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1.  Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene 
BMC Research Notes  2014;7:953.
Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes.
The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (FST = 0.005), moderate differentiation between sali and jum (FST = 0.108) and high differentiation between jum and boro (FST = 0.230) ecotypes.
The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.
Electronic supplementary material
The online version of this article (doi:10.1186/1756-0500-7-953) contains supplementary material, which is available to authorized users.
PMCID: PMC4320456  PMID: 25547027
Boro; Ecotype; Genetic relatedness; Indigenous rice varieties; Jum; Sali
2.  The validation of Fibit Zip™ physical activity monitor as a measure of free-living physical activity 
BMC Research Notes  2014;7(1):952.
The new generation of activity monitors allow users to upload their data to the internet and review progress. The aim of this study is to validate the Fitbit Zip as a measure of free-living physical activity.
Participants wore a Fitbit Zip, ActiGraph GT3X accelerometer and a Yamax CW700 pedometer for seven days. Participants were asked their opinion on the utility of the Fitbit Zip. Validity was assessed by comparing the output using Spearman’s rank correlation coefficients, Wilcoxon signed rank tests and Bland-Altman plots. 59.5% (25/47) of the cohort were female. There was a high correlation in steps/day between the Fitbit Zip and the two reference devices (r = 0.91, p < 0.001). No statistically significant difference between the Fitbit and Yamax steps/day was observed (Median (IQR) 7477 (3597) vs 6774 (3851); p = 0.11). The Fitbit measured significantly more steps/day than the Actigraph (7477 (3597) vs 6774 (3851); p < 0.001). Bland-Altman plots revealed no systematic differences between the devices.
Given the high level of correlation and no apparent systematic biases in the Bland Altman plots, the use of Fitbit Zip as a measure of physical activity. However the Fitbit Zip recorded a significantly higher number of steps per day than the Actigraph.
PMCID: PMC4307145  PMID: 25539733
Physical activity; Pedometer; Accelerometer; Validation
3.  A validation study: assessing the reliability of the hand held StatStripXPress lactate meter to test lactate in amniotic fluid 
BMC Research Notes  2014;7(1):935.
The level of lactate in amniotic fluid may provide useful clinical information when assessing whether a woman in labour is experiencing labour dystocia. If so, a rapid, reliable method to assess the concentration of amniotic fluid lactate at the bedside will be required in order to be clinically relevant. To assess efficacy, we compared the hand held StatStripXPreass lactate meter (Nova Biomedical) to the reference laboratory analyser ABX Pentra 400 (Horiba) in a controlled environment. Baseline biological lactate concentration was measured in triplicate and samples of a known quantity of thawed amniotic fluid spiked with lactate substrate (62 mmol/L) from the LDH12 kit (Roche, SUI) to yield a predetermined lactate concentration above baseline then measured in triplicate. Deming Regression was used to determine the linear agreement and a Bland Altman plot used to determine the paired agreement across the range of values.
The mean difference with Bland-Altman plot between hand held meter and lab instrument was -1.0 mmol/L (SD 3.0 mmol/L) with 95% CI limits of agreement between -6.9 mmol/L to 4.9 mmol/L. The Deming regression co-efficient or slope of agreement was 0.91 (SD of 0.21).
The measurement of amniotic fluid lactate using the StatStripXPress hand held meter was reliable compared to reference laboratory methods for measuring lactate levels in amniotic fluid.
PMCID: PMC4300832  PMID: 25523193
Dystocia; Lactate; Amniotic fluid; Labour; Point of care
4.  From consultation to participation in public health research: reflections on a community-based research partnership 
BMC Research Notes  2014;7(1):936.
Road traffic crashes and their outcomes are substantial global public health issues and public health initiatives are increasingly involving relevant community members in order to create sustainable change. This paper describes an applied research project utilizing participatory methods to establish a road trauma support service in Western Australia and reflects on the extent of participation in the community-based research partnership. Community-based participatory research (CBPR) provided the basis for the research project conducted in partnership with 34 government and non-government agency representatives and people affected personally by road trauma and which resulted in 22 recommendations for establishing the service.
Attempts to position the group as co-researchers highlighted the dynamic interplay of factors that hinder and enable participation in participatory research. Barriers to participation within the research process included the limited time and funds, reluctance to share authorship, and a lack of clarity regarding roles and processes. Factors that enabled participation were the recognition of each member’s expertise, providing different forms and methods of communication, and the reimbursement of costs according to role.
