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1.  Current status and trend of the publication to the SCI and SCIE journals in the field of radiation oncology in Korea for 30 years 
Radiation Oncology Journal  2012;30(1):14-19.
Purpose
We collected the data of Science Citation Index (SCI) and SCI Expended (SCIE) papers written by the members of the Korean Society of Radiation Oncology (KOSRO) to analyze the current status and the future trend.
Materials and Methods
We searched the database of SCIE for the period from 1981 to 2011 at the Web of Knowledge site. Articles, reviews or proceedings written by KOSRO members as the first or corresponding authors were included. Search terms were the following combination of subject headings: therapeut radiol, radiat oncol, Korea. For National Cancer Center, combined search terms such as natl canc ctr, Korea and the names of faculties were applied.
Results
The total number of SCIE papers was 547. Numbers of the published papers in 1995, 2000, 2005, and 2010, were increased continuously, which was 2, 14, 40, and 83, respectively. The average impact factor was 2.9. The papers were published at the 134 different journals. The proportion of "International Journal of Radiation Oncology Biology Physics" was 23.4% of all the papers. The number and proportions of papers by subject categories were 87 (15.9%) in biology, 73 (13.3%) in physics and 387 (70.6%) in clinics. The papers of the top five institutions, based on the number of published papers, occupied 66.3%.
Conclusion
The number of SCIE papers is increasing rapidly in the field of radiation oncology in Korea. To improve the quality of papers, multi-institutional retrospective or prospective randomized studies should be done for the common cancers in Korea.
doi:10.3857/roj.2012.30.1.14
PMCID: PMC3475958  PMID: 23120739
Science Citation Index; Korean Society of Radiation Oncology; Web of Knowledge
2.  Korea's Contribution to Radiological Research Included in Science Citation Index Expanded, 1986-2010 
Korean Journal of Radiology  2012;13(5):523-529.
Objective
To evaluate scientific papers published by Korean radiologists in the Science Citation Index Expanded (SCIE) radiology journals, between 1986 and 2010.
Materials and Methods
The Institute for Scientific Information Web of Knowledge-Web of Science (SCIE) database was searched for all articles published by Korean radiologists, in SCIE radiology journals, between 1986 and 2010. We performed the analysis by typing "Korea" and "radiol" in the address section and selecting the subject area of "Radiology, Nuclear Medicine, and Medical Imaging" with the use of the general search function of the software. Analyzed parameters included the total number of publications, document types, journals, and institutions. In addition, we analyzed where Korea ranks, compared to other countries, in terms of the number of published articles. All these data were analyzed according to five time periods: 1986-1990, 1991-1995, 1996-2000, 2001-2005, and 2006-2010.
Results
Overall, 4974 papers were published by Korean radiologists, in 99 different SCIE journals, between 1986 and 2010, of which 4237 (85.2%) were article-type papers. Of the total 115395 articles, worldwide, published in radiology journals, Korea's share was 3.7%, with an upward trend over time (p < 0.005). The journal with the highest number of articles was the American Journal of Roentgenology (n = 565, 13.3%). The institution which produced the highest number of publications was Seoul National University (n = 932, 22.0%).
Conclusion
The number of scientific articles published by Korean radiologists in the SCIE radiology journals has increased significantly between 1986 and 2010. Korea was ranked 4th among countries contributing to radiology research during the last 5 years.
doi:10.3348/kjr.2012.13.5.523
PMCID: PMC3435847  PMID: 22977317
Citation analysis; Publication; Radiologic research; Korea
3.  DISCOVER: Dutch Iliac Stent trial: COVERed balloon-expandable versus uncovered balloon-expandable stents in the common iliac artery: study protocol for a randomized controlled trial 
Trials  2012;13:215.
Background
Iliac artery atherosclerotic disease may cause intermittent claudication and critical limb ischemia. It can lead to serious complications such as infection, amputation and even death. Revascularization relieves symptoms and prevents these complications. Historically, open surgical repair, in the form of endarterectomy or bypass, was used. Over the last decade, endovascular repair has become the first choice of treatment for iliac arterial occlusive disease. No definitive consensus has emerged about the best endovascular strategy and which type of stent, if any, to use. However, in more advanced disease, that is, long or multiple stenoses or occlusions, literature is most supportive of primary stenting with a balloon-expandable stent in the common iliac artery (Jongkind V et al., J Vasc Surg 52:1376-1383,2010). Recently, a PTFE-covered balloon-expandable stent (Advanta V12, Atrium Medical Inc., Hudson, NH, USA) has been introduced for the iliac artery. Covering stents with PTFE has been shown to lead to less neo-intimal hyperplasia and this might lower restenosis rates (Dolmatch B et al. J Vasc Interv Radiol 18:527-534,2007, Marin ML et al. J Vasc Interv Radiol 7:651-656,1996, Virmani R et al. J Vasc Interv Radiol 10:445-456,1999). However, only one RCT, of mediocre quality has been published on this stent in the common iliac artery (Mwipatayi BP et al. J Vasc Surg 54:1561-1570,2011, Bekken JA et al. J Vasc Surg 55:1545-1546,2012). Our hypothesis is that covered balloon-expandable stents lead to better results when compared to uncovered balloon-expandable stents.
Methods/Design
This is a prospective, randomized, controlled, double-blind, multi-center trial. The study population consists of human volunteers aged over 18 years, with symptomatic advanced atherosclerotic disease of the common iliac artery, defined as stenoses longer than 3 cm and occlusions. A total of 174 patients will be included.
The control group will undergo endovascular dilatation or revascularization of the common iliac artery, followed by placement of one or more uncovered balloon-expandable stents. The study group will undergo the same treatment, however one or more PTFE-covered balloon-expandable stents will be placed. When necessary, the aorta, external iliac artery, common femoral artery, superficial femoral artery and deep femoral artery will be treated, using the standard treatment.
The primary endpoint is absence of binary restenosis rate. Secondary endpoints are reocclusion rate, target-lesion revascularization rate, clinical success, procedural success, hemodynamic success, major amputation rate, complication rate and mortality rate. Main study parameters are age, gender, relevant co-morbidity, and several patient, disease and procedure-related parameters.
