ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

RNA-Seq and microarray platforms have emerged as important tools for detecting changes in gene expression and RNA processing in biological samples. We present ExpressionPlot, a software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets. Download and installation instructions, a user's manual, discussion group, and a prototype are available at http://expressionplot.com/ webcite.ALS Therapy Allianc

Quality of Recovery After Rotator Cuff Repair With Interscalene Liposomal Bupivacaine Versus Interscalene Nerve Catheter

Background: Interscalene nerve catheters have been proven to be effective in managing pain after rotator cuff repair (RCR) surgery. Liposomal bupivacaine is a newer approved therapy for use around the interscalene brachial plexus, but its analgesic efficacy has limited supporting data in various patient populations. Purpose/Hypothesis: The purpose of this study was to investigate the quality of recovery after arthroscopic RCR in patients who received either single-injection interscalene liposomal bupivacaine or an interscalene peripheral nerve catheter. It was hypothesized that interscalene peripheral nerve catheters would provide more reliable analgesia and improved patient satisfaction 48 hours after surgery. Study Design: Cohort study; Level of evidence, 2.Methods:Enrolled were 93 consecutive patients who underwent arthroscopic rotator cuff surgery at a single ambulatory surgery center between October 2020 and June 2021. Of these patients, 13 were lost to follow-up; thus, 80 patients were included in statistical analysis. One group of patients (n = 48) received a preoperative interscalene nerve block placed with 10 mL 0.5% bupivacaine and 10 mL 1.3% liposomal bupivacaine. The second group (n = 32) received a preoperative interscalene catheter with an initial bolus of 20 mL 0.25% bupivacaine and a 0.2% ropivacaine infusion by an elastomeric pump set at 10 mL/hr for 48 hours. The primary outcome was the difference between preoperative and 48-hour postoperative quality of recovery-15 (QoR-15) scores. Secondary outcomes included visual analog pain scores, opioid use, and patient satisfaction. Complications and adverse effects were also noted. The Kruskal-Wallis test was used to analyze means and standard deviations for continuous endpoints; Fisher exact test was used to analyze counts and proportions for categorical endpoints. Results: The liposomal bupivacaine group had a mean reduction of 3.9 in their postoperative QoR-15 scores, and the catheter group had a mean reduction of 25.1 in their postoperative QoR-15 scores, indicating a significantly worse functional recovery period compared with liposomal bupivacaine within the first 48 hours (P < .001). Patients who received liposomal bupivacaine also had significantly lower pain scores on the second postoperative day, improved quality of sleep, and improved satisfaction with analgesia (P < .05 for all). Conclusion: The use of interscalene liposomal bupivacaine demonstrated significantly improved quality of recovery when compared with interscalene nerve catheter after RCR

RNA Captor: A Tool for RNA Characterization

Background: In the genome era, characterizing the structure and the function of RNA molecules remains a major challenge. Alternative transcripts and non-protein-coding genes are poorly recognized by the current genome-annotation algorithms and efficient tools are needed to isolate the less-abundant or stable RNAs. Results: A universal RNA-tagging method using the T4 RNA ligase 2 and special adapters is reported. Based on this system, protocols for RACE PCR and full-length cDNA library construction have been developed. The RNA tagging conditions were thoroughly optimized and compared to previous methods by using a biochemical oligonucleotide tagging assay and RACE PCRs on a range of transcripts. In addition, two large-scale full-length cDNA inventories relying on this method are presented. Conclusion: The RNA Captor is a straightforward and accessible protocol. The sensitivity of this approach was shown to be higher compared to previous methods, and applicable on messenger RNAs, non-protein-coding RNAs, transcription-start sites and microRNA-directed cleavage sites of transcripts. This strategy could also be used to study other classes of RNA and in deep sequencing experiments

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

<p>Abstract</p> <p>Background</p> <p>RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments.</p> <p>Results</p> <p>We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data. In contrast to other existing tools, the software does not require a reference genome. Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome. Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads. On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene.</p> <p>Conclusions</p> <p>RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.</p

Measurement of the Total Active 8B Solar Neutrino Flux at the Sudbury Neutrino Observatory with Enhanced Neutral Current Sensitivity

The Sudbury Neutrino Observatory (SNO) has precisely determined the total active (nu_x) 8B solar neutrino flux without assumptions about the energy dependence of the nu_e survival probability. The measurements were made with dissolved NaCl in the heavy water to enhance the sensitivity and signature for neutral-current interactions. The flux is found to be 5.21 +/- 0.27 (stat) +/- 0.38 (syst) x10^6 cm^{-2}s^{-1}, in agreement with previous measurements and standard solar models. A global analysis of these and other solar and reactor neutrino results yields Delta m^{2} = 7.1^{+1.2}_{-0.6}x10^{-5} ev^2 and theta = 32.5^{+2.4}_{-2.3} degrees. Maximal mixing is rejected at the equivalent of 5.4 standard deviations.Comment: Submitted to Phys. Rev. Let