In May 2012, the Government of Western Australia announced it would fund the recommendations and Road Trauma Support Western Australia was launched in November 2013. Notwithstanding this successful outcome, there were varied experiences of participation in the research process, and this was despite the use of a research methodology that is by definition participatory, with explicit and embedded participatory structures and processes. The research project shows that elements of CBPR can be incorporated into public health research, even in projects with externally-imposed time and budget constraints.
PMCID: PMC4302106  PMID: 25527083
Participatory action research; Community-based participatory research; Trauma; Injury; Bereavement; Consumer involvement
5.  The extracellular N-terminal domain of G-protein coupled receptor 83 regulates signaling properties and is an intramolecular inverse agonist 
BMC Research Notes  2014;7(1):913.
Recently, the orphan G-protein coupled receptor 83 (GPR83) was identified as a new participant in body weight regulation. This receptor is highly expressed in the hypothalamic arcuate nucleus and is regulated in response to nutrient availability. Gpr83 knock-out mice are protected from diet-induced obesity. Moreover, in a previous study, we designed and characterized several artificial constitutively activating mutations (CAMs) in GPR83. A particular CAM was located in the extracellular N-terminal domain (eNDo) that is highly conserved among GPR83 orthologs. This suggests the contribution of this receptor part into regulation of signaling, which needed a more detailed investigation.
In this present study, therefore, we further explored the role of the eNDo in regulating GPR83-signaling and demonstrate a proof-of-principle approach in that deletion mutants are characterized by a strong increase in basal Gq/11-mediated signaling, whilst none of the additionally characterized signaling pathways (Gs, Gi, G12/13) were activated by the N-terminal deletion variants. Of note, we detected basal GPR83 MAPK-activity of the wild type receptor, which was not increased in the deletion variants.
Finally, the extracellular portion of GPR83 has a strong regulatory function on this receptor. A suppressive - inverse agonistic - effect of the eNDo on GPR83 signaling activity is demonstrated here, which also suggests a putative link between extracellular receptor activation and proteolytic cleavage. These new insights highlight important aspects of GPR83-regulation and might open options in the development of tools to modulate GPR83-signaling.
PMCID: PMC4300838  PMID: 25516095
G-protein coupled receptor 83; Signaling mechanism; Inverse agonist; Antagonist; Constitutive activation
6.  Different conceptual constructs for modelling sedentary behaviour and physical activity: the impact on the correlates of behaviour 
BMC Research Notes  2014;7(1):921.
Research on the correlates of physical activity (PA) and sedentary behaviour (SB) to date has used independent prediction equations for each behaviour, without considering that they are both part of the same continuum of movement. This assumption of independence might lead to inaccurate estimates because common underlying latent variables may simultaneously influence the propensity to engage in PA and SB. This study tests empirically the interdependent nature of PA and SB by comparing independent equations (current approach in the literature), and joint estimators (a novel but unexplored approach). Using Health Survey for England 2008 data, accelerometry-accessed PA and SB were separately modelled (using ordinary least squared regressions - OLS) and then jointly (using seemingly unrelated regressions -SUR). We tested for diagonality, specification, and goodness of fit.
The best fit models were the ones that allowed for interdependence of the two movement-related behaviours (rho = −0.156; p < 0.001). The SUR showed more favourable properties compared to OLS models; producing lower standard errors and more consistent and efficient coefficients. The efficiency gain was more pronounced in the SB equation (Chi2 = 92.75; p < 0.001).
Evidence from a large national population-wide accelerometry study suggests that accounting for the interdependent nature of PA and SB in prediction equations leads to more efficient modelling estimates. Further research using different samples is, however, required to fully understand the magnitude of efficiency gains accruable from using the joint estimators.
PMCID: PMC4301058  PMID: 25515233
7.  Implementing an electronic medication overview in Belgium 
BMC Research Notes  2014;7(1):915.
An accurate medication overview is essential to reduce medication errors. Therefore, it is essential to keep the medication overview up-to-date and to exchange healthcare information between healthcare professionals and patients. Digitally shared information yields possibilities to improve communication. However, implementing a digitally shared medication overview is challenging. This articles describes the development process of a secured, electronic platform designed for exchanging medication information as executed in a pilot study in Belgium, called “Vitalink”.
