Improvement of peptide identification with considering the abundance of mRNA and peptide

Scripts used for data analysis in this study. (DOCX 35 kb

Association between hypertension and prognosis of patients with COVID-19: A systematic review and meta-analysis

Background To investigate the association between hypertension and clinical outcomes, including in-hospital mortality, intensive care unit (ICU) admission, and invasive ventilation in patients with coronavirus disease 2019 (COVID-19) pneumonia. Methods We implemented a systematic search of PubMed for articles that assessed clinical outcomes of hypertensive patients infected with SARS-CoV-2. The primary outcomes evaluated included: in-hospital mortality, ICU admission, and the use of invasive ventilation. Results A total of 18 studies were included, involving 13,293 patients and covering from January 25, 2020, to April 20, 2020. The relationship between hypertension and prognosis in COVID-19 patients was evaluated. Results showed that hypertension was a risk factor for in-hospital mortality in COVID-19 patients (RR: 2.20, 95% CI, 1.83–2.65, P < .001). Moreover, patients with hypertension were more likely to be admitted to ICU (RR: 1.86, 95% CI, 1.13–3.07, P = .001) and to use invasive ventilation (RR: 2.99, 95% CI, 1.73–5.17, P < .001). Conclusions Among COVID-19 patients, those combined with hypertension had a significantly higher risk of in-hospital deaths, admission to ICU, and need for invasive ventilation

Overview of the MEMS Pirani Sensors

Vacuum equipment has a wide range of applications, and vacuum monitoring in such equipment is necessary in order to meet practical applications. Pirani sensors work by using the effect of air density on the heat conduction of the gas to cause temperature changes in sensitive structures, thus detecting the pressure in the surrounding environment and thus vacuum monitoring. In past decades, MEMS Pirani sensors have received considerable attention and practical applications because of their advances in simple structures, long service life, wide measurement range and high sensitivity. This review systematically summarizes and compares different types of MEMS Pirani sensors. The configuration, material, mechanism, and performance of different types of MEMS Pirani sensors are discussed, including the ones based on thermistors, thermocouples, diodes and surface acoustic wave. Further, the development status of novel Pirani sensors based on functional materials such as nanoporous materials, carbon nanotubes and graphene are investigated, and the possible future development directions for MEMS Pirani sensors are discussed. This review is with the purpose to focus on a generalized knowledge of MEMS Pirani sensors, thus inspiring the investigations on their practical applications

sapFinder:an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments

Summary: Single nucleotide variations (SNVs) located within a reading frame can result in single amino acid polymorphisms (SAPs), leading to alteration of the corresponding amino acid sequence as well as function of a protein. Accurate detection of SAPs is an important issue in proteomic analysis at the experimental and bioinformatic level. Herein, we present sapFinder, an R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. This package automates the construction of variation-associated databases from public SNV repositories or sample-specific next-generation sequencing (NGS) data and the identification of SAPs through database searching, post-processing and generation of HTML-based report with visualized interface. Availability and implementation: sapFinder is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at http://bioconductor.org/packages/devel/bioc/html/sapFinder.html and are provided under a GPL-2 license. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Dynamic Plasma Lipidomic Analysis Revealed Cholesterol Ester and Amides Associated with Sepsis Development in Critically Ill Patients after Cardiovascular Surgery with Cardiopulmonary Bypass

Background: Sepsis in patients after cardiovascular surgery with cardiopulmonary bypass (CPB) has a high rate of mortality. We sought to determine whether changes in lipidomics can predict sepsis after cardiac surgery. Methods: We used high-performance liquid chromatography coupled to tandem mass spectrometry to explore global lipidome changes in samples from a prospective case-control cohort (30 sepsis vs. 30 nonsepsis) hospitalized with cardiovascular surgery. All patients were sampled before and within 48&ndash;72 h after surgery. A bioinformatic pipeline was applied to acquire reliable features and MS/MS-driven identifications. Furthermore, a multiple-step machine learning framework was performed for signature discovery and performance evaluation. Results: Compared with preoperative samples, 94 features were upregulated and 282 features were downregulated in the postoperative samples of the sepsis group, and 73 features were upregulated and 265 features were downregulated in the postoperative samples of the nonsepsis group. &ldquo;Autophagy&rdquo;, &ldquo;pathogenic Escherichia coli infection&rdquo; and &ldquo;glycosylphosphatidylinositol-anchor biosynthesis&rdquo; pathways were significantly enriched in the pathway enrichment analysis. A multistep machine learning framework further confirmed that two cholesterol esters, CE (18:0) and CE (16:0), were significantly decreased in the sepsis group (p &lt; 0.05). In addition, oleamide and stearamide were increased significantly in the postoperative sepsis group (p &lt; 0.001). Conclusions: This study revealed characteristic lipidomic changes in the plasma of septic patients before and after cardiac surgery with CPB. We discovered two cholesterol esters and two amides from peripheral blood that could be promising signatures for sepsis within a dynamic detection between the preoperative and postoperative groups

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets.

Rice (Oryza sativa) is one of the most important worldwide crops. The genome has been available for over 10 years and has undergone several rounds of annotation. We created a comprehensive database of transcripts from 29 public RNA sequencing data sets, officially predicted genes from Ensembl plants, and common contaminants in which to search for protein-level evidence. We re-analyzed nine publicly accessible rice proteomics data sets. In total, we identified 420K peptide spectrum matches from 47K peptides and 8,187 protein groups. 4168 peptides were initially classed as putative novel peptides (not matching official genes). Following a strict filtration scheme to rule out other possible explanations, we discovered 1,584 high confidence novel peptides. The novel peptides were clustered into 692 genomic loci where our results suggest annotation improvements. 80% of the novel peptides had an ortholog match in the curated protein sequence set from at least one other plant species. For the peptides clustering in intergenic regions (and thus potentially new genes), 101 loci were identified, for which 43 had a high-confidence hit for a protein domain. Our results can be displayed as tracks on the Ensembl genome or other browsers supporting Track Hubs, to support re-annotation of the rice genome

Optimization of frequency shifts in optically detected magnetic-state-selection cesium beam atomic clocks

In this paper, we report a new method to suppress the AC Stark effect (light shift) in compact cesium beam atomic clocks. The clock used in experiment uses the optically detected magnetic-state-selection scheme independently proposed and developed by Peking University. This method compensates the AC Stark effect by introducing a detuned laser into the detection light. We demonstrate theoretically that the AC Stark effect can be strongly suppressed with properly chosen detuned light. In addition, we experiment this scheme and the α-coefficient (the sensitivity of the AC Stark effect to laser power fluctuation) is successfully reduced from $1.23 \times 10^{-12}/\mathrm{mW}$ to $8 \times 10^{-14}/\mathrm{mW}$ . We also test the long-term frequency stability with additional laser intensity noise. It is shown that the fractional Allan deviation at 20000 s is reduced from $2.0\times10^{-13}$ to $5.9\times10^{-14}$ , which reveals the suppression of the light shift with our method. These results are relevant for improving the long-term frequency stability of compact cesium beam atomic clocks