We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment ...indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets,
N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.
The precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics. Owing to the complexity of glycosylation, the current overall throughput, data quality and ...accessibility of intact glycopeptide identification lack behind those in routine proteomic analyses. Here, we propose a workflow for the precise high-throughput identification of intact N-glycopeptides at the proteome scale using stepped-energy fragmentation and a dedicated search engine. pGlyco 2.0 conducts comprehensive quality control including false discovery rate evaluation at all three levels of matches to glycans, peptides and glycopeptides, improving the current level of accuracy of intact glycopeptide identification. The N-glycoproteome of samples metabolically labeled with
N/
C were analyzed quantitatively and utilized to validate the glycopeptide identification, which could be used as a novel benchmark pipeline to compare different search engines. Finally, we report a large-scale glycoproteome dataset consisting of 10,009 distinct site-specific N-glycans on 1988 glycosylation sites from 955 glycoproteins in five mouse tissues.Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale.
Doped nanocarbon materials ( e.g. , carbon nanotubes, graphene) are considered as effective electrocatalyst supports for fuel cells, and their electrochemical properties are closely related to the ...synthetic methods and the types of doping elements. In the current paper, we report a novel approach to synthesize sulfur-doped multi-walled carbon nanotubes (S-MWCNTs) as a highly efficient support material for Pt nanoparticle catalysts. The S-MWCNTs are obtained by annealing poly(3,4-ethylenedioxythiophene) (PEDOT) functionalized multi-walled carbon nanotubes at 800 °C. The prepared nanohybrids were physically characterized by Raman spectroscopy, Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). It has been found that the doping of sulfur into MWCNTs could significantly improve the dispersion of supported Pt nanoparticles of 2.37 nm in size and increase the electrochemically active surface area (ECSA, 161.4 m 2 g −1 ). The doped sulfur atoms not only provide uniformly dispersed anchoring sites for the deposition of Pt nanoparticles on the surface of MWCNTs but also enhance the electron transfer interaction between Pt nanoparticles and the S-MWCNT support. The electrochemical properties of the catalysts were evaluated by using cyclic voltammetry (CV) and chronoamperometry (CA) techniques. The results demonstrate that the as-prepared Pt/S-MWCNTs exhibit much higher electrocatalytic activity, long-term durability and CO-tolerance ability for the methanol oxidation reaction (MOR) compared to the undoped MWCNT supported Pt and commercial Pt/C catalysts.
Background
This meta-analysis aimed to investigate the value of preoperative sarcopenia in predicting complications after esophagectomy. Clinicopathologic characteristics of sarcopenia patients, ...which may support sarcopenia management, also were studied.
Methods
This study searched for articles describing an association between sarcopenia and short-term outcomes after esophagectomy using PubMed, EMBASE, and the Cochrane Library. Mantel–Haenszel and inverse variance models were used for the meta-analyses of end points.
Results
The meta-analysis included 14 studies comprising a total of 2387 patients. Sarcopenia was significantly associated with advanced age (weighted mean difference WMD, 3.48; 95% confidence interval CI, 2.22–4.74), lower body mass index (WMD − 2.22; 95% CI − 2.65 to − 1.79), squamous cell carcinoma (odds ratio OR, 2.78; 95% CI 1.72–4.47), advanced clinical tumor stage (OR 1.65; 95% CI 1.28–2.15), and neoadjuvant therapy (OR 1.87; 95% CI 1.38–2.53). The sarcopenia patients showed lower preoperative albumin levels (WMD − 0.11; 95% CI − 0.19 to − 0.04) than the nonsarcopenia patients. Sarcopenia was significantly predictive of pneumonia (OR 2.58; 95% CI 1.75–3.81) and overall complications (OR 1.52; 95% CI 1.07–2.15) after esophagectomy. The sarcopenia patients also showed nonsignificant increases in the risks of anastomotic leakage (OR 1.29; 95% CI 0.99–1.67), vocal cord palsy (OR 2.03; 95% CI 0.89–4.64), and major complications (≥ Clavien-Dindo grade III; OR 1.30; 95% CI 0.95–1.79) but not increased operation time, blood loss, or mortality.
Conclusions
Preoperative sarcopenia assessment showed considerable potential for predicting postoperative complications for esophageal cancer patients. To realize this potential, more effective diagnostic criteria and severity classifications for sarcopenia are warranted.
The water‐soluble polypyridine copper complex Cu(F3TPA)(ClO4)2 1; F3TPA=tris(2‐fluoro‐6‐pyridylmethyl)amine catalyzes water oxidation in a pH 8.5 borate buffer at a relatively low overpotential of ...610 mV. Assisted by photosensitizer and an electron acceptor, 1 also exhibits activity as a homogeneous catalyst for photo‐induced O2 evolution with a maximum turnover frequency (TOF) of (1.58±0.03)×10−1 s−1 and a maximum turnover number (TON) of 11.61±0.23. In comparison, the reference Cu(TPA)(ClO4)2 TPA=tris(2‐pyridylmethyl)amine displayed almost no activity under either set of conditions, implying the crucial role of the ligand in determining the behavior of the catalyst. Experimental evidence indicate the molecular catalytic nature of 1, leading to a potentially practical strategy to apply the copper complex in a photoelectrochemical device for water oxidation.
A water‐soluble copper polypyridine complex performs as a homogeneous catalyst for both photo‐induced and electrocatalytic O2 evolution, which allows a derivative to be assembled into a photoelectrochemical device for water oxidation (see figure; ITO=indium–tin oxide, bpy=bipyridine).