Trial registration
Dutch Trial Register, NTR3381.
doi:10.1186/1745-6215-13-215
PMCID: PMC3576320  PMID: 23164097
Peripheral arterial occlusive disease; Atherosclerotic disease; Common Iliac Artery; Intermittent Claudication; Critical Limb Ischemia; Endovascular; Stenting; Covered stent
4.  Trends in television time, non-gaming PC use and moderate-to-vigorous physical activity among German adolescents 2002–2010 
BMC Public Health  2014;14:351.
Background
Studies in youth highlight that moderate-to-vigorous physical activity (MVPA) and screen-time behaviours such as television viewing and PC use are associated with a range of health outcomes. However, little is known about recent trends in these behaviours in adolescents. This paper presents time trends in German adolescents’ television time, non-gaming PC use as well as MVPA from 2002 to 2010.
Methods
Data were derived from the cross-sectional German Health Behaviour in School-aged Children (HBSC) study in 2002, 2006 and 2010. Analyses were based on 16,918 11-to 15-year olds boys (49.1%) and girls. Outcome variables were time spent in TV viewing and using a PC (weekday and weekend day) as well as the number of days achieving 60 minutes of MVPA. Changes in both screen-time behaviours and MVPA over time were analysed using sex-specific linear regression, controlling for age and family affluence.
Results
TV viewing on weekdays, but not at weekends, declined steadily over time with a difference between 2002 and 2010 of 12.4 min/day in girls and 18.3 min/day in boys (p for trend < .01). We found a strong increase in PC use for non-gaming purposes over time for girls only, with a difference between 2002 and 2010 of 54.1 min/weekday and 68.8 min/weekend day (p < .001). For MVPA we found a slight statistically significant increase in terms of meeting PA guidelines as well as days/week in MVPA for boys and girls (p < .001). In 2010 14.0% of girls and 19.9% of boys met PA guideline.
Conclusion
Although MVPA increased from 2002 to 2010 in German adolescents, the time spent in MVPA was still low. Despite the observed decrease in TV viewing, there was no overall decline in the observed screen-based behaviours, especially for girls. This is mainly due to a marked increase in use of a PC for chatting on-line, internet, emailing, homework etc. among girls during the last ten years which outweighs the corresponding decrease in TV viewing. The findings highlight a need for strategies and interventions aimed at reducing screen-time behaviours and promoting MVPA.
doi:10.1186/1471-2458-14-351
PMCID: PMC3990022  PMID: 24725269
Television time; Non-gaming PC use; Moderate-to-vigorous physical activity; Trends; Germany; HBSC
5.  Describing randomisation: patients' and the public's preferences compared with clinicians' practice 
British Journal of Cancer  2002;87(8):854-858.
Explaining the concept of randomisation in simple terms to patients during the discussion of randomised clinical trials can be a difficult task for many health care professionals. We report the results of a questionnaire-based survey, using seven descriptions of randomisation taken from Corbett's study. We examined the preferences of the general public and patients towards the descriptions and compared the results with the clinicians' choice. Participants in the survey were 341 lay people without cancer, 200 patients with cancer and 200 oncologists from cancer centres throughout the UK. It was difficult to identify ‘the best’ way to describe the process of randomisation. The two most favoured statements for patients and members of the public included a very explicit statement that mentioned ‘a computer’, ‘chance’ and ‘not the doctor's or patient's decision’ and a succinct statement that played down the role of ‘chance’. Clinicians chose neither of these statements as closely resembling their own practice. Patients and members of the public most disliked the statement ‘a computer will perform the equivalent of tossing a coin to allocate you to one of two methods of treatment’. This analogy used by 26% of oncologists, was viewed as trivialising and upsetting in the context of determining treatment for life threatening disease.
British Journal of Cancer (2002) 87, 854–858. doi:10.1038/sj.bjc.6600527 www.bjcancer.com
© 2002 Cancer Research UK
doi:10.1038/sj.bjc.6600527
PMCID: PMC2376175  PMID: 12373599
randomisation; cancer; patients' preferences
6.  Artificial Regulation of Water Level and Its Effect on Aquatic Macrophyte Distribution in Taihu Lake 
PLoS ONE  2012;7(9):e44836.
Management of water levels for flood control, water quality, and water safety purposes has become a priority for many lakes worldwide. However, the effects of water level management on the distribution and composition of aquatic vegetation has received little attention. Relevant studies have used either limited short-term or discrete long-term data and thus are either narrowly applicable or easily confounded by the effects of other environmental factors. We developed classification tree models using ground surveys combined with 52 remotely sensed images (15–30 m resolution) to map the distributions of two groups of aquatic vegetation in Taihu Lake, China from 1989–2010. Type 1 vegetation included emergent, floating, and floating-leaf plants, whereas Type 2 consisted of submerged vegetation. We sought to identify both inter- and intra-annual dynamics of water level and corresponding dynamics in the aquatic vegetation. Water levels in the ten-year period from 2000–2010 were 0.06–0.21 m lower from July to September (wet season) and 0.22–0.27 m higher from December to March (dry season) than in the 1989–1999 period. Average intra-annual variation (CVa) decreased from 10.21% in 1989–1999 to 5.41% in 2000–2010. The areas of both Type 1 and Type 2 vegetation increased substantially in 2000–2010 relative to 1989–1999. Neither annual average water level nor CVa influenced aquatic vegetation area, but water level from January to March had significant positive and negative correlations, respectively, with areas of Type 1 and Type 2 vegetation. Our findings revealed problems with the current management of water levels in Taihu Lake. To restore Taihu Lake to its original state of submerged vegetation dominance, water levels in the dry season should be lowered to better approximate natural conditions and reinstate the high variability (i.e., greater extremes) that was present historically.
doi:10.1371/journal.pone.0044836
PMCID: PMC3445588  PMID: 23028639
7.  Pharmacokinetics, oral bioavailability, and metabolism in mice and cynomolgus monkeys of (2'R,5'S-)-cis-5-fluoro-1-[2-(hydroxymethyl)-1,3-oxathiolan-5-yl] cytosine, an agent active against human immunodeficiency virus and human hepatitis B virus. 
Antimicrobial Agents and Chemotherapy  1994;38(12):2722-2729.
