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26.  Genetic polymorphism at an odorant receptor gene (Or39) among mosquitoes of the Anopheles gambiae complex in Senegal (West Africa) 
BMC Research Notes  2014;7:321.
Olfaction plays a significant role in insect behavior during critical steps of their life-cycle, such as host-seeking during foraging or the search for a mate. Here, we explored genetic polymorphism within and divergence between sibling species of the African malaria mosquito, Anopheles gambiae sensu lato in the gene sequence and encoded peptides of an odorant receptor, Or39. This study included sympatric specimens of An. gambiae sensu stricto, An. coluzzii and An. arabiensis sampled together in the village of Dielmo, Senegal.
A 1,601 bp genomic sequence composed of 6 exons and 5 introns was obtained for Or39 from 6–8 mosquitoes in each of the 3 species. DNA sequence analysis revealed a high level of molecular polymorphism (π = 0.0154; Haplotype diversity = 0.867) and high overall genetic differentiation between taxa (Fst > 0.92, P < 0.01). In total, 50 parsimony informative sites were recorded. Throughout the whole dataset, there were 13 non-synonymous mutations resulting in aminoacid changes in the encoded protein. Each of the 6 different identified peptides was species-specific and none was shared across species. Most aminoacid changes were located on the intracellular domains of the protein. However, intraspecific polymorphisms in An. gambiae and An. arabiensis as well as species-specific mutations also occurred in the first extracellular domain.
Although obtained from a limited number of specimens, our results point towards genetic differences between cryptic species within the An. gambiae complex in a gene of biological relevance that might be of evolutionary significance when exposed to disruptive selective forces.
PMCID: PMC4048261  PMID: 24886539
Mosquito; Malaria; Anopheles gambiae; Speciation; Olfactory receptor
27.  Life-space mobility assessment in older people in Finland; measurement properties in winter and spring 
BMC Research Notes  2014;7:323.
Life-space mobility refers to the spatial area an individual moves through, the frequency and need for assistance. Based on the assumption that measurement scale properties are context-specific, we tested the scale distribution, responsiveness, and reproducibility of the 15-item University of Alabama at Birmingham Study of Aging Life-Space Assessment in older people in Finland, specifically accounting for season.
Community-dwelling older men and women in central Finland aged 75-90 years were interviewed to determine life-space mobility (score range 0-120). Baseline (January-June 2012) and one-year follow-up data (January-June 2013; n = 806) from the cohort study “Life-space mobility in old age” were used to investigate the scale distribution and responsiveness over a period of one year. In addition, with a sub-sample in conjunction with the one-year follow-up, we collected data to study the two-week test-retest reproducibility (n = 18 winter and n = 21 spring 2013).
The median life-space mobility score at baseline was 64. The median change in score over the one-year follow-up was zero. However, participants reporting a decline in health (repeated measures ANOVA p = .016) or mobility (p = .002) status demonstrated a significantly larger decrease in life-space mobility score than those reporting no or positive changes over the year. The two-week intra-class correlation (ICC) coefficient was .72. Lower ICC was found in the winter than in the spring sample and for items that represent higher life-space levels.
The test-retest reproducibility of the Life-Space Assessment was fair but somewhat compromised in the winter. Mobility of older people at the life-space levels of “town” and “beyond town” may be more variable. Life-space mobility was responsive to change, regardless of season. Further study is warranted to obtain insight in the factors contributing to seasonal effects.
PMCID: PMC4055210  PMID: 24886670
Reliability; Scale; Methods; Psychometrics; Mobility; Life-space; Aging; Season
28.  Changes in public health preparedness services provided to local health departments by regional offices in North Carolina: a comparison of two cross-sectional studies 
BMC Research Notes  2014;7:319.
In 2011, seven decentralized Public Health Regional Surveillance Teams (PHRSTs) were restructured into four centralized Public Health Preparedness and Response (PHP&R) regional offices to realign preparedness priorities and essential services with appropriate infrastructure; field-based staff was reduced, saving approximately $1 million. The objective of this study was to understand the impact that restructuring had on services provided to local health departments (LHDs) throughout North Carolina.
A survey to document services that regional offices provide to LHDs in North Carolina was administered by the North Carolina Preparedness and Emergency Response Research Center in 2013. The results were compared to a similar survey from 2009, which identified services provided by regional teams prior to restructuring.
Of 69 types of assistance, 14 (20%) were received by 50% or more LHDs in 2012. Compared to 2009, there was a significant decrease in the proportion of LHDs receiving 67% (n = 47) of services. The size of the region served by regional offices was shown to inversely impact the proportion of LHDs receiving services for 25% of services. There was a slight significant decline in perceived quality of the services provided by regional teams in 2012 as comparison to 2009.
Following a system-wide review of preparedness in North Carolina, the state’s regional teams were reorganized to refine their focus to planning, exercises, and training. Some services, most notably under the functions of epidemiology and surveillance and public health event response, are now provided by other state offices. However, the study results indicate that several services that are still under the domain of the regional offices were received by fewer LHDs in 2012 than 2009. This decrease may be due to the larger number of counties now served by the four regional offices.
PMCID: PMC4047551  PMID: 24886311
Public health; Preparedness; Regionalization
29.  Vincristine-induced vocal cord palsy and successful re-treatment in a patient with diffuse large B cell Lymphoma: a case report 
BMC Research Notes  2014;7:318.
