BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery

Small-scale temporal variation in propagule supply of an intertidal red alga

Information on the variability in supply of algal propagules is scarce, hindered by the difficulty in identifying propagules, but this variability may affect the distribution and abundance of algal assemblages. This study examined the small-scale (&frac12; hourly to hourly) temporal variation in propagule supply of Chondrus verrucosus (Gigartinaceae, Rhodophyta) over a dense, isolated bed in south-eastern Japan in summer and winter of 1999. Either 0.5 litre scoop samples or 5 litre pump samples were collected &frac12; hourly to hourly over 13, 22.5, and 30 h on three occasions in summer (June &amp; July) and 32 h on one occasion in winter (December). Sampling was conducted around either the new moon (two occasions in summer) or full moon (one occasion in both summer and winter) and incorporated full tidal sequences including daytime (summer) and nighttime (winter) low-low (LL) tides. Chondrus verrucosus was the only red alga with spores within the size range of 15&ndash;20 &mu;m that was fertile in the study area and surrounds at the time of sampling facilitating identification of spores. Spores in scoop samples were settled onto Petri dishes and identified on the basis of cell shape, colour and size. Pump samples were filtered onto transparent membrane filters and identified using epifluorescence microscopy: C. verrucosus spores fluoresced bright yellow and were easily distinguished from other micro-organisms of similar size, which fluoresced red or green. Results showed that while propagules could be found in the water column at most times, propagule supply of C. verrucosus was greatest during the 1&ndash;2 h period following LL tides. Variability in propagule supply was less than in previous studies examining surface or offshore waters. Spore release is thought to be stimulated by either desiccation or salinity changes associated with periods of emersion at low tide followed by re-immersion on incoming tides.<br /

Association Between Diastolic Blood Pressure During Pediatric In-Hospital Cardiopulmonary Resuscitation and Survival

BackgroundOn the basis of laboratory cardiopulmonary resuscitation (CPR) investigations and limited adult data demonstrating that survival depends on attaining adequate arterial diastolic blood pressure (DBP) during CPR, the American Heart Association recommends using blood pressure to guide pediatric CPR. However, evidence-based blood pressure targets during pediatric CPR remain an important knowledge gap for CPR guidelines.MethodsAll children ≥37 weeks' gestation and &lt;19 years old in Collaborative Pediatric Critical Care Research Network intensive care units with chest compressions for ≥1 minute and invasive arterial blood pressure monitoring before and during CPR between July 1, 2013, and June 31, 2016, were included. Mean DBP during CPR and Utstein-style standardized cardiac arrest data were collected. The hypothesis was that DBP ≥25 mm Hg during CPR in infants and ≥30 mm Hg in children ≥1 year old would be associated with survival. Primary outcome was survival to hospital discharge. Secondary outcome was survival to hospital discharge with favorable neurological outcome, defined as Pediatric Cerebral Performance Categories 1 to 3 or no worse than prearrest baseline. Multivariable Poisson regression models with robust error estimates were used to estimate the relative risk of outcomes.ResultsBlinded investigators analyzed blood pressure waveforms during CPR from 164 children, including 60% &lt;1 year old, 60% with congenital heart disease, and 54% after cardiac surgery. The immediate cause of arrest was hypotension in 67%, respiratory decompensation in 44%, and arrhythmia in 19%. Median duration of CPR was 8 minutes (quartiles, 3 and 27 minutes). Ninety percent survived the event, 68% with return of spontaneous circulation and 22% by extracorporeal life support. Forty-seven percent survived to hospital discharge, and 43% survived to discharge with favorable neurological outcome. Maintaining mean DBP ≥25 mm Hg in infants and ≥30 mm Hg in children ≥1 year old occurred in 101 of 164 children (62%) and was associated with survival (adjusted relative risk, 1.7; 95% confidence interval, 1.2-2.6; P=0.007) and survival with favorable neurological outcome (adjusted relative risk, 1.6; 95% confidence interval, 1.1-2.5; P=0.02).ConclusionsThese data demonstrate that mean DBP ≥25 mm Hg during CPR in infants and ≥30 mm Hg in children ≥1 year old was associated with greater likelihood of survival to hospital discharge and survival with favorable neurological outcome

Association Between Diastolic Blood Pressure During Pediatric In-Hospital Cardiopulmonary Resuscitation and Survival

