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opencc-zeroAug 2019View details →

Data from: Calculating maximum morphine equivalent daily dose from prescription directions for use in the electronic health record: a case report

Objective To demonstrate a process of calculating the maximum potential morphine milligram equivalent daily dose (MEDD) based on the prescription Sig for use in quality improvement initiatives. Methods To calculate an opioid prescription's maximum potential Sig-MEDD, we developed SQL code to determine a prescription's maximum units/day using discrete field data and text-parsing in the prescription instructions. We validated the derived units/day calculation using 3,000 Sigs, then compared the Sig-MEDD calculation against the Epic MEDD calculator. Results Of the 101,782 outpatient opioid prescriptions ordered over one year, 80% used discrete-field Sigs, 7% used free-text Sigs, and 3% used both types. We determined units/day and calculated a Sig-MEDD for 98.3% of all prescriptions, 99.99% of discrete-Sig prescriptions, and 81.5% of free-text-Sig prescriptions. Conclusion Analyzing opioid prescription Sigs to determine a maximum potential Sig-MEDD provides greater insight into a patient's risk for opioid exposure.

opencc-zeroDec 2016View details →

Data from: Do failures in non-technical skills contribute to fatal medical accidents in Japan? A review of the 2010–2013 national accident reports

Objectives: We sought to clarify how large a proportion of fatal medical accidents can be considered to be caused by poor Non-Technical Skills, and to support development of a policy to reduce numbers of such accidents by making recommendations about possible training requirements. Design: Summaries of reports of fatal medical accidents, published by the Japan Medical Safety Research Organization, were reviewed individually. Three experienced clinicians and one patient safety expert conducted the reviews to determine the cause of death. Views of the patient safety expert were given additional weight in the overall determination. Setting: A total of 73 summary reports of fatal medical accidents were reviewed. These reports had been submitted by healthcare organisations across Japan to the Japan Medical Safety Research Organization between April 2010 and March 2013. Primary and secondary outcome measures: The cause of death in fatal medical accidents, categorised into technical skills, non-technical skills, and inevitable progress of disease were evaluated. Non-technical skills were further sub-divided into situation awareness, decision-making, communication, team working, leadership, managing stress, and coping with fatigue. Results: Overall, the cause of death was identified as non-technical skills in 34 cases (46.6%), disease progression in 33 cases (45.2%), and technical skills in two cases (5.5%). In two cases, no consensual determination could be achieved. Further categorisation of cases of non-technical skills were identified 14 cases (41.2%) of problems with situation awareness, eight (23.5%) with team-working, and three (8.8%) with decision-making. These three sub-categories, or combinations of them, were identified as the cause of death in 33 cases (97.1%). Conclusions: Poor non-technical skills were considered to be a significant cause of adverse events in nearly half of the fatal medical accidents examined. Improving non-technical skills may be effective for reducing accidents, and training in particular sub-categories of non-technical skills may be especially relevant.

opencc-zeroDec 2011View details →

Data from: A call for more transparent reporting of error rates: the quality of AFLP data in ecological and evolutionary research

Despite much discussion of the importance of quantifying and reporting genotyping error in molecular studies, it is still not standard practice in the literature. This is particularly a concern for amplified fragment length polymorphism (AFLP) studies, where differences in laboratory, peak-calling and locus-selection protocols can generate data sets varying widely in genotyping error rate, the number of loci used and potentially estimates of genetic diversity or differentiation. In our experience, papers rarely provide adequate information on AFLP reproducibility, making meaningful comparisons among studies difficult. To quantify the extent of this problem, we reviewed the current molecular ecology literature (470 recent AFLP articles) to determine the proportion of studies that report an error rate and follow established guidelines for assessing error. Fifty-four per cent of recent articles do not report any assessment of data set reproducibility. Of those studies that do claim to have assessed reproducibility, the majority (~90%) either do not report a specific error rate or do not provide sufficient details to allow the reader to judge whether error was assessed correctly. Even of the papers that do report an error rate and provide details, many (≥23%) do not follow recommended standards for quantifying error. These issues also exist for other marker types such as microsatellites, and next-generation sequencing techniques, particularly those which use restriction enzymes for fragment generation. Therefore, we urge all researchers conducting genotyping studies to estimate and more transparently report genotyping error using existing guidelines and encourage journals to enforce stricter standards for the publication of genotyping studies.

opencc-zeroDec 2013View details →

Data from: Outcome of assisted reproductive technology (ART) and subsequent self-reported life satisfaction