Vincristine, a type of vinca alkaloid, is widely used in the treatment of various childhood and adult malignancies. A well-known side effect of vincristine is its neurotoxicity and it is rarely indicted in vagus nerve involvement. Vincristine induced vocal cord palsy is a potentially reversible condition, with the mainstay of therapy being withdrawal of the offending drug. However, there are no clear guidelines regarding the possibility of re-treatment with the causative agent.
Case presentation
A 58 year old Asian male presented with constipation and abdominal distension. Diagnostic investigations revealed stage IVB diffuse large B cell lymphoma (DLBCL). The patient was subsequently started on R-CHOP (Rituximab, Cyclophosphamide, Doxorubicin, Vincristine, and Prednisolone). On day twelve of receiving course four of R-CHOP, our patient presented to the hospital with a history of hoarseness of voice. Clinical and radiological examination revealed bilateral vocal cord palsy. Tracheostomy was done in view of a compromised airway. The patient subsequently went on to receive two more cycles of R-CHOP. Two weeks later Flexible laryngoscopy showed no lesion and the vocal cords were moving normally. The tracheostomy was removed. His voice has improved since and the patient is currently in remission.
The occurrence of vincristine induced vocal cord palsy has been well reported in the literature. We strongly believe that our patient developed vocal cord palsy secondary to vincristine. The uniqueness of our patient’s case lies in successful re-treatment of our patient with the offending drug. To the best of our knowledge this is the third instance where a patient was successfully re-treated with vincristine after having developed vocal cord palsy as a result of its use.
PMCID: PMC4045940  PMID: 24886197
Vincristine; Vocal cord palsy; Re-treatment
30.  Combined effect of teriparatide and low-intensity pulsed ultrasound for nonunion: a case report 
BMC Research Notes  2014;7:317.
Low-intensity pulsed ultrasound is a pain-free therapy performed daily at home by the patient and has been shown to promote fracture healing. Teriparatide is a parathyroid hormone preparation that activates osteoblastic bone formation and is also reported to be effective in promoting bony union.
Case presentation
We report the case of a 56-year-old Japanese male with a femoral shaft fracture who underwent intramedullary osteosynthesis nailing initially. He had no radiologic or clinical sign of healing 3 months later and low-intensity pulsed ultrasound was initiated at that time. He was reassessed in another 3 months, with evidence of mild bone consolidation but the fracture gap persisted. Subsequent treatment with human parathyroid hormone was initiated in combination with low-intensity pulsed ultrasound. Full fracture healing was present 6 months after beginning the combination low-intensity pulsed ultrasound and teriparatide. It is hypothesized that the potential additive effects of low-intensity pulsed ultrasound and teriparatide therapy ultimately triggered sufficient bone formation to support osseous union.
The case reported herein is a femoral shaft atrophic nonunion in which traditional interventions failed. Successful fracture healing was finally achieved with low-intensity pulsed ultrasound and teriparatide therapy. This is the first reported case of diaphyseal nonunion with deterioration of bone quality in long bones resolved with teriparatide and low-intensity pulsed ultrasound.
PMCID: PMC4059730  PMID: 24886079
Teriparatide; Low-intensity pulsed ultrasound (LIPUS); Nonunion; Bone quality
31.  GFF-Ex: a genome feature extraction package 
BMC Research Notes  2014;7:315.
Genomic features of whole genome sequences emerging from various sequencing and annotation projects are represented and stored in several formats. Amongst these formats, the GFF (Generic/General Feature Format) has emerged as a widely accepted, portable and successfully used flat file format for genome annotation storage. With an increasing interest in genome annotation projects and secondary and meta-analysis, there is a need for efficient tools to extract sequences of interests from GFF files.
We have developed GFF-Ex to automate feature-based extraction of sequences from a GFF file. In addition to automated sequence extraction of the features described within a feature file, GFF-Ex also assigns boundaries for the features (introns, intergenic, regions upstream to genes), which are not explicitly specified in the GFF format, and exports the corresponding primary sequence information into predefined feature specific output files. GFF-Ex package consists of several UNIX Shell and PERL scripts.
Compared to other available GFF parsers, GFF-Ex is a simpler tool, which permits sequence retrieval based on additional inferred features. GFF-Ex can also be integrated with any genome annotation or analysis pipeline. GFF-Ex is freely available at
PMCID: PMC4045924  PMID: 24885931
GFF; Genomics; Annotation; Sequence parser
32.  Efficacy of adalimumab in young children with juvenile idiopathic arthritis and chronic uveitis: a case series 
BMC Research Notes  2014;7:316.
Juvenile idiopathic arthritis is a relatively common chronic disease of childhood, and is associated with persistent morbidity and extra-articular complications, one of the most common being uveitis. The introduction of biologic therapies, particularly those blocking the inflammatory mediator tumor necrosis factor-α, provided a new treatment option for juvenile idiopathic arthritis patients who were refractory to standard therapy such as non-steroidal anti-inflammatory drugs, corticosteroids and/or methotrexate.
