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1.  Bone temperature during cementation with a heatsink: a bovine model pilot study 
BMC Research Notes  2014;7:494.
Background
Bone cement is an effective means of supporting implants, but reaches high temperatures while undergoing polymerisation. Bone has been shown to be sensitive to thermal injury with osteonecrosis reported after one minute at 47°C. Necrosis during cementing may lead to loosening of the prosthesis. Some surgeons fill the joint cavity with cool irrigation fluid to provide a heatsink during cementing, but this has not been supported by research. This paper assesses a simple technique to investigate the efficacy of this method.
Findings
We used a model acetabulum in a bovine humerus to allow measurement of bone temperatures in cementing. Models were prepared with a 50 mm diameter acetabulum and three temperature probe holes; two as close as possible to the acetabular margin at half the depth of the acetabulum and at the full depth of the acetabulum, and one 10 mm from the acetabular rim. Four warmed models were cemented with Palacos RG using a standard mixing system and a 10 mm polyethylene disc to represent an acetabular component. Two of the acetabular models were filled with room temperature water to provide a heatsink. An electronic probe measured temperature at 5 second intervals from the moment of cementing.
In the models with no heatsink, peak temperature was 40.3°C. The mean temperature rise was 10.9°C. In the models with a heatsink, there was an average fall in the bone temperature during cementing of 4.4°C.
Conclusions
These results suggest that using a heatsink while cementing prostheses may reduce the peak bone temperature. This study demonstrates a simple, repeatable technique which may be useful for larger trials.
doi:10.1186/1756-0500-7-494
PMCID: PMC4126909  PMID: 25099248
Arthroplasty; Bone cements; Osteonecrosis; Heatsink
2.  Biofilm and fluoroquinolone resistance of canine Escherichia coli uropathogenic isolates 
BMC Research Notes  2014;7:499.
Background
Escherichia coli is the most common uropathogen involved in urinary tract infection (UTI). Virulence of strains may differ, and may be enhanced by antimicrobial resistance and biofilm formation, resulting in increased morbidity and recurrent infections. The aim of this study was to evaluate the in vitro biofilm forming capacity of E. coli isolates from dogs with UTI, by using fluorescent in situ hybridization, and its association with virulence genes and antimicrobial resistance.
Findings
The proportion of biofilm-producing isolates significantly increased with the length of incubation time (P < 0.05). Biofilm production was significantly associated with fluoroquinolone resistance at all incubation time points and was independent of the media used (P < 0.05). Biofilm production was not associated with cnf1, hly, pap and sfa genes (P > 0.05), but was significantly associated with afa, aer and the β-lactamase genes (P < 0.05).
Conclusions
To the best of our knowledge, this is the first report showing significant association between biofilm production and fluoroquinolone resistance in E. coli isolates from dogs with UTI. Biofilm formation may contribute to UTI treatment failure in dogs, through the development of bacterial reservoirs inside bladder cells, allowing them to overcome host immune defenses and to establish recurrent infections.
doi:10.1186/1756-0500-7-499
PMCID: PMC4132243  PMID: 25099929
Biofilm; Dogs; Escherichia coli; Fluoroquinolone resistance; Urinary tract infection
3.  Preliminary characterization of IL32 in basal-like/triple negative compared to other types of breast cell lines and tissues 
BMC Research Notes  2014;7:501.
Background
Triple negative breast cancer (TNBC) and often basal-like cancers are defined as negative for estrogen receptor, progesterone receptor and Her2 gene expression. Over the past few years an incredible amount of data has been generated defining the molecular characteristics of both cancers. The aim of these studies is to better understand the cancers and identify genes and molecular pathways that might be useful as targeted therapies. In an attempt to contribute to the understanding of basal-like/TNBC, we examined the Gene Expression Omnibus (GEO) public datasets in search of genes that might define basal-like/TNBC. The Il32 gene was identified as a candidate.
Findings
Analysis of several GEO datasets showed differential expression of IL32 in patient samples previously designated as basal and/or TNBC compared to normal and luminal breast samples. As validation of the GEO results, RNA and protein expression levels were examined using MCF7 and MDA MB231 cell lines and tissue microarrays (TMAs). IL32 gene expression levels were higher in MDA MB231 compared to MCF7. Analysis of TMAs showed 42% of TNBC tissues and 25% of the non-TNBC were positive for IL32, while non-malignant patient samples and all but one hyperplastic tissue sample demonstrated lower levels of IL32 protein expression.
Conclusion
Data obtained from several publically available GEO datasets showed overexpression of IL32 gene in basal-like/TNBC samples compared to normal and luminal samples. In support of these data, analysis of TMA clinical samples demonstrated a particular pattern of IL32 differential expression. Considered together, these data suggest IL32 is a candidate suitable for further study.
doi:10.1186/1756-0500-7-501
PMCID: PMC4132244  PMID: 25100201
Triple negative; Basal breast cancers; Gene expression analysis; IL32
4.  Employing whole genome mapping for optimal de novo assembly of bacterial genomes 
BMC Research Notes  2014;7:484.