(2'R,5'S-)-cis-5-Fluoro-1-[2-(hydroxymethyl)-1,3-oxathiolan-5-yl] cytosine (524W91) is a nucleoside analog with potent anti-human immunodeficiency virus and anti-human hepatitis B virus activities in vitro. The pharmacokinetics and bioavailability of 524W91 after oral dosing were studied in mice dosed with 10, 100, and 600 mg of 524W91 per kg of body weight by the oral and intravenous routes. Cynomolgus monkeys were dosed with 10 and 80 mg of 524W91 per kg. In both species, the clearance of 524W91 was rapid, via the kidney, and was independent of dose. In monkeys, the total body clearance of 10 mg of 524W91 per kg was 0.7 +/- 0.1 liter/h/kg, and the volume of distribution at steady state was 0.8 +/- 0.02 liter/kg. The terminal elimination half-life was 1.0 +/- 0.2 h. The absolute bioavailability after oral dosing was 63% +/- 4% at 10 mg/kg. Concentrations of 524W91 in the cerebrospinal fluid were 4% +/- 0.7% of the corresponding levels in plasma. In mice, the total clearance of 10 mg of 524W91 per kg was 2.3 liters/kg/h, and the volume of distribution at steady state was 0.9 liter/kg. Absolute bioavailability in mice after oral dosing was 96% at a dose of 10 mg/kg. The metabolism of orally administered [6-3H]524W91 was studied in cynomolgus monkeys at a dose of 80 mg/kg and in mice at a dose of 120 mg/kg. Monkeys excreted 41% +/- 6% of the radioactive dose in the 0- to 72-h urine, 33% +/- 10% in the feces, and 10% +/- 7% in the cage wash. Unchanged 524W91 was 64% of the total radiolabeled drug recovered in the urine. The glucuronide was a minor urinary metabolite. 5-Fluorouracil was not detected (less than 0.02% of the dose). Mice dosed orally with 120 mg of [6-3H]524W91 per kg excreted 67% +/- 7% of the radiolable in the )- to 48-h urine. Small amounts of the 3' -sulfoxide and glucuronide metabolites were observed in the urine, but 5-fluorouracil was not detected. Good bioavailability after oral dosing and resistance to metabolism recommend 524W91 for further preclinical evaluation.
PMCID: PMC188276  PMID: 7695253
8.  Unusual proximal dislocation without fracture: a case report 
Hand (New York, N.Y.)  2012;7(4):454-456.
Carpal instability includes a broad spectrum of osseous and ligamentous injuries which have been subclassified into greater and lesser arc injuries, in addition to combinations of both (Mayfield et al. J Hand Surg [Am] 5:226–241, 1980; Yaeger et al. Skeletal Radiol 13(2):120–30, 1985). The injuries typically occur from a fall on the outstretched hand with the wrist in ulnar deviation, hyperextension, and intercarpal supination (Yaeger et al. Skeletal Radiol 13(2):120–30, 1985). The force classically propagates from the radial to the ulnar side of the wrist resulting in a fracture (greater arc) or dislocation (lesser arc) pattern with the extent of the injury occurring in an orderly pattern depending upon the degree of hyperextension and the duration and magnitude of the force (Mayfield et al. J Hand Surg [Am] 5:226–241, 1980; Yaeger et al. Skeletal Radiol 13(2):120–30, 1985). Multiple variations occur, including transradial styloid fractures as well as fractures through carpal bones surrounding the lunate (Mayfield et al. J Hand Surg [Am] 5:226–241, 1980; Yaeger et al. Skeletal Radiol 13(2):120–30, 1985; Kozin SH. J Am Acad Orthop Surg 6 (2): 114–20, 1998. Although carpal dislocations have been noted for many years, the mechanisms and classification have only been recently clarified. We report a case of a complex dislocation involving the entire proximal carpal row without an associated fracture. While this type of complex carpal dislocation has been previously described, to our knowledge, it has never been reported without a fracture of the forearm, wrist, or hand.
doi:10.1007/s11552-012-9449-6
PMCID: PMC3508026  PMID: 24294171
9.  Certifying the cause of death: an audit of wording inaccuracies. 
Journal of Clinical Pathology  1993;46(3):232-234.
AIMS: To audit wording and formulation inaccuracies in certifying the cause of death. METHODS: Five hundred causes of death were analysed from the counterfoils of medical death certificates (Form 66). Wording and formulation inaccuracies were defined as terms contrary to the notes given to doctors in books on death certificates. RESULTS: One or more inaccuracies were identified in 29% of cases. In 5.8% of cases, the inaccuracies were sufficiently serious to warrant further action or enquiry by the Registrar of Births and Deaths, including referral to Her Majesty's Coroner. CONCLUSIONS: Most inaccuracies could have been avoided by adhering to the notes for medical practitioners contained in books of death certificates. The wording and formulation of causes of death warrants special prominence in under-graduate and postgraduate medical education. The topic should be audited and medical practitioners should pay particular attention to cases worthy of referral to HM Coroner.
PMCID: PMC501176  PMID: 8463416
10.  Interventions for preventing neuropathy caused by cisplatin and related compounds 
Background
Cisplatin and several related antineoplastic agents used to treat many types of solid tumors are neurotoxic, and most patients completing a full course of cisplatin chemotherapy develop a clinically detectable sensory neuropathy. Effective neuroprotective therapies have been sought.
Objectives
To examine the efficacy of purported chemoprotective agents to prevent or limit the neurotoxicity of cisplatin and related agents.
Search methods
We searched the Cochrane Neuromuscular Disease Group Specialized Register (25 August 2010), the Cochrane Central Register of Controlled Trials (Issue 3, 2010 in The Cochrane Library), MEDLINE (January 1966 to August 2010), EMBASE (January 1980 to August 2010), LILACS (January 1982 to August 2010), CINAHL (January 1982 to August 2010) for randomized trials designed to evaluate neuroprotective agents used to prevent or limit neurotoxicity of cisplatin and related agents among human patients.
Selection criteria
Quasi-randomized or randomized controlled trials whose participants received cisplatin (or related compounds) chemotherapy with or without a potential chemoprotectant (acetylcysteine, amifostine, ACTH, BNP7787, calcium and magnesium, diethyldithiocarbamate, glutathione, Org 2766, oxcarbazepine, or vitamin E) and were evaluated zero to six months after completing chemotherapy using quantitative sensory testing (primary) or other measures including nerve conduction studies or neurological impairment rating using validated scales (secondary).