Case presentations
The first case was a 2-year-old girl with juvenile idiopathic arthritis and uveitis who failed to respond to treatment with anti-inflammatories, low-dose corticosteroids and methotrexate, and had growth retardation. Adalimumab 24 mg/m2 every 2 weeks and prednisone 0.5 mg/kg/day were added to methotrexate therapy; steroid tapering and withdrawal started after 1 month. After 2 months the patient showed good control of articular and ocular manifestations, and she remained in remission for 1 year, receiving adalimumab and methotrexate with no side effects, and showing significant improvement in growth. Case 2 was a 9-year-old boy with an 8-year history of juvenile idiopathic arthritis and uveitis that initially responded to infliximab, but relapse occurred after 2 years off therapy. After switching to adalimumab, and adjusting doses of both adalimumab and methotrexate based on body surface area, the patient showed good response and corticosteroids were tapered and withdrawn after 6 months; the patient remained in remission taking adalimumab and methotrexate. The final case was a 5-year-old girl with juvenile idiopathic arthritis for whom adalimumab was added to methotrexate therapy after three flares of uveitis. The patient had two subsequent episodes of uveitis that responded well to local therapy, but was then free of both juvenile idiopathic arthritis and uveitis symptoms, allowing methotrexate and then adalimumab to be stopped; the patient remained in drug-free remission.
This report includes the first published case of the use of adalimumab in a child aged <3 years. Our clinical experience further supports the use of biologic therapy for the management of juvenile idiopathic arthritis and uveitis in children as young as two years of age.
PMCID: PMC4045933  PMID: 24886032
Adalimumab; Juvenile idiopathic arthritis; Children; Uveitis
33.  Implementation of Cloud based Next Generation Sequencing data analysis in a clinical laboratory 
BMC Research Notes  2014;7:314.
The introduction of next generation sequencing (NGS) has revolutionized molecular diagnostics, though several challenges remain limiting the widespread adoption of NGS testing into clinical practice. One such difficulty includes the development of a robust bioinformatics pipeline that can handle the volume of data generated by high-throughput sequencing in a cost-effective manner. Analysis of sequencing data typically requires a substantial level of computing power that is often cost-prohibitive to most clinical diagnostics laboratories.
To address this challenge, our institution has developed a Galaxy-based data analysis pipeline which relies on a web-based, cloud-computing infrastructure to process NGS data and identify genetic variants. It provides additional flexibility, needed to control storage costs, resulting in a pipeline that is cost-effective on a per-sample basis. It does not require the usage of EBS disk to run a sample.
We demonstrate the validation and feasibility of implementing this bioinformatics pipeline in a molecular diagnostics laboratory. Four samples were analyzed in duplicate pairs and showed 100% concordance in mutations identified. This pipeline is currently being used in the clinic and all identified pathogenic variants confirmed using Sanger sequencing further validating the software.
PMCID: PMC4036707  PMID: 24885806
Next generation sequencing; Cloud computing; Variant detection; Molecular diagnostics
34.  Paraneoplastic granulocyte colony-stimulating factor secretion in soft tissue sarcoma mimicking myeloproliferative neoplasia: a case report 
BMC Research Notes  2014;7:313.
While paraneoplastic leukocytosis is a common phenomenon in solid tumors, extreme elevations of white blood counts (WBC) in the range of more than 100,000/μl are uncommon in patients with non-hematologic malignancies. Leukocytosis with mature neutrophils due to a granulocyte colony-stimulating factor (G-CSF) producing tumor is only seen on rare occasions.
Case presentation
Massive neutrophil leukocytosis of approximately 100,000/μl was diagnosed in a 57-year-old Caucasian woman with metastatic undifferentiated endometrial sarcoma. A bone marrow trephine biopsy revealed massively increased granulopoiesis, but no evidence of monoclonal myeloproliferative disease. After the primary tumor had been resected, white blood count (WBC) plummeted and went back to nearly normal levels within one week. With progressive metastatic disease, granulocyte colony-stimulating factor (G-CSF) plasma levels were found to be increased by 10-fold. White blood count (WBC) strictly correlated with tumor burden and response to chemotherapy. In the final stage of treatment resistent disease, white blood count (WBC) approximated 300,000/μl.
We report on a granulocyte colony-stimulating factor (G-CSF) secreting undifferentiated endometrial sarcoma, which was associated with extreme neutrophil counts. White blood count (WBC) were closely correlated with tumor burden and associated with an aggressive clinical course. We suggest that paraneoplastic neutrophilia represents a poor prognostic sign in soft tissue sarcoma. In patients with similar constellations, antitumor therapy must not be delayed.
PMCID: PMC4039653  PMID: 24885681
Paraneoplastic leukocytosis; Neutrophilia; G-CSF; Sarcoma
35.  Bilateral chylothorax following neck dissection: a case report 
BMC Research Notes  2014;7:311.
Chylothorax is an extremely rare but potentially life-threatening complication after radical neck dissection. We report the case of a bilateral chylothorax after total thyroidectomy and cervico-central and cervico-lateral lymphadenectomy for thyroid carcinoma.
Case presentation
A 40-year-old European woman underwent total thyroidectomy and neck dissection for papillary thyroid carcinoma. Postoperatively she developed dyspnoea and pleural effusion. A chylothorax was found and the initial conservative therapy was not successful. She had to be operated on again and the thoracic duct was legated.
The case presentation reports a very rare complication after total thyroidectomy and neck dissection, but it has to be kept in mind to prevent dangerous complications.