The goal of “Vitalink” is to improve the exchange of medication information between professionals working in healthcare and patients in order to achieve a more efficient cooperation and better quality of care. Healthcare professionals of primary and secondary health care and patients of four Belgian regions participated in the project. In each region project groups coordinated implementation and reported back to the steering committee supervising the pilot study. The electronic medication overview was developed based on consensus in the project groups. The steering committee agreed to establish secured and authorized access through the use of electronic identity documents (eID) and a secured, eHealth-platform conform prior governmental regulations regarding privacy and security of healthcare information.
A successful implementation of an electronic medication overview strongly depends on the accessibility and usability of the tool for healthcare professionals. Coordinating teams of the project groups concluded, based on their own observations and on problems reported to them, that secured and quick access to medical data needed to be pursued. According to their observations, the identification process using the eHealth platform, crucial to ensure secured data, was very time consuming. Secondly, software packages should meet the needs of their users, thus be adapted to daily activities of healthcare professionals. Moreover, software should be easy to install and run properly. The project would have benefited from a cost analysis executed by the national bodies prior to implementation.
PMCID: PMC4301824  PMID: 25516258
General practice/family medicine; Quality of care; Health care organisation and management; Communication; Pharmacotherapy
8.  The multiple sclerosis visual pathway cohort: understanding neurodegeneration in MS 
BMC Research Notes  2014;7(1):910.
Multiple Sclerosis (MS) is an immune-mediated disease of the Central Nervous System with two major underlying etiopathogenic processes: inflammation and neurodegeneration. The latter determines the prognosis of this disease. MS is the main cause of non-traumatic disability in middle-aged populations.
The MS-VisualPath Cohort was set up to study the neurodegenerative component of MS using advanced imaging techniques by focusing on analysis of the visual pathway in a middle-aged MS population in Barcelona, Spain. We started the recruitment of patients in the early phase of MS in 2010 and it remains permanently open. All patients undergo a complete neurological and ophthalmological examination including measurements of physical and disability (Expanded Disability Status Scale; Multiple Sclerosis Functional Composite and neuropsychological tests), disease activity (relapses) and visual function testing (visual acuity, color vision and visual field). The MS-VisualPath protocol also assesses the presence of anxiety and depressive symptoms (Hospital Anxiety and Depression Scale), general quality of life (SF-36) and visual quality of life (25-Item National Eye Institute Visual Function Questionnaire with the 10-Item Neuro-Ophthalmic Supplement). In addition, the imaging protocol includes both retinal (Optical Coherence Tomography and Wide-Field Fundus Imaging) and brain imaging (Magnetic Resonance Imaging). Finally, multifocal Visual Evoked Potentials are used to perform neurophysiological assessment of the visual pathway.
The analysis of the visual pathway with advance imaging and electrophysilogical tools in parallel with clinical information will provide significant and new knowledge regarding neurodegeneration in MS and provide new clinical and imaging biomarkers to help monitor disease progression in these patients.
PMCID: PMC4300678  PMID: 25512202
Multiple Sclerosis; Visual pathway; Neurodegeneration; Cohort studies
9.  Experimental validation of predicted subcellular localizations of human proteins 
BMC Research Notes  2014;7(1):912.
Computational methods have been widely used for the prediction of protein subcellular localization. However, these predictions are rarely validated experimentally and as a result remain questionable. Therefore, experimental validation of the predicted localizations is needed to assess the accuracy of predictions so that such methods can be confidently used to annotate the proteins of unknown localization. Previously, we published a method called ngLOC that predicts the localization of proteins targeted to ten different subcellular organelles. In this short report, we describe the accuracy of these predictions using experimental validations.
We have experimentally validated the predicted subcellular localizations of 114 human proteins corresponding to nine different organelles in normal breast and breast cancer cell lines using live cell imaging/confocal microscopy. Target genes were cloned into expression vectors as GFP fusions and cotransfected with RFP-tagged organelle-specific gene marker into normal breast epithelial and breast cancer cell lines. Subcellular localization of each target protein is confirmed by colocalization with a co-expressed organelle-specific protein marker. Our results showed that about 82.5% of the predicted subcellular localizations coincided with the experimentally validated localizations. The highest agreement was found in the endoplasmic reticulum proteins, while the cytoplasmic location showed the least concordance. With the exclusion of cytoplasmic location, the average prediction accuracy increased to 90.4%. In addition, there was no difference observed in the protein subcellular localization between normal and cancer breast cell lines.
The experimentally validated accuracy of ngLOC method with (82.5%) or without cytoplasmic location (90.4%) nears the prediction accuracy of 89%. These results demonstrate that the ngLOC method can be very useful for large-scale annotation of the unknown subcellular localization of proteins.