BackgroundOn the basis of laboratory cardiopulmonary resuscitation (CPR) investigations and limited adult data demonstrating that survival depends on attaining adequate arterial diastolic blood pressure (DBP) during CPR, the American Heart Association recommends using blood pressure to guide pediatric CPR. However, evidence-based blood pressure targets during pediatric CPR remain an important knowledge gap for CPR guidelines.MethodsAll children ≥37 weeks' gestation and &lt;19 years old in Collaborative Pediatric Critical Care Research Network intensive care units with chest compressions for ≥1 minute and invasive arterial blood pressure monitoring before and during CPR between July 1, 2013, and June 31, 2016, were included. Mean DBP during CPR and Utstein-style standardized cardiac arrest data were collected. The hypothesis was that DBP ≥25 mm Hg during CPR in infants and ≥30 mm Hg in children ≥1 year old would be associated with survival. Primary outcome was survival to hospital discharge. Secondary outcome was survival to hospital discharge with favorable neurological outcome, defined as Pediatric Cerebral Performance Categories 1 to 3 or no worse than prearrest baseline. Multivariable Poisson regression models with robust error estimates were used to estimate the relative risk of outcomes.ResultsBlinded investigators analyzed blood pressure waveforms during CPR from 164 children, including 60% &lt;1 year old, 60% with congenital heart disease, and 54% after cardiac surgery. The immediate cause of arrest was hypotension in 67%, respiratory decompensation in 44%, and arrhythmia in 19%. Median duration of CPR was 8 minutes (quartiles, 3 and 27 minutes). Ninety percent survived the event, 68% with return of spontaneous circulation and 22% by extracorporeal life support. Forty-seven percent survived to hospital discharge, and 43% survived to discharge with favorable neurological outcome. Maintaining mean DBP ≥25 mm Hg in infants and ≥30 mm Hg in children ≥1 year old occurred in 101 of 164 children (62%) and was associated with survival (adjusted relative risk, 1.7; 95% confidence interval, 1.2-2.6; P=0.007) and survival with favorable neurological outcome (adjusted relative risk, 1.6; 95% confidence interval, 1.1-2.5; P=0.02).ConclusionsThese data demonstrate that mean DBP ≥25 mm Hg during CPR in infants and ≥30 mm Hg in children ≥1 year old was associated with greater likelihood of survival to hospital discharge and survival with favorable neurological outcome

Chest compression rates and pediatric in-hospital cardiac arrest survival outcomes

AimThe primary aim of this study was to evaluate the association between chest compression rates and 1) arterial blood pressure and 2) survival outcomes during pediatric in-hospital cardiopulmonary resuscitation (CPR).MethodsProspective observational study of children ≥37 weeks gestation and &lt;19 years old who received CPR in an intensive care unit (ICU) as part of the Pediatric Intensive Care Unit Quality of CPR Study (PICqCPR) of the Collaborative Pediatric Critical Care Research Network (CPCCRN). Arterial blood pressure and compression rate were determined from manually extracted arterial line waveform data during the first 10 min of CPR. The primary outcome was survival to hospital discharge. Modified Poisson regression models assessed the association between rate categories (80-&lt;100, 100-120 [Guidelines], &gt;120-140, &gt;140) and outcomes.ResultsCompression rate data were available for 164 patients. More than half (98/164; 60%) were &lt;1 year old. Return of circulation was achieved in 148/164 (90%); survival to hospital discharge in 77/164 (47%). Percentage of events with average rate within Guidelines was 32.9%. Compared to Guidelines, higher rate categories were associated with lower systolic blood pressures (&gt;120-140, p = 0.010; &gt;140, p = 0.077), but not survival. A rate between 80-&lt;100 per minute was associated with a higher rate of survival to hospital discharge (aRR 1.92, CI95 1.13, 3.29, p = 0.017) and survival with favorable neurological outcome (aRR 2.12, CI95 1.09, 4.13, p = 0.027) compared to Guidelines.ConclusionNon-compliance with compression rate Guidelines was common in this multicenter cohort. Among ICU patients, slightly lower rates were associated with improved outcomes compared to Guidelines

Functional outcomes among survivors of pediatric in-hospital cardiac arrest are associated with baseline neurologic and functional status, but not with diastolic blood pressure during CPR

