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1.  Procalcitonin as a prognostic marker for sepsis: a prospective observational study 
BMC Research Notes  2014;7:458.
Background
Procalcitonin is useful for the diagnosis of sepsis but its prognostic value regarding mortality is unclear. This prospective observational study was designed to study the prognostic value of procalcitonin in prediction of 28 day mortality in patients of sepsis. Fifty-four consecutive patients of sepsis, severe sepsis and septic shock defined using the 2001 Consensus Conference SCCM/ESICM/ACCP/ATS/SIS criteria from medical Intensive Care Unit (ICU) of a tertiary care center in New Delhi, India were enrolled from July 2011 to June 2013. Procalcitonin (PCT), C-reactive protein (CRP) measurements were recorded on day 1, day 7 and day 28 of follow up.
Results
Procalcitonin value was a better predictor of all-cause short-term mortality than C-reactive protein. Those patients with Procalcitonin levels <7 ng/ml showed higher cumulative survival than those with level [greater than or equal to]7 ng/ml (69.1% vs. 39.5%, p = 0.02). No such effect was observed in relation to C-reactive protein. Procalcitonin levels [greater than or equal to]7 ng/ml predicted mortality with a hazard ratio of 2.6(1.1-6.3).
Conclusions
A Procalcitonin value [greater than or equal to]7 ng/ml obtained at the time of admission to the ICU is a predictor of short-term mortality and thus may allow the identification of those septic patients at increased mortality risk, and help improve their treatment.
doi:10.1186/1756-0500-7-458
PMCID: PMC4105100  PMID: 25034373
Sepsis; Prognosis; Procalcitonin; C-reactive protein
2.  Training obstetrics and gynecology residents to be effective communicators in the era of the 80-hour workweek: a pilot study 
BMC Research Notes  2014;7:455.
Background
To ensure optimal patient care, physicians must establish effective patient-physician relationships and thoughtfully incorporate their patients’ perspectives into their counseling. Historically, these skills are acquired with increasing clinical experience. However, given increasing work-hour restrictions, OB/GYN residents have fewer opportunities to develop these skills. Therefore, the objective of this study was to determine if an interactive learning method is an effective tool by which to teach OB/GYN residents how to communicate with complicated patients.
Methods
An experiential simulation model was developed to teach OB/GYN residents effective communication skills for dealing with patients experiencing a pregnancy-related complication. A simulated patient interaction was designed for first-year residents. Specific scenarios were constructed based on challenging clinical scenarios identified by second-year residents. Non-judgmental communication, culture competency awareness and reflective listening were key skills that were taught as part of the clinical scenarios. Both acceptability and utility of the exercise with the first-years was assessed by a follow-up survey.
Results
Seven first-year residents participated in the education session consisting of four physician-patient interactions with specific learning objectives for each. These first-year residents all indicated that they would employ the skills practiced during the intervention into their future practice of medicine, and that their comfort level in caring for complex obstetric patients had increased. Moreover, all first-year residents endorsed that this educational strategy was potentially applicable to other aspects of their training.
Conclusions
Simulated patient exercises can be utilized in multiple arenas to teach OB/GYN residents communication skills, while simultaneously addressing their clinical knowledge deficits. Early implementation of such a curriculum in an OB/GYN residency will lay the foundation for the development of empathetic and culturally competent physicians.
doi:10.1186/1756-0500-7-455
PMCID: PMC4105231  PMID: 25030271
Role-playing; Professionalism; Physician-patient relationship; Simulated patient encounters; Obstetrics and gynecology; ACGME milestones
3.  Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation 
BMC Research Notes  2014;7:444.
Background
Mass spectrometry (MS) is a very sensitive and specific method for protein identification, biomarker discovery, and biomarker validation. Protein identification is commonly carried out by comparing MS data with public databases. However, with the development of high throughput and accurate genomic sequencing technology, public databases are being overwhelmed with new entries from different species every day. The application of these databases can also be problematic due to factors such as size, specificity, and unharmonized annotation of the molecules of interest. Current databases representing liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based searches focus on enzyme digestion patterns and sequence information and consequently, important functional information can be missed within the search output. Protein variants displaying similar sequence homology can interfere with database identification when only certain homologues are examined. In addition, recombinant DNA technology can result in products that may not be accurately annotated in public databases. Curated databases, which focus on the molecule of interest with clearer functional annotation and sequence information, are necessary for accurate protein identification and validation. Here, four cases of curated database application have been explored and summarized.
Findings
The four presented curated databases were constructed with clear goals regarding application and have proven very useful for targeted protein identification and biomarker application in different fields. They include a sheeppox virus database created for accurate identification of proteins with strong antigenicity, a custom database containing clearly annotated protein variants such as tau transcript variant 2 for accurate biomarker identification, a sheep-hamster chimeric prion protein (PrP) database constructed for assay development of prion diseases, and a custom Escherichia coli (E. coli) flagella (H antigen) database produced for MS-H, a new H-typing technique. Clearly annotating the proteins of interest was essential for highly accurate, specific, and sensitive sequence identification, and searching against public databases resulted in inaccurate identification of the sequence of interest, while combining the curated database with a public database reduced both the confidence and sequence coverage of the protein search.