Data collection and analysis
We identified 16 randomized trials involving five possible chemoprotective agents in the initial 2006 review. Each study was reviewed by two authors who extracted the data and reached consensus. The 2010 update identified 11 additional randomized trials consisting of nine possible chemoprotective agents, including three treatments (acetylcysteine, calcium and magnesium, and oxcarbazepine) not among those described in the 2006 review. The included trials in the updated review involved eight unrelated treatments and included many disparate measures of neuropathy, resulting in insufficient data for any one measure to combine the results in most instances.
Main results
One of four eligible amifostine trials (541 total participants in all four trials) used quantitative sensory testing and demonstrated a favorable outcome in terms of amifostine neuroprotection, but the vibration perception threshold result was based on data from only 14 participants receiving amifostine who completed the post-treatment evaluation and should be regarded with caution. Of the six eligible glutathione trials (354 participants), one used quantitative sensory testing but reported only qualitative analyses. Four eligible Org 2766 trials (311 participants) employed quantitative sensory testing reported disparate results; meta-analyses of three trials using comparable measures showed no significant vibration perception threshold neuroprotection. The remaining trial reported only descriptive analyses. The single eligible trials involving acetylcysteine (14 participants), diethyldithiocarbamate (195 participants), calcium and magnesium (33 participants), and oxcarbazepine (32 participants) and the two eligible trials involving vitamin E (57 participants) did not perform quantitative sensory testing. In all, data from 1,537 participants were included.
Authors' conclusions
At present, the data are insufficient to conclude that any of the purported chemoprotective agents (acetylcysteine, amifostine, calcium and magnesium, diethyldithiocarbamate, glutathione, Org 2766, oxycarbazepine, or Vitamin E) prevent or limit the neurotoxicity of platin drugs among human patients.
doi:10.1002/14651858.CD005228.pub3
PMCID: PMC3715044  PMID: 21328275
Antineoplastic Agents [*adverse effects]; Cisplatin [*adverse effects analogs & derivatives]; Neuroprotective Agents [*therapeutic use]; Peptide Fragments [therapeutic use]; Peripheral Nervous System Diseases [chemically induced; *prevention & control]; Humans
11.  Transsexualism: a legal perspective. 
Journal of Medical Ethics  1980;6(2):92-97.
This paper begins with a discussion of the current legal definition of sex laid down in Corbett v Corbett. The implications of this test for three areas of the law, marriage, birth certificates and employment are then examined. Solutions from the United States of America and West Germany are studied and the suitability of similar solutions being transplanted into British law discussed.
PMCID: PMC1154808  PMID: 7420377
12.  The burden and quality of life of caregivers of sickle cell anemia patients taking hydroxyurea versus those not taking hydroxyurea 
Objective
To assess the burden and quality of life of caregivers of patients with sickle cell anemia taking hydroxyurea versus those of patients not taking hydroxyurea.
Methods
A cross-sectional study was performed of caregivers of outpatients with sickle cell anemia in two public hospitals in Campo Grande, MS, from January through June 2010. The World Health Organization Quality of Life-BREF Scale and the Caregiver Burden Scale were used.
Results
Of the 37 caregivers in this study, 81.1% were women, 73.0% were mothers, 59.5% were married, 54.1%were mulattos, 48.6% were housewives, 54.1% had family incomes of up to one minimum wage and 75.7% had onlycompleted elementary education. The mean duration of care provided (time after diagnosis) was 16.08 ± 9.88 yearsand 89.2% reported that they provided 24-hour care. Regarding health, 27.0% of study participants reported having physical and 13.5% emotional problems. There were no significant relationships between these variables either with the different domains or the total score of the WHOQOL-BREF comparing caregivers of patients taking hydroxyurea versusthose of patients not taking hydroxyurea. There was a moderate negative linear correlation between the WHOQOL-BREF and the Caregiver Burden Scale scores (linear correlation test of Pearson: p-value = 0.003, r = -0.477). The burden of caregivers of patients who did not take hydroxyurea was significantly higher than those of patients who took the medication in terms of general tension, disappointment, environment and total score (student t-test: p-value < 0.05).
Conclusion
In the perception of the caregiver, looking after sickle cell anemia patients represents a moderate negative burden.
doi:10.5581/1516-8484.20120070
PMCID: PMC3460397  PMID: 23049439
Anemia, sickle cell; Caregivers; Quality of life; Hydroxyurea
13.  Some features of the distribution of birthweight of human infants 
This paper is concerned with the distribution of birthweight of some 18,700 singleton live and still births taking place in Cornwall, Devon, Plymouth, and Exeter in 1965. Information collected as part of the statutory birth registration process was linked to the corresponding information about the birth recorded by the local authority health department. The birthweights were originally recorded in ounces, but the irregularities in the pattern of results suggest that the observations are subject to substantial observer error and are accurate at best to the nearest quarter pound.
The general form of the birthweight distribution is examined and it is shown that the overall distribution can be effectively summarized by a mixture of two normal components. Because of the inaccuracies of the basic data concerning birthweight, it is not possible to obtain reliable estimates of all the five parameters necessary to describe a mixture of two normal components. However, the distribution (which we convert to the metric scale) can be described adequately in terms of the mean and standard deviation of the primary or major component and the proportion of births weighing less than 2,000 g, the corresponding figures for all single births being 3,380 g, 500 g, and 2·0% respectively.
The population of single births was subdivided in turn on the basis of sex, social class, parity, and maternal age. The mean of the primary component was about 120 g higher in males than in females, about 130 g higher in parity 1 births than in parity 0 births, about 110 g higher in births to mothers of 30-34 years of age than in births to mothers of less than 20 years, and about 150 g higher in social classes 1 and 2 than in social class 5. When two or more attributes are considered in combination, the social class gradient is present in most of the various subpopulations formed by subdivision of the population in terms of the other attributes. However, there seem to be complex interactions in terms of sex, parity, and maternal age. For example, the estimates of the mean of the primary component for males of parity 0 increase with increasing maternal age, whereas the corresponding estimates for females of parity 0 decrease. The variability of the primary distribution is greater for males than for females and increases with decreasing social class, increasing parity, and increasing maternal age. The proportion of births weighing less than 2,000 g was similar in males and females but decreased with increasing social class. In terms of parity, the proportion was higher for parity 0 than for parity 1 but subsequently increased with increasing parity. A similar pattern exists for maternal age in male infants, the proportion decreasing with age to reach a minimum in the 25-29 years age group and subsequently increasing as maternal age increases further. Female infants, on the other hand, show a totally different pattern in the lowest maternal age groups.