Background
De novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. Often users are not bio-informaticians and, in a black box approach, utilise assembly parameters such as contig length and N50 to generate whole genome sequences, potentially resulting in mis-assemblies.
Findings
Utilising several assembly tools based on de Bruijn graphs like Velvet, SPAdes and IDBA, we demonstrate that at the optimal N50, mis-assemblies do occur, even when using the multi-k-mer approaches of SPAdes and IDBA. We demonstrate that whole genome mapping can be used to identify these mis-assemblies and can guide the selection of the best k-mer size which yields the highest N50 without mis-assemblies.
Conclusions
We demonstrate the utility of whole genome mapping (WGM) as a tool to identify mis-assemblies and to guide k-mer selection and higher quality de novo genome assembly of bacterial genomes.
doi:10.1186/1756-0500-7-484
PMCID: PMC4118782  PMID: 25077983
De-novo assembly; Whole genome mapping; k-mer; Microbial genomes; de bruijn graph; SPAdes and Velvet
5.  Genetic diversity of Brucella ovis isolates from Rio Grande do Sul, Brazil, by MLVA16 
BMC Research Notes  2014;7:447.
Background
Ovine epididymitis is predominantly associated with Brucella ovis infection. Molecular characterization of Brucella spp. achieved by multi-locus variable number of tandem repeats (VNTR) analyses (MLVA) have proved to be a powerful tool for epidemiological trace-back studies. Thus, the aim of this study was to evaluate the genetic diversity of Brucella ovis isolates from Rio Grande do Sul State, Brazil, by MLVA16.
Findings
MLVA16 genotyping identified thirteen distinct genotypes and a Hunter-Gaston diversity index of 0.989 among the fourteen B. ovis genotyped strains. All B. ovis MLVA16 genotypes observed in the present study represented non-previously described profiles. Analyses of the eight conserved loci included in panel 1 (MLVA8) showed three different genotypes, two new and one already described for B. ovis isolates. Among ten B. ovis isolates from same herd only two strains had identical pattern, whereas the four isolates with no epidemiologic information exhibited a single MLVA16 pattern each. Analysis of minimal spanning tree, constructed using the fourteen B. ovis strains typed in this study together with all nineteen B. ovis MLVA16 genotypes available in the MLVAbank 2014, revealed the existence of two clearly distinct major clonal complexes.
Conclusions
In conclusion, the results of the present study showed a high genetic diversity among B. ovis field isolates from Rio Grande do Sul State, Brazil, by MLVA16.
doi:10.1186/1756-0500-7-447
PMCID: PMC4124495  PMID: 25015223
Genotyping; Brucella ovis; MLVA16; Ovine brucellosis
6.  The use of a low cost 3D scanning and printing tool in the manufacture of custom-made foot orthoses: a preliminary study 
BMC Research Notes  2014;7:443.
Background
Custom foot orthoses are currently recognized as the gold standard for treatment of foot and lower limb pathology. While foam and plaster casting methods are most widely used in clinical practice, technology has emerged, permitting the use of 3D scanning, computer aided design (CAD) and computer aided manufacturing (CAM) for fabrication of foot molds and custom foot orthotic components. Adoption of 3D printing, as a form of CAM, requires further investigation for use as a clinical tool.
This study provides a preliminary description of a new method to manufacture foot orthoses using a novel 3D scanner and printer and compare gait kinematic outputs from shod and traditional plaster casted orthotics.
Findings
One participant (male, 25 years) was included with no lower extremity injuries. Foot molds were created from both plaster casting and 3D scanning/printing methods. Custom foot orthoses were then fabricated from each mold. Lower body plug-in-gait with the Oxford Foot Model on the right foot was collected for both orthotic and control (shod) conditions. The medial longitudinal arch was measured using arch height index (AHI) where a decrease in AHI represented a drop in arch height. The lowest AHI was 21.2 mm in the running shoes, followed by 21.4 mm wearing the orthoses made using 3D scanning and printing, with the highest AHI of 22.0 mm while the participant wore the plaster casted orthoses.
Conclusion
This preliminary study demonstrated a small increase in AHI with the 3D printing orthotic compared to the shod condition. A larger sample size may demonstrate significant patterns for the tested conditions.
doi:10.1186/1756-0500-7-443
PMCID: PMC4114407  PMID: 25015013
Custom-made foot orthoses; 3D printing; Microsoft Kinect; plaster casting
7.  Comparative assessment of commercial ELISA kits for detection of HIV in India 
BMC Research Notes  2014;7:436.
Background
India harbors the 3rd highest HIV infected population globally. The magnitude of the HIV detection challenge is enormous. ELISA is the most commonly used screening technique for HIV. There is always an acute need for good quality ELISA kits. However, the quality evaluation data on Indian kits are very limited in comparison with internationally recognized kits. This study aimed to evaluate the performance and diagnostic usefulness of five commercially available ELISA kits which are frequently used in India.