Conclusion
Curated protein sequence databases incorporating clear annotations are very useful for accurate protein identification and fit-for-purpose application through MS-based biomarker validation.
doi:10.1186/1756-0500-7-444
PMCID: PMC4102332  PMID: 25011440
Curated database; Targeted protein identification; Sheeppox virus; Flagellar typing; Tau; Recombinant prion protein
4.  Anemia in a cohort of HIV-infected Hispanics: prevalence, associated factors and impact on one-year mortality 
BMC Research Notes  2014;7:439.
Background
Anemia occurs frequently in HIV-infected patients and has been associated with an increased risk of death in this population. For Hispanic subjects, information describing this blood disorder during HIV is scarce. Therefore, the present study examined data from a cohort of HIV-positive Hispanics to determine the prevalence of anemia, identify its associated factors, and evaluate its relationship with one-year mortality.
Methods
This study included 1,486 patients who enrolled between January, 2000 and December, 2010 in an HIV-cohort in Bayamón, Puerto Rico. Data were collected through personal interviews and medical record abstractions. To determine the factors independently associated with anemia, a multivariable logistic regression model was used. Kaplan-Meier and Cox proportional hazards models were also performed to estimate survival time and to predict death risk.
Results
The prevalence of anemia at enrollment was 41.5%. Factors independently associated with increased odds of anemia were: unemployment (OR = 2.02; 95% CI 1.45-2.79), CD4 count <200 cells/μL (OR = 2.66; 95% CI 1.94-3.66), HIV viral load ≥100,000 copies/mL (OR = 1.94; 95% CI 1.36-2.78), white blood cell count <4,000 cells/μL (OR = 2.42; 95% CI 1.78-3.28) and having clinical AIDS (OR = 2.39; 95% CI 1.39-4.09). Overweight (OR = 0.43; 95% CI 0.32-0.59) and obese (OR = 0.44; 95% CI 0.29-0.67) BMI’s were independently associated with reduced odds of anemia. Survival differed significantly by anemia status (log-rank test: p < 0.001). One-year mortality estimates were: 30.8%, 23.3%, 8.4% and 2.5%, for patients with severe, moderate, mild and no anemia, respectively. Having anemia at baseline was independently associated with an increased one-year mortality risk (severe anemia: HR = 9.06; 95% CI: 4.16-19.72; moderate anemia: HR = 6.51; 95% CI: 3.25-13.06; mild anemia: HR = 2.53; 95% CI: 1.35-4.74).
Conclusions
A high prevalence of anemia at enrollment was observed in this cohort of HIV-infected Hispanics. Unemployment and several adverse prognostic features of HIV infection were independently associated with this blood disorder. Anemia resulted to be the strongest predictor of one-year mortality, evidencing a dose–response effect. Further investigations are needed to evaluate whether recovering from anemia is associated with longer survival, and to identify the types of anemia affecting this particular group of HIV patients.
doi:10.1186/1756-0500-7-439
PMCID: PMC4099091  PMID: 25005803
Anemia; HIV; Hispanics; Prevalence; Mortality; Puerto Rico
5.  Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure 
BMC Research Notes  2014;7:435.
Background
Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) has been identified recently as a novel regulator of estrogen signalling in breast cancer cells. Despite being a potential target for new breast cancer treatment, its amino acid sequence suggests no association with any well-characterized protein family and provides little clues as to its molecular function. In this paper, we predicted the structure, function and interactions of BIG3 using a range of bioinformatic tools.
Results
Homology search results showed that BIG3 had distinct features from its paralogues, BIG1 and BIG2, with a unique region between the two shared domains, Sec7 and DUF1981. Although BIG3 contains Sec7 domain, the lack of the conserved motif and the critical glutamate residue suggested no potential guaninyl-exchange factor (GEF) activity. Fold recognition tools predicted BIG3 to adopt an α-helical repeat structure similar to that of the armadillo (ARM) family. Using state-of-the-art methods, we predicted interaction sites between BIG3 and its partner PHB2.
Conclusions
The combined results of the structure and interaction prediction led to a novel hypothesis that one of the predicted helices of BIG3 might play an important role in binding to PHB2 and thereby preventing its translocation to the nucleus. This hypothesis has been subsequently verified experimentally.
doi:10.1186/1756-0500-7-435
PMCID: PMC4096751  PMID: 24997568
Breast cancer; Estrogen receptor-alpha; BIG3; PHB2; Protein-protein interaction; Bioinformatics
6.  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
7.  Highly specific and efficient primers for in-house multiplex PCR detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma hominis and Ureaplasma urealyticum 
BMC Research Notes  2014;7:433.
Background
Although sophisticated methodologies are available, the use of endpoint polymerase chain reaction (PCR) to detect 16S rDNA genes remains a good approach for estimating the incidence and prevalence of specific infections and for monitoring infections. Considering the importance of the early diagnosis of sexually transmitted infections (STIs), the development of a sensitive and affordable method for identifying pathogens in clinical samples is needed. Highly specific and efficient primers for a multiplex polymerase chain reaction (m-PCR) system were designed in silico to detect the 16S rDNA genes of four bacteria that cause genital infections, and the PCR method was developed.
