Validation of a nomogram for predicting the risk of inadvertent intraoperative hypothermia in colorectal surgery patients
Ontology highlight
ABSTRACT:
DISEASE(S): Colorectal Cancer
PROVIDER: 2760520 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
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Project description:Microarrays have evolved from low-density cDNA or oligonucleotide arrays to high-density platforms, for several study species even covering the complete transcriptome. At the same time, transcriptomics experiments have become more complex and multifactorial in nature, requiring many microarrays to assess multiple biologically relevant hypotheses. Scientists using this technology are therefore painfully aware of the high financial cost of a typical microarray experiment. Unfortunately, this often leads to either a suboptimal experimental design in an effort to reduce the cost by using fewer microarrays, or to abandoning microarray technology altogether. In this study, we argue that for many studies high-density full genome microarrays are in fact technical overkill. By selectively reducing full genome probe sets to a lower number of probes, it is possible to significantly reduce the total cost of a microarray experiment. The study consists of four microarray analyses: a cadmium probe selection experiment, a temperature probe selection experiment, a cadmium validation experiment and a cadmium validation experiment.
2009-12-31 | GSE17086 | GEO
Project description:Microarrays have evolved from low-density cDNA or oligonucleotide arrays to high-density platforms, for several study species even covering the complete transcriptome. At the same time, transcriptomics experiments have become more complex and multifactorial in nature, requiring many microarrays to assess multiple biologically relevant hypotheses. Scientists using this technology are therefore painfully aware of the high financial cost of a typical microarray experiment. Unfortunately, this often leads to either a suboptimal experimental design in an effort to reduce the cost by using fewer microarrays, or to abandoning microarray technology altogether. In this study, we argue that for many studies high-density full genome microarrays are in fact technical overkill. By selectively reducing full genome probe sets to a lower number of probes, it is possible to significantly reduce the total cost of a microarray experiment. The study consists of four microarray analyses: a cadmium probe selection experiment, a temperature probe selection experiment, a cadmium validation experiment and a cadmium validation experiment.
2009-12-31 | GSE17085 | GEO
Project description:Intervention1: Rectus sheath block: A USG machine with linear array probe (5-12MHz) with an imaging depth of 4-6cm will be used for performing the block.
The ultrasound probe will be placed transverse on abdomen, immediately lateral (3 cm) to umbilicus.
A 20-gauge needle will be inserted in-plane in a medial to lateral orientation, through the subcutaneous tissue, to pierce through the anterior rectus sheath.
Upon identification of the rectus muscle and hyperechoic twin lines deep to it (posterior rectus sheath and fascia transversalis) in the ultrasound image the needle tip will be advanced to the desired position, posterior to the rectus muscle and above the underlying posterior rectus sheath under direct vision.
Following con�rmation of the correct position of the needle tip with hydro dissection of the rectus muscle away from the posterior rectus by administration of 0.51ml of normal saline; 20ml of 0.25% bupivacaine will be administered for block performance.
The procedure will be repeated on the opposite side.
Intervention2: oblique subcostal Transversus abdominis plane block: A USG linear array probe with high- or an intermediate-frequency linear probe of 35 to 40 mm will provide adequate imaging.
A needle of up to 15 to 20 cm in length , bend into a slight curve will be required , decribed by Hebbard et al .15
The operator will stand on the left side of the patient in the supine position, and both sides are blocked from this position, with the right hand holding the needle and the left hand holding the probe.
To perform the block, the rectus abdominis and underlying transversus abdominis muscles will be identified near the costal margin and xyphoid.
Local anesthetic is injected incrementally in the TAP (hydrodissection) by a needle passing along the obliq
Primary outcome(s): â?¢To assess the analgesic efficacy of rectus sheath block.
â?¢To assess the analgesic efficacy of oblique subcostal TAP block.
â?¢To compare the analgesic efficacy of both blocks.
Timepoint: 24 hrs
Study Design: Randomized, Parallel Group Trial
Method of generating randomization sequence:Coin toss, Lottery, toss of dice, shuffling cards etc Method of allocation concealment:An Open list of random numbers Blinding and masking:Participant and Investigator Blinded
| 2605115 | ecrin-mdr-crc
Project description:Interventions: Gold Standard:Gastroscopy, colonoscopy, pathological diagnosis;Index test:Plasma exosome extraction: commercial plasma exosome extraction kit (EZB company) extraction.