Electronic supplementary material
The online version of this article (doi:10.1186/1756-0500-7-912) contains supplementary material, which is available to authorized users.
PMCID: PMC4301851  PMID: 25510246
Protein subcellular localization; ngLOC prediction; Gene cloning; Experimental validation; GFP fusion; Live cell imaging/confocal microscopy
10.  Efficacy and tolerability of a low-dose, 2-week administration of sunitinib followed by a week rest (2/1 schedule) for metastatic renal cell carcinoma: a single center experience of six cases 
BMC Research Notes  2014;7(1):872.
Sunitinib, an oral multitarget tyrosine kinase inhibitor and standard first-line treatment for metastatic renal cell carcinoma (mRCC), is generally administered on a 6-week schedule (4 weeks on/2 weeks off). However, drug toxicity often leads to temporary treatment interruption, resulting in reduced treatment efficacy. In this report, we investigated whether sunitinib administration of at a dose of 25 mg/day in a 2-weeks-on/1-week-off cycle would reduce the incidence of drug-related side effects while maintaining drug efficacy.
A total of six patients with mRCC were orally administered sunitinib at a dose of 25 mg/day in a 2-weeks-on/1-week-off regimen until intolerable toxicities occurred. All enrolled patients were assessed for toxicity and response. The median treatment period was 24 months (range, 9–40 months). Objective responses were as follows: disease stabilization of >6 months was achieved in all patients. The most important toxicities were neutropenia, fatigue, and proteinuria, but all were controlled.
Oral sunitinib at 25 mg/day in a 2-weeks-on/1-week-off regimen to Japanese patients can avoid drug-related toxicities while achieving the same dose intensity as a 6-week schedule. Because these data were derived from a small number of patients, future prospective studies of modified sunitinib administration schedules are warranted.
PMCID: PMC4289163  PMID: 25471941
Sunitinib; Metastatic renal cell carcinoma; Renal cancer medical treatment; Treatment toxicity; Tyrosine kinase inhibitors
11.  Testing the sexual imagination hypothesis for gender differences in response to infidelity 
BMC Research Notes  2014;7(1):860.
Evolutionary psychologists hypothesized that men are more upset by sexual infidelity than women are, whereas women are more upset by emotional infidelity than men are. On the other hand, the sexual imagination hypothesis states that gender differences in infidelity responses are derived from explicit men’s sexual imagery. Based on the latter hypothesis, we hypothesized that although men would report being more distressed by sexual infidelity than women who were not in a committed relationship (NCR), no gender difference would be reported in a committed relationship (CR).
These two hypotheses were tested with 598 participants in a CR and 1,643 participants in a NCR. No significant gender difference was found sexual infidelity response in the CR group (d = 0.008, a power of .956), whereas men were more upset than women about sexual infidelity in the NCR group. Moreover, a significant interaction between gender and infidelity type was found in the NCR, whereas no significant interaction between gender and infidelity type was observed in the CR group (partial η2 = 0.005, a power of .943).
Our findings supported the sexual imagination hypothesis but were inconsistent with the EJM hypothesis.
PMCID: PMC4258009  PMID: 25432800
Sexual infidelity; Jealousy; Evolutionary psychology; Sexual imagination hypothesis; Gender difference
12.  The novel surfactant protein SP-H enhances the phagocytosis efficiency of macrophage-like cell lines U937 and MH-S 
BMC Research Notes  2014;7(1):851.
Surfactant proteins (SP) secreted by alveolar type 2 cells, play an essential role in maintaining the air-liquid barrier of the lung and are also involved in the opsonisation and clearance of bacteria by phagocytes. We have recently described a novel surfactant protein, SP-H (SFTA3). Expression of SP-H was earlier demonstrated to be upregulated by LPS and negatively regulated by IL-1β and IL-23 in vitro. The influence of SP-H on phagocytosis was measured using a murine and a human phagocytic cell line and fluorescent latex beads.
SP-H markedly increases phagocytosis in vitro in the murine-derived alveolar macrophage cell lines MH-S and in human-derived differentiated U937 cells.
It can be assumed that SP-H is involved in regulating phagocytic activity of macrophages. SP-H is a new player in pulmonary host defence.
PMCID: PMC4256058  PMID: 25427765
13.  First-generation linkage map for the European tree frog (Hyla arborea) with utility in congeneric species 
BMC Research Notes  2014;7(1):850.