We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method ...detects peptides with higher precision and speed than seven other search engines. Open-pFind identified 70-85% of the tandem mass spectra in four large-scale datasets and 14,064 proteins, each supported by at least two protein-unique peptides, in a human proteome dataset.
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, ...structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially.
The application of Pt alloy catalysts for oxygen reduction reactions (ORRs) in proton-exchange membrane fuel cells is severely impeded by base metal leaching, since the produced metal ions can result ...in the degradation of a Nafion membrane by replacing H+ and inducing a Fenton reaction. Doping Pt with nonmetal elements can significantly mitigate such problems due to the relative harmlessness of the corrosion products of anions. Herein, we developed a phosphorus-doping strategy, which can greatly boost the ORR performance of Pt. Phosphorus was introduced into the near-surface of commercial Pt/C (denoted as PNS-Pt/C) via a surfactant-free method. High-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) and X-ray photoelectron spectrum (XPS) tests indicate that the introduction of phosphorus induced distortion of the Pt lattice and the downshift of the d-band center. In situ electrochemical Fourier transform infrared (FTIR) spectroscopy with adsorbed CO as a molecule probe further revealed that the introduction of phosphorus can lower the adsorption ability. The ORR mass activity of PNS-Pt/C is as high as 1.00 mA μgPt –1@0.90 V, which is enhanced by 7 times in comparison with the initial Pt/C catalyst. Meanwhile, the durability is also enhanced. After 10 000 potential cycles, PNS-Pt/C only lost 14% of the ORR mass activity, while Pt/C lost 51%. More importantly, a H2–air fuel cell with a PNS-Pt/C cathode achieves a power density of 1.06 W cm–2 at a current density of 2.0 A cm–2 with a low Pt loading of 0.15 mg cm–2. The current density at 0.60 V (practical working potential) is 1.54 A cm–2, 2 times higher than that of commercial Pt/C. Density functional theory (DFT) calculations indicate that near-surface phosphorus doping can induce the distortion of the Pt surface, on which some concave Pt sites have optimal binding energy of OH for the ORR. Furthermore, this phosphorus-doping strategy is also valid for a PtNi alloy catalyst to further boost the ORR performance.
Malaria importation can be caused by cross-border movement either of both people and anopheline mosquitoes. However, there still lacks robust evidence of imported malaria caused by Plasmodium spp. ...infected anopheles along international border areas (border-spill malaria). The objectives of this study were to confirm whether an outbreak of Plasmodium vivax malaria is border-spill malaria and assess the effects of China's public health response along China-Myanmar border.
Epidemiological, parasitological and entomological investigations were conducted to investigate the outbreak of border-spill malaria. Meanwhile, comprehensive interventions were carried out to prevent further transmission and reintroduction of malaria.
Rapid diagnostic testing, microscopy and polymerase chain reaction were performed and the infections were confirmed as P. vivax. A total of 22 (9.21%) of 239 workers contracted P. vivax during the outbreak. Multivariate logistic regression analysis identified that the distance of worker shelters in China within 300 meters to the internally displaced person (IDP) camps in Myanmar was a risk factors associated with malaria infection (adjusted odds ratio 7.5920; 95% confidence interval, 2.6079-22.1013; P = 0.0002). After comprehensive interventions, malaria transmission was successfully interpreted and prevented at the project site till the completion of project on 14 January 2020, and recurrence of P. vivax malaria was not detected by the end of 2020.
This study provided robust evidence of border-spill malaria along China-Myanmar border. Malaria parasite reservoir and distance travelled by female anopheline mosquitoes are two determinants for border-spill malaria. The public health response to the outbreak indicates that the malaria surveillance and response system works well in preventing reintroduction of malaria. However, prevention of border-spill malaria is still a major challenge in the Yunnan border area, China.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
OBJECTIVE:Our objective was to evaluate the impact of early oral feeding (EOF) on postoperative cardiac, respiratory, and gastrointestinal (CRG) complications after McKeown minimally invasive ...esophagectomy for esophageal cancer.
SUMMARY BACKGROUND DATA:Nil-by-mouth with enteral tube feeding is routinely practiced after esophagectomy.
METHODS:Patients were randomly allocated to receive oral feeding on the first postoperative day (EOF group) or late oral feeding (LOF group) 7 days after surgery. The primary endpoint was the occurrence of postoperative CRG complications, and the secondary outcomes included bowel function recovery and short-term quality of life (QOL).
RESULTS:Between February 2014 and October 2015, 280 patients were enrolled in this study. There were 140 patients in the EOF group and 140 patients in the LOF group. EOF was noninferior to LOF for CRG complications (30.0% in the EOF group vs. 32.9% in the LOF group; 95% confidence interval of the difference−13.8% to 8.0%). Compared with the LOF group, the EOF group showed significantly shorter time to first flatus (median of 2 days vs. 3 days, P = 0.001) and bowel movement (median of 3 vs. 4 days, P < 0.001). Two weeks after the operation, patients in the EOF group reported higher global QOL and function scores and lower symptom scores than patients in the LOF group.
CONCLUSIONS:In patients after McKeown minimally invasive esophagectomy is noninferior to the standard of care with regard to postoperative CRG complications. In addition, patients in the EOF group had a quicker recovery of bowel function and improved short-term QOL.
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