Interhospital Sepsis Code in Catalonia (Spain): Territorial model for initial care of patients with sepsis

Sepsis is a syndromic entity with high prevalence and mortality. The management of sepsis is standardized and exhibits time-dependent efficiency. However, the management of patients with sepsis is complex. The heterogeneity of the forms of presentation can make it difficult to detect and manage such cases, in the same way as differences in training, professional competences or the availability of health resources. The Advisory Commission for Patient Care with Sepsis (CAAPAS), comprising 7 scientific societies, the Emergency Medical System (SEM) and the Catalan Health Service (CatSalut), have developed the Interhospital Sepsis Code (CSI) in Catalonia (Spain). The general objective of the CSI is to increase awareness, promote early detection and facilitate initial care and interhospital coordination to attend septic patients in a homogeneous manner throughout Catalonia.

High Temporal-Resolution Transcriptome Landscape of Early Maize Seed Development

The early maize (Zea mays) seed undergoes several developmental stages after double fertilization to become fully differentiated within a short period of time, but the genetic control of this highly dynamic and complex developmental process remains largely unknown. Here, we report a high temporal-resolution investigation of transcriptomes using 31 samples collected at an interval of 4 or 6 h within the first six days of seed development. These time-course transcriptomes were clearly separated into four distinct groups corresponding to the stages of double fertilization, coenocyte formation, cellularization, and differentiation. A total of 22,790 expressed genes including 1415 transcription factors (TFs) were detected in early stages of maize seed development. In particular, 1093 genes including 110 TFs were specifically expressed in the seed and displayed high temporal specificity by expressing only in particular period of early seed development. There were 160, 22, 112, and 569 seed-specific genes predominantly expressed in the first 16 h after pollination, coenocyte formation, cellularization, and differentiation stage, respectively. In addition, network analysis predicted 31,256 interactions among 1317 TFs and 14,540 genes. The high temporal-resolution transcriptome atlas reported here provides an important resource for future functional study to unravel the genetic control of seed development.

Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer

Determining the complete Arabidopsis (Arabidopsis thaliana) protein-protein interaction network is essential for understanding the functional organization of the proteome. Numerous small-scale studies and a couple of large-scale ones have elucidated a fraction of the estimated 300,000 binary protein-protein interactions in Arabidopsis. In this study, we provide evidence that a docking algorithm has the ability to identify real interactions using both experimentally determined and predicted protein structures. We ranked 0.91 million interactions generated by all possible pairwise combinations of 1,346 predicted structure models from an Arabidopsis predicted "structure-ome" and found a significant enrichment of real interactions for the top-ranking predicted interactions, as shown by cosubcellular enrichment analysis and yeast two-hybrid validation. Our success rate for computationally predicted, structure-based interactions was 63% of the success rate for published interactions naively tested using the yeast two-hybrid system and 2.7 times better than for randomly picked pairs of proteins. This study provides another perspective in interactome exploration and biological network reconstruction using protein structural information. We have made these interactions freely accessible through an improved Arabidopsis Interactions Viewer and have created community tools for accessing these and ∼2.8 million other protein-protein and protein-DNA interactions for hypothesis generation by researchers worldwide. The Arabidopsis Interactions Viewer is freely available at http://bar.utoronto.ca/interactions2/.

An updated gene atlas for maize reveals organ-specific and stress-induced genes

Maize (Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide. The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA-sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36 207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4154 organ-specific and 7704 differentially expressed (DE) genes following stress treatment. Gene co-expression network analyses revealed 12 modules associated with distinct biological processes containing 13 590 genes providing a resource for further association of gene function based on co-expression patterns. Presence-absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ-specific and stress-induced DE genes suggesting that PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average have significantly fewer co-expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. To facilitate use by the community, we developed the Maize Genomics Resource website (maize.plantbiology.msu.edu) for viewing and data-mining these resources and deployed two new views on the maize electronic Fluorescent Pictograph Browser (bar.utoronto.ca/efp_maize).

HIF pathway and c-Myc as biomarkers for response to sunitinib in metastatic clear-cell renal cell carcinoma

BACKGROUND

Clear-cell renal cell carcinoma (ccRCC) is a heterogeneous disease with a different clinical behavior and response to targeted therapies. Differences in hypoxia-inducible factor (HIF) expression have been used to classify von Hippel-Lindau gene (VHL)-deficient ccRCC tumors. c-Myc may be driving proliferation in HIF-2α-expressing tumors in a growth factor-independent manner.

OBJECTIVE

To explore the HIF-1α, HIF-2α and c-Myc baseline expression as potential predictors of sunitinib outcome as well as the effectiveness and safety with sunitinib in patients with metastatic ccRCC in routine clinical practice.