Extraction of plasma exosomal miRNA: Advanced probe method RT-qPCR extraction kit (Thermo Company).
Primary outcome(s): exosome microRNA
Study Design: Cohort study
| 40619 | ecrin-mdr-crc
Project description:We performed global scale microarray analysis to identify detailed mechanisms by which nonpermissive temperature induces cell differentiation in testicular Sertoli TTE3 cells harboring temperature-sensitive SV40 large T-antigen by using an Affymetrix GeneChip system. Testicular Sertoli TTE3 cells used in the present study were derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen. In the TTE3 cells, inactivation of the T-antigen by a nonpermissive temperature at 39˚C led to cell differentiation accompanying elevation of transferrin and cyclin-dependent kinase inhibitor CDKN1A. Of the 22, 690 probe sets analyzed, nonpermissive temperature up-regulated 729 probe sets and down-regulated 471 probe sets by >2.0-fold. Keywords: Sertoli cell; differentiation; temperature-sensitive SV40 large T-antigen; nonpermissive temperature
2007-02-23 | GSE6961 | GEO
Project description:Intervention1: Continuous Bilateral Quadratus Lumborum Block: Patients in CQL (II) group will undergo ultrasound-guided QL (II) block as described by Quiang Zhu et al. The patient should be placed in the left lateral position and a roll to be placed in between the rib cage and transverse process of the left side to open up the opposite space. (22) Then a low frequency convex probe (SonoSite edge transducer, 25 MHz) will be placed at the L2 transverse level near posterior axillary line of the right side to locate the sham-rock sign. The thoracolumbar fascia between the quadratus lumborum and psoas major is identified by optimising the gain. A 19G nerve block needle will be used (PlexoLong Nanoline continuous nerve block Kit, PAJUNK Inc.) to insert by in-plane method from the dorsal to ventral direction. After reaching the front edge of the quadratus lumborum, hydrodissection with 5 ml of normal saline will be done to separate the muscle and the fascia which will indicate that the needle tip has reached the appropriate position. Ropivacaine 0.2% at 0.3 ml·kg 1 will be injected after negative aspiration and then, a 20 G catheter will be placed through the sheath tube at a depth of approximately 5 cm. A subcutaneous tunnel of 3 cm will be made to prevent catheter dislodgment. The same procedure will be followed in the right side.
Control Intervention1: Continuous Epidural Block: Patients in the EPI group will undergo epidural placement (in between T9 and T11 level in patients undergoing left-sided hemicolectomy and anorectal surgery and between T8 and T10 in patients undergoing right-sided hemicolectomy) as per the institutional protocol.
Patients with block height above T7 level 30 min after completion of the block (in both groups) will be included in the stu
Primary outcome(s): 1.To compare NRS scores (at rest) between the continuous quadratus lumborum (CQLâ?¡) and Epidural (Ep) groups at 24 hours after surgery.Timepoint: 1.To compare NRS scores (at rest) between the continuous quadratus lumborum (CQLâ?¡) and Epidural (Ep) groups at 24 hours after surgery.
Study Design: Randomized, Parallel Group Trial
Method of generating randomization sequence:Computer generated randomization Method of allocation concealment:On-site computer system Blinding and masking:Outcome Assessor Blinded
| 2606371 | ecrin-mdr-crc
Project description:Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes
2011-10-31 | GSE32518 | GEO
Project description:BACKGROUND:This study aimed to externally validate and upgrade the recent difficulty scoring system (DSS) proposed by Halls et al. to predict intraoperative complications (IOC) during laparoscopic liver resection (LLR). METHODS:The DSS was validated in a cohort of 128 consecutive patients undergoing pure LLRs between 2008 and 2019 at a single tertiary referral center. The validated DSS includes four difficulty levels based on five risk factors (neoadjuvant chemotherapy, previous open liver resection, lesion type, lesion size and classification of resection). As established by the validated DSS, IOC was defined as excessive blood loss (>?775?mL), conversion to an open approach and unintentional damage to surrounding structures. Additionally, intra- and postoperative outcomes were compared according to the difficulty levels with usual statistic methods. The same five risk factors were used for validation done by linear and advanced nonlinear (artificial neural network) models. The study was supported by mathematical computations to obtain a mean risk curve predicting the probability of IOC for every difficulty score. RESULTS:The difficulty level of LLR was rated as low, moderate, high and extremely high in 36 (28.1%), 63 (49.2%), 27 (21.1%) and 2 (1.6%) patients, respectively. IOC was present in 23 (17.9%) patients. Blood loss of >775?mL occurred in 8 (6.2%) patients. Conversion to open approach was required in 18 (14.0%) patients. No patients suffered from unintentional damage to surrounding structures. Rates of IOC (0, 9.5, 55.5 and 100%) increased gradually with statistically significant value among difficulty levels (P?<?0.001). The relations between the difficulty level, need for transfusion, operative time, hepatic pedicle clamping, and major postoperative morbidity were statistically significant (P?<?0.05). Linear and nonlinear validation models showed a strong correlation (correlation coefficients 0.914 and 0.948, respectively) with the validated DSS. The Weibull cumulative distribution function was used for predicting the mean risk probability curve of IOC. CONCLUSION:This external validation proved this DSS based on patient's, tumor and surgical factors enables us to estimate the risk of intra- and postoperative complications. A surgeon should be aware of an increased risk of complications before starting with more complex procedures.