Western Palearctic tree frogs (Hyla arborea group) represent a strong potential for evolutionary and conservation genetic research, so far underexploited due to limited molecular resources. New microsatellite markers have recently been developed for Hyla arborea, with high cross-species utility across the entire circum-Mediterranean radiation. Here we conduct sibship analyses to map available markers for use in future population genetic applications.
We characterized eight linkage groups, including one sex-linked, all showing drastically reduced recombination in males compared to females, as previously documented in this species. Mapping of the new 15 markers to the ~200 My diverged Xenopus tropicalis genome suggests a generally conserved synteny with only one confirmed major chromosome rearrangement.
The new microsatellites are representative of several chromosomes of H. arborea that are likely to be conserved across closely-related species. Our linkage map provides an important resource for genetic research in European Hylids, notably for studies of speciation, genome evolution and conservation.
Electronic supplementary material
The online version of this article (doi:10.1186/1756-0500-7-850) contains supplementary material, which is available to authorized users.
PMCID: PMC4258042  PMID: 25430653
Conservation; Heterochiasmy; Hylid frogs; Microsatellites; Population genetics; Recombination; Transcriptome
14.  Frequency distribution of genes encoding aminoglycoside modifying enzymes in uropathogenic E. coli isolated from Iranian hospital 
BMC Research Notes  2014;7(1):842.
Escherichia coli is considered as the most common cause of urinary tract infection (UTI) and acquired multiple resistances to a wide range of antibiotics such as aminoglycosides. Enzymatic alteration of aminoglycosides (AMEs) by aminoglycoside- modifying enzymes is the main mechanism of resistance to these antibiotics in E. coli. The aim of this study was detection and investigation of frequency of genes encoding aminoglycoside modifying enzymes (aac(3)-IIa and ant(2′′)-Ia) in UPEC isolated from hospitalized patients in teaching hospital of Tehran, Iran.
A total of 276 UPEC were obtained from Urine samples in a hospital from Tehran. Antibiotic susceptibility to aminoglycosides was determined by disk diffusion method according CLSI guidelines in UPEC isolates. MICs of target antibiotics were determined by agar dilution method. All isolates were screened for the presence of the AMEs genes using the PCR. The results of disk diffusion showed 21%, 24.6%, 23.18%, 3.62% and 6.15% of isolates were resistant to Gentamicin, Tobramycin, Kanamicin, Amikacin and Netilmicin respectively. The agar dilution’s results (MICs) were high, 66.19% for Gentamicin. The aac (3)-IIa and ant(2″)-Ia genes were detected in (78.87%) and 47.88% of isolates respectively.
This study shows the high frequency of genes encoding (AMEs) aac(3)-IIa and ant(2”)-Ia genes and their relationship between different aminoglycoside resistance phenotypes.
PMCID: PMC4258249  PMID: 25424607
UPEC; Aminoglycoside modifying enzymes and UTI
15.  A review of software for analyzing molecular sequences 
BMC Research Notes  2014;7(1):830.
Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454 sequencers and Illumina platforms are available. But for a new researcher, it is difficult to know which package to choose. We present a systematic review of packages for the analysis of molecular sequences used to describe and compare microbial communities. This review gives students and researchers information to help choose the best analytic pipeline for their project. To the best of our knowledge, this is the first review of such software.
Seven software packages met our inclusion criteria of being cost free and publically available, offering analysis functions from platform sequencing to results presentation, and included documentation and data security. We installed and executed each of the software packages and describe the installation, documentation, features, and functions of each.
For the user, pipeline choices may be limited because some packages only run on select operating systems. Users should be aware of the availability of features and functions of each package. Of utmost importance is that the user must be aware of the default settings and underlying assumptions of each function. All packages are lacking sufficient methods for longitudinal analysis.
Researchers can do well using any one of these seven packages. However, two packages are outstanding; mothur and QIIME, due not only to the comprehensive suite of functions and procedures incorporated into the pipelines but also because of the accompanying documentation.
PMCID: PMC4258797  PMID: 25421430
Microbiome; Molecular sequencing; Analytic pipelines; 16S gene
16.  Zoonotic parapoxviruses detected in symptomatic cattle in Bangladesh 
BMC Research Notes  2014;7(1):816.
Application of molecular diagnostic methods to the determination of etiology in suspected poxvirus-associated infections of bovines is important both for the diagnosis of the individual case and to form a more complete understanding of patterns of strain occurrence and spread. The objective of this study was to identify and characterize bovine-associated zoonotic poxviruses in Bangladesh which are relevant to animal and human health.