Objective: To compare life satisfaction between women with successful or unsuccessful outcome after assisted reproductive treatment (ART) by taking into account the time since the last ART. Design: Cohort study. Setting: Tertiary hospital. Patients: A total of 987 consecutive women who had undergone ART during 1996–2007 were invited and altogether 505 women participated in the study. Interventions: A postal enquiry with a life satisfaction scale. Main Outcome Measure: Self-reported life satisfaction in respect to the time since the last ART. Results: In general, women who achieved a live birth after ART had a significantly higher life satisfaction than those who had unsuccessful ART, especially when compared in the first three years. The difference disappeared in the time period of 6–9 years after ART. The unsuccessfully treated women who had a child by some other means before or after the unsuccessful ART had comparable life satisfaction with successfully treated women even earlier. Conclusions: Even if unsuccessful ART outcome is associated with subsequent lower level of life satisfaction, it does not seem to threaten the long-term wellbeing.

opencc-zeroOct 2019View details →

A vigiPoint characterisation of female versus male reports in VigiBase, the WHO global database of individual case safety reports

General information This data is supplementary material to the paper by Watson et al. on sex differences in global reporting of adverse drug reactions [1]. Readers are referred to this paper for a detailed description of the context in which the data was generated. Anyone intending to use this data for any purpose should read the publicly available information on the VigiBase source data [2, 3]. The conditions specified in the caveat document [3] must be adhered to. Source dataset The dataset published here is based on analyses performed in VigiBase, the WHO global database of individual case safety reports [4]. All reports entered into VigiBase from its inception in 1967 up to 2 January 2018 with patient sex coded as either female or male have been included, except suspected duplicate reports [5]. In total, the source dataset contained 9,056,566 female and 6,012,804 male reports. Statistical analysis The characteristics of the female reports were compared to those of the male reports using a method called vigiPoint [6]. This is a method for comparing two or more sets of reports (here female and male reports) on a large set of reporting variables, and highlight any feature in which the sets are different in a statistically and clinically relevant manner. For example, patient age group is a reporting variable, and the different age groups 0 - 27 days, 28 days - 23 months et cetera are features within this variable. The statistical analysis is based on shrinkage log odds ratios computed as a comparison between the two sets of reports for each feature, including all reports without missing information for the variable under consideration. The specific output from vigiPoint is defined precisely below. Here, the results for 18 different variables with a total of 44,486 features are presented. 74 of these features were highlighted as so called vigiPoint key features, suggesting a statistically and clinically significant difference between female and male reports in VigiBase. Description of published dataset The dataset is provided in the form of a MS Excel spreadsheet (.xlsx file) with nine columns and 44,486 rows (excluding the header), each corresponding to a specific feature. Below follows a detailed description of the data included in the different columns. Variable: This column indicates the reporting variable to which the specific feature belongs. Six of these variables are described in the original publication by Watson et al.: country of origin, geographical region of origin, type of reporter, patient age group, MedDRA SOC, ATC level 2 of reported drugs, seriousness, and fatality [1]. The remaining 12 are described here: <ul> <li> MedDRA HLGT (high-level group term), MedDRA HLT (high-level term) and MedDRA PT (preferred term) are defined analogously to the MedDRA SOC (system organ class) [1], only at lower levels of the <a href="https://www.meddra.org/">MedDRA </a>(Medical Dictionary for Regulatory Activities) hierarchy. Here, MedDRA version 20.1 has been used.</li> <li> ATC level 3 of reported drugs is defined analogously to the variable ATC level 2 of reported drugs [1], only one step further down in the <a href="https://www.whocc.no/atc/structure_and_principles">ATC</a> (Anatomical Therapeutical Classification) hierarchy.</li> <li>The vigiGrade completeness score is a measure of how complete each report is with respect to certain report fields useful for causality assessment [7]. The completeness score has been dichotomised into two features, 'Above or equal to 0.8' and 'Below 0.8'. The maximum possible score for an individual report is 1.0.</li> <li>The date of VigiBase entry is simply the time when a report was entered into VigiBase. This variable is divided into 14 features that are either individual years or ranges of years.</li> <li> The number of reported drugs is the number of unique drugs that are coded on a report as either suspected, interacting, or concomitant. A drug is here defined as an entry at the preferred base (i.e. substance) level of the WHODRUG terminology. The variable is divided into four features: 'One drug', 'Two drugs', '3-5 drugs', and 'More than 5 drugs'.