Methods
The Genosensor Probe Designer (GPD) (version 1.0a) software was initially used to design highly specific and efficient primers for in-house m-PCR. Single-locus PCR reactions were performed and standardised, and then primers for each locus in turn were added individually in subsequent amplifications until m-PCR was achieved. Amplicons of the expected size were obtained from each of the four bacterial gene fragments. Finally, the analytical specificity and limits of detection were tested.
Results
Because they did not amplify any product from non-STI tested species, the primers were specific. The detection limits for the Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma hominis and Ureaplasma urealyticum primer sets were 5.12 × 105, 3.9 × 103, 61.19 × 106 and 6.37 × 105 copies of a DNA template, respectively.
Conclusions
The methodology designed and standardised here could be applied satisfactorily for the simultaneous or individual detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma hominis and Ureaplasma urealyticum. This method is at least as efficient as other previously described methods; however, this method is more affordable for low-income countries.
doi:10.1186/1756-0500-7-433
PMCID: PMC4099392  PMID: 24997675
Multiplex PCR; Cervicitis; Detection; 16S rDNA genes
8.  A qualitative study of the factors that influence mothers when choosing drinks for their young children 
BMC Research Notes  2014;7:430.
Background
The consumption of sweetened beverages is a known common risk factor for the development of obesity and dental caries in children and children consume sweet drinks frequently and in large volumes from an early age. The aim of this study was to examine factors that influence mothers when choosing drinks for their children.
Method
Semi-structured interviews (n = 32) were conducted with a purposive sample of mothers of young children from Victoria’s Barwon South Western Region (selected from a larger cohort study to include families consuming different types of water, and different socioeconomic status and size). Inductive thematic analysis was conducted on transcribed interviews.
Results
Several themes emerged as influencing child drink choice. Child age: Water was the main beverage for the youngest child however it was seen as more acceptable to give older children sweetened beverages. Child preference and temperament: influencing when and if sweet drinks were given; Family influences such as grandparents increased children’s consumption of sweet drinks, often providing children drinks such as fruit juice and soft drinks regardless of maternal disapproval. The Setting: children were more likely to be offered sweetened drinks either as a reward or treat for good behaviour or when out shopping, out for dinner or at parties.
Conclusions
Limiting intake of sweet drinks is considered an important step for child general and oral health. However, the choice of drinks for children has influences from social, environmental and behavioural domains, indicating that a multi-strategy approach is required to bring about this change.
doi:10.1186/1756-0500-7-430
PMCID: PMC4097085  PMID: 24997015
9.  The role of Staphylococcus aureus carriage in the pathogenesis of bloodstream infection 
BMC Research Notes  2014;7:428.
Background
Staphylococcus aureus (SA) colonisation is associated with development of bloodstream infection (BSI), with the majority of colonising and infecting strains identical by pulsed-field gel electrophoresis (PFGE). We examined SA colonisation in patients with SABSI to delineate better the relationship between the two.
Methods
Patients with SABSI were swabbed in the nose, throat, groin, axilla and rectum. Isolates were typed using PFGE. Logistic regression was performed to determine factors associated with positive swabs.
Results
79 patients with SABSI had swabs taken. 46 (58%) had ≥ 1 screening swab positive for S. aureus; of these 37 (80%) were in the nose, 11 (24%) in the throat, 12 (26%) in the groin, 11 (24%) in the axilla and 8 (17%) in the rectum. On multivariate analysis, days from blood culture to screening swabs (OR 0.5, 95% CI 0.32-0.78, P = 0.003) and methicillin resistance (OR 9.5, 95% CI 1.07-84.73, P = 0.04) were associated with having positive swabs. Of 46 participants who had a blood sample and 1 other sample subtyped, 33 (72%, 95% CI 57-84%) had all identical subtypes, 1 (2%) had subtypes varying by 1–3 bands and 12 (26%) had subtypes ≥ 3 bands different. 30/36 (83%) blood-nose pairs were identical.
Conclusion
Overall, 58% of patients with SABSI had positive screening swabs. Of these, only 80% had a positive nose swab ie less than half (37/79, 47%) of all SABSI patients were nasally colonised. This may explain why nasal mupirocin alone has not been effective in preventing SA infection. Measures to eradicate non-nasal carriage should also be included.
doi:10.1186/1756-0500-7-428
PMCID: PMC4099385  PMID: 24996783
Staphylococcus aureus; Blood stream infection; Colonisation
10.  Characterization of DNase activity and gene in Streptococcus suis and evidence for a role as virulence factor 
BMC Research Notes  2014;7:424.
Background
The Gram-positive bacterium Streptococcus suis serotype 2 is an important swine pathogen and emerging zoonotic agent. Multilocus sequence typing allowed dividing S. suis serotype 2 into sequence types (STs). The three major STs of S. suis serotype 2 from North America are 1 (most virulent), 25 (intermediate virulence) and 28 (less virulent). Although the presence of DNase activity in S. suis has been previously reported, little data is available. The aim of this study was to investigate DNase activity in S. suis according to STs, to characterize the activity and gene, and to provide evidence for a potential role in virulence.