Investigators from the International Center Diarrhoeal Disease Research (icddr,b), the US Centers for Disease Control and Prevention (CDC), and the Bangladesh Department of Livestock Services traveled to three districts in Bangladesh—Siranjganj, Rangpur and Bhola–to collect diagnostic specimens from dairy cattle and buffalo that had symptoms consistent with poxvirus-associated infections. Bovine papular stomatitis virus (BPSV) DNA was obtained from lesion material (teat) and an oral swab collected from an adult cow and calf (respectively) from a dairy production farm in Siranjganj. Pseudocowpox virus (PCPV) DNA signatures were obtained from a scab and oral swab collected from a second dairy cow and her calf from Rangpur.
We report the first detection of zoonotic poxviruses from Bangladesh and show phylogenetic comparisons between the Bangladesh viruses and reference strains based on analyses of the B2L and J6R loci (vaccinia orthologs). Understanding the range and diversity of different species and strains of parapoxvirus will help to spotlight unusual patterns of occurrence that could signal events of significance to the agricultural and public health sectors.
PMCID: PMC4246640  PMID: 25410770
Bangladesh; Bovine papular stomatitis virus; Parapoxvirus; Zoonosis; Pseudocowpox virus
17.  Operational research capacity building using ‘The Union/MSF’ model: adapting as we go along 
BMC Research Notes  2014;7(1):819.
We have conducted 23 operational research (OR) courses since 2009, based on ‘The Union/ Médecins Sans Frontières (MSF)’ model, now popularly known as SORT-IT (Structured Operational Research and Training Initiative) model - wherein participants are mentored through the whole research process from protocol development (module 1) to data analysis (module 2) to publication (module 3) over a period of 9–12 months. We have faced a number of challenges including shortage of time, especially for data analysis and interpretation, and a heavy mentorship burden on limited numbers of experienced facilitators. To address these challenges, we have made several modifications to the structure of the OR course. In this article, we describe the revised structure and our experience (successes and challenges) of implementing it in Asia in 2013.
The key changes introduced included extending the duration of the course modules (by a day each in module 1 and 2 and by three days in module 3), increasing the numbers of facilitators and standardizing milestones related to data entry and analysis. We successfully implemented this revised structure in the second Asian OR Course held in Nepal in 2013. Eleven of twelve participants successfully completed all the milestones and submitted 13 scientific manuscripts (two participants completed two projects) to international peer-reviewed journals. Though, this posed two challenges – increased costs and increased time away for faculty and participants.
The revised structure of ‘The Union/MSF’ model of OR capacity building addressed previous issues of insufficient time and overburdened mentors and we intend to continue with this model for future courses.
PMCID: PMC4253003  PMID: 25409542
Operational research; Training; Asia; Capacity building; SORT IT
18.  Proteolytic activity of the nematophagous fungus Arthrobotrys sinensis on Angiostrongylus vasorum larvae 
BMC Research Notes  2014;7(1):811.
The predatory nematophagous fungus Arthrobotrys sinensis (SF53) produces three proteases with nematicidal activity when grown on solid media culture. However, the proteolytic profile produced by this fungus, when grown in liquid culture medium remains unknown.
Thus, the objective of this work was to evaluate the production of proteases from nematophagous fungus Arthrobotrys sinensis in liquid medium and its nematicidal activity on first stage larvae of A. vasorum. Proteases were obtained in its crude form, using Whatman no.1 filter paper, followed by centrifugation for 5 min at 10 × g and 4°C. A zymogram was performed with co-polymerized casein in an acrylamide gel as substrate. An in vitro assay to evaluate the nematicidal action of the proteases of A. sinensis (SF53) produced in liquid medium on A. vasorum L1 was conducted. By the analysis of the zymogram, it was observed a single halo at the beginning of digestion of the gel, suggesting that the three proteases of SF53 are produced in an enzymatic complex of large molecular weight. Regarding nematicidal activity, within 24 hours, the proteases produced in liquid medium of A. sinensis (SF53) showed a percentage reduction of 64% on the number of L1 of A. vasorum.
In the present work, it is suggested that the three proteases of SF53 are produced in an enzymatic complex and was also demonstrated that these enzymes were effective in destroying A. vasorum L1.
PMCID: PMC4242478  PMID: 25406419
Nematophagous fungi; Angiostrongylus vasorum; Protease
19.  Na/K-ATPase assay in the intact mice lung subjected to perfusion 
BMC Research Notes  2014;7(1):798.