</li> <li> The number of reported MedDRA PTs is the number of unique MedDRA preferred terms that are coded as events on a report. This variable is divided into four features in exactly the same way as the reported drugs.</li> <li> A reported drug is a drug coded on a report as either suspected, interacting, or concomitant. As above, a drug is defined as an entry at the preferred base (i.e. substance) level of the WHODRUG terminology. This variable has almost 23,000 features, one for each drug that occurs in at least one female or one male report.</li> <li> The type of report indicates the type of individual case report. The vast majority belongs to the feature 'Spontaneous', but there are four other possible features for this variable.</li> </ul> The Variable column can be useful for filtering the data, for example if one is interested in one or a few specific variables. Feature: This column contains each of the 44,486 included features. The vast majority should be self-explanatory, or else they have been explained above, or in the original paper [1]. Female reports and Male reports: These columns show the number of female and male reports, respectively, for which the specific feature is present. Proportion among female reports and Proportion among male reports: These columns show the proportions within the female and male reports, respectively, for which the specific feature is present. Comparing these crude proportions is the simplest and most intuitive way to contrast the female and male reports, and a useful complement to the specific vigiPoint output. Odds ratio: The odds ratio is a basic measure of association between the classification of reports into female and male reports and a given reporting feature, and hence can be used to compare female and male reports with respect to this feature. It is formally defined as a / (bc / d), where <ul> <li> a is the number of female reports with the feature</li> <li> b is the number of female reports without the feature (excluding reports where the variable is missing)</li> <li> c is the number of male reports with the feature</li> <li> d is the number of male reports without the feature (excluding reports where the variable is missing).</li> </ul> This crude odds ratio can also be computed as (pfemale / (1-pfemale)) / (pmale / (1-pmale)), where pfemale and pmale are the proportions described earlier. If the odds ratio is above 1, the feature is more common among the female than the male reports; if below 1, the feature is less common among the female than the male reports. Note that the odds ratio can be mathematically undefined, in which case it is missing in the published data. vigiPoint score: This score is defined based on an odds ratio with added statistical shrinkage, defined as (a + k) / ((bc / d) + k), where k is 1% of the total number of female reports, or about 9,000. While the shrinkage adds robustness to the measure of association, it makes interpretation more difficult, which is why the crude proportions and unshrunk odds ratios are also presented. Further, 99% credibility intervals are computed for the shrinkage odds ratios, and these intervals are transformed onto a log2 scale [6]. The vigiPoint score is then defined as the lower endpoint of the interval, if that endpoint is above 0; as the higher endpoint of the interval, if that endpoint is below 0; and otherwise as 0. The vigiPoint score is useful for sorting the features from strongest positive to strongest negative associations, and/or to filter the features according to some user-defined criteria. vigiPoint key feature: Features are classified as vigiPoint key features if their vigiPoint score is either above 0.5 or below -0.5. The specific thereshold of 0.5 is arbitrary, but chosen to identify features where the two sets of reports (here female and male reports) differ in a clinically significant way. References <ol> <li>Watson S, Caster O, Rochon PA, den Ruijter H. Reported adverse drug reactions in women and men: Aggregated evidence from globally collected individual case reports during half a decade. EClinicalMedicine 2019.</li> <li>Uppsala Monitoring Centre. <a href="https://www.who-umc.org/media/164772/guidelineusingvigibaseinstudies.pdf">Guideline for using VigiBase data in studies</a>.</li> <li>Uppsala Monitoring Centre. <a href="https://www.who-umc.org/media/164610/umc_caveat.pdf">Caveat document: Statement of reservations, limitations, and conditions relating to data released from VigiBase, the WHO global database of individual case safety reports (ICSRs)</a>.</li> <li>Lindquist M. VigiBase, the WHO Global ICSR Database System: Basic Facts. The Drug Information Journal 2008; 42(5): 409-19.</li> <li>Norén GN, Orre R, Bate A, Edwards IR. Duplicate detection in adverse drug reaction surveillance. Data Mining and Knowledge Discovery 2007; 14(3): 305-28.</li> <li>Juhlin K, Star K, Norén GN. A method for data-driven exploration to pinpoint key features in medical data and facilitate expert review. Pharmacoepidemiology and Drug Safety 2017; 26(10): 1256-65.</li> <li>Bergvall T, Norén GN, Lindquist M. vigiGrade: A tool to identify well-documented individual case reports and highlight systematic data quality issues. Drug Safety 2014; 37(1): 65-77.</li> </ol>

opencc-zeroJun 2021View details →

CLSM data of CLE40, CLV3, WUS, BAM1, and CLV1 reporter lines in Arabidopsis thaliana