Results
We showed that ST1 and ST28 strains exhibited DNase activity that was absent in ST25 strains. The lack of activity in ST25 isolates was associated with a 14-bp deletion resulting in a shifted reading frame and a premature stop codon. The DNase of S. suis P1/7 (ST1) was cell-associated and active on linear DNA. A DNase-deficient mutant of S. suis P1/7 was found to be less virulent in an amoeba model. Stimulation of macrophages with the DNase mutant showed a decreased secretion of pro-inflammatory cytokines and matrix metalloproteinase-9 compared to the parental strain.
Conclusions
This study further expands our knowledge of S. suis DNase and its potential role in virulence.
doi:10.1186/1756-0500-7-424
PMCID: PMC4094637  PMID: 24996230
Streptococcus suis; nuclease; DNase activity; Virulence factor; SsnA
11.  Primary immunodeficiency diagnosed at autopsy: a case report 
BMC Research Notes  2014;7:425.
Background
DiGeorge syndrome may manifest as severe immunodeficiency diagnosed at infancy. The diagnosis of primary immunodeficiency is based on characteristic clinical features, immunophenotyping by flow cytometry, molecular diagnostics and functional lymphocyte evaluation. At autopsy, gross evaluation, conventional histology and immunohistochemistry may be useful for the diagnosis of primary immunodeficiency. This case report illustrates the application of autopsy and immunohistochemistry in the diagnosis of DiGeorge syndrome.
Case presentation
A four-month-old African female infant died while undergoing treatment at Kenyatta National Hospital, a Referral and Teaching Hospital in Nairobi, Kenya. She presented with a month’s history of recurrent respiratory infections, a subsequent decline in the level of consciousness and succumbed to her illness within four days. Her two older siblings died following similar circumstances at ages 3 and 5 months respectively. Autopsy revealed thymic aplasia, bronchopneumonia and invasive brain infection by Aspergillus species. Microbial cultures of cerebrospinal fluid, jejunal contents, spleen and lung tissue revealed multi drug resistant Klebsiella spp, Pseudomonas spp, Serratia spp and Escherichia coli. Immunohistochemistry of splenic tissue obtained from autopsy confirmed reduction of T lymphocytes.
Conclusion
Use of immunohistochemistry on histological sections of tissues derived from autopsy is a useful adjunct for post mortem diagnosis of DiGeorge syndrome.
doi:10.1186/1756-0500-7-425
PMCID: PMC4094674  PMID: 24996427
Primary immunodeficiency; DiGeorge syndrome; autopsy; Immunohistochemistry
12.  Effect of teaching with or without mirror on balance in young female ballet students 
BMC Research Notes  2014;7:426.
Background
In literature there is a general consensus that the use of the mirror improves proprioception. During rehabilitation the mirror is an important instrument to improve stability. In some sports, such as dancing, mirrors are widely used during training. The purpose of this study is to evaluate the effectiveness of the use of a mirror on balance in young dancers. Sixty-four young dancers (ranging from 9–10 years) were included in this study. Thirty-two attending lessons with a mirror (mirror- group) were compared to 32 young dancers that attended the same lessons without a mirror (non-mirror group). Balance was evaluated by BESS (Balance Error Scoring System), which consists of three stances (double limb, single limb, and tandem) on two surfaces (firm and foam). The errors were assessed at each stance and summed to create the two subtotal scores (firm and foam surface) and the final total score (BESS). The BESS was performed at recruitment (T0) and after 6 months of dance lessons (T1).
Results
The repeated measures ANOVA analysis showed that for the BESS total score there is a difference due to the time (F = 3.86; p < 0.05). No other differences due to the group or to the time of measurement were found (p > 0.05). The analysis of the multiple regression model showed the influence of the values at T0 for every BESS items and the dominance of limb for stability on an unstable surface standing on one or two legs.
Conclusions
These preliminary results suggest that the use of a mirror in a ballet classroom does not improve balance acquisition of the dancer. On the other hand, improvement found after 6 months confirms that at the age of the dancers studied motor skills and balance can easily be trained and improved.
doi:10.1186/1756-0500-7-426
PMCID: PMC4102331  PMID: 24996519
Dancing; Postural balance; Mirror neurons; Feedback; Sensory
13.  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
14.  Evaluation of microleakage of class II dental composite resin restorations cured with LED or QTH dental curing light; Blind, Cluster Randomized, In vitro cross sectional study 
BMC Research Notes  2014;7:416.
Background
The aim of this study is to compare the microleakage of Class II dental composite resin restorations which have been cured by three different LED (light emitting diode) light curing modes compared to control samples cured by QTH (quartz tungsten halogen) light curing units (LCUs), to determine the most effective light curing unit and mode of curing.
Results
In this experimental study, class II cavities were prepared on 100 sound human premolars which have been extracted for orthodontic treatment. The teeth were randomly divided into four groups; three experimental and one control group of 25 teeth each. Experimental groups were cured by either conventional, pulse-delay, or ramped curing modes of LED. The control group was cured for 20 seconds by QTH. The restorations were thermocycled (1000 times, between 5 and 55°C, for 5 seconds dwell time), dyed, sectioned mesio-distally and viewed under stereo-microscope (40×) magnification. Teeth were then scored on a 0 to 4 scale based on the amount of microleakage. The data were analyzed by Chi-square test.
No significant difference was demonstrated between the different LCUs (light curing units), or modes of curing, at the enamel side (p > 0.05). At the dentin side, all modes of LED curing could significantly reduce microleakage (p < 0.05). The results suggest that slow start curing improves marginal integrity and seal. High intense curing endangers those aims.
Conclusions
Comparison between the three LED mode cured composite resin restorations and QTH curing showed LED curing in all modes is more effective than QTH for reducing microleakage. Both LED and QTH almost completely eliminate the microleakage on the enamel side, however none of them absolutely eliminated microleakage on the dentin side.
doi:10.1186/1756-0500-7-416
PMCID: PMC4085696  PMID: 24990296
Class II cavity; Composite restoration; Microleakage; LED; QTH
15.  Clinical, immunological, and virological outcomes of pediatric antiretroviral therapy in central China 
BMC Research Notes  2014;7:419.
Background
Antiretroviral therapy (ART) reduces HIV-related mortality and morbidity substantially in children. The clinical characteristics, immunological and virological outcomes were evaluated in HIV-infected children receiving ART.
Methods
Twenty-six HIV-1-infected children receiving ART in Hubei province, China, were enrolled retrospectively in this study. During the period of ART, plasma viral load, lymphocyte phenotype of CD4 and CD8 cells and clinical events were assessed.
Results
The median duration of ART was 41 months (18–72.3 months). In children showing clinical improvement, high viral suppression rate below log10 (2.7) copies/ml by the third months of ART was observed. The median CD4 cell counts reached to 820.5/μl by 12 months and the median ratio of CD4/CD8 increased to 0.6 by 21 months. The counts of peripheral white blood cells and red blood cells decreased in the first 12 months, while Hb concentration, MCV and MCH increased (P < 0.001).
Conclusions
Despite the limited small sample size, ART is an effective strategy for inhibiting HIV replication and reconstructing the immunological response in children with AIDS.
doi:10.1186/1756-0500-7-419
PMCID: PMC4086285  PMID: 24994004
HIV/AIDS; Medical practice; Pediatrics; Antiretroviral therapy; Infectious diseases outcomes
16.  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
17.  ‘All in a box’ a concept for optimizing microbiological diagnostic sampling in prosthetic joint infections 
BMC Research Notes  2014;7:418.
Background
Accurate microbial diagnosis is crucial for effective management of prosthetic joint infections. Culturing of multiple intraoperative tissue samples has increased diagnostic accuracy, but new preparatory techniques and molecular methods hold promise of further improvement. The increased complexity of sampling is, however, a tough challenge for surgeons and assistants in the operation theatre, and therefore we devised and tested a new concept of pre-packed boxes with a complete assortment of swabs, vials and additional tools needed in the operating theatre for non-standard samples during a clinical study of prosthetic joint infections.
Findings
The protocol for the clinical study required triplicate samples of joint fluid, periprosthetic tissue, bone tissue, and swabs from the surface of the prosthesis. Separate boxes were prepared for percutaneous joint puncture and surgical revision; the latter included containers for prosthetic components or the entire prosthesis. During a 2-year project period 164 boxes were used by the surgeons, 98 of which contained a complete set of samples. In all, 1508 (89%) of 1685 scheduled samples were received.
Conclusion
With this concept a high level of completeness of sample sets was achieved and thus secured a valid basis for evaluation of new diagnostics. Although enthusiasm for the project may have been a contributing factor, the extended project period suggests that the ‘All in a box’ concept is equally applicable in routine clinical settings with standardized but complex diagnostic sampling.
doi:10.1186/1756-0500-7-418
PMCID: PMC4105167  PMID: 24993888
Prosthesis; Infections; Specimen handling; Specimen types; Transport media
18.  Chronic kidney disease in US adults with type 2 diabetes: an updated national estimate of prevalence based on Kidney Disease: Improving Global Outcomes (KDIGO) staging 
BMC Research Notes  2014;7:415.
Background
Kidney Disease Improving Global Outcomes (KDIGO) 2013 updated the classification and risk stratification of chronic kidney disease (CKD) to include both the level of renal function and urinary albumin excretion (UAE). The update subclassifies the previous category of moderate renal impairment. There is currently limited information on the prevalence of CKD based on this new classification in United States (US) adults with type 2 diabetes mellitus (T2DM). The objective of this study was to provide such estimates, for T2DM both overall and in those ≥ 65 years of age. We used the continuous National Health and Nutrition Examination Survey (NHANES) 1999–2012 to identify participants with T2DM. Estimated glomerular filtration rate (eGFR) and UAE were calculated using laboratory results and data collected from the surveys, and categorized based on the KDIGO classification. Projections for the US T2DM population were based on NHANES sampling weights.
Results
A total of 2915 adults diagnosed with T2DM were identified from NHANES, with 1466 being age ≥ 65 years. Prevalence of CKD based on either eGFR or UAE was 43.5% in the T2DM population overall, and 61.0% in those age ≥ 65 years. The prevalence of mildly decreased renal function or worse (eGFR < 60/ml/min/1.73 m2) was 22.0% overall and 43.1% in those age ≥ 65 years. Prevalence of more severe renal impairment (eGFR < 45 ml/min/1.73 m2) was 9.0% overall and 18.6% in those age ≥ 65 years. The prevalence of elevated UAE (> 30 mg/g) was 32.2% overall and 39.1% in those age ≥ 65 years. The most common comorbidities were hypertension, retinopathy, coronary heart disease, myocardial infarction, and congestive heart failure.
Conclusions
This study confirms the high prevalence of CKD in T2DM, impacting 43.5% of this population. Additionally, this study is among the first to report US prevalence estimates of CKD based on the new KDIGO CKD staging system.
doi:10.1186/1756-0500-7-415
PMCID: PMC4091951  PMID: 24990184
Diabetes; Type 2 diabetes mellitus; Chronic kidney disease; Prevalence; Estimated glomerular filtration rate; Albuminuria
19.  Induction of hairy roots by various strains of Agrobacterium rhizogenes in different types of Capsicum species explants 
BMC Research Notes  2014;7:414.
Background
Capsicum annuum and Capsicum frutescens, also known as “chilies”, belong to the Solanaceae family and have tremendous beneficial properties. The application of hairy root culture may become an alternative method for future development of these species by adding value, such as by increasing secondary metabolites and improving genetic and biochemical stability compared with normal Capsicum plants. Therefore, in this research, different types of explants of both species were infected with various Agrobacterium rhizogenes strains to provide more information about the morphology and induction efficiency of hairy roots. After 2 weeks of in vitro seed germination, young seedling explants were cut into three segments; the cotyledon, hypocotyl, and radical. Then, the explants were co-cultured with four isolated A. rhizogenes strains in Murashige & Skoog culture media (MS) containing decreasing carbenicillin disodium concentrations for one month.
Results
In this experiment, thick and short hairy roots were induced at all induction sites of C. annuum while thin, elongated hairy roots appeared mostly at wound sites of C. frutescens. Overall, the hairy root induction percentages of C. frutescens were higher compared with C. annuum. Hairy root initiation was observed earliest using radicles (1st week), followed by cotyledons (2nd week), and hypocotyls (3rd week). Cotyledon explants of both species had the highest induction frequency with all strains compared with the other explants types. Strains ATCC 13333 and ATCC 15834 were the most favourable for C. frutescens while ATCC 43056 and ATCC 43057 were the most favourable for C. annuum. The interactions between the different explants and strains showed significant differences with p-values < 0.0001 in both Capsicum species.
Conclusions
Both Capsicum species were amenable to A. rhizogenes infection and hairy root induction is recommended for use as an alternative explants in future plant-based studies.
doi:10.1186/1756-0500-7-414
PMCID: PMC4083348  PMID: 24981787
Capsicum annuum; Capsicum frutescens; Agrobacterium rhizogenes; Hairy root culture; Hairy root induction; Explant type
20.  Accrual to a randomised trial of adjuvant whole brain radiotherapy for treatment of melanoma brain metastases is feasible 
BMC Research Notes  2014;7:412.
Background
Brain metastases (BMs) are common in melanoma patients. Adjuvant whole brain radiotherapy (WBRT) following local treatment of intracranial melanoma metastases with neurosurgery and/or stereotactic radiosurgery is controversial. A randomised trial is needed. However, accrual to WBRT trials has been problematic. A pilot study by Australia and New Zealand Melanoma Trials Group (ANZMTG) was conducted to see if accrual was feasible.
Methods
Sites canvassed for interest included those who treat melanoma patients, had a proven accrual in previous melanoma trials and who had the relevant infrastructure support. Feasibility forecasts from interested sites were sought. These were compared to the patient numbers documented in the research contracts. A target accrual of 60 patients in 2 years was set. Funding was sought for the pilot study. Basic demographics of the pilot study cohort were collected.
Results
The first centre opened December 2008; the first patient was randomised in April 2009. The pilot accruing period concluded in September, 2011. In 30 months, 54 patients from 10 of a total of 17 activated sites in Australia (39, 72%) and in Norway (15, 28%) had been accrued. Feasibility forecasts predicted 133 trial eligible patients per year (including 108 Australian + 25 International patients). Site estimates generally overestimated accrual with 4 of 17 active sites estimating within 50% of target numbers. Sites with patient estimates calculated from records were more accurate than those estimated from memory. The overall recruitment target was lower in the research contracts when compared to the feasibility evaluation. Basic demographics of the pilot study revealed 62% of patients were males; 58% had a single metastasis, 28% had two and 14% had three metastases. 12-month overall survival was 50%.