Among the characteristics of acute respiratory distress syndrome (ARDS) is edema formation and its resolution depends on pneumocyte Na/K-ATPase activity. Increased concentration of oleic acid (OA) in plasma induces lung injury by targeting Na/K-ATPase and, thus, interfering in sodium transport.
Presently, we adapted a radioactivity-free assay to detect Na/K-ATPase activity in perfused lung mice, comparing the inhibitory effect of ouabain and OA. We managed to perfuse only the lung, avoiding the systemic loss of rubidium. Rb+ incorporation into lung was measured by inductively coupled plasma optical emission spectrometry (ICP OES) technique, after lung tissue digestion. Na/K-ATPase activity was the difference between Rb+ incorporation with or without ouabain. Lung Na/K-ATPase was completely inhibited by perfusion with ouabain. However, OA caused a partial inhibition.
In the present work the amount of incorporated Rb+ was greater than seen in our previous report, showing that the present technique is trustworthy. This new proposed assay may allow researchers to study the importance of Na/K-ATPase activity in lung pathophysiology.
PMCID: PMC4242599  PMID: 25399325
Lung; Na/K-ATPase; Inductively coupled plasma optical emission spectrometer
20.  Ophthalmic infections in children presenting to Angkor Hospital for Children, Siem Reap, Cambodia 
BMC Research Notes  2014;7(1):784.
Ophthalmic infections cause significant morbidity in Cambodian children but aetiologic data are scarce. We investigated the causes of acute eye infections in 54 children presenting to the ophthalmology clinic at Angkor Hospital for Children, Siem Reap between March and October 2012.
The median age at presentation was 3.6 years (range 6 days – 16.0 years). Forty two patients (77.8%) were classified as having an external eye infection, ten (18.5%) as ophthalmia neonatorum, and two (3.7%) as intra-ocular infection. Organisms were identified in all ophthalmia neonatorum patients and 85.7% of patients with an external eye infection. Pathogens were not detected in either of the intra-ocular infection patients. Most commonly isolated bacteria were Staphylococcus aureus (23 isolates), coagulase-negative staphylococci (13), coliforms (7), Haemophilus influenzae/parainfluenzae (6), Streptococcus pneumoniae (4), and Neisseria gonorrhoeae (2). Chlamydia trachomatis DNA was detected in 60% of swabs taken from ophthalmia neonatorum cases.
This small study demonstrates the wide range of pathogens associated with common eye infections in Cambodian children. The inclusion of molecular assays improved the spectrum of detectable pathogens, most notably in neonates.
PMCID: PMC4228269  PMID: 25369774
Paediatric; Ophthalmic; Infection; Chlamydia
21.  Effects of senktide, a neurokinin 3 receptor agonist, on luteinizing hormone secretion and follicular development in anestrous Shiba goats: a pilot study 
BMC Research Notes  2014;7(1):773.
Recent studies suggest that neurokinin B and its receptor, neurokinin 3 receptor, have an essential role in the regulation of gonadotropin-releasing hormone and luteinizing hormone (LH) release in several mammalian species. As the first trial, this pilot study reports the effect of intravenous treatment with senktide, a selective agonist of neurokinin 3 receptor, on LH secretion, follicular development in female goats that were clinically diagnosed with anestrus.
Anestrous goats were intravenously administered 200 nmol senktide at 4-h intervals for 24 h. Most of them examined (5/6 cases) showed a pulsatile increase in LH secretion after each injection of senktide, whereas the remaining one case showed a surge-like increase of LH secretion. Ovulation was confirmed in 5/6 cases at the range of 48–96 h after the beginning of treatment.
This pilot study demonstrated that intravenous treatment with senktide has therapeutic action in goats with anestrus by inducing LH release, which could promote follicular development and ovulation.
PMCID: PMC4228059  PMID: 25362998
Anestrus; Goats; Senktide; LH; Ovulation
22.  Cytomegalovirus viral and antibody correlates in young children 
BMC Research Notes  2014;7(1):776.
Young, healthy children shedding cytomegalovirus (CMV) in urine and saliva appear to be the leading source of CMV in primary infection of pregnant women.