Stem cell homeostasis in plant shoot meristems requires tight coordiantion between stem cell proliferation and cell differentiation. In Arabidopsis, stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which signals through the leucine-rich repeat (LRR)–receptor kinase CLAVATA1 (CLV1) and related CLV1-family members to downregulate expression of the homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from cells below the stem cell domain to the meristem tip and promotes stem cell identity, together with CLV3 expression, generating a negative feedback loop. How stem cell activity in the meristem centre is coordinated with organ initiation and cell differentiation at the periphery is unknown. We show here that the CLE40 gene, encoding a secreted peptide closely related to CLV3, is expressed in the SAM in differentiating cells in a pattern complementary to that of CLV3. CLE40 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40 expression is in turn repressed in a WUS-dependent manner. Together, CLE40-BAM1-WUS establish a second negative feedback loop. We propose that stem cell homeostasis is achieved through two intertwined pathways that adjust WUS activity and incorporate information on the size of the stem cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.

opennotspecifiedDec 2016View details →

FIGURES 3–4. Tambitnotia peruviana n in A new species of Tambitnotia from Peru, with the first reported female of the genus (Lepidoptera: Tortricidae: Olethreutinae)

FIGURES 3–4. Tambitnotia peruviana n. sp., male, head close-ups (lateral and dorsal views).

opennotspecifiedDec 2005View details →

FIGURE 1 in First report of Aethaloptera dispar Brauer 1875 (Trichoptera: Hydropsychidae) from IleIfe, southwestern Nigeria, West Africa

FIGURE 1. Map of Africa showing the location of IleIfe in southwestern Nigeria.

opennotspecifiedDec 2006View details →

FIGURE 7 in First Asian report of the genus Chilibathynella Noodt, 1963 (Bathynellacea, Syncarida), with the description and biogeographic significance of a new species from Kotumsar Cave, India

FIGURE 7. Map to show the distribution of the three known species of Chilibathynella.

opennotspecifiedDec 2006View details →

FIGURE 1 in First Asian report of the genus Chilibathynella Noodt, 1963 (Bathynellacea, Syncarida), with the description and biogeographic significance of a new species from Kotumsar Cave, India

FIGURE 1. Location map of the Kotumsar Cave (adapted from Pati & Agrawal, 2002).

opennotspecifiedDec 2008View details →

FIGURE 5 in A summary of reports of abyssal and hadal Monoplacophora and Polyplacophora (Mollusca) *

FIGURE 5. Depth range (m) of abyssal and hadal Polyplacophora.

opennotspecifiedDec 2008View details →

FIGURE 3 in A summary of reports of abyssal and hadal Monoplacophora and Polyplacophora (Mollusca) *

FIGURE 3. Depth range (m) of abyssal and hadal Monoplacophora.

FIGURE21. Brama brama MZUSP 80495 41.8 in First report of rare pomfrets (Teleostei: Bramidae) from Brazilian waters, with a key to Western Atlantic species

FIGURE21. Brama brama MZUSP 80495 41.8 mm SL.

FIGURE 18 C & D in First report of rare pomfrets (Teleostei: Bramidae) from Brazilian waters, with a key to Western Atlantic species

FIGURE 18 C & D Taractichthys longipinnis, UF 168739, young, 50.0 mm SL, from Bahamas.

FIGURE 13. Pteraclis aesticola MZUSP 61590, 59.7 in First report of rare pomfrets (Teleostei: Bramidae) from Brazilian waters, with a key to Western Atlantic species

FIGURE 13. Pteraclis aesticola MZUSP 61590, 59.7 mm SL.

FIGURE 16. Pterycombus brama MZUSP 61623, 84.2 in First report of rare pomfrets (Teleostei: Bramidae) from Brazilian waters, with a key to Western Atlantic species

FIGURE 16. Pterycombus brama MZUSP 61623, 84.2 mm SL.

FIGURE 20. Brama dussumieri MZUSP 61634, 94.3 in First report of rare pomfrets (Teleostei: Bramidae) from Brazilian waters, with a key to Western Atlantic species

FIGURE 20. Brama dussumieri MZUSP 61634, 94.3 mm SL.

FIGURE 15. Pterycombus petersii MZUSP 61586, 65.2 in First report of rare pomfrets (Teleostei: Bramidae) from Brazilian waters, with a key to Western Atlantic species

FIGURE 15. Pterycombus petersii MZUSP 61586, 65.2 mm SL.

FIGURE 3 The Tropical Pomfret becomes a in First report of rare pomfrets (Teleostei: Bramidae) from Brazilian waters, with a key to Western Atlantic species

FIGURE 3 The Tropical Pomfret becomes a daily catch off Bahia, Northeast Brazil.

FIGURE 17 Taractichthys longipinnis MZUSP 78303, 29.3 in First report of rare pomfrets (Teleostei: Bramidae) from Brazilian waters, with a key to Western Atlantic species

FIGURE 17 Taractichthys longipinnis MZUSP 78303, 29.3 mm SL.