Findings
The ELISA kits evaluated using an in-house well characterized 100 member sera panel revealed 100% sensitivity for all the batches. However, batch to batch variation in terms of specificity, positive predictive value (PPV) and efficiency, although not statistically significant (p > 0.05), was observed. For specificity, the 3rd generation kits (mean 99.6% to 99.3%) were comparatively better than the 4th generation assays (97.2% to 96.9%). But the 4th generation kits performed far better in the ability for early detection post HIV infection in the 25 member commercial seroconversion panel with a margin of at least 22 days and as high as 35 days than the 3rd generation assays.
Conclusions
The commercial ELISA kits with 100% sensitivity seem appropriate for HIV screening. The ability of early detection post HIV infection favors use of 4th generation kits for ensuring HIV free blood for transfusion. Lot to lot variations, especially kits having the specificity level ≤98.0%, indicate the need for a regular mechanism of kit evaluation for each batch for procuring kits appropriate for intended use.
doi:10.1186/1756-0500-7-436
PMCID: PMC4112990  PMID: 25001981
HIV; ELISA; Sensitivity; Specificity; Efficiency; Sera panel; Seroconversion panel
8.  Potential causes of black-stained peritoneal dialysis tubing: an analysis from nurse practitioner’s prospect 
BMC Research Notes  2014;7:434.
Background
Continuous Ambulatory Peritoneal dialysis (CAPD) has been promoted to be the main method of treatment for Thai End-Stage Renal Disease (ESRD) patients; however, a national survey of dialysis centers reported an annual incidence of black-stained particle of 57.6 per 1,000 CAPD cases. The objective of this study was to identify potential causes of the stain in the nurse practitioners’ prospect.
Findings
This study applied three-round Delphi technique. In the first round, the questionnaire was sent to 127 nurses in all dialysis centers. Their responses were analyzed to come up with an anonymous summary, which was presented in the second and third round of the survey among 80 and 200 nurses. The response rates of the three rounds of Delphi were 57.5%, 81.3%, and 75.0%, respectively. Nurses consistently believed that the contamination was caused by spilled-out povidone-iodine solution during transfer set change. Other potential causes were previous peritonitis, inadequate dialysis, low serum albumin, transfer set soaking with antiseptics, patient history of diabetes, dressing technique, and existence of dry abdomen period.
Conclusions
Black-stained particle is a common contamination of dialysis tube in CAPD patients. This study proposed some potential determinants, most of which were relevant to care process.
doi:10.1186/1756-0500-7-434
PMCID: PMC4098673  PMID: 24997794
Contamination; Delphi; Peritoneal dialysis; Nurse practitioner
9.  Low seroprevalence of Coxiella burnetii in Boer goats in Missouri 
BMC Research Notes  2014;7:421.
Background
Goats are known reservoirs of Coxiella burnetii, the etiologic agent of Q fever. However, there has been very little research on the prevalence of C. burnetii exposure and risk in meat goats farmed in the US. Banked serum samples were secondarily tested for C. burnetii specific antibodies.
Findings
The animal and herd-level seroprevalence estimates for C. burnetii were 1.2% (3/249) and 4.2% (1/24) respectively. Within-herd seroprevalence ranged from 0% to 1.2%.
Conclusions
This study indicates that seroprevalence of C. burnetii in Boer goats raised in Missouri was low, but it does not preclude the existence of a higher level of infection in Missouri’s meat goat herds. This result is inconclusive because this study was disadvantaged by the small number of individual animal and herds tested, which compromised the statistical power of this study to detect a possible higher seroprevalence of C. burnetii in this population, if present. More research is warranted to corroborate the preliminary findings reported here in order to determine the public health significance C. burnetii infection risks associated with contemporary goat production systems in the US.
doi:10.1186/1756-0500-7-421
PMCID: PMC4102339  PMID: 24994554
Coxiella burnetii; Goats; Q fever; Missouri; United States
10.  Ubiquinol reduces gamma glutamyltransferase as a marker of oxidative stress in humans 
BMC Research Notes  2014;7:427.
Background
The reduced form of Coenzyme Q10 (CoQ10), ubiquinol (Q10H2), serves as a potent antioxidant in mitochondria and lipid membranes. There is evidence that Q10H2 protects against oxidative events in lipids, proteins and DNA. Serum gamma-glutamyltransferase (GGT) activity is associated with cardiovascular diseases. In a physiological range, activity of GGT is a potential early and sensitive marker of inflammation and oxidative stress.
In this study, we first examined the relationship between CoQ10 status and serum GGT activity in 416 healthy participants between 19 and 62 years of age in a cross-sectional study (cohort I). In the second step, 53 healthy males (21–48 years of age; cohort II) underwent a 14-day Q10H2 supplementation (150 mg/d) to evaluate the effect of Q10H2 supplementation on serum GGT activity and GGT1 gene expression.
Findings
There was a strong positive association between CoQ10 status and serum GGT activity in cohort I. However, a gender-specific examination revealed differences between male and female volunteers regarding the association between CoQ10 status and serum GGT activity. Q10H2 supplementation (cohort II) caused a significant decrease in serum GGT activity from T0 to T14 (p < 0.001). GGT1 mRNA levels declined 1.49-fold after Q10H2 supplementation. Of note, other liver enzymes (i.e., aspartate aminotransferase, AST) were not affected by Q10H2 supplementation.
