Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies

High-throughput post-genomic studies are now routinely and promisingly investigated in biological and biomedical research. The main statistical approach to select genes differentially expressed between two groups is to apply a t-test, which is subject of criticism in the literature. Numerous alternatives have been developed based on different and innovative variance modeling strategies. However, a critical issue is that selecting a different test usually leads to a different gene list. In this context and given the current tendency to apply the t-test, identifying the most efficient approach in practice remains crucial. To provide elements to answer, we conduct a comparison of eight tests representative of variance modeling strategies in gene expression data: Welch's t-test, ANOVA [1], Wilcoxon's test, SAM [2], RVM [3], limma [4], VarMixt [5] and SMVar [6]. Our comparison process relies on four steps (gene list analysis, simulations, spike-in data and re-sampling) to formulate comprehensive and robust conclusions about test performance, in terms of statistical power, false-positive rate, execution time and ease of use. Our results raise concerns about the ability of some methods to control the expected number of false positives at a desirable level. Besides, two tests (limma and VarMixt) show significant improvement compared to the t-test, in particular to deal with small sample sizes. In addition limma presents several practical advantages, so we advocate its application to analyze gene expression data

The tundra phenology database: More than two decades of tundra phenology responses to climate change

Observations of changes in phenology have provided some of the strongest signals of the effects of climate change on terrestrial ecosystems. The International Tundra Experiment (ITEX), initiated in the early 1990s, established a common protocol to measure plant phenology in tundra study areas across the globe. Today, this valuable collection of phenology measurements depicts the responses of plants at the colder extremes of our planet to experimental and ambient changes in temperature over the past decades. The database contains 150,434 phenology observations of 278 plant species taken at 28 study areas for periods of 1 to 26 years. Here we describe the full dataset to increase the visibility and use of these data in global analyses, and to invite phenology data contributions from underrepresented tundra locations. Portions of this tundra phenology database have been used in three recent syntheses, some datasets are expanded, others are from entirely new study areas, and the entirety of these data are now available at the Polar Data Catalogue (https://doi.org/10.21963/13215)

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700

A comparison of prehospital lactate and systolic blood pressure for predicting the need for resuscitative care in trauma transported by ground.

BACKGROUND: Reliance on prehospital trauma triage guidelines misses patients with serious injury. Lactate is a biomarker capable of identifying high-risk trauma patients. Our objective was to compare prehospital point-of-care lactate (P-LAC) with systolic blood pressure (SBP) for predicting the need for resuscitative care (RC) in trauma patients transported by ground emergency medical services. METHODS: This is a prospective observational study at nine sites within the Resuscitation Outcomes Consortium conducted from March 2011 to August 2012. Lactate was measured on patients with a prehospital SBP of 100 mm Hg or less who were transported by emergency medical services to a Level I or II trauma center. Patients were followed up for the need for RC, defined as any of the following within 6 hours of emergency department arrival: blood transfusion of 5 U or greater; intervention for hemorrhage including thoracotomy, laparotomy, pelvic fixation, or interventional radiology embolization; or death. RESULTS: A total of 387 patients had a lactate value and presented with SBP between 71 mm Hg and 100 mm Hg, and 70 (18%) required RC. With the use of a P-LAC decision rule (≥2.5 mmol/L) that yielded the same specificity as that of SBP of 90 mm Hg or less (48%), the observed sensitivities for RC were 93% (95% confidence interval [CI], 84-98%) for P-LAC of 2.5 mmol/L or greater and 67% (95% CI, 55-78%) for SBP of 90 mm Hg or less (McNemars test, p < 0.001). P-LAC has an estimated area under the curve of 0.78 (95% CI, 0.73-0.83), which is statistically superior to that of SBP (0.59; 95% CI, 0.53-0.66) and shock index (heart rate / SBP) (0.66; 95% CI, 0.60-0.74). CONCLUSION: P-LAC obtained at the scene is associated with the need for RC. P-LAC is superior to other early surrogates for hypoperfusion (SBP and shock index) in predicting the need for RC in trauma patients with 70 mm Hg < SBP ≤ 100 mm Hg. LEVEL OF EVIDENCE: Prognostic study, level II

Risk Factors for the Development of Acute Respiratory Distress Syndrome Following Hemorrhage

BackgroundThe Pragmatic Randomized Optimal Platelet and Plasma Ratios (PROPPR) study evaluated the effects of plasma and platelets on hemostasis and mortality after hemorrhage. The pulmonary consequences of resuscitation strategies that mimic whole blood, remain unknown.MethodsA secondary analysis of the PROPPR study was performed. Injured patients predicted to receive a massive transfusion were randomized to 1:1:1 versus 1:1:2 plasma-platelet-red blood cell ratios at 12 Level I North American trauma centers. Patients with survival >24 h, an intensive care unit (ICU) stay, and a recorded PaO2/FiO2 (P/F) ratio were included. Acute respiratory distress syndrome (ARDS) was defined as a P/F ratio < 200, with bilateral pulmonary infiltrates, and adjudicated by investigators.ResultsFour hundred fifty-four patients were reviewed (230 received 1:1:1, 224 1:1:2). Age, sex, injury mechanism, and regional abbreviated injury scale (AIS) scores did not differ between cohorts. Tidal volume, positive end-expiratory pressure, and lowest P/F ratio did not differ. No significant differences in ARDS rates (14.8% vs. 18.4%), ventilator-free (24 vs. 24) or ICU-free days (17.5 vs. 18), hospital length of stay (22 days vs. 18 days), or 30-day mortality were found (28% vs. 28%). ARDS was associated with blunt injury (OR 3.61 [1.53-8.81] P < 0.01) and increasing chest AIS (OR 1.40 [1.15-1.71] P < 0.01). Each 500 mL of crystalloid infused during hours 0 to 6 was associated with a 9% increase in the rate of ARDS (OR 1.09 [1.04-1.14] P < 0.01). Blood given at 0 to 6 or 7 to 24 h were not risk factors for lung injury.ConclusionAcute crystalloid exposure, but not blood products, is a potentially modifiable risk factor for the prevention of ARDS following hemorrhage

Kuluttajabarometri maakunnittain 2000, 2. neljännes

Suomen virallinen tilasto (SVT

Use of failure-to-rescue to identify international variation in postoperative care in low-, middle- and high-income countries: a 7-day cohort study of elective surgery

This was an investigator-initiated study funded by Nestle Health Sciences through an unrestricted research grant and by a National Institute for Health Research (UK) Professorship held by R.P. The study was sponsored by Queen Mary University of London