. Lack of community support to migrants is the major barrier in accessing the health services.