Conclusions
CoQ10 level is positively associated with serum GGT activity. Supplementation with Q10H2 reduces serum GGT activity. This effect might be caused by gene expression. Overall, we provide preliminary evidence that higher Q10H2 levels improve oxidative stress via reduction of serum GGT activity in humans.
Trial registration
Current Controlled Trials ISRCTN26780329.
doi:10.1186/1756-0500-7-427
PMCID: PMC4105833  PMID: 24996614
Coenzyme Q10; Ubiquinol; Gene expression; Supplementation study; Liver enzymes; Oxidative stress; Antioxidants
11.  Dry eye in LASIK patients 
BMC Research Notes  2014;7:420.
Background
Increasing age is a known risk factor for developing dry eye. The specific aims of the present study were to determine the prevalence of dry eye syndrome (DES) and use of post-operative dry eye medications in a relatively young population presenting for LASIK surgery at an academic ophthalmology clinic.
Findings
A retrospective, analysis of 948 de-identified patient charts (median age 39 years, not age stratified) was performed to extract pre-LASIK diagnoses and post-LASIK medication lists. Clinical evaluation for DES and the results of Schirmer’s reflex tear flow test were used to assign LASIK patients into Normal, Pre-dry eye (Pre-DES), and Dry Eye Syndrome (DES) groups; which were then compared for use of dry eye medications.
Based on pre-operative diagnoses, only 2% (CI: 1.3 – 3.1) of LASIK patients presented with overt DES. Unexpectantly, 25% (CI: 22.2 – 27.6) of LASIK patients labeled Pre-DES were not classified by the clinician as having overt DES, yet they showed poor reflex tear flow rates ≤ 5 mm before surgery, and frequently used post-operative lubricant dry eye medications.
Conclusions
Although the number of patients with pre-existing eye conditions was unknown, a sizable portion of relatively young LASIK patients displays poor reflex tear flow without overt DES. Such patients could go on to develop more serious consequences of poor tear flow, such as corneal abrasion and erosion. More specific, dry eye medications may be needed for ideal treatment.
doi:10.1186/1756-0500-7-420
PMCID: PMC4088369  PMID: 24994125
Dry eye; Human; LASIK; Schirmer’s reflex tear flow; Dry eye medication
12.  A pilot study of depression among older people in Rawalpindi, Pakistan 
BMC Research Notes  2014;7:409.
Background
Depression is common among elderly in developed countries and it is more pronounced in institutional settings. In Pakistan there is a lack of empirical data on depression among this segment of the population particularly with reference to their living arrangements.
The objectives of the present study are to report the magnitude of depression among elderly having two different residential arrangements and to examine the association of depression and its established demographic factors.
Findings
Data were collected from 141 respondents. 108 were community residents (m = 57 and f = 51) and 33 were living in the care homes (m = 29 and f = 4).
Prevalence of depression as assessed by Geriatric Depression Scale (GDS) among community and Care Homes (CHs) participants was 31.5 percent and 60.6 percent, respectively.
On Centre of Epidemiological Studies Depression Scale (CES-D), 42.6 percent of the community and 69.7 percent of the CH respondents were deemed depressed. Before adjusting for any other potential risk factors the odds of being depressed was significantly increased if the study participants were living in CH, relatively older, female, not currently married, had low educational level, had lower Mini Mental State Examination (MMSE) scores, and reported lower perceived emotional and practical support. In a partially adjusted logistic regression model an increased risk of depression was not confounded by any of the above mentioned risk factors.
However, the risk associated was not significant when it was adjusted for social support.
Conclusions
The findings of the current study are consistent with previous research and throws light on the dire need for interventions to address mental health needs of Pakistani elderly.
Implications for improving the mental health status of elderly are also presented.
doi:10.1186/1756-0500-7-409
PMCID: PMC4119248  PMID: 24973800
Elderly mental health; Social support; Living arrangement
13.  Identification of pathogens from blood culture bottles in spiked and clinical samples using matrix-assisted laser desorption ionization time-of-flight mass-spectrometry analysis 
BMC Research Notes  2014;7:405.
Background
Blood stream infections significantly contribute to mortality. An early most appropriate antimicrobial therapy is crucial for a favourable outcome of the patient. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) may speed up the diagnostic of causative micro organisms.
Findings
MALDI-TOF MS using the SARAMIS database was applied to 37 spiked blood culture samples. Identification rates of spiked samples were as follows: The species level was determined in 16 of 21 (76.2%) Gram negative bacteria and in 11 of 13 (84.6%) Gram positive bacteria. Genus level only was determined in additional 2 Gram negative and for the 2 Gram positive strains. Yeast species could not be identified.
MALDI-TOF MS was also compared to cultured-based results in standard routine diagnostic. Identification rates of patient samples were as follows: The species level was determined in 41 of 47 (87.2%) Gram negative bacteria and in 63 of 123 (51.2%) Gram positive bacteria. Genus level only was determined in additional 2 Gram negative bacteria. Once again no yeasts were identified.
A prolonged incubation of BC bottles for 16 hours after primary positive alert did not influence the concentration of bacteria and identification rates.