Conclusions
Despite only 54 patients and not the full 60 patient target being accrued in two years the Trial Management Committee and Data Safely Monitoring Committee approved the continuation of the pilot study to the main trial. On the basis of this successful pilot study, funding was achieved for the full study. 143 patients of a target of 200 have been randomised by June 2014.
doi:10.1186/1756-0500-7-412
PMCID: PMC4083364  PMID: 24981506
Radiotherapy; Metastases; Melanoma; Brain; Trial; Pilot project; Feasibility; Whole brain radiotherapy; Randomised trial
21.  Secondary loss of a cis-spliced intron during the divergence of Giardia intestinalis assemblages 
BMC Research Notes  2014;7:413.
Background
Giardia intestinalis is a parasitic unicellular eukaryote with a highly reduced genome, in which only six cis-spliced and four trans-spliced introns have been discovered. However, we anticipate that more cis- and trans-spliced introns likely remain unidentified in genes encoding hypothetical proteins that occupy ca. 2/3 of all of the open reading frames (ORFs) in the Giardia genome. Consequently, comprehensive surveys of introns in ORFs for hypothetical proteins are critical for better understanding of the intron evolution in this organism.
Results
In this study, we identified two novel cis-spliced introns in the draft genome data of G. intestinalis strain WB, by surveying the conserved sequence motifs shared amongst the previously known introns. G. intestinalis strains can be divided into phylogenetically distinct assemblages A–H, and all the introns identified in past studies are shared among the published genome data from strains WB, DH, GS, and P15 representing assemblages A1, A2, B, and E, respectively. Nevertheless one of the two novel introns identified in this study was found to be absent in strain P15.
Conclusion
By considering the organismal relationship among G. intestinalis assemblages A1, A2, B, and E, one of the two introns identified in this study has highly likely been lost after the divergence of the assemblages. On the basis of a sequence comparison between the intron-bearing loci in WB, DH, and GS genomes and the homologous but intron-free locus in P15 genome, we propose that the loss of this particular intron was mediated by integration of the DNA fragment reverse-transcribed from mature mRNAs.
doi:10.1186/1756-0500-7-413
PMCID: PMC4085374  PMID: 24981682
Intron loss; Homologous recombination; Reduced genome; Reverse transcription
22.  Hirschsprung’s disease in children: a five year experience at a University teaching hospital in northwestern Tanzania 
BMC Research Notes  2014;7:410.
Background
Hirschsprung’s disease (HD) is the commonest cause of functional intestinal obstruction in children and poses challenges to pediatricians and pediatric surgeons practicing in resource-limited countries. This study describes the clinical characteristics and outcome of management of this disease in our setting and highlights challenges associated with the care of these patients and proffer solutions for improved outcome.
Methods
This was a descriptive prospective study of children aged ≤ 10 years who were histologically diagnosed and treated for HD at our centre between July 2008 and June 2013.
Results
A total of 110 patients (M: F ratio= 3.6:1) with a median age of 24 months were studied. Six (5.5%) patients were in the neonatal period. Sixty-four (58.2%) patients had complete intestinal obstruction whereas 42 (38.2%) and 4 (3.6%) patients had chronic intestinal obstruction and intestinal perforation respectively. No patient had enterocolitis. Constipation (94.5%) was the most common complaints. 109 (99.1%) patients had colostomy prior to the definitive pull-through. The median duration of colostomy before definitive pull-through was 4 months. The majority of patients (67.3%) had short segment of aganglionosis localized to the recto-sigmoid region. The definitive pull-through was performed in 94 (85.5%) patients (Swenson’s pull-through 76 (80.9%), Duhamel’s pull-through (12.8%) and Soave’s pull-through 4 (4.3%) patients). Postoperative complication rate was 47.3%. The median length of hospital stay was 26 days. Patients who developed complications stayed longer in the hospital and this was statistically significant (p <0.001). Mortality rate was 21.8%. The age < 4 weeks, delayed presentation and surgical site infection were the main predictors of mortality (p < 0.001). During the follow-up period, the results of Swenson’s and Duhamel’s pull through procedures were generally good in 87.8% and 42.9% of patients respectively. The result of Soave’s procedures was generally poor in this study.
Conclusion
HD remains the commonest cause of functional intestinal obstruction in children and contributes significantly to high morbidity and mortality in our setting. The majority of patients present late when the disease becomes complicated. Early diagnosis and timely definitive pull through procedure are essential in order to decrease the morbidity and mortality associated with this disease.
doi:10.1186/1756-0500-7-410
PMCID: PMC4083133  PMID: 24973940
Hirschsprung’s disease; Clinical presentation; Management; Outcome; Tanzania
23.  Acute subdural haemorrhage in the postpartum period as a rare manifestation of possible HELLP (haemolysis, elevated liver enzymes, and low-platelet count) syndrome: a case report 
BMC Research Notes  2014;7:408.
Background
The HELLP syndrome (haemolysis, elevated liver enzymes, and low-platelet count) occurs in about 0.5 to 0.9% of all pregnancies. With occurrence of thrombocytopaenia, it signals for several potentially lethal conditions such as complete or partial HELLP syndrome, thrombotic thrombocytopaenic purpura and acute fatty liver of pregnancy.