PMCID: PMC478809  PMID: 4816582
14.  Mapping Species Distributions with MAXENT Using a Geographically Biased Sample of Presence Data: A Performance Assessment of Methods for Correcting Sampling Bias 
PLoS ONE  2014;9(5):e97122.
MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one “virtual” derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases.
doi:10.1371/journal.pone.0097122
PMCID: PMC4018261  PMID: 24818607
15.  Neurogenesis suggests independent evolution of opercula in serpulid polychaetes 
Background
The internal phylogenetic relationships of Annelida, one of the key lophotrochozoan lineages, are still heavily debated. Recent molecular analyses suggest that morphologically distinct groups, such as the polychaetes, are paraphyletic assemblages, thus questioning the homology of a number of polychaete morphological characters. Serpulid polychaetes are typically recognized by having fused anterior ends bearing a tentacular crown and an operculum. The latter is commonly viewed as a modified tentacle (= radiole) and is often used as an important diagnostic character in serpulid systematics.
Results
By reconstructing the developmental neuroanatomy of the serpulid polychaete Spirorbis cf. spirorbis (Spirorbinae), we found striking differences in the overall neural architecture, the innervation pattern, and the ontogenetic establishment of the nervous supply of the operculum and the radioles in this species. Accordingly, the spirorbin operculum might not be homologous to the radioles or to the opercula of other serpulid taxa such as Serpula and Pomatoceros and is thus probably not a part of the tentacular crown.
Conclusion
We demonstrate that common morphological traits such as the prostomial appendages may have evolved independently in respective serpulid sublineages and therefore require reassessment before being used in phylogenetic analyses. Our findings corroborate recent molecular studies that argue for a revision of serpulid systematics. In addition, our data on Spirorbis neurogenesis provide a novel set of characters that highlight the developmental plasticity of the segmented annelid nervous system.
doi:10.1186/1471-2148-9-270
PMCID: PMC2785788  PMID: 19930667
16.  Perceptual accuracy of upper airway compromise in children: Clinical relevance and future directions for research 
Allergy & Rhinology  2013;4(2):e54-e62.
Approximately 80% of children with asthma have coexisting allergic rhinitis. The accurate recognition and assessment of asthma and rhinitis symptoms is an integral component of guideline-based treatment for both conditions. This article describes the development and preliminary evaluation of a novel paradigm for testing the accuracy of children's assessment of their upper airway (rhinitis) symptoms. This work is guided by our previous research showing the clinical efficacy of tools to evaluate children's perceptual accuracy of asthma symptoms and linking accurate asthma symptom perception to decreased asthma morbidity (Fritz G, et al., Ethnic differences in perception of lung function: A factor in pediatric asthma disparities? Am J Respir Crit Care Med 182:12–18, 2010; Klein RB, et al., The Asthma Risk Grid: Clinical interpretation of symptom perception, Allergy Asthma Proc 251–256, 2004). The pilot study tests a paradigm that allows for the examination of the correspondence of children's assessment of their upper airway functioning with actual values of upper airway flow through the use of a portable, handheld nasal peak flowmeter. Nine children with persistent asthma were evaluated over a 4-week period. The article describes the rhinitis perceptual accuracy paradigm and reviews the results of a pilot study, showing a large proportion of inaccurate rhinitis symptoms “guesses” by the sample of children with persistent asthma. Patterns of inaccuracy, rhinitis control, and asthma morbidity are also described. Directions for future work are reviewed. The development of clinical tools to evaluate children's accuracy of rhinitis symptoms are needed, given the central role of the self-assessment of symptoms in guideline-based care. Accurate perception of the severity of rhinitis symptoms may enhance rhinitis control, lessen the burden of asthma, and prevent unnecessary emergency use among this high-risk group of children.
doi:10.2500/ar.2013.4.0060
PMCID: PMC3793113  PMID: 24124637
Allergy; asthma; children; perceptual accuracy; rhinitis; treatment; upper airway
17.  Improved Response to Disasters and Outbreaks by Tracking Population Movements with Mobile Phone Network Data: A Post-Earthquake Geospatial Study in Haiti 
PLoS Medicine  2011;8(8):e1001083.
Linus Bengtsson and colleagues examine the use of mobile phone positioning data to monitor population movements during disasters and outbreaks, finding that reports on population movements can be generated within twelve hours of receiving data.
Background
Population movements following disasters can cause important increases in morbidity and mortality. Without knowledge of the locations of affected people, relief assistance is compromised. No rapid and accurate method exists to track population movements after disasters. We used position data of subscriber identity module (SIM) cards from the largest mobile phone company in Haiti (Digicel) to estimate the magnitude and trends of population movements following the Haiti 2010 earthquake and cholera outbreak.
Methods and Findings
Geographic positions of SIM cards were determined by the location of the mobile phone tower through which each SIM card connects when calling. We followed daily positions of SIM cards 42 days before the earthquake and 158 days after. To exclude inactivated SIM cards, we included only the 1.9 million SIM cards that made at least one call both pre-earthquake and during the last month of study. In Port-au-Prince there were 3.2 persons per included SIM card. We used this ratio to extrapolate from the number of moving SIM cards to the number of moving persons. Cholera outbreak analyses covered 8 days and tracked 138,560 SIM cards.
An estimated 630,000 persons (197,484 Digicel SIM cards), present in Port-au-Prince on the day of the earthquake, had left 19 days post-earthquake. Estimated net outflow of people (outflow minus inflow) corresponded to 20% of the Port-au-Prince pre-earthquake population. Geographic distribution of population movements from Port-au-Prince corresponded well with results from a large retrospective, population-based UN survey. To demonstrate feasibility of rapid estimates and to identify areas at potentially increased risk of outbreaks, we produced reports on SIM card movements from a cholera outbreak area at its immediate onset and within 12 hours of receiving data.
Conclusions
Results suggest that estimates of population movements during disasters and outbreaks can be delivered rapidly and with potentially high validity in areas with high mobile phone use.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Every year, millions of people are affected by disasters—sudden calamitous events that disrupt communities and cause major human, material, economic, and environmental losses. Disasters can be natural (for example, earthquakes and infectious disease outbreaks) or man-made (for example, terrorist attacks and industrial accidents). Whenever a disaster strikes, governments, international bodies, and humanitarian agencies swing into action to help the affected population by providing food, water, shelter, and medical assistance. Within days of the earthquake that struck Haiti on January 12, 2010, for instance, many governments pledged large sums of money to help the Haitians, and humanitarian agencies such as Oxfam and the International Federation of Red Cross and Red Crescent Societies sent tons of food and hundreds of personnel into the country. And when a cholera outbreak began in Haiti in October 2010, the world responded by sending further assistance.