Conclusions
The SARAMIS database used in our experiments mainly confirms previous findings that were obtained with the MALDI-TOF MS BRUKER system by others.
doi:10.1186/1756-0500-7-405
PMCID: PMC4091744  PMID: 24972877
Mass spectrometry; Blood culture; Bloodstream infection
14.  Effect of the Y chromosome on plasma high-density lipoprotein-cholesterol levels in Y-chromosome-consomic mouse strains 
BMC Research Notes  2014;7:393.
Background
Plasma high-density lipoprotein (HDL)-cholesterol level is a clinically important quantitative phenotype that widely varies among inbred mouse strains. Several genes or loci associated with plasma HDL-cholesterol levels have been identified on autosomes and the X chromosome. In contrast, genes or loci on the Y chromosome have not attracted significant attention hitherto. Therefore, we investigated the effects of the Y chromosome on plasma HDL-cholesterol levels in Y- chromosome-consomic (Y-consomic) mouse strains.
Findings
Plasma HDL-cholesterol level data from 16 Y-consomic strains demonstrated that the Y chromosome substitutions significantly altered plasma HDL-cholesterol levels, i.e., variations in the plasma HDL-cholesterol level could be partially explained by Y chromosome genes. We obtained the following results from the genotype data on 30 single nucleotide polymorphisms (SNPs), including nonsynonymous and synonymous SNPs and 9 polymorphisms in Sry: (1) Variation in rs46947134 of Uty was significantly associated with plasma HDL-cholesterol levels. (2) A CAG repeat number polymorphism in Sry was significantly associated with plasma HDL-cholesterol levels. (3) Strains with a certain haplotype of the Mus musculus domesticus-type Y chromosome had significantly lower plasma HDL-cholesterol levels than strains with a certain haplotype of the M. m. musculus-type Y chromosome.
Conclusions
The effect of the Y chromosome on plasma HDL-cholesterol levels was confirmed in the Y-consomic strains. We identified several variants associated with plasma HDL-cholesterol levels. Because the physiological significance of various Y-linked genes remains unclear, the results of this study will provide further insights into the functions of Y-linked genes in lipid metabolism.
doi:10.1186/1756-0500-7-393
PMCID: PMC4080985  PMID: 24962540
HDL-cholesterol; Sry; Uty; Y-chromosome-consomic mouse strains
15.  Long term outcome of acute kidney injury due to leptospirosis? A longitudinal study in Sri Lanka 
BMC Research Notes  2014;7:398.
Background
Leptospirosis is an important zoonotic disease of variable severity and is a common cause of acute kidney injury (AKI) in tropics. However the knowledge on long term renal outcome in leptospirosis is scarce. This study aims to assess the long-term renal outcome of AKI caused by leptospirosis.
Findings
Hospital records of patients who had developed AKI following leptospirosis (Serologically confirmed) presented to two Teaching Hospitals in Kandy district over 3 years from 2007 were studied. A total of 44 patients were included and they had been followed up at least for one year in out patient clinics with regular assessment including renal status. Renal histology was studied in two patients. The primary outcome measure was normalization of renal function at one year. Of the 44 patients, 31 were in the risk and injury stage (Group 1), and the rest of them were in the failure stage (Group 2) under RIFLE criteria. Of group 2 patients, 11 had abnormal renal functions on discharge. Their mean serum creatinine and GFR values on discharge were 392 mmol/l and 20 ml/min/1.73 m2. Other two patients had full renal recovery whilst in the hospital. Nine in the group 2 required renal replacement therapy by means of peritoneal dialysis, intermittent haemodialysis or haemofiltration. Seventeen out of the total had persistently abnormal renal functions on discharge. Of them 13 recovered their renal functions to normal. Four patients (9%) who belonged to group 2, had persistently abnormal renal functions after first year compatible with stage 3 chronic kidney disease (CKD). Renal histology of two patients showed tubulointerstitial lymphocyte infiltrate, tubular atrophy and interstitial fibrosis.
Conclusion
The long term renal outcome of AKI following leptospirosis is satisfactory as only 9% of patients had abnormal renal functions compatible with early stage of CKD. Even among them, advanced CKD or dialysis dependency had not been observed.
doi:10.1186/1756-0500-7-398
PMCID: PMC4080986  PMID: 24964804
Leptospirosis; Acute kidney injury; Chronic kidney disease; Long term renal outcome; Sri Lanka
16.  What time-lag for a retraction search on PubMed? 
BMC Research Notes  2014;7:395.
Background
To investigate fraud and errors, scientists have studied cohorts of retraction notices. These researches have been performed using a PubMed search on publication type “retraction of publication” which retrieves the notices of the retractions. We assessed the stability of the indexation of retraction notices over a 15-month period and what was the time-lag to get stability.
Findings
A search on notices of retraction issued in 2008 was repeated every 3 months during 15 months from February 2011. The first search resulted in 237 notices of retraction. Throughout the study period, 14 discrepancies with the initial search were observed (6%). We found that the number of retraction notices became stable 35 months after the retraction.