PMCID: PMC4036830  PMID: 24885488
Thyroidectomy; Neck dissection; Bilateral chylothorax
36.  Primary care at Swiss universities - current state and perspective 
BMC Research Notes  2014;7:308.
There is increasing evidence that a strong primary care is a cornerstone of an efficient health care system. But Switzerland is facing a shortage of primary care physicians (PCPs). This pushed the Federal Council of Switzerland to introduce a multifaceted political programme to strengthen the position of primary care, including its academic role. The aim of this paper is to provide a comprehensive overview of the situation of academic primary care at the five Swiss universities by the end of year 2012.
Although primary care teaching activities have a long tradition at the five Swiss universities with activities starting in the beginning of the 1980ies; the academic institutes of primary care were only established in recent years (2005 – 2009). Only one of them has an established chair. Human and financial resources vary substantially. At all universities a broad variety of courses and lectures are offered, including teaching in private primary care practices with 1331 PCPs involved. Regarding research, differences among the institutes are tremendous, mainly caused by entirely different human resources and skills.
So far, the activities of the existing institutes at the Swiss Universities are mainly focused on teaching. However, for a complete academic institutionalization as well as an increased acceptance and attractiveness, more research activities are needed. In addition to an adequate basic funding of research positions, competitive research grants have to be created to establish a specialty-specific research culture.
PMCID: PMC4037554  PMID: 24885148
Primary care; Swiss universities; Research output; Teaching; Academic career; Medical education
37.  Low prevalence of IgA anti-transglutaminase 1, 2, and 3 autoantibodies in children with atopic dermatitis 
BMC Research Notes  2014;7:310.
Atopic dermatitis (AD) is a multifactorial chronic inflammatory skin disease presenting with a relapsing clinical pattern similar to chronic autoimmune disease. Several human transglutaminases have been defined and keratinocyte transglutaminase (TG1) and epidermal transglutaminase (TG3) expressed in the epidermis are associated with epidermal barrier dysfunction. Since impairments to the epidermal barrier represent an important factor in AD, we hypothesized that IgA autoantibodies specific for TG1 (IgA-anti-TG1) and TG3 (IgA-anti-TG3) may affect AD development during childhood.
Active AD patients (n = 304), 28 patients with biopsy-confirmed coeliac disease (CD), 5 patients with active AD and CD, and 55 control patients without CD and skin diseases were enrolled into the study. IgA-anti-TG1 and IgA-anti-TG3 reactivity was determined using an enzyme-linked immunosorbent assay. IgA-anti-TG2 were defined using a fluoroenzyme immunoassay.
IgA-anti-TG1 antibodies were found in 2% and IgA-anti-TG3 antibodies in 3% of patients with active AD. Two out of the 5 patients with AD and concomitant CD had IgA-anti-TG1 and IgA-anti-TG2 antibodies. In CD patients, 36% of individuals presented with elevated IgA-anti-TG1 antibodies and 18% presented with elevated IgA-anti-TG3 antibodies and all CD patients presented with IgA-anti-TG2 antibodies (significantly different from AD patients and controls, p < 0.05). In CD patients, IgA-anti-TG1 and/or IgA-anti-TG3 seropositivity tended to appear concurrently, whereas only one patient with AD had both types of autoantibodies.
IgA-anti-TG1 and IgA-anti-TG3 seropositivity was rare in active AD but frequent in CD patients. The level of circulating antibodies related to skin lesions could be studied by determining the levels of IgA-anti-TG1 and IgA-anti-TG3 in skin biopsies of AD patients.
PMCID: PMC4045883  PMID: 24885370
Autoantibodies; Atopic dermatitis; Coeliac disease; Transglutaminase 1; Transglutaminase 2; Transglutaminase 3
38.  Determinant and outcome of early diagnosis of HIV infection among HIV-exposed infants in southwest Ethiopia 
BMC Research Notes  2014;7:309.
Preventing mother-to-child transmission (PMTCT) of human immunodeficiency virus infection (HIV) has been a fundamental advancement in the acquired immunodeficiency syndrome (AIDS) response for the past decade. Several countries have made great strides in the efforts to prevent HIV through mother-to-child transmission. The objective of this study is to assess the determinant and outcome of early diagnosis of HIV infection among HIV-exposed infants in southwest Ethiopia.
An institutional based retrospective cohort study was conducted in a hospital. Medical records of HIV-exposed infants and their mothers enrolled into the program were reviewed. Data entry and analysis was carried out using SPSS version 20 for Windows.
A total of 426 HIV exposed infant-mother pairs where both mother and infants received a minimum ARV intervention for PMTCT were included in the study. Two hundred fifty-four (59.6%) of mothers had attended antenatal care (ANC). Of all participants, 234(54.9%) mothers did not receive any PMTCT prophylaxis during ANC, while only 104(24.4) received antiretroviral (ART) as PMTCT prophylaxis and 163(38.3%) claimed that did not observe any infant PMTCT interventions while 135(31.7%) of the infants received single-dose NVP + AZT. About 385(90.4%) infants were not infected at their final infection status. Those mothers who did not attended ANC follow-up, infants on mixed and complementary feeding and infants weaned off and mothers who were in WHO clinical stage III and IV were more likely to have HIV sero positive infant.