Why Was This Study Done?
An instinctive response to any disaster is to flee the affected area, but such population movements after a disaster can increase the loss of human life by complicating the provision of relief assistance, the assessment of needs, and infectious disease surveillance. Unfortunately, there are no rapid or accurate methods available to track population movements after disasters. Relief coordinators currently rely on slow, potentially biased methods such as eye witness accounts and aerial images of shelters to track population movements. In this geospatial analysis, the researchers investigate whether position data from mobile phone SIMs (subscriber identity modules) can be used to estimate the magnitude and trends of population movements by retrospectively following the positions of SIMs in Haiti before and after the earthquake and tracking SIMs during the first few days of the cholera outbreak. Every time a SIM makes a call, the mobile phone network database records which mobile phone tower connected the call. Thus, the database can provide a geographic position for each mobile phone caller.
What Did the Researchers Do and Find?
The researchers obtained anonymized data on the position of 1.9 million SIMs in Haiti from 42 days before the earthquake to 158 days afterwards. Nearly 200,000 SIMs that were present in Haiti's capital Port-au-Prince when the earthquake struck had left 19 days post-earthquake. Just under a third of Port-au-Prince's inhabitants were mobile phone subscribers at the time of the earthquake, so this movement of SIMs equates to the movement of about 630,000 people. Notably, although the SIM-based estimates of numbers leaving Port-au-Prince matched the estimates reported by the Haitian National Civil Protection Agency (NPCA), which were largely based on counting ship and bus movements and which were used during the relief operation, the estimated geographical distribution of displaced people reported by the NPCA was very different to that obtained by analyzing SIM movements. By contrast, the geographical distribution of the population obtained from SIM movements closely matched that reported by a retrospective United Nations Population Fund household survey. Finally, to demonstrate the feasibility of producing rapid estimates of population movements during disasters, the researchers tracked nearly 140,000 SIMs during the first 8 days of the Haitian cholera outbreak and showed that they could distribute analyses of SIM movements within 12 hours of receiving data from the mobile phone company.
What Do These Findings Mean?
These findings suggest that estimates of population movements during disasters and infectious disease outbreaks can be delivered rapidly and accurately in areas of high mobile use by analyzing mobile phone data. 86% of the world's population now has mobile phone network coverage and, in 2009, there were already 3.2 billion mobile phone subscriptions in the developing world, which has a population of 5.5 billion people. Thus, this tracking method could be useful in many parts of the world, including those particularly vulnerable to disasters. However, because mobile phone use varies between sections of society, because some areas have a low density of mobile phone towers, and because disasters can destroy these towers, this approach may not be effective in all disasters. The researchers recommend, therefore, that the use of mobile phone data for tracking population movements is evaluated further and that relationships are built up with mobile phone companies to ensure rapid implementation of the approach after future disasters.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001083.
Internal Displacement Monitoring Centre provides information on population displacement during natural disasters
The International Federation of Red Cross and Red Crescent Societies provides information in several languages about disaster management and about the 2010 earthquake in Haiti
Oxfam also has information on conflicts and natural disasters and the Haiti earthquake and cholera outbreak (in several languages)
EM-DAT, the International Disaster Database contains essential core information on 18,000 mass disasters in the world from 1990 until the present
doi:10.1371/journal.pmed.1001083
PMCID: PMC3168873  PMID: 21918643
18.  Deformable Image Registration of Sliding Organs Using Anisotropic Diffusive Regularization 
Traditional deformable image registration imposes a uniform smoothness constraint on the deformation field. This is not appropriate when registering images visualizing organs that slide relative to each other, and therefore leads to registration inaccuracies. In this paper, we present a deformation field regularization term that is based on anisotropic diffusion and accommodates the deformation field discontinuities that are expected when considering sliding motion. The registration algorithm was assessed first using artificial images of geometric objects. In a second validation, monomodal chest images depicting both respiratory and cardiac motion were generated using an anatomically-realistic software phantom and then registered. Registration accuracy was assessed based on the distances between corresponding segmented organ surfaces. Compared to an established diffusive regularization approach, the anisotropic diffusive regularization gave deformation fields that represented more plausible image correspondences, while giving rise to similar transformed moving images and comparable registration accuracy.
doi:10.1109/ISBI.2011.5872434
PMCID: PMC3141338  PMID: 21785755
Deformable image registration; regularization; sliding organs; medical imaging
19.  Molecular Evidence for Spread of Two Major Methicillin-Resistant Staphylococcus aureus Clones with a Unique Geographic Distribution in Chinese Hospitals▿  
Methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) is a serious problem worldwide. To investigate the molecular epidemiology of MRSA isolates in China, a total of 702 MRSA isolates collected from 18 teaching hospitals in 14 cities between 2005 and 2006 were characterized by antibiogram analysis, pulsed-field gel electrophoresis (PFGE), staphylococcal cassette chromosome mec (SCCmec) typing, and spa typing; and 102 isolates were selected for multilocus sequence typing (MLST). Overall, SCCmec type III was the most popular type and was found in 541 isolates (77.1%), followed by SCCmec type II (109/702; 15.5%). Twenty-four PFGE types were obtained among 395 isolates collected in 2005, and 18 spa types were obtained among 702 isolates. spa type t030, which corresponded to PFEG types A to E, constituted 52.0% (365/702) of all isolates, and isolates of this type were present in all 14 cities; spa type t037, which corresponded to PFGE types F and G, accounted for 25.5% (179/702) of all isolates, and isolates of this type were identified in 12 cities. The two spa genotypes belonged to sequence type 239 (ST239) and carried SCCmec type III. spa type t002, which included isolates of PFGE types L to T, made up 16.0% (112/702) of the isolates that belonged to ST5 and SCCmec type II, and isolates of this type were distributed in 12 cities. The distribution of spa types varied among the regions. spa type t002 was the most common in Dalian (53.4%) and Shenyang (44.4%); spa type t037 was predominant in Shanghai (74.8%), whereas spa type t030 was the most common in the other cities. Two isolates from Guangzhou that harbored SCCmec type IVa with ST59 and ST88 were identified as community-associated MRSA. The prevalence of the Panton-Valentine leukocidin gene was 2.3%. The data documented two major epidemic MRSA clones, ST239-MRSA-SCCmec type III and ST5-MRSA-SCCmec type II, with unique geographic distributions across China.