We screened 48 children 6 months – 5 years old for CMV IgG and measured levels of CMV IgG, IgM and IgG avidity antibodies, frequency of CMV shedding, and viral loads in blood, urine, and saliva. Thirteen of the 48 children (27%) were CMV IgG positive, among whom 3 were also CMV IgM positive with evidence of recent primary infection. Nine of the 13 seropositive children (69%) were shedding 102-105 copies/ml of CMV DNA in one or more bodily fluid. Among seropositive children, low IgG antibody titer (1:20–1:80) was associated with the absence of shedding (p = 0.014), and enrollment in daycare was associated with the presence of CMV shedding (p = 0.037).
CMV antibody profiles correlated with CMV shedding. The presence of CMV IgM more often represents primary infection in children than in adults. Correlating antibodies with primary infection and viral shedding in healthy children adds to the understanding of CMV infection in children that can inform the prevention of CMV transmission to pregnant women.
PMCID: PMC4236479  PMID: 25367101
Cytomegalovirus; Viral load; Serology; Avidity
23.  Reproducibility of exhaled nitric oxide measurements in overweight and obese adults 
BMC Research Notes  2014;7(1):775.
Exhaled nitric oxide is a noninvasive measure of airway inflammation that can be detected by a handheld device. Obesity may influence the reproducibility of exhaled nitric oxide measurements, by - for instance – decreased expiratory reserve volume.
We analyzed triple exhaled nitric oxide measurements from 553 participants (aged 45 to 65 years with a body mass index ≥27 kg/m2) of the Netherlands Epidemiology of Obesity Study. The interclass correlation coefficient (single measurement reliability) was 0.965 (95% CI: 0.960, 0.970).
We conclude that for assessment of exhaled nitric oxide in large cohorts of overweight and obese adults a single measurement suffices.
PMCID: PMC4237750  PMID: 25366981
Reproducibility; Exhaled nitric oxide; Obesity
24.  Growth differentiation Factor 11 is an encephalic regionalizing factor in neural differentiated mouse embryonic stem cells 
BMC Research Notes  2014;7(1):766.
The central nervous system has a complex structural organization and consists of different subdomains along the antero-posterior axis. However, questions remain about the molecular mechanisms leading to the regionalization of this organ. We used a previously developed methodology to identify the novel patterning role of GDF11, a TGF-β signaling factor.
Using an assay based on neural differentiated mouse embryonic stem cells, GDF11 is shown to induce diencephalic (posterior forebrain), mesencephalic (midbrain) and metencephalic (anterior hindbrain) fates at the expense of telencephalic (anterior forebrain) specification. GDF11 has not previously been implicated in the early patterning of the nervous system. In addition, inhibition of the TGF-β type I receptors Alk4, Alk5 and Alk7 by the pharmacological inhibitor SB431542 caused a strong anteriorization of the cells.
Our findings suggest that GDF11 is involved in the earliest steps of the brain patterning during neurogenesis in the vertebrate embryo and is shown to be a regionalizing factor of the regional fate in the developing brain. This regionalization is not a typical posteriorizing signal as seen with retinoic acid, FGF or BMP molecules. To our knowledge, this is the first time that GDF11 is implicated in the earliest steps of the patterning of the neural plate.
PMCID: PMC4228095  PMID: 25352416
Mouse ES cells; Brain patterning; GDF11
25.  Photosynthetic carbon from algal symbionts peaks during the latter stages of embryonic development in the salamander Ambystoma maculatum 
BMC Research Notes  2014;7(1):764.
It was recently discovered that symbiotic algae in the eggs of the salamander Ambystoma maculatum translocate fixed carbon from photosynthesis to developing embryos. Fixed carbon translocation was shown in embryos at one time point during development, however, it was unknown if fixed carbon translocation occurs throughout all developmental stages.
In this study, fixed carbon translocation was measured in salamander eggs at six time points over the latter half of development. Fixed carbon translocation did not occur until the middle tailbud portion of development (stages 26–30), and translocation was measured in 20% or less of eggs sampled. Peak carbon translocation occurred during the late tailbud phase of development (stages 31–35), where as much as 87% of eggs sampled showed translocation, and average percent translocation was 6.5%. During the final stages of development, fixed carbon translocation declined, and translocation was not detected in embryos five days prior to hatching.
The onset of fixed carbon translocation from Oophila to A. maculatum embryos during the second half of embryonic development is likely due to the corresponding settlement and concentration of Oophila in the inner egg envelope. In addition, carbon translocation ceases in late stage embryos as the inner egg envelope thins and ruptures in preparation for hatching.
PMCID: PMC4221728  PMID: 25348817
Algae; Symbiosis; Salamander; Carbon translocation

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