| S-EPMC6882247 | biostudies-literature
Project description:The aim of this study is to provide an extended, retrospective validation of a previously described 4-gene signature (MMP1, COL4A1, P4HA2, and THBS2) predictive of oral carcinoma recurrence. We assessed an independent cohort including 245 histologically normal surgical margins from 62 patients with OSCC. Gene expression was determined using a color-coded probe assay for quantitative gene expression analysis. All margins and tumor blocks were cut (4-5µm tick) and stained with Hematoxylin-Eosin and tissues were subjected to needle microdissection using the stereo microscope Leica EZ4 (Leica Microsystems, Wetzlar, Germany) before RNA extraction, in order to isolate pure tumor or normal cell populations. RNA from FFPE samples was isolated using the RecoverAll Total Nucleic Acid Isolation kit (Ambion/Life Technologies, Carlsbad, CA, USA), following our previously reported protocol with modifications to improve RNA yield [PMID:23835716]. RNA was stored at -80ºC until RNA extraction and gene expression validation. In addition, tumor tissues from the same patients were collected for further analysis (not in scope of the presented study). Probes were designed for the 4-gene signature (MMP1, COL4A1, P4HA2 and THBS2) and contained one capture probe linked to biotin and one reporter probe attached to a color-coded molecular tag for each gene sequence, according to the nCounterTM code-set design. RNA samples were randomized using a numerical ID and were then subjected to NanoString nCounterTM analysis by the Princess Margaret Genomics Centre (https://www.pmgenomics.ca), Toronto, ON, Canada. Patient samples were analyzed in two batches consisting of 125 and 152 margins tissue samples. The detailed protocol for mRNA transcript quantification analysis, including sample preparation, hybridization, detection and scanning followed the manufacturer’s recommendations and was described in [PMID: 21549012]. We used 400 ng of total RNA isolated from FFPE tissues for detection of probe signals. Raw data were analyzed using the nCounterTM digital analyzer software (http://www.nanostring.com/support/ncounter/) and gene expression levels were subjected to further bioinformatic and statistical analyses.
2020-02-07 | GSE108712 | GEO
Project description:Zebrafish eggs were collected at 28 °C, and split into three embryonic incubation temperature groups (24 °C, 28 °C, 32 °C). When larvae reaching first feeding, the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C, and all fish were kept at 28 °C for later development until adulthood. At 100 d post-fertilization, 7 replicates from each temperature group were intraperitoneally (i.p.) injected with 2 μl of 50 mg/ml lipopolysaccharide (LPS) from Pseudomonas aeruginosa 10, while another 7 replicates were i.p. injected with 2 μl phosphate-buffered saline as control. At 12 h post-injection, the spleen was dissected, and total RNA was extracted. Five LPS-treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures (24 °C vs 28 °C; 32 °C vs 28 °C), and between LPS treatment and control within each temperature group (24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control). Totally, 251 differentially expressed genes (DEGs, 71 up-/180 down-regulated) were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C (DESeq2, adjusted p-value < 0.05, |fold change| > 1.5); and 660 DEGs (385 up-/275 down-regulated) were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS-treated fish to control, 567 DEGs (271 up-/296 down-regulated) were identified in fish from embryonic incubation temperature of 24 °C, 140 DEGs (80 up-/60 down-regulated) were identified in fish kept at constant 28 °C; and 49 DEGs (11 up-/38 down-regulated) were identified in fish from the 32 °C embryonic incubation temperature group.
2023-10-01 | GSE121163 | GEO