doi:10.1128/AAC.00804-08
PMCID: PMC2630620  PMID: 19029328
20.  From phase-based to displacement-based gating: a software tool to facilitate respiration-gated radiation treatment 
Background
The Varian Real-Time Position Management (RPM) system allows respiratory gating based on either the phase or displacement (amplitude) of the breathing waveform. A problem in clinical application is that phase-based gating, required for respiration-correlated (4D-CT) simulation, is not robust to irregular breathing patterns during treatment, and a widely used system version (1.6) does not provide an easy means to change from a phase-based gate into an equivalent displacement-based one. We report on the development and evaluation of a robust method to convert phase-gate thresholds, set by the physician, into equivalent displacement-gate thresholds to facilitate its clinical application to treatment.
Methods
The software tool analyzes the respiration trace recorded during the 4D-CT simulation and determines a relationship between displacement and phase through a functional fit. The displacement- gate thresholds are determined from an average of two values of this function, corresponding to the start and end thresholds of the original phase gate. The software tool was evaluated in two ways: first, whether in-gate residual target motion and predicted treatment beam duty cycle are equivalent between displacement-gating and phase-gating during 4D-CT simulation (using retrospective phase recalculation); second, whether residual motion is improved with displacement-gating during treatment relative to phase-gating (using real-time phase calculation). Residual target motion was inferred from the respiration traces and quantified in terms of mean and standard deviation in-gate displacement measured relative to the value at the start of the recorded trace. For retrospectively-calculated breathing traces compared with real-time-calculated breathing traces, we evaluate the inaccuracies of real-time phase calculation by measuring the phase gate position in each trace as well as the mean in-gate displacement and standard deviation of the displacement.
Results
Retrospectively calculated data from 10 patients were analyzed. The patient-averaged in-gate mean ± standard deviation displacement (representing residual motion) was reduced from 0.16 ± 0.14 cm for phase-gating under simulation conditions to 0.12 ± 0.08 cm for displacement-gating. Evaluation of respiration traces under treatment conditions (real-time phase calculation) showed that the average displacement gate threshold results in a lower in-gate mean and residual motion (variance) for all patients studied. The patient-averaged in-gate mean ± standard deviation displacement was reduced from 0.26 ± 0.18 cm for phase-gating (under treatment conditions) to 0.15 ± 0.09 cm for displacement-gating.
Conclusions
Real-time phase gating sometimes leads to gating on incorrect portions of the breathing cycle when the breathing trace is irregular. Displacement gating is less prone to such errors, as evidenced by the lower in-gate residual motion in a large majority of cases. In terms of duty cycle and residual motion, displacement-based gating is equivalent to phase-based gating for retrospectively-calculated phase information.
PMCID: PMC2826245  PMID: 19918227
21.  Clinical and Imaging Characteristics Associated with Discordance Between CT Angiography and Quantitative Coronary Angiography on the Diagnosis of Significant Coronary Artery Disease 
JACC. Cardiovascular imaging  2013;6(9):963-972.
Objectives
To investigate clinical and imaging characteristics associated with diagnostic inaccuracy of computed tomography angiography (CTA) for detecting obstructive coronary artery disease (CAD) defined by quantitative coronary angiography (QCA).
Background
While diagnostic performance metrics of CTA have been reported, there are sparse data on predictors of diagnostic inaccuracy by CTA.
Methods
Clinical characteristics of 291 patients enrolled in the CorE-64 study were examined. Pre-defined CTA segment-level characteristics of all true-positive (N=237), false-positive (N=115), false-negative (N=159), and a random subset of true-negative segments (N=511) for ≥50% stenosis with QCA as reference standard were blindly abstracted in a central core-laboratory. Factors independently associated with corresponding levels of CTA diagnostic inaccuracies were determined.
Results
A calcium score of ≥1 per patient (OR=5.2, 95% confidence interval [CI] =1.1–24.6) and the presence of within-segment calcification (OR=10.2 [5.2–19.8]) predicted false-positive diagnoses. Conversely, absence of within-segment calcification was an independent predictor of false-negative diagnosis (OR=2.0 [1.2–3.5]). Prior percutaneous revascularization was independently associated with patient-level misdiagnosis of obstructive CAD (OR=4.2 [1.6–11.2]). Specific segment characteristics on CTA, notably segment tortuosity (OR=3.5 [2.4–5.1], smaller luminal caliber (OR=0.48 [0.36–0.63] per 1-mm increment) and juxta-arterial vein conspicuity (OR=2.1 [1.4–3.2]) were independently associated with segment-level misdiagnoses. Attaining greater intra-luminal contrast enhancement independently lowered the risk for false-negative diagnosis (OR=0.96 [0.94–0.99], per 10-Hounsfield-Unit increment).
Conclusions
We identified clinical and readily-discernable imaging characteristics predicting inaccurate CT angiography diagnosis of obstructive CAD defined by QCA. Knowledge and appropriate considerations of these features may improve accuracy in clinical CTA interpretation.