Conclusions
The time-lag observed in this study has to be taken into account when performing a PubMed search.
doi:10.1186/1756-0500-7-395
PMCID: PMC4105554  PMID: 24965905
Retraction; Time-lag
17.  Zinc and copper levels in low birth weight deliveries in Medani Hospital, Sudan 
BMC Research Notes  2014;7:386.
Background
Low birth weight (LBW) is a worldwide health problem, especially in developing countries. We conducted a case–control study at Medani Hospital, Sudan. Cases were women who delivered a LBW (<2500 g) newborn and consecutive women who delivered a normal weight (>2500 g) newborn were controls. Questionnaires were used to collect clinical data. Zinc and copper levels were measured by an atomic absorption spectrophotometer.
Findings
The two groups (50 in each arm) were well matched in their basic characteristics. Median (25–75th interquartile range) maternal zinc (62.9 [36.3–96.8] vs. 96.2 [84.6–125.7] μg/dl; P <0.001) and copper (81.6 [23.7–167.5] vs. 139.8 [31.9–186.2] μg/dl; P = 0.04) levels were significantly lower in cases than in controls. Cord copper levels in cases were significantly lower than those in controls (108 [55.1–157.9] vs. 147.5 [84.5–185.2] μg/dl; P = 0.02). There were significant direct correlations between birth weight and maternal copper levels and maternal and cord zinc levels.
Conclusions
Maternal zinc and copper levels, as well as cord copper levels, are lower in LBW newborns than in those with normal weight.
doi:10.1186/1756-0500-7-386
PMCID: PMC4081538  PMID: 24958541
Zinc; Copper; Low birth weight; Sudan
18.  Effects of flavonoid-induced oxidative stress on anti-H5N1 influenza a virus activity exerted by baicalein and biochanin A 
BMC Research Notes  2014;7:384.
Background
Different flavonoids are known to interfere with influenza A virus replication. Recently, we showed that the structurally similar flavonoids baicalein and biochanin A inhibit highly pathogenic avian H5N1 influenza A virus replication by different mechanisms in A549 lung cells. Here, we investigated the effects of both compounds on H5N1-induced reactive oxygen species (ROS) formation and the role of ROS formation during H5N1 replication.
Findings
Baicalein and biochanin A enhanced H5N1-induced ROS formation in A549 cells and primary human monocyte-derived macrophages. Suppression of ROS formation induced by baicalein and biochanin A using the antioxidant N-acetyl-L-cysteine strongly increased the anti-H5N1 activity of both compounds in A549 cells but not in macrophages.
Conclusions
These findings emphasise that flavonoids induce complex pharmacological actions some of which may interfere with H5N1 replication while others may support H5N1 replication. A more detailed understanding of these actions and the underlying structure-activity relationships is needed to design agents with optimised anti-H5N1 activity.
doi:10.1186/1756-0500-7-384
PMCID: PMC4080993  PMID: 24958200
H5N1; Biochanin A; Baicalein; Antiviral; Reactive oxygen species; N-acetyl-L-cysteine
19.  Evaluation of coding-independent functions of the transcribed bovine aromatase pseudogene CYP19P1 
BMC Research Notes  2014;7:378.
Background
CYP19A1 encodes the aromatase which catalyzes the final reaction of estrogen biosynthesis. The bovine genome also contains a non-coding copy of CYP19A1, the transcribed pseudogene CYP19P1. Whereas CYP19A1 is transcribed in all estrogen-producing tissues, mainly in the placenta and gonads, the CYP19P1 transcript so far was detected in the placenta. Strikingly, one sequence segment of both transcripts exhibits an exceptional high identity of 98%, which implies selective pressure and suggests some kind of function. Only recently, indeed, coding-independent functions of several transcribed pseudogenes were reported. Therefore, we analyzed CYP19P1 and CYP19A1 transcripts with the aim to detect clues for gene–pseudogene interference.
Findings
The CYP19P1 transcript was first examined in silico for the presence of microRNA coding sequences and microRNA targets. Further, to identify tissues where CYP19P1 and CYP19A1 transcripts are co-expressed, as a pre-requisite for transcript interference, expression profiling was performed in a variety of bovine tissues. Our in silico analyses did neither reveal potential microRNA coding sequences, nor microRNA targets. Co-expression of the CYP19 loci was demonstrated in placental cotyledons and granulosa cells of dominant follicles. However, in granulosa cells of dominant follicles the concentration of CYP19P1 mRNA was very low compared to CYP19A1 mRNA.
Conclusions
CYP19P1 and CYP19A1 transcripts might interfere in placental cotyledons. However, in granulosa cells of dominant follicles relevant interference between gene and pseudogene transcripts is unlikely to occur because of the very low CYP19P1/CYP19A1 transcript ratio.
doi:10.1186/1756-0500-7-378
PMCID: PMC4076500  PMID: 24947985
CYP19A1; Placenta; Granulosa; Gene-pseudogene interference
20.  Antimicrobial resistance in urinary isolates from inpatients and outpatients at a tertiary care hospital in South-Kivu Province (Democratic Republic of Congo) 
BMC Research Notes  2014;7:374.