This study showed that 385(90.4%) of the infants were not infected at their final infection status. Therefore, encouraging pregnant women to visit health facilities during their course of pregnancy, focusing on exclusive breast feeding counseling and promotion, and early initiation of antiretroviral treatment to HIV infected pregnant women are recommend.
PMCID: PMC4045956  PMID: 24885260
Outcome; EID; HIV infection; HIV-exposed infants; Ethiopia
39.  A method for generating highly multiplexed ChIP-seq libraries 
BMC Research Notes  2014;7:312.
The barcoding of next generation sequencing libraries has become an essential part of the experimental design. Barcoding not only allows the sequencing of more than one sample per lane, but also reduces technical bias. However, current barcoding strategies impose significant limitations and/or technical barriers in their implementation for ChIP-sequencing.
Converting Y-shaped sequencing adapters to double stranded DNA prior to agarose gel size selection reduces adapter dimer contamination and quantitating the number of cycles required for amplification of the library with qPCR prior to library amplification eliminates library over-amplification.
We describe an efficient and cost effective method for making barcoded ChIP-seq libraries for sequencing on the Illumina platform.
PMCID: PMC4048252  PMID: 24885602
Chromatin immunoprecipitation; ChIP-seq; Next generation sequencing; Genomics; Epigenetics
40.  The psychological impact of a dual-disaster caused by earthquakes and radioactive contamination in Ichinoseki after the Great East Japan Earthquake 
BMC Research Notes  2014;7:307.
The psychological impact of dual-disasters (earthquakes and a nuclear accident), on affected communities is unknown. This study investigated the impact of a dual-disaster (earthquakes and radioactive contamination) on the prevalence of psychological distress in a landlocked city within the Tohoku area, Japan.
A cross-sectional mail-in survey with a random sample of inhabitants from Ichinoseki city was conducted eleven months after the disasters, and data from 902 respondents were analyzed by logistic regression models, with multiple imputation methodology. The K6 was used to determine psychological distress.
The estimated prevalence of psychological distress was 48.0 percent. House damage due to earthquakes and anxiety about radioactive contamination were significantly associated with psychological distress (p < 0.05), while an interactive effect between house damage and anxiety about radioactive contamination was not significant. Being female, middle-to-low educational status and unemployed were additional risk factors for psychological distress.
This dual-disaster was associated with a moderate prevalence of psychological distress in the area. The impact of the earthquake and radioactive contamination appeared additive.
PMCID: PMC4037272  PMID: 24885053
Psychological distress; PTSD; K6; Dual-disaster; Natural disaster; Nuclear accident; Fukushima Daiichi atomic power plant; Disaster psychiatry
41.  Development and validation of the Japanese version of the obsessive-compulsive inventory 
BMC Research Notes  2014;7:306.
The Obsessive-Compulsive Inventory (OCI) was designed to evaluate the severity of obsessive-compulsive symptoms in both clinical and non-clinical samples. The aim of the study was to develop a Japanese version of this scale (OCI-J) and validate it in both non-clinical and clinical Japanese samples.
In Study 1, the OCI-J, the Maudsley Obsessional Compulsive Inventory (MOCI), and measures of anxiety and depression were administered to 150 undergraduate students (non-clinical sample) in order to investigate the internal consistency and convergent validity of the OCI-J. Furthermore, 118 non-clinical participants completed the OCI-J after a 2-week interval to determine the test-retest reliability. In Study 2, OCD participants (n = 35), anxiety control participants with panic disorder (n = 22), and healthy control participants (n = 37) completed the OCI-J in order to test its clinical discrimination ability.
Correlational analysis indicated moderate to high correlations between the subscales and total scores of the OCI-J and MOCI. In addition, the OCI-J and its subscales demonstrated satisfactory test-retest reliabilities. Finally, the OCI-J showed good clinical discrimination for patients with OCD from healthy and anxiety controls.
The OCI-J is a valid and reliable instrument for measuring OCD symptoms in both clinical and non-clinical samples of Japanese.
PMCID: PMC4045934  PMID: 24884936
42.  Incidences and clinical outcomes of acute kidney injury in ICU: a prospective observational study in Sri Lanka 
BMC Research Notes  2014;7:305.
Acute kidney injury (AKI) is a common and a serious complication among patients admitted to intensive care units (ICUs), and has been the focus of many studies leading to recent advances in diagnosis and classification. The incidence and outcome of AKI in Sri Lankan ICUs is largely unknown. The aim of this study was to describe the incidence, severity and outcome of AKI among patients admitted to the medical ICU, National Hospital, Colombo, Sri Lanka (NHSL).
Patients admitted to the medical ICU, NHSL, over a period of 6 months were studied prospectively.
Standard demographic, physiological and clinical data were collected. Severity of illness was assessed using SOFA (Sequential Organ Failure Assessment) score. Diagnosis of AKI was based on Acute Kidney Injury Network (AKIN) criteria.
