Incidence and outcomes of surgical pulmonary embolectomy in the UK.

BACKGROUND: Surgical pulmonary embolectomy is rarely used for the treatment of massive acute pulmonary embolism. The aim of this study was to assess the incidence and outcomes of this operation by undertaking a retrospective analysis of a large national registry in the UK. METHODS: All acute pulmonary embolectomies performed between 1996 and 2018 were captured in the National Institute of Cardiovascular Outcomes Research central database. Trends in the number of operations performed during this interval and reported in-hospital outcomes were analysed retrospectively. Multivariable logistic regression was used to identify independent risk factors for in-hospital death. RESULTS: All 256 patients treated surgically for acute pulmonary embolism during the study interval were included in the analysis. Median age at presentation was 54 years, 55.9% of the patients were men, 48.0% had class IV heart failure symptoms, and 37.5% had preoperative cardiogenic shock. The median duration of bypass was 73 min, and median cross-clamp time was 19 min. Cardioplegic arrest was used in 53.1% of patients. The median duration of hospital stay was 11 days. The in-hospital mortality rate was 25%, postoperative stroke occurred in 5.4%, postoperative dialysis was required in 16%, and the reoperation rate for bleeding was 7.5%. Risk-adjusted multivariable analysis revealed cardiogenic shock (OR 2.54, 95% c.i. 1.05 to 6.21; P = 0.038), preoperative ventilation (OR 5.85, 2.22 to 16.35; P < 0.001), and duration of cardiopulmonary bypass exceeding 89 min (OR 7.82, 3.25 to 20.42; P < 0.001) as significant independent risk factors for in-hospital death. CONCLUSION: Surgical pulmonary embolectomy is rarely performed in the UK, and is associated with significant mortality and morbidity. Preoperative ventilation, cardiogenic shock, and increased duration of bypass were significant predictors of in-hospital death.

A blood clot in the lung can prevent the lungs from working properly and put pressure on the heart to work harder. Small clots can be treated with medications taken at home and are not a danger to life. Larger blood clots can put a lot of pressure on the heart and need immediate hospital treatment. Large blood clots can be treated with 'clot busting' medications, the delivery of a small tube into the blood vessels of the lung to suck up the clot or deliver medications directly on to its surface, and finally a form of open-heart surgery. With this surgery, a surgeon opens the chest, make a cut into the large vessels containing the clot, and physically removes the large piece of obstructing clot. The aim of this study was to describe and analyse the outcomes of this operation done in the UK over a long period. A database was used to find out how often and where this operation took place and its results. The available data were studied to try to understand how helpful this operation is to patients with lung blood clots. Between 1996 and 2018, 256 people had this operation. One in four patients did not survive the operation, 5.4% developed a clot or bleed in the brain, 16% needed to go on to a dialysis machine, and 7.5% had to be rushed back into theatre because of bleeding. Needing a ventilator machine for help with breathing, being in a sudden state of heart failure, and a long time on the heart bypass machine were all linked with patients who did not survive. This operation is rarely performed in the UK, and is often linked to a high chance of death or serious complication. In this study, the points described above were linked to a bad outcome.

Clinical correlation but no elevation of striatal dopamine synthesis capacity in two independent cohorts of medication-free individuals with schizophrenia.

Dysregulation of dopamine systems has been considered a foundational driver of pathophysiological processes in schizophrenia, an illness characterized by diverse domains of symptomatology. Prior work observing elevated presynaptic dopamine synthesis capacity in some patient groups has not always identified consistent symptom correlates, and studies of affected individuals in medication-free states have been challenging to obtain. Here we report on two separate cohorts of individuals with schizophrenia spectrum illness who underwent blinded medication withdrawal and medication-free neuroimaging with [18F]-FDOPA PET to assess striatal dopamine synthesis capacity. Consistently in both cohorts, we found no significant differences between patient and matched, healthy comparison groups; however, we did identify and replicate robust inverse relationships between negative symptom severity and tracer-specific uptake widely throughout the striatum: [18F]-FDOPA specific uptake was lower in patients with a greater preponderance of negative symptoms. Complementary voxel-wise and region of interest analyses, both with and without partial volume correction, yielded consistent results. These data suggest that for some individuals, striatal hyperdopaminergia may not be a defining or enduring feature of primary psychotic illness. However, clinical differences across individuals may be significantly linked to variability in striatal dopaminergic tone. These findings call for further experimentation aimed at parsing the heterogeneity of dopaminergic systems function in schizophrenia.

Degenerated extensor hallucis brevis accessorius: A case report.

The extensor hallucis brevis accessorius has rarely been mentioned in the extant medical literature. Here, we present the case of a cadaver found to have such a muscle and discuss the findings. Specifically, the muscle was observed to be degenerated both grossly and histologically. Therefore, both the gross and histological findings are presented. Such unusual cases are of archival value for future authors to compare their findings.

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning.

In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral library matching. The lack of accurate predictive models for fragment ion intensities impairs the realization of the full potential of these approaches. Here, we extended the ProteomeTools synthetic peptide library to 550,000 tryptic peptides and 21 million high-quality tandem mass spectra. We trained a deep neural network, termed Prosit, resulting in chromatographic retention time and fragment ion intensity predictions that exceed the quality of the experimental data. Integrating Prosit into database search pipelines led to more identifications at >10× lower false discovery rates. We show the general applicability of Prosit by predicting spectra for proteases other than trypsin, generating spectral libraries for data-independent acquisition and improving the analysis of metaproteomes. Prosit is integrated into ProteomicsDB, allowing search result re-scoring and custom spectral library generation for any organism on the basis of peptide sequence alone.

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues.

Genome-, transcriptome- and proteome-wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein-level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue-specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation.

The Peacock study: feasibility of the dynamic characterisation of the paediatric hypothalamic-pituitary-adrenal function during and after cardiac surgery.

BACKGROUND: Cortisol is the main stress hormone mobilised during surgery to establish homