SciCombinator

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Journal: BMC research notes

193

BACKGROUND: Cola is an extremely popular caffeinated soft drink. The media have recently cited a poll in which 16% of the respondents considered themselves to be addicted to cola soft drinks. We find the contrast between the apparent prevalence of cola addiction and the lack of scientific literature on the subject remarkable. To our knowledge, this is the first case of cola dependency described in the scientific literature. CASE PRESENTATION: The patient is a 40-year-old woman, who when feeling down used cola to give her an energy boost and feel better about herself. During the past seven years her symptoms increased, and she was prescribed antidepressant medication by her family doctor. Due to worsening of symptoms she was hospitalised and later referred to a specialised outpatient clinic for affective disorders. At entry to the clinic she suffered from constant tiredness, lack of energy, failing concentration, problems falling asleep as well as interrupted sleep. She drank about three litres of cola daily, and she had developed a metabolic syndrome.The patient fulfilled the ICD-10 criteria for dependency, and on the Yale Food Addiction Scale (YFAS) she scored 40 points. Her clinical mental status was at baseline assessed by the Major Depression Inventory (MDI) = 41, Hamilton Depression - 17 item Scale (HAMD-17) = 14, Young Mania Rating Scale (YMRS) = 2 and the Global Assessment of Functioning (GAF) Scale = 45.During cognitive therapy sessions she was guided to stop drinking cola and was able to moderate her use to an average daily consumption of 200 ml of cola Her concentration improved and she felt mentally and physically better. At discharge one year after entry her YFAS was zero. She was mentally stable (MDI =1, HAMD-17 = 0, YMRS = 0 and GAF = 85) and without antidepressant medication. She had lost 7.2 kg, her waistline was reduced by 13 cm and the metabolic syndrome disappeared. CONCLUSION: This case serves as an example of how the overconsumption of a caffeinated soft drink likely was causing or accentuating the patient’s symptoms of mental disorder. When diagnosing and treating depression, health professionals should pay attention to potential overuse of cola or other caffeinated beverages.

Concepts: Coffee, Addiction, Caffeine, Bipolar disorder, Major depressive disorder, Soft drink, Energy drink, Coca-Cola

176

BACKGROUND: RNA sequencing (RNA-Seq) is emerging as a highly accurate method to quantify transcript abundance. However, analyses of the large data sets obtained by sequencing the entire transcriptome of organisms have generally been performed by bioinformatics specialists. Here we provide a step-by-step guide and outline a strategy using currently available statistical tools that results in a conservative list of differentially expressed genes. We also discuss potential sources of error in RNA-Seq analysis that could alter interpretation of global changes in gene expression. FINDINGS: When comparing statistical tools, the negative binomial distribution-based methods, edgeR and DESeq, respectively identified 11,995 and 11,317 differentially expressed genes from an RNA-seq dataset generated from soybean leaf tissue grown in elevated O3. However, the number of genes in common between these two methods was only 10,535, resulting in 2,242 genes determined to be differentially expressed by only one method. Upon analysis of the non-significant genes, several limitations of these analytic tools were revealed, including evidence for overly stringent parameters for determining statistical significance of differentially expressed genes as well as increased type II error for high abundance transcripts. CONCLUSIONS: Because of the high variability between methods for determining differential expression of RNA-Seq data, we suggest using several bioinformatics tools, as outlined here, to ensure that a conservative list of differentially expressed genes is obtained. We also conclude that despite these analytical limitations, RNA-Seq provides highly accurate transcript abundance quantification that is comparable to qRT-PCR.

Concepts: DNA, Gene, Gene expression, Transcription, Statistics, Molecular biology, RNA, RNA-Seq

173

There are several well-described causes of a painful mass following total hip arthroplasty including polyethylene and metal wear debris, infection, expanding hematoma, dislocation, and synovial cysts. In addition to causing pain, these lesions, when large enough, may cause neurologic and vascular compromise. Rapid growth of the mass may clinically and radiographically resemble a sarcoma. Here, we report a case of a large painful hip mass which developed after total hip arthroplasty. The well-circumscribed mass was overlying and extending into the hip joint containing thousands of highly organized fibrin-containing “rice bodies”. To our knowledge, this is the first report of a large, highly organized (rice-body-containing) cyst complicating total hip arthroplasty.

Concepts: Causality, Hip replacement, Hip, Pelvis, Orthopedic surgery, Joint replacement, Synovial joint, Polyethylene

170

BACKGROUND: This study examined the effects of bovine colostrum on exercise –induced modulation of antioxidant parameters in the skeletal muscles in mice. Adult male BALB/c mice were randomly divided into four groups (control, colostrum alone, exercise and exercise with colostrum) and each group had three subgroups (day 0, 21 and 42). Colostrum groups of mice were given a daily oral supplement of 50 mg/kg body weight of bovine colostrum and the exercise group of mice were made to exercise on the treadmill for 30 minutes per day. Total antioxidants, lipid hydroperoxides, xanthine oxidase and super oxide dismutase level was assayed from the homogenate of hind limb skeletal muscles. RESULTS: Exercise—induced a significant oxidative stress in skeletal muscles as evidenced by the elevated lipid hydroperoxides and xanthine oxidase levels. There was a significant decrease in skeletal muscle total antioxidants and superoxide dismutase levels. Daily colostrum supplement significantly reduced the lipid hydroperoxides and xanthine oxidase enzyme level and increased the total antioxidant levels in the leg muscle. CONCLUSION: Thus, the findings of this study showed that daily bovine colostrum supplementation was beneficial to the skeletal muscle to reduce the oxidant-induced damage during muscular exercise.

Concepts: Metabolism, Antioxidant, Oxidative stress, Reactive oxygen species, Superoxide dismutase, Glycogen, Muscular system, Superoxide

170

Cerebrospinal fluid leaks (CSF) result from an abnormal communication between the subarachnoid space and the extracranial space. Approximately 90% of CSF leak at the anterior skull base manifests as rhinorrhea and can become life-threatening condition. Endoscopic sinus surgery (ESS) has become a common otolaryngologist procedure. The aim of this article is to consider our experience and to evaluate the outcomes in patients who underwent a purely endoscopic repair of CSF leaks of the anterior skull base.

Concepts: Spinal cord, Cerebrospinal fluid, Meninges, Spontaneous cerebrospinal fluid leak

170

BACKGROUND: To evaluate institutional nursing care performance in the context of national comparative statistics (benchmarks), approximately one in every three major healthcare institutions (over 1,800 hospitals) across the United States, have joined the National Database for Nursing Quality Indicators[REGISTERED SIGN] (NDNQI[REGISTERED SIGN]). With over 18,000 hospital units contributing data for nearly 200 quantitative measures at present, a reliable and efficient input data screening for all quantitative measures for data quality control is critical to the integrity, validity, and on-time delivery of NDNQI reports. METHODS: With Monte Carlo simulation and quantitative NDNQI indicator examples, we compared two ad-hoc methods using robust scale estimators, Inter Quartile Range (IQR) and Median Absolute Deviation from the Median (MAD), to the classic, theoretically-based Minimum Covariance Determinant (FAST-MCD) approach, for initial univariate outlier detection. RESULTS: While the theoretically based FAST-MCD used in one dimension can be sensitive and is better suited for identifying groups of outliers because of its high breakdown point, the ad-hoc IQR and MAD approaches are fast, easy to implement, and could be more robust and efficient, depending on the distributional property of the underlying measure of interest. CONCLUSION: With highly skewed distributions for most NDNQI indicators within a short data screen window, the FAST-MCD approach, when used in one dimensional raw data setting, could overestimate the false alarm rates for potential outliers than the IQR and MAD with the same pre-set of critical value, thus, overburden data quality control at both the data entry and administrative ends in our setting.

Concepts: Median, Dimension, Absolute deviation, Normal distribution, Standard deviation, Robust statistics, Outlier, Median absolute deviation

170

BACKGROUND: Takayasu arteritis is a large vessel vasculitis occurring in young females. We report a rare presentation of Takayasu arteritis in a Sri Lankan woman. She presented with bronchiectasis and left recurrent laryngeal nerve palsy prior to the onset of vascular symptoms. This case illustrates an atypical presentation of this disease and the diagnostic dilemma that the physician may be faced with. CASE PRESENTATION: A 39-year-old woman presented with chronic cough, haemoptysis and hoarseness of voice. She had left recurrent laryngeal nerve palsy and high inflammatory markers on investigation. CT thorax revealed aortic wall thickening and traction bronchiectasis. 2 D echocardiogram revealed grade 1 aortic regurgitation compatible with aortitis. She did not have weak peripheral pulses or a blood pressure discrepancy and did not meet American College of Rheumatology (ACR) criteria for diagnosis of Takayasu arteritis at this stage. Tuberculosis, syphilis and sarcoidosis was excluded. While awaiting angiography, she developed left arm claudication and a pericardial effusion. Angiography revealed evidence of Takayasu arteritis and absence of flow in the left subclavian artery. Takayasu arteritis was diagnosed at this stage after a period of eight months from the onset of initial symptoms. She is currently on prednisolone, azathioprine and aspirin. CONCLUSION: Bronchiectasis and recurrent laryngeal nerve palsy is a rare presentation of Takayasu arteritis. Atypical presentations can occur in Takayasu arteritis prior to the onset of vascular symptoms. Elevation of inflammatory markers are an early finding. A high degree of suspicion is needed to identify these patients in the early course of the disease.