Of 212 patients screened, 108 satisfied the inclusion criteria; males 67(61.5%); mean age 47.8 years(SD 19.4, range 12-94). Mean duration of ICU stay was 11.6 days (SD 10.6, range 2-55). Eighty one (75.0%) received mechanical ventilation. Forty nine (45.4%) had sepsis. ICU mortality was 38.9% and AKI was present in 60.2%. The majority of AKI patients (38, 58.5%) had AKI stage 3. Patients with AKI were at higher risk of death (p < 0.01). Neither age, gender, nor the presence of co-morbidities were associated with increased risk of AKI. Patients with AKI had significantly longer ICU stay (Log-Rank Chi Square: 23.186, p < 0.0001). Both the incidence of AKI and ICU mortality were higher in patients with SOFA scores over 9 (Pearson Chi-Square 7.581, p = 0.006, and 11.288, p = 0.001 respectively).
The incidence of AKI is high at 60% among our ICU patients, and those with AKI had higher mortality and longer duration of ICU stay. Age, gender or the presence of co-morbidities was not associated with a higher risk of AKI. Patients with SOFA scores over 9 within the first 24 hours were more likely to develop AKI and had higher risk of death.
PMCID: PMC4049500  PMID: 24884808
Acute kidney injury; Intensive care; Critical care; Sepsis; Mortality; ICU stay
43.  Validation of reference genes for gene expression analysis in olive (Olea europaea) mesocarp tissue by quantitative real-time RT-PCR 
BMC Research Notes  2014;7:304.
Gene expression analysis using quantitative reverse transcription PCR (qRT-PCR) is a robust method wherein the expression levels of target genes are normalised using internal control genes, known as reference genes, to derive changes in gene expression levels. Although reference genes have recently been suggested for olive tissues, combined/independent analysis on different cultivars has not yet been tested. Therefore, an assessment of reference genes was required to validate the recent findings and select stably expressed genes across different olive cultivars.
A total of eight candidate reference genes [glyceraldehyde 3-phosphate dehydrogenase (GAPDH), serine/threonine-protein phosphatase catalytic subunit (PP2A), elongation factor 1 alpha (EF1-alpha), polyubiquitin (OUB2), aquaporin tonoplast intrinsic protein (TIP2), tubulin alpha (TUBA), 60S ribosomal protein L18-3 (60S RBP L18-3) and polypyrimidine tract-binding protein homolog 3 (PTB)] were chosen based on their stability in olive tissues as well as in other plants. Expression stability was examined by qRT-PCR across 12 biological samples, representing mesocarp tissues at various developmental stages in three different olive cultivars, Barnea, Frantoio and Picual, independently and together during the 2009 season with two software programs, GeNorm and BestKeeper. Both software packages identified GAPDH, EF1-alpha and PP2A as the three most stable reference genes across the three cultivars and in the cultivar, Barnea. GAPDH, EF1-alpha and 60S RBP L18-3 were found to be most stable reference genes in the cultivar Frantoio while 60S RBP L18-3, OUB2 and PP2A were found to be most stable reference genes in the cultivar Picual.
The analyses of expression stability of reference genes using qRT-PCR revealed that GAPDH, EF1-alpha, PP2A, 60S RBP L18-3 and OUB2 are suitable reference genes for expression analysis in developing Olea europaea mesocarp tissues, displaying the highest level of expression stability across three different olive cultivars, Barnea, Frantoio and Picual, however the combination of the three most stable reference genes do vary amongst individual cultivars. This study will provide guidance to other researchers to select reference genes for normalization against target genes by qPCR across tissues obtained from the mesocarp region of the olive fruit in the cultivars, Barnea, Frantoio and Picual.
PMCID: PMC4062307  PMID: 24884716
Reference genes; qRT-PCR; Olea europaea; Gene expression
44.  Mechanic’s hands revisited: is this sign still useful for diagnosis in patients with lung involvement of collagen vascular diseases? 
BMC Research Notes  2014;7:303.
The presence of “mechanic’s hands” is one of the clinical clues for collagen vascular diseases. However, the exact relevance of “mechanic’s hands” in collagen vascular diseases has not been well documented. The aim of this study was to clarify the relevance of “mechanic’s hands” to collagen vascular diseases including various skin lesions and interstitial pneumonia.
A retrospective review of the medical records of patients with “mechanic’s hands” at our hospital between April 2011 and December 2012 was conducted. A PubMed search was also conducted using the term “mechanic’s hands”.
Four patients in our institution and 40 patients obtained from PubMed who had “mechanic’s hands” were identified. The most frequent diseases were DM/amyopathic DM (n = 24, 54.5%) and anti-ARS syndrome (n = 17, 38.6%). In these patients, the major skin lesions associated with “mechanic’s hands” were periungual erythema (n = 23, 52.3%), Gottron’s sign (n = 17, 38.6%), heliotrope rash (n = 10, 22.7%), Raynaud’s phenomenon (n = 9, 20.5%), and anti-ARS syndrome (n = 17, 38.6%). Six cases (2 DM, 4 anti-ARS syndrome) had only “mechanic’s hands”. Antibodies to anti-ARS (n = 24) were Jo-1 (n = 19), PL-7 (n = 3), OJ (n = 1), and PL-12 (n = 1).
The presence of “mechanic’s hands” together with diverse skin lesions could be a clinical clue to the diagnosis of lung involvement associated with collagen vascular diseases, especially in anti-ARS syndrome or DM/amyopathic DM.
PMCID: PMC4035896  PMID: 24886713
Anti-aminoacyl-transfer RNA synthetase (ARS) syndrome; Dermatomyositis; Mechanic’s hands; Skin lesions
45.  Comparison of performance of Sri Lankan and US children on cognitive and motor scales of the Bayley scales of infant development 
BMC Research Notes  2014;7:300.