doi:10.1016/j.jcmg.2013.02.011
PMCID: PMC4162406  PMID: 23932641
Computed tomography angiography; accuracy; false-positive; false-negative
22.  Validation of a New Model-Based Tracking Technique for Measuring Three-Dimensional, In Vivo Glenohumeral Joint Kinematics 
Shoulder motion is complex and significant research efforts have focused on measuring glenohumeral joint motion. Unfortunately, conventional motion measurement techniques are unable to measure glenohumeral joint kinematics during dynamic shoulder motion to clinically significant levels of accuracy. The purpose of this study was to validate the accuracy of a new model-based tracking technique for measuring three-dimensional, in vivo glenohumeral joint kinematics. We have developed a model-based tracking technique for accurately measuring in vivo joint motion from biplane radiographic images that tracks the position of bones based on their three-dimensional shape and texture. To validate this technique, we implanted tantalum beads into the humerus and scapula of both shoulders from three cadaver specimens and then recorded biplane radiographic images of the shoulder while manually moving each specimen’s arm. The position of the humerus and scapula were measured using the model-based tracking system and with a previously validated dynamic radiostereometric analysis (RSA) technique. Accuracy was reported in terms of measurement bias, measurement precision, and overall dynamic accuracy by comparing the model-based tracking results to the dynamic RSA results. The model-based tracking technique produced results that were in excellent agreement with the RSA technique. Measurement bias ranged from −0.126 to 0.199 mm for the scapula and ranged from −0.022 to 0.079 mm for the humerus. Dynamic measurement precision was better than 0.130 mm for the scapula and 0.095 mm for the humerus. Overall dynamic accuracy indicated that rms errors in any one direction were less than 0.385 mm for the scapula and less than 0.374 mm for the humerus. These errors correspond to rotational inaccuracies of approximately 0.25 deg for the scapula and 0.47 deg for the humerus. This new model-based tracking approach represents a non-invasive technique for accurately measuring dynamic glenohumeral joint motion under in vivo conditions. The model-based technique achieves accuracy levels that far surpass all previously reported non-invasive techniques for measuring in vivo glenohumeral joint motion. This technique is supported by a rigorous validation study that provides a realistic simulation of in vivo conditions and we fully expect to achieve these levels of accuracy with in vivo human testing. Future research will use this technique to analyze shoulder motion under a variety of testing conditions and to investigate the effects of conservative and surgical treatment of rotator cuff tears on dynamic joint stability.
doi:10.1115/1.2206199
PMCID: PMC3072582  PMID: 16813452
shoulder; kinematics; accuracy; glenohumeral joint; rotator cuff
23.  Non-response in a nationwide follow-up postal survey in Finland: a register-based mortality analysis of respondents and non-respondents of the Health and Social Support (HeSSup) Study 
BMJ Open  2012;2(2):e000657.
Objective
To examine difference in mortality between postal survey non-respondents and respondents.
Design
A prospective cohort study with baseline survey in 1998 and comprehensive linkage to national mortality registers until 2005, the Health and Social Support study.
Setting
A population-based postal survey of the working-aged population in Finland in 1998.
Participants
The original random sample comprised 64 797 working-aged individuals in Finland (20–24, 30–34, 40–44, 50–54 years of age; 32 059 women and 32 716 men), yielding 25 898 (40.0%) responses in the baseline postal survey in 1998.
Primary outcome measure
Registry-based primary causes of death encoded with the International Classification of Diseases (ICD-10).
Results
In women, HR for total mortality was 1.75 (95% CI 1.40 to 2.19) times higher among the non-respondents compared with the respondents. In men, non-response was associated with a 1.41-fold (1.21–1.65) excess risk of total mortality. Non-response associated in certain age groups with deaths due to diseases in women and with deaths due to external causes in men. The most prominent excess mortality was seen for total mortality for both genders and for mortality due to external causes among men.
Conclusions
Postal surveys result in slight underestimation of illness prevalence.
Article summary
Article focus
Women and individuals from upper social strata tend to participate more actively in postal health surveys.
What this exactly means in terms of health selection among respondents is unclear.
Postal health surveys are believed to produce underestimates of illness prevalence.
Key messages
Total mortality was consistently and for women in the age group ≥50 years and for men in the age groups ≥40 years significantly higher among non-respondents compared with respondents during a 7-year follow-up among a total Finnish nationwide sample in working age comprising almost 65 000 individuals.
The excess mortality observed was 1.5–2 fold. Among men, it was explained by external causes, whereas among women, it was due to diseases and was statistically significant only in the age group 50–54 years.
Postal surveys result in slight underestimation of illness prevalence.
Strengths and limitations of the study
The linkage to mortality data was successful for virtually all individuals of the original sample comprising nearly 65 000 individuals. The sample size secures the reliability of the conclusions drawn. Furthermore, the registry data on mortality in Finland can be considered as reliable. To the best of the authors' knowledge, a corresponding study based on an as large a sample as in this study has not previously been carried out.
Some inaccuracy concerning the final diagnosis of death is possible. A further study limitation is that data of socioeconomic status or educational level of non-respondents were not available, and hence, adjustments of the statistical analyses for these variables were not possible.
doi:10.1136/bmjopen-2011-000657
PMCID: PMC3307122  PMID: 22422917
24.  ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data 
BMC Bioinformatics  2012;13:221.
Background
Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results.
Results
Here we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration. We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. We also compare ReQON to other available recalibration tools and show that ReQON is less biased and performs favorably in terms of quality score accuracy.
Conclusion
ReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. ReQON produces a new BAM file with more accurate quality scores, which can improve the results of downstream analysis, and produces several diagnostic plots showing the effectiveness of the recalibration.
doi:10.1186/1471-2105-13-221
PMCID: PMC3447716  PMID: 22946927
Next-generation sequencing; Quality score; Recalibration; Bioinformatics; Bioconductor
25.  Consequences of EEG electrode position error on ultimate beamformer source reconstruction performance 
Inaccuracy of EEG electrode coordinates forms an error term in forward model generation and ultimate source reconstruction performance. This error arises from the combination of both intrinsic measurement noise of the digitization apparatus and manual coregistration error when selecting corresponding points on anatomical MRI volumes. A common assumption is that such an error would lead only to displacement of localized sources. Here, we measured electrode positions on a 3D-printed full-scale replica head, using three different techniques: a fringe projection 3D scanner, a novel “Flying Triangulation” 3D sensor, and a traditional electromagnetic digitizer. Using highly accurate fringe projection data as ground truth, the Flying Triangulation sensor had a mean error of 1.5 mm while the electromagnetic digitizer had a mean error of 6.8 mm. Then, again using the fringe projection as ground truth, individual EEG simulations were generated, with source locations across the brain space and a range of sensor noise levels. The simulated datasets were then processed using a beamformer in conjunction with the electrode coordinates registered with the Flying Triangulation and electromagnetic digitizer methods. The beamformer's output SNR was severely degraded with the digitizer-based positions but less severely with the Flying Triangulation coordinates. Therefore, the seemingly innocuous error in electrode registration may result in substantial degradation of beamformer performance, with output SNR penalties up to several decibels. In the case of low-SNR signals such as deeper brain structures or gamma band sources, this implies that sensor coregistration accuracy could make the difference between successful detection of such activity or complete failure to resolve the source.
doi:10.3389/fnins.2014.00042
PMCID: PMC3949288  PMID: 24653671
electroencephalography; beamformer; head model; inverse problem; source localization; optical 3D metrology

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