AimDiastolic blood pressure (DBP) during cardiopulmonary resuscitation (CPR) is associated with survival following pediatric in-hospital cardiac arrest. The relationship between intra-arrest haemodynamics and neurological status among survivors of pediatric cardiac arrest is unknown.MethodsThis study represents analysis of data from the prospective multicenter Pediatric Intensive Care Quality of cardiopulmonary resuscitation (PICqCPR) Study. Primary predictor variables were median DBP and median systolic blood pressure (SBP) over the first 10min of CPR. The primary outcome measure was "new substantive morbidity" determined by Functional Status Scale (FSS) and defined as an increase in the FSS of at least 3 points or increase of 2 in a single FSS domain. Univariable analyses were completed to investigate the relationship between new substantive morbidity and BPs during CPR.Results244 index CPR events occurred during the study period, 77 (32%) CPR events met all inclusion criteria as well as having both DBP and FSS data available. Among 77 survivors, 32 (42%) had new substantive morbidity as measured by the FSS score. No significant differences were identified in DBP (median 30.5mmHg vs. 30.9mmHg, p=0.5) or SBP (median 76.3mmHg vs. 63.0mmHg, p=0.2) between patients with and without new substantive morbidity. Children who developed new substantive morbidity were more likely to have lower pre-arrest FSS than those that did not (median [IQR]: 7.5 [6.0-9.0] versus 9.0 [7.0-13.0], p=0.01).ConclusionNew substantive morbidity determined by FSS after a pediatric IHCA was associated with baseline functional status, but not DBP during CPR

Association between time of day and CPR quality as measured by CPR hemodynamics during pediatric in-hospital CPR

IntroductionPatients who suffer in-hospital cardiac arrest (IHCA) are less likely to survive if the arrest occurs during nighttime versus daytime. Diastolic blood pressure (DBP) as a measure of chest compression quality was associated with survival from pediatric IHCA. We hypothesized that DBP during CPR for IHCA is lower during nighttime versus daytime.MethodsThis is a secondary analysis of data collected from the Pediatric Intensive Care Quality of Cardiopulmonary Resuscitation Study. Pediatric or Pediatric Cardiac Intensive Care Unit patients who received chest compressions for ≥1 min and who had invasive arterial BP monitoring were enrolled. Nighttime was defined as 11:00PM to 6:59AM and daytime as 7:00AM until 10:59PM. Primary outcome was attainment of DBP ≥ 25 mmHg in infants &lt;1 year and ≥30 mmHg in older children. Secondary outcomes were mean DBP, ROSC, and survival to hospital discharge. Univariable and multivariate analyses evaluated the relationships between time (nighttime vs. daytime) and outcomes.ResultsBetween July 1, 2013 and June 30, 2016, 164 arrests met all inclusion/exclusion criteria: 45(27%) occurred at nighttime and 119(73%) during daytime. Average DBPs achieved were not different between groups (DBP: nighttime 28.3 mmHg[25.3, 36.5] vs. daytime 29.6 mmHg[21.8, 38.0], p = 0.64). Relative risk of DBP threshold met during nighttime vs. daytime was 1.27, 95%CI [0.80, 1.98], p = 0.30. There was no significant nighttime vs. daytime difference in ROSC (28/45[62%] vs. 84/119[71%] p = 0.35) or survival to hospital discharge (16/45[36%] vs. 61/119[51%], p = 0.08).ConclusionsIn this cohort of pediatric ICU patients with IHCA, there was no significant difference in DBP during CPR between nighttime and daytime

The association of immediate post cardiac arrest diastolic hypertension and survival following pediatric cardiac arrest

AimIn-hospital cardiac arrest occurs in &gt;5000 children each year in the US and almost half will not survive to discharge. Animal data demonstrate that an immediate post-resuscitation burst of hypertension is associated with improved survival. We aimed to determine if systolic and diastolic invasive arterial blood pressures immediately (0-20 min) after return of spontaneous circulation (ROSC) are associated with survival and neurologic outcomes at hospital discharge.MethodsThis is a secondary analysis of the Pediatric Intensive Care Quality of CPR (PICqCPR) study of invasively measured blood pressures during intensive care unit CPR. Patients were eligible if they achieved ROSC and had at least one invasively measured blood pressure within the first 20 min following ROSC. Post-ROSC blood pressures were normalized for age, sex and height. "Immediate hypertension" was defined as at least one systolic or diastolic blood pressure &gt;90th percentile. The primary outcome was survival to hospital discharge.ResultsOf 102 children, 70 (68.6%) had at least one episode of immediate post-CPR diastolic hypertension. After controlling for pre-existing hypotension, duration of CPR, calcium administration, and first documented rhythm, patients with immediate post-CPR diastolic hypertension were more likely to survive to hospital discharge (79.3% vs. 54.5%; adjusted OR = 2.93; 95%CI, 1.16-7.69).ConclusionsIn this post hoc secondary analysis of the PICqCPR study, 68.6% of subjects had diastolic hypertension within 20 min of ROSC. Immediate post-ROSC hypertension was associated with increased odds of survival to discharge, even after adjusting for covariates of interest