Case presentation
A previously healthy 27-year-old, Sinhala ethnic primigravida with pregnancy-induced hypertension was admitted at 38 weeks of gestation with lower abdominal pain and a blood pressure of 140/90 mmHg. She underwent emergency Caesarian section due to faetal distress giving birth to a healthy baby girl. Since postpartum day one, she was having intermittent fever spikes. All the routine investigations were normal in the first three weeks. Platelet count started dropping from post-partum day-20 onwards. On day-23, she had developed a seizure and computed tomography scan brain showed a subdural haemorrhage. She had a platelet count of 22,000 × 109/liter and was managed conservatively. She also had elevated liver enzymes, lactate dehydrogenase and bilirubin levels. Blood picture on day-24 showed haemolytic anemia. On day- 36, patient again developed seizures and she was having intermittent fever with generalized headache and signs of meningism. Computed tomography scan revealed an acute on chronic subdural haemorrhage.
Conclusions
Hypertensive disorders in pregnancy should be managed as high-risk throughout the postpartum period. Development of thrombocytopaenia can be considered as an early warning sign for HELLP, thrombotic thrombocytopaenic purpura or acute fatty liver of pregnancy which are lethal conditions. Prompt recognition of intracranial haemorrhages and early neurosurgical intervention is lifesaving.
doi:10.1186/1756-0500-7-408
PMCID: PMC4083337  PMID: 24972626
Intracranial haemorrhage; Thrombocytopaenia; HELLP Syndrome; Pregnancy; Postpartum period
24.  Biological pattern and transcriptomic exploration and phylogenetic analysis in the odd floral architecture tree: Helwingia willd 
BMC Research Notes  2014;7:402.
Background
Odd traits in few of plant species usually implicate potential biology significances in plant evolutions. The genus Helwingia Willd, a dioecious medical shrub in Aquifoliales order, has an odd floral architecture-epiphyllous inflorescence. The potential significances and possible evolutionary origin of this specie are not well understood due to poorly available data of biological and genetic studies. In addition, the advent of genomics-based technologies has widely revolutionized plant species with unknown genomic information.
Results
Morphological and biological pattern were detailed via anatomical and pollination analyses. An RNA sequencing based transcriptomic analysis were undertaken and a high-resolution phylogenetic analysis was conducted based on single-copy genes in more than 80 species of seed plants, including H. japonica. It is verified that a potential fusion of rachis to the leaf midvein facilitates insect pollination. RNA sequencing yielded a total of 111450 unigenes; half of them had significant similarity with proteins in the public database, and 20281 unigenes were mapped to 119 pathways. Deduced from the phylogenetic analysis based on single-copy genes, the group of Helwingia is closer with Euasterids II and rather than Euasterids, congruent with previous reports using plastid sequences.
Conclusions
The odd flower architecture make H. Willd adapt to insect pollination by hosting those insects larger than the flower in size via leave, which has little common character that other insect pollination plants hold. Further the present transcriptome greatly riches genomics information of Helwingia species and nucleus genes based phylogenetic analysis also greatly improve the resolution and robustness of phylogenetic reconstruction in H. japonica.
doi:10.1186/1756-0500-7-402
PMCID: PMC4083144  PMID: 24969969
Biological pattern; Helwingia Willd; Phylogenetic analysis; Transcriptome
25.  A mutation in a splicing factor that causes retinitis pigmentosa has a transcriptome-wide effect on mRNA splicing 
BMC Research Notes  2014;7:401.
Background
Substantial progress has been made in the identification of sequence elements that control mRNA splicing and the genetic variants in these elements that alter mRNA splicing (referred to as splicing quantitative trait loci – sQTLs). Genetic variants that affect mRNA splicing in trans are harder to identify because their effects can be more subtle and diffuse, and the variants are not co-located with their targets. We carried out a transcriptome-wide analysis of the effects of a mutation in a ubiquitous splicing factor that causes retinitis pigmentosa (RP) on mRNA splicing, using exon microarrays.
Results
Exon microarray data was generated from whole blood samples obtained from four individuals with a mutation in the splicing factor PRPF8 and four sibling controls. Although the mutation has no known phenotype in blood, there was evidence of widespread differences in splicing between cases and controls (affecting approximately 20% of exons). Most probesets with significantly different inclusion (defined as the expression intensity of the exon divided by the expression of the corresponding transcript) between cases and controls had higher inclusion in cases and corresponded to exons that were shorter than average, AT rich, located towards the 5’ end of the gene and flanked by long introns. Introns flanking affected probesets were particularly depleted for the shortest category of introns, associated with splicing via intron definition.
Conclusions
Our results show that a mutation in a splicing factor, with a phenotype that is restricted to retinal tissue, acts as a trans-sQTL cluster in whole blood samples. Characteristics of the affected exons suggest that they are spliced co-transcriptionally and via exon definition. However, due to the small sample size available for this study, further studies are required to confirm the widespread impact of this PRPF8 mutation on mRNA splicing outside the retina.
doi:10.1186/1756-0500-7-401
PMCID: PMC4084799  PMID: 24969741
mRNA splicing; Retinitis pigmentosa; Exon array; PRPF8

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