Background
The rate of antimicrobial resistant isolates among pathogens causing urinary tract infections (UTIs) in Democratic Republic of Congo (DRC) is not known. The aim of the current study was to determine this rate at the Bukavu Provincial General Hospital (province of South-Kivu, DRC).
Findings
A total of 643 isolates (both from inpatients and outpatients) collected from September 2012 to August 2013 were identified using biochemical methods, and tested for antimicrobial susceptibility. The isolates were further screened for Extended-Spectrum Beta-Lactamases (ESBL) production. Beta-lactamase AmpC phenotype was investigated in 20 antibiotic-resistant isolates.
Escherichia coli (58.5%), Klebsiella spp. (21.9%) and Enterobacter spp. (16.2%) were the most frequent uropathogens encountered. Rare uropathogens included Citrobacter spp., Proteus spp., and Acinetobacter spp. Resistance was significantly more present in inpatients isolates (22.1% of isolates) when compared to outpatients isolates (8.4% of isolates), (p-value <0.001). Antibiotic-resistant isolates displayed resistance to common antimicrobial drugs used for UTIs treatment in South Kivu province, namely: ciprofloxacin, ampicillin and third generation cephalosporins. ESBL-phenotype was present in 92.9% of antibiotic-resistant isolates. Only amikacin, nitrofurantoin and imipenem displayed satisfactory activity against antibiotic resistant isolates.
Conclusions
This study confirms the presence of antibiotic-resistant uropathogens (mainly ESBL-producers isolates) at the Bukavu General Hospital. This study should serve as a wake-up call and help to raise awareness about the threat to public health of antibiotic resistance in this DRC province.
doi:10.1186/1756-0500-7-374
PMCID: PMC4074390  PMID: 24943866
Urinary tract infections; South-Kivu; Democratic Republic of Congo; Multidrug resistance; Prevalence; Extended spectrum beta-lactamases; Antibotics
21.  Characterization of microsatellite markers developed from Prosopis rubriflora and Prosopis ruscifolia (Leguminosae - Mimosoideae), legume species that are used as models for genetic diversity studies in Chaquenian areas under anthropization in South America 
BMC Research Notes  2014;7:375.
Background
Prosopis rubriflora and Prosopis ruscifolia are important species in the Chaquenian regions of Brazil. Because of the restriction and frequency of their physiognomy, they are excellent models for conservation genetics studies. The use of microsatellite markers (Simple Sequence Repeats, SSRs) has become increasingly important in recent years and has proven to be a powerful tool for both ecological and molecular studies.
Findings
In this study, we present the development and characterization of 10 new markers for P. rubriflora and 13 new markers for P. ruscifolia. The genotyping was performed using 40 P. rubriflora samples and 48 P. ruscifolia samples from the Chaquenian remnants in Brazil. The polymorphism information content (PIC) of the P. rubriflora markers ranged from 0.073 to 0.791, and no null alleles or deviation from Hardy-Weinberg equilibrium (HW) were detected. The PIC values for the P. ruscifolia markers ranged from 0.289 to 0.883, but a departure from HW and null alleles were detected for certain loci; however, this departure may have resulted from anthropic activities, such as the presence of livestock, which is very common in the remnant areas.
Conclusions
In this study, we describe novel SSR polymorphic markers that may be helpful in future genetic studies of P. rubriflora and P. ruscifolia.
doi:10.1186/1756-0500-7-375
PMCID: PMC4079167  PMID: 24941887
Prosopis; Pantanal; Chaco; Population Genetics; Conservation; Short Tandem Repeats
22.  Development of a BALB/c 3T3 neutral red uptake cytotoxicity test using a mainstream cigarette smoke exposure system 
BMC Research Notes  2014;7:367.
Background
Tobacco smoke toxicity has traditionally been assessed using the particulate fraction under submerged culture conditions which omits the vapour phase elements from any subsequent analysis. Therefore, methodologies that assess the full interactions and complexities of tobacco smoke are required. Here we describe the adaption of a modified BALB/c 3T3 neutral red uptake (NRU) cytotoxicity test methodology, which is based on the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) protocol for in vitro acute toxicity testing. The methodology described takes into account the synergies of both the particulate and vapour phase of tobacco smoke. This is of particular importance as both phases have been independently shown to induce in vitro cellular cytotoxicity.
Findings
The findings from this study indicate that mainstream tobacco smoke and the gas vapour phase (GVP), generated using the Vitrocell® VC 10 smoke exposure system, have distinct and significantly different toxicity profiles. Within the system tested, mainstream tobacco smoke produced a dilution IC50 (dilution (L/min) at which 50% cytotoxicity is observed) of 6.02 L/min, whereas the GVP produced a dilution IC50 of 3.20 L/min. In addition, we also demonstrated significant dose-for-dose differences between mainstream cigarette smoke and the GVP fraction (P < 0.05). This demonstrates the importance of testing the entire tobacco smoke aerosol and not just the particulate fraction, as has been the historical preference.
