507 research outputs found
55 Investigation of the RetS–GacAS regulatory network in clinical Pseudomonas aeruginosa isolates reveals evolutionary adaptation
Digitalitzat per Artypla
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics
Funding Information: This work was supported by a research grant from the Danish Cardiovascular Academy, which is funded by the Novo Nordisk Foundation, grant number NNF20SA0067242 and the Danish Heart Foundation. Publisher Copyright: © 2023 The Authors. Proteomics published by Wiley-VCH GmbH.Clinical biomarker discovery is often based on the analysis of human plasma samples. However, the high dynamic range and complexity of plasma pose significant challenges to mass spectrometry-based proteomics. Current methods for improving protein identifications require laborious pre-analytical sample preparation. In this study, we developed and evaluated a TMTpro-specific spectral library for improved protein identification in human plasma proteomics. The library was constructed by LC-MS/MS analysis of highly fractionated TMTpro-tagged human plasma, human cell lysates, and relevant arterial tissues. The library was curated using several quality filters to ensure reliable peptide identifications. Our results show that spectral library searching using the TMTpro spectral library improves the identification of proteins in plasma samples compared to conventional sequence database searching. Protein identifications made by the spectral library search engine demonstrated a high degree of complementarity with the sequence database search engine, indicating the feasibility of increasing the number of protein identifications without additional pre-analytical sample preparation. The TMTpro-specific spectral library provides a resource for future plasma proteomics research and optimization of search algorithms for greater accuracy and speed in protein identifications in human plasma proteomics, and is made publicly available to the research community via ProteomeXchange with identifier PXD042546.publishersversionepub_ahead_of_prin
Impact of age on morbidity and outcome of concurrent radiochemotherapy in high-risk FIGO stage I to IVA carcinoma of the uterine cervix following laparoscopic surgery
The ALICE TPC, a large 3-dimensional tracking device with fast readout for ultra-high multiplicity events
The design, construction, and commissioning of the ALICE Time-Projection
Chamber (TPC) is described. It is the main device for pattern recognition,
tracking, and identification of charged particles in the ALICE experiment at
the CERN LHC. The TPC is cylindrical in shape with a volume close to 90 m^3 and
is operated in a 0.5 T solenoidal magnetic field parallel to its axis.
In this paper we describe in detail the design considerations for this
detector for operation in the extreme multiplicity environment of central
Pb--Pb collisions at LHC energy. The implementation of the resulting
requirements into hardware (field cage, read-out chambers, electronics),
infrastructure (gas and cooling system, laser-calibration system), and software
led to many technical innovations which are described along with a presentation
of all the major components of the detector, as currently realized. We also
report on the performance achieved after completion of the first round of
stand-alone calibration runs and demonstrate results close to those specified
in the TPC Technical Design Report.Comment: 55 pages, 82 figure
The response of perennial and temporary headwater stream invertebrate communities to hydrological extremes
The headwaters of karst rivers experience considerable hydrological variability, including spates and streambed drying. Extreme summer flooding on the River Lathkill (Derbyshire, UK) provided the opportunity to examine the invertebrate community response to unseasonal spate flows, flow recession and, at temporary sites, streambed drying. Invertebrates were sampled at sites with differing flow permanence regimes during and after the spates. Following streambed drying at temporary sites, dewatered surface sediments were investigated as a refugium for aquatic invertebrates. Experimental rehydration of these dewatered sediments was conducted to promote development of desiccation-tolerant life stages. At perennial sites, spate flows reduced invertebrate abundance and diversity, whilst at temporary sites, flow reactivation facilitated rapid colonisation of the surface channel by a limited number of invertebrate taxa. Following streambed drying, 38 taxa were recorded from the dewatered and rehydrated sediments, with Oligochaeta being the most abundant taxon and Chironomidae (Diptera) the most diverse. Experimental rehydration of dewatered sediments revealed the presence of additional taxa, including Stenophylax sp. (Trichoptera: Limnephilidae) and Nemoura sp. (Plecoptera: Nemouridae). The influence of flow permanence on invertebrate community composition was apparent despite the aseasonal high-magnitude flood events
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