METHODS

This was an observational and prospective study involving 10 Spanish hospitals. Formalin-fixed, paraffin-embedded primary tumor samples from metastatic ccRCC patients who received sunitinib as first-line treatment were analyzed. Association between biomarker expression and sunitinib treatment outcomes was evaluated. Kaplan-Meier method was applied to measure progression-free survival (PFS) and overall survival.

RESULTS

Eighty-one patients were included: median PFS was 10.8 months (95% CI: 7.4-13.5 months), median overall survival was 21.8 months (95% CI: 14.7-29.8 months) and objective response rate was 40.7%, with 7.4% of patients achieving a complete response. Molecular marker staining was performed in the 69 available tumor samples. Significant association with lower PFS was identified for double c-Myc/HIF-2α-positive staining tumors (median 4.3 vs 11.5 months, hazard ratio =2.64, 95% CI: 1.03-6.80, P=0.036). A trend toward a lower PFS was found in positive c-Myc tumors (median 5.9 vs 10.9 months, P=0.263). HIF-1α and HIF-2α expression levels were not associated with clinical outcome.

CONCLUSION

These preliminary results suggest that predictive subgroups might be defined based on biomarkers such as c-Myc/HIF-2α. Further validation with more patients will be needed in order to confirm it. Outcomes with sunitinib in metastatic ccRCC in daily clinical practice resemble those obtained in clinical trials.

Epidermal growth factor receptor and epididymis invasion as prognostic biomarkers in clinical stage I testicular germ cell tumours

Background

Inguinal orchiectomy is curative in 70–80% of clinical stage I testicular germ cell tumours (CS I TGCT). The identification of patients who are at low risk of relapse is critical to avoid unnecessary treatment. The aim of this study is to explore EGFR, hMLH-1/hMSH-2 and microsatellite instability (MSI) as potential prognostic factors of recurrence in CS I TGCT.

Methods

Fifty-six CS I TGCT patients who underwent inguinal orchiectomy were included in this study. We analysed the relationship between clinicopathological and molecular factors with survival. Analysis of hMLH1, hMSH2 and EGFR expression was carried out by immunohistochemistry. Methylation status of the hMLH1 promoter was determined by pyrosequencing analysis in selected cases. EGFR exons 19, 20, 21 were analysed by PCR labeled-fragments and MSI status was determined using standard Multiplex MSI assays.

Results

Classical pathological factors such as lymphovascular invasion, high percentage of embryonal carcinoma, rete testis invasion or tumour size ≥4 cm showed a significant relationship with a higher risk of relapse. Additionally, it was found that an epididymis invasion proved to be a significant independent poor prognostic factor of recurrence (p = 0.001). hMLH1 or hMSH2 expression showed no significant association with risk of relapse and no MSI was found. EGFR expression was observed in 30.4% of samples and its expression was associated with higher risk of relapse (HR 3.5; 95% CI 1.3–9.8; p = 0.016). None of the cases presented EGFR kinase domain mutations.

Conclusions

Epididymis invasion and EGFR expression, but not hMLH-1/hMSH-2 or MSI, could be potentially useful as new prognostic factors of recurrence for CS I TGCT.

Electronic supplementary material

The online version of this article (doi:10.1186/s12967-017-1162-3) contains supplementary material, which is available to authorized users.

Use of radiometric indices to evaluate Zn and Pb stress in two grass species (Festuca rubra L. and Vulpia myuros L.)

Vegetation indices obtained from radiometric measurements have been used to estimate the stress response of plants grown in contaminated sites. The phytotoxicity of Pb and Zn in Festuca rubra L. and Vulpia myuros L. plants grown under hydroponic conditions was evaluated using vegetation indices obtained from radiometric measurements. The plants were supplied with 3 mM Zn (+Zn), 500 μM Pb (+Pb) and 500 μM Pb with EDTA (+PbEDTA) for 3 months. Significantly higher Zn concentrations in F. rubra shoots compared with V. myuros shoots were detected for Zn and Pb treatments. EDTA increased Pb transport to the shoots for both grasses, while Pb-treated plants retained Pb primarily in the roots. All vegetation indices tested showed the highest differences in F. rubra under +PbEDTA treatment and minor effects under +Zn, whereas the major variations for V. myuros corresponded to +Zn treatment, followed by +PbEDTA. Red edge normalized difference vegetation index, yellowness index and anthocyanin concentration index were the most sensitive indices to report Zn and Pb phytotoxicity in these grasses. According to the results obtained, both metal concentrations and radiometric indices suggested that Pb is more phytotoxic to F. rubra, which tolerates high Zn levels, whereas V. myuros was strongly affected by high Zn levels and markedly tolerant to Pb, even when applied in a mobile form (PbEDTA). Both species could be used in the phytostabilization of Zn- and Pb-contaminated soils. The abilities of F. rubra to accumulate Zn and V. myuros to accumulate Pb in the roots would facilitate a more efficient phytoremediation strategy when used in combination.