There is no validated scale to assess neurodevelopment of infants and children in Sri Lanka. The Bayley III scales have used widely globally but it has not been validated for Sri Lankan children. We administered the Cognitive and Motor Scales of the Bayley III to 150 full-term children aged 6, 12 and 24 months from the Gampaha District of Sri Lanka. We compared the performance of Sri Lankan children 6, 12 and 24 months of age on the cognitive and motor scales of the Bayley III with that of US children.
Compared to the US norms, at 12 months, Sri Lankan children had significantly higher cognitive scores and lower gross motor scores, and at 24 months significantly lower cognitive scores. The test had a high test-retest reliability among Sri Lankan children.
There were small differences in the cognitive and motors scores between Sri Lankan and US children. It is feasible to use Bayley III scales to assess neurodevelopment of Sri Lankan children. However, we recommend that the tool be validated using a larger representative sample of all population groups.
PMCID: PMC4025536  PMID: 24886547
Bayley III scales; Cognitive; Motor; Sri Lanka; Children 6–24 months
46.  CDK9 inhibition strategy defines distinct sets of target genes 
BMC Research Notes  2014;7:301.
CDK9 is the catalytic subunit of the Positive Transcription Elongation Factor b (P-TEFb), which phosphorylates the CTD of RNAPII and negative elongation factors enabling for productive elongation after initiation. CDK9 associates with T-type cyclins and cyclin K and its activity is tightly regulated in cells at different levels. CDK9 is also the catalytic subunit of TAK (Tat activating Kinase), essential for HIV1 replication. Because of CDK9′s potential as a therapeutic target in AIDS, cancer, inflammation, and cardiomyophathy it is important to understand the consequences of CDK9 inhibition. A previous gene expression profiling study performed with human glioblastoma T98G cells in which CDK9 activity was inhibited either with a dominant negative mutant form of CDK9 (dnCDK9) or the pharmacological inhibitor Flavopiridol unveiled striking differences in gene expression effects. In the present report we extended these studies by (1) using both immortalized normal human fibroblasts and primary human astrocytes, (2) eliminating potential experimental variability due to transduction methodology and (3) also modulating CDK9 activity with siRNA.
Striking differences in the effects on gene expression resulting from the strategy used to inhibit CDK9 activity (dnCDK9 or FVP) remain even when potential variability due to viral transduction is eliminated. siRNA mediated CDK9 knockdown in human fibroblasts and astrocytes efficiently reduced CDK9 expression and led to potent changes in gene expression that exhibit little correlation with the effects of dnCDK9 or FVP. Interestingly, HEXIM1 a validated CDK9 target gene, was found to be potently downregulated by dnCDK9, FVP and siCDK9, but the cluster of genes with expression profiles similar to HEXIM1 was small. Finally, cluster analysis of all treatments revealed higher correlation between treatments than cell type origin.
The nature of the strategy used to inhibit CDK9 profoundly affects the patterns of gene expression resulting from CDK9 inhibition. These results suggest multiple variables that affect outcome, including kinetics of inhibition, potency, off-target effects, and selectivity issues. This is particularly important when considering CDK9 as a potential target for therapeutic intervention.
PMCID: PMC4045923  PMID: 24886624
Transcription; CDK9; RNA polymerase II; CDKs; Control of gene expression
47.  Sexual experience and HIV-related knowledge among Belgian university students: a questionnaire study 
BMC Research Notes  2014;7:299.
Adolescents are a risk group for acquiring sexually transmitted diseases, including HIV. Correct knowledge about transmission mechanisms is a prerequisite to taking appropriate precautions to avoid infection. This study aimed at assessing the level of HIV-related knowledge among university students as a first step in developing targeted interventions. We used a self-developed HIV knowledge questionnaire, supplemented with socio-demographic and sexual behaviour questions. The questionnaire was composed of 59 items from different existing questionnaires. It included general statements and statements about prevention, transmission and treatment of HIV.
There were 357 (79.7%) female and 93 (20.3%) male participants and their median age was 20 (IQR 19–21). On average 42/59 (71.2%) questions were answered correctly, 5/59 (8.5%) were answered incorrectly and 12/59 (20.3%) were unknown . The best and worse scores were seen on the prevention questions and the treatment questions, respectively. HIV-related knowledge is higher in older students and in students with a health-related education. Students with sexual experience, with five or more partners and students who have been tested on STDs have a higher HIV-related knowledge.
Knowledge on prevention and transmission of HIV is fairly good among university students and knowledge is higher among students with more sexual experience. They still have some misconceptions (e.g. HIV is spread by mosquitoes) and they are ignorant of a substantial number of statements (e.g. risk for infection through oral sex).
PMCID: PMC4026820  PMID: 24886447
HIV; Acquired Immunodeficiency Syndrome; Knowledge; Sexual behaviour; Adolescent
48.  Lone workers attitudes towards their health: views of Ontario truck drivers and their managers 
BMC Research Notes  2014;7:297.