Conclusions
We have adapted the NRU methodology based on the ICCVAM protocol to capture the full interactions and complexities of tobacco smoke. This methodology could also be used to assess the performance of traditional cigarettes, blend and filter technologies, tobacco smoke fractions and individual test aerosols.
doi:10.1186/1756-0500-7-367
PMCID: PMC4067082  PMID: 24935030
Tobacco smoke; Whole smoke; Gas vapour phase; Smoke exposure system; Neutral red; BALB/c3T3
23.  Assessing professional behaviour: Overcoming teachers’ reluctance to fail students 
BMC Research Notes  2014;7:368.
Background
Developing professional behaviour is an important goal of medical education in which teachers play a significant part. Many teachers can be reluctant to fail students demonstrating unprofessional behaviour. We hypothesize that supporting teachers in teaching and assessing professional behaviour and involving them in remediation will reduce this reluctance.
Findings
In 2010, VUmc School of Medical Sciences Amsterdam introduced an educational theme on professional behaviour for the bachelor's and master's programmes in medicine with a special emphasis on supporting teachers in teaching and assessing professional behaviour and involving them in the remediation process. Information was extracted from the student database on the number of unprofessional behaviour judgments awarded over 2008-2010 (before the intervention), and 2010-2013 (after introducing the intervention), which was compared. To find out if teachers' reluctance to fail had decreased, qualitative feedback from the teachers was gathered and analysed. Since the implementation of the educational theme, the number of unprofessional behaviour judgments has risen. The teachers are positive about the implemented system of teaching and assessing professional behaviour, and feel less reluctant to award an unsatisfactory professional behaviour judgment.
Conclusions
Supporting teachers in teaching and assessing professional behaviour and involving them in students' remediation appears to reduce their reluctance to fail students demonstrating unprofessional behaviour.
doi:10.1186/1756-0500-7-368
PMCID: PMC4080734  PMID: 24938392
Professionalism; Professional behaviour; Faculty development
24.  Unanswered questions about the Middle East respiratory syndrome coronavirus (MERS-CoV) 
BMC Research Notes  2014;7:358.
Background
The Middle East respiratory syndrome coronavirus (MERS-CoV) represents a current threat to the Arabian Peninsula, and potential pandemic disease. As of June 3, 2014, MERS CoV has reportedly infected 688 people and killed 282. We briefly summarize the state of the outbreak, and highlight unanswered questions and various explanations for the observed epidemiology.
Findings
The continuing but infrequent cases of MERS-CoV reported over the past two years have been puzzling and difficult to explain. The epidemiology of MERS-CoV, with many sporadic cases and a few hospital outbreaks, yet no sustained epidemic, suggests a low reproductive number. Furthermore, a clear source of infection to humans remains unknown. Also puzzling is the fact that MERS-CoV has been present in Saudi Arabia over several mass gatherings, including the 2012 and 2013 Hajj and Umrah pilgrimages, which predispose to epidemics, without an epidemic arising.
Conclusions
The observed epidemiology of MERS-CoV is quite distinct and does not clearly fit either a sporadic or epidemic pattern. Possible explanations of the unusual features of the epidemiology of MERS-CoV include sporadic ongoing infections from a non-human source; human to human transmission with a large proportion of undetected cases; or a combination of both. The virus has been identified in camels; however the mode of transmission of the virus to humans remains unknown, and many cases have no history of animal contact. In order to gain a better understanding of the epidemiology of MERS CoV, further investigation is warranted.
doi:10.1186/1756-0500-7-358
PMCID: PMC4068970  PMID: 24920393
MERS-CoV; Emerging infectious disease; Epidemiology
25.  Analysis of BRCA1and BRCA2 large genomic rearrangements in Sri Lankan familial breast cancer patients and at risk individuals 
BMC Research Notes  2014;7:344.
Background
Majority of mutations found to date in the BRCA1/BRCA2 genes in breast and/or ovarian cancer families are point mutations or small insertions and deletions scattered over the coding sequence and splice junctions. Such mutations and sequence variants of BRCA1 and BRCA2 genes were previously identified in a group of Sri Lankan breast cancer patients. Large genomic rearrangements have been characterized in BRCA1 and BRCA2 genes in several populations but these have not been characterized in Sri Lankan breast cancer patients.
Findings
A cohort of familial breast cancer patients (N = 57), at risk individuals (N = 25) and healthy controls (N = 23) were analyzed using multiplex ligation-dependent probe amplification method to detect BRCA1 and BRCA2 large genomic rearrangements. One familial breast cancer patient showed an ambiguous deletion in exon 6 of BRCA1 gene. Full sequencing of the ambiguous region was used to confirm MLPA results. Ambiguous deletion detected by MLPA was found to be a false positive result confirming that BRCA1 large genomic rearrangements were absent in the subjects studied. No BRCA2 rearrangement was also identified in the cohort.
Conclusion
Thus this study demonstrates that BRCA1 and BRCA2 large genomic rearrangements are unlikely to make a significant contribution to aetiology of breast cancer in Sri Lanka.
doi:10.1186/1756-0500-7-344
PMCID: PMC4057568  PMID: 24906410
BRCA1; BRCA2; Large genomic rearrangements; Breast cancer

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