CT scan prior to radiotherapy in unresectable, locally advanced, non-small cell carcinoma of the lung: is it always necessary?

PURPOSE

There is broad consensus regarding evaluating response to chemotherapy (CHT) by means of computerized tomography (CT) in patients with localized or locally advanced non-small cell lung carcinoma (NSCLC). We present a study comparing the usefulness of CT versus chest X-ray (XR) and clinical findings when indicating radiotherapy (RT) following CHT.

METHODS

Ninety-eight of 150 subjects with unresectable locally advanced NSCLC were blindly and independently evaluated by XR and CT, with pairs of chest XR and CT (before and after CHT). A null hypothesis (H0) was established of the conditioned probability of detecting progression by CT and not by XR of 10 % or more, with a statistical power of 80 %.

RESULTS

Sensitivity, specificity, positive and negative predictive value of XR versus CT were 98, 89, 99, and 80 % respectively. A 4 % (p = 0.0451) probability of improvement of CT versus XR was calculated, enabling the H0 to be ruled out.

CONCLUSION

The CT failed to prove to be significantly superior to the chest XR + clinical picture in indicating a change in treatment approach in patients with unresectable locally advanced NSCLC after CHT.

Effects of droperidol and ondansetron on dispersion of ventricular repolarization: A randomized double-blind clinical study in anesthetized adult patients

BACKGROUND AND OBJECTIVE

Droperidol and ondansetron prolong QT interval, a circumstance that has raised some concerns regarding the possibility of inducing torsades de pointes (TdP). However drug-induced spatial dispersion of ventricular repolarization has been shown to be the principal arrhythmogenic substrate for TdP. The aim of this study is to explore the effects of droperidol and ondansetron on the dispersion of repolarization, measured using the T peak-to-end interval (Tp-e) and Tp-e/QT and Tp-e/RR(1/2) ratios in surgical anesthetized patients.

METHODS

A randomized, double-blind study carried out on sixty-three adult patients without cardiac disease or factors favoring QT prolongation and undergoing non-cardiac surgery were randomly assigned to the droperidol or ondansetron group. Under propofol anesthesia, a 12-lead EKG was obtained, and 1.25mg droperidol or 4mg ondansetron was injected. Five minutes later, a new 12-lead EKG was recorded. EKG analyses were independently performed by two cardiologists blinded to the state of the traces or group allocation. QT, RR and Tp-e intervals were measured by averaging five successive beats in leadII (QT) or V5 (Tp-e). The mean value for each measurement was calculated for statistical analysis.

RESULTS

Thirty-two patients (19 women) received droperidol, and 31 (22 women) ondansetron. Droperidol and ondansetron prolonged the QTcF interval (Fridericia formula) by 6.8 and 7.2ms (mean values) respectively, but neither droperidol nor ondansetron increased the Tp-e interval or Tp-e/QT and Tp-e/RR(1/2) ratios.

CONCLUSION

At antiemetic doses, neither ondansetron (4mg) nor droperidol (1.25mg) increases the dispersion of ventricular repolarization in healthy adult patients anesthetized with propofol.

IL8 polymorphisms and overall survival in pazopanib- or sunitinib-treated patients with renal cell carcinoma

BACKGROUND

We evaluated germline single nucleotide polymorphisms (SNPs) for association with overall survival (OS) in pazopanib- or sunitinib-treated patients with advanced renal cell carcinoma (aRCC).

METHODS

The discovery analysis tested 27 SNPs within 13 genes from a phase III pazopanib trial (N=241, study 1). Suggestive associations were then pursued in two independent datasets: a phase III trial (COMPARZ) comparing pazopanib vs sunitinib (N=729, study 2) and an observational study of sunitinib-treated patients (N=89, study 3).

RESULTS

In study 1, four SNPs showed nominally significant association (P≤0.05) with OS; two of these SNPs (rs1126647, rs4073) in IL8 were associated (P≤0.05) with OS in study 2. Because rs1126647 and rs4073 were highly correlated, only rs1126647 was evaluated in study 3, which also showed association (P≤0.05). In the combined data, rs1126647 was associated with OS after conservative multiple-test adjustment (P=8.8 × 10(-5); variant vs reference allele hazard ratio 1.32, 95% confidence interval: 1.15-1.52), without evidence for heterogeneity of effects between studies or between pazopanib- and sunitinib-treated patients.

CONCLUSIONS

Variant alleles of IL8 polymorphisms are associated with poorer survival outcomes in pazopanib- or sunitinib-treated patients with aRCC. These findings provide insight in aRCC prognosis and may advance our thinking in development of new therapies.