Noise Characterization and Filtering in the MicroBooNE Liquid Argon TPC

The low-noise operation of readout electronics in a liquid argon time projection chamber (LArTPC) is critical to properly extract the distribution of ionization charge deposited on the wire planes of the TPC, especially for the induction planes. This paper describes the characteristics and mitigation of the observed noise in the MicroBooNE detector. The MicroBooNE's single-phase LArTPC comprises two induction planes and one collection sense wire plane with a total of 8256 wires. Current induced on each TPC wire is amplified and shaped by custom low-power, low-noise ASICs immersed in the liquid argon. The digitization of the signal waveform occurs outside the cryostat. Using data from the first year of MicroBooNE operations, several excess noise sources in the TPC were identified and mitigated. The residual equivalent noise charge (ENC) after noise filtering varies with wire length and is found to be below 400 electrons for the longest wires (4.7 m). The response is consistent with the cold electronics design expectations and is found to be stable with time and uniform over the functioning channels. This noise level is significantly lower than previous experiments utilizing warm front-end electronics.Comment: 36 pages, 20 figure

Evaluating methods for ranking differentially expressed genes applied to microArray quality control data

<p>Abstract</p> <p>Background</p> <p>Statistical methods for ranking differentially expressed genes (DEGs) from gene expression data should be evaluated with regard to high sensitivity, specificity, and reproducibility. In our previous studies, we evaluated eight gene ranking methods applied to only Affymetrix GeneChip data. A more general evaluation that also includes other microarray platforms, such as the Agilent or Illumina systems, is desirable for determining which methods are suitable for each platform and which method has better inter-platform reproducibility.</p> <p>Results</p> <p>We compared the eight gene ranking methods using the MicroArray Quality Control (MAQC) datasets produced by five manufacturers: Affymetrix, Applied Biosystems, Agilent, GE Healthcare, and Illumina. The area under the curve (AUC) was used as a measure for both sensitivity and specificity. Although the highest AUC values can vary with the definition of "true" DEGs, the best methods were, in most cases, either the weighted average difference (WAD), rank products (RP), or intensity-based moderated <it>t </it>statistic (ibmT). The percentages of overlapping genes (POGs) across different test sites were mainly evaluated as a measure for both intra- and inter-platform reproducibility. The POG values for WAD were the highest overall, irrespective of the choice of microarray platform. The high intra- and inter-platform reproducibility of WAD was also observed at a higher biological function level.</p> <p>Conclusion</p> <p>These results for the five microarray platforms were consistent with our previous ones based on 36 real experimental datasets measured using the Affymetrix platform. Thus, recommendations made using the MAQC benchmark data might be universally applicable.</p

Interdependent Infrastructure as Linked Social, Ecological, and Technological Systems (SETSs) to Address Lock‐in and Enhance Resilience

Traditional infrastructure adaptation to extreme weather events (and now climate change) has typically been techno‐centric and heavily grounded in robustness—the capacity to prevent or minimize disruptions via a risk‐based approach that emphasizes control, armoring, and strengthening (e.g., raising the height of levees). However, climate and nonclimate challenges facing infrastructure are not purely technological. Ecological and social systems also warrant consideration to manage issues of overconfidence, inflexibility, interdependence, and resource utilization—among others. As a result, techno‐centric adaptation strategies can result in unwanted tradeoffs, unintended consequences, and underaddressed vulnerabilities. Techno‐centric strategies that lock‐in today\u27s infrastructure systems to vulnerable future design, management, and regulatory practices may be particularly problematic by exacerbating these ecological and social issues rather than ameliorating them. Given these challenges, we develop a conceptual model and infrastructure adaptation case studies to argue the following: (1) infrastructure systems are not simply technological and should be understood as complex and interconnected social, ecological, and technological systems (SETSs); (2) infrastructure challenges, like lock‐in, stem from SETS interactions that are often overlooked and underappreciated; (3) framing infrastructure with a SETS lens can help identify and prevent maladaptive issues like lock‐in; and (4) a SETS lens can also highlight effective infrastructure adaptation strategies that may not traditionally be considered. Ultimately, we find that treating infrastructure as SETS shows promise for increasing the adaptive capacity of infrastructure systems by highlighting how lock‐in and vulnerabilities evolve and how multidisciplinary strategies can be deployed to address these challenges by broadening the options for adaptation