Concepts: Cardiology, Common carotid artery, Brachiocephalic artery, Subclavian vein, Vertebral artery, Subclavian artery

169

BACKGROUND: Tea has been suggested to promote oral health by inhibiting bacterial attachment to the oral cavity. Most studies have focused on prevention of bacterial attachment to hard surfaces such as enamel. FINDINGS: This study investigated the effect of five commercial tea (green, oolong, black, pu-erh and chrysanthemum) extracts and tea components (epigallocatechin gallate and gallic acid) on the attachment of five oral pathogens (Streptococcus mutans ATCC 25175, Streptococcus mutans ATCC 35668, Streptococcus mitis ATCC 49456, Streptococcus salivarius ATCC 13419 and Actinomyces naeslundii ATCC 51655) to the HGF-1 gingival cell line. Extracts of two of the teas (pu-erh and chrysanthemum) significantly (p < 0.05) reduced attachment of all the Streptococcus strains by up to 4 log CFU/well but effects of other teas and components were small. CONCLUSIONS: Pu-erh and chrysanthemum tea may have the potential to reduce attachment of oral pathogens to gingival tissue and improve the health of oral soft tissues.

Concepts: Bacteria, Streptococcus, Tea, Camellia sinensis, Gram positive bacteria, Streptococcaceae, Pu-erh tea, Oolong

169

BACKGROUND: Accurate interpretation of HIV drug resistance (HIVDR) testing is challenging, yet important for patient care. We compared genotyping interpretation, based on the Stanford University HIV Drug Resistance Database (Stanford HIVdb), and virtual phenotyping, based on the Janssen Diagnostics BVBA’s vircoTYPETM HIV-1, and investigated their level of agreement in antiretroviral (ARV) naive patients in Asia, where non-B subtypes predominate. METHODS: Sequences from 1301 ARV-naive patients enrolled in the TREAT Asia Studies to Evaluate Resistance – Monitoring Study (TASER-M) were analysed by both interpreting systems. Interpretations from both Stanford HIVdb and vircoTYPETM HIV-1 were initially grouped into 2 levels: susceptible and non-susceptible. Discrepancy was defined as a discordant result between the susceptible and non-susceptible interpretations from the two systems for the same ARV. Further analysis was performed when interpretations from both systems were categorised into 3 levels: susceptible, intermediate and resistant; whereby discrepancies could be categorised as major discrepancies and minor discrepancies. Major discrepancy was defined as having a susceptible result from one system and resistant from the other. Minor discrepancy corresponded to having an intermediate interpretation in one system, with a susceptible or resistant result in the other. The level of agreement was analysed using the prevalence adjusted bias adjusted kappa (PABAK). RESULTS: Overall, the agreement was high, with each ARV being in “almost perfect agreement”, using Landis and Koch’s categorisation. Highest discordance was observed for efavirenz (75/1301, 5.8 %), all arising from susceptible Stanford HIVdb versus non-susceptible vircoTYPETM HIV-1 predictions. Protease Inhibitors had highest level of concordance with PABAKs all above 0.99, followed by Nucleoside Reverse Transcriptase Inhibitors with PABAKs above 0.97 and non-NRTIs with the lowest PABAK of 0.88. The 68/75 patients with discordant efavirenz results harboured the V179D/E mutations compared to 7/1226 with no efavirenz discrepancy (p-value <0.001). In the 3-level comparison, all but one of the discrepancies was minor. CONCLUSIONS: The two systems agreed well with lowest concordance observed for efavirenz. When interpreting HIVDR, especially in non-B subtypes, clinical correlation is crucial, in particular when efavirenz resistance is interpreted based on V179D/E.

Concepts: Antiretroviral drug, HIV, Reverse transcriptase inhibitor, Phenotype, Subtypes of HIV, Reverse transcriptase, Interpretation, HIV Drug Resistance Database

169

BACKGROUND: Plantar fibromatosis is a benign disease creating nodules on the medial plantar side of affected patients. While surgical removal is regarded as the therapeutic mainstay, recurrence rates and impairment of daily activities remains substantial. High-energy focussed extracorporeal shockwave therapy has been suggested to be potentially effective in plantar fibromatosis in terms of pain reduction.HypothesisHigh-energy focussed extracorporeal shockwave therapy reduces pain in plantar fibromatosis. FINDINGS: A total number of six patients (5 males, 58+/-4 years) were included with plantar fibromatosis (Ledderhose’s disease) associated with pain. Three patients were operated on previously, one had concomitant Dupuytren’s contracture. High-energy focussed ESWT was applied using a Storz Duolith SD1 (2000 impulses, 3 Hz, 1.24mJ/mm2) in two sessions with 7 days between. Pain was 6+/-2 at baseline, 2+/-1 after 14 days and 1+/-1 after 3 months. Softening of the nodules was noted by all patients. No adverse effects were noted. CONCLUSIONS: High-energy focussed extracorporeal shockwave energy reduces pain in painful plantar fibromatosis (Morbus Ledderhose). Further large-scale prospective trials are warranted to elucidate the value of high-energy focussed extracorporeal shockwave therapy (ESWT) in plantar fibromatosis in terms of recurrence and efficacy.

Concepts: Medicine, Rare diseases, Dupuytren's contracture, Plantar fasciitis, Dermal and subcutaneous growths, Plantar fibromatosis, Fibromatosis, Extracorporeal shockwave therapy