Truck driving is the second most common occupation among Canadian men. Transportation of goods via roads is of crucial importance for the Canadian economy. The industry is responsible annually for $17 billion in GDP and is projected to increase by 28% over the next 10 years. Recruitment is an issue with 20% of drivers projected to retire or leave the profession in the next 10 years. Despite the reliance on transport truck drivers for the delivery of goods which affects Canada’s economy and daily living of residents, little is known about the health care needs of this large cohort of primarily male lone workers from a drivers’ perspective. Transport truck drivers are independent workers whose non traditional workplace is their tractor, the truck stops and the journey on the road.
The objective of this study was to obtain a contextually informed description of lifestyle issues, health and disease risk factors experienced by drivers and perceived by their managers in the truck driving occupation.
Using a grounded theory approach, 4 focus groups were conducted with drivers (n = 16) and managers (n = 10) from two trucking companies in Southwestern Ontario to identify the lived experience of the drivers as it relates to preventable risks to health and wellness. A semi structured guided interview was used to explore the lifestyle context of transport truck driving and organizational aspects of the occupation (workplace culture, working conditions and health and wellness promotion).
The predominant themes described stress, workplace, communication, lifestyle, driving culture, family, and fatigue concerns. In terms of the transportation work environment, drivers and managers were aware of the profession’s potential to foster lifestyle related chronic diseases but described challenges in making the profession more amenable to a healthy lifestyle.
Workplace environmental determinants are significant in shaping health behaviours. Chronic disease health risks were the main health concerns identified. Health risks were exacerbated by working conditions (job demands, work hours, financial pressure and the sedentary nature of the job). Workplace health strategies will need to take into account the unique challenges of the occupation.
PMCID: PMC4023166  PMID: 24886231
Truck drivers; Health and wellness; Chronic disease risk factors; Lifestyle; Workplace health
49.  Prevalence of bruxism in children with episodic migraine - a case–control study with polysomnography 
BMC Research Notes  2014;7:298.
Parents of children with migraine have described a higher prevalence of sleep bruxism and other sleep disturbances in their children. The objective of this study was to use polysomnography to investigate the prevalence of bruxism during sleep in children with episodic migraine relative to controls.
Controls and patients were matched by sex, age, years of formal education, presence of snoring, arousals per hour, and respiratory events per hour.
A total of 20 controls, between 6 and 12 years old, with no history of headache, recruited from public schools in Sao Paulo between 2009 and 2012, and 20 patients with episodic migraine recruited from the Headache Clinic at the Federal University of Sao Paulo between 2009 and 2012 underwent polysomnography.
No intervention was performed before sleep studies.
Among migraine patients, 27.5% experienced aura prior to migraine onset. The sleep efficiency, sleep latency, REM sleep latency, arousals per hour, percentage of sleep stages, and breathing events per hour were similar between groups. Five children (25%) with episodic migraine exhibited bruxism during the sleep study while this finding was not observed in any control (p = 0.045).
Our data demonstrate that bruxism during sleep is more prevalent in children with episodic migraine. Further prospective studies will help elucidate the underlying shared pathogenesis between bruxism and episodic migraine in children.
PMCID: PMC4026587  PMID: 24886343
Bruxism; Sleep; Migraine; Polysomnography
50.  Smear-positive pulmonary tuberculosis and AFB examination practices according to the standard checklist of WHO’s tuberculosis laboratory assessment tool in three governmental hospitals, Eastern Ethiopia 
BMC Research Notes  2014;7:295.
Using the Directly Observed Treatment-Short course (DOTS) program the World Health Organization’s global target was to detect 70% of new sputum-smear positive PTB cases. Smear positive PTB cases are more infectious than the smear negative cases. The TB case detection rate remains very low in Ethiopia, but there are increases in smear-negative PTB diagnosis which could be attributed to several factors including poor quality of sputum smear-microscopy.
A five years retrospective record review of data between September, 2007 and August, 2012 and an in-depth assessment of AFB staining practices of sputum smear using a standard checklist were made. The proportion of smear positive cases relative to overall Acid Fast Bacilli (AFB) screened was determined over a five year period to indicate the overall prevalence and the trend. Odds ratio with 95 percent confidence interval was calculated for categorical variables using multivariate Logistic Regression model to assess the strength of association.
A total of 1266 individuals’ data were reviewed. The majority of the study participants were male, 704 (55.6%), and rural residents, 690 (54.5%). The overall prevalence rate of smear positive PTB was 21.6%. Age categories between 15–24 and 25–34 years were independent predictors of smear positive PTB with adjusted odds ratio of 2.246 [95% CI (1.098-4.597)] and 2.267 [95% CI (1.107-4.642)], respectively. More males were affected by PTB than females with an adjusted odds ratio of 1.426 [95% CI (1.083-1.879)]. An in-depth interview with the respective laboratory chiefs showed that quality control measures for sputum smear microscopy were used at different levels of the testing activities; however, equipment function verification as a quality control measure was not accomplished regularly in all of the study hospital laboratories.
The smear positive PTB case detection rate indicated in this study is significantly lower than the countries which met the 70% target of the World Health Organization. Lack of feedback mechanisms in the External Quality Assurance schemes of sputum smear microscopy render the opportunity for improvement difficult; Serial sputum examination showed a considerable rate of positivity in the second sputum sample when compared with the others.
PMCID: PMC4024114  PMID: 24885987
Smear positive pulmonary tuberculosis; AFB staining practices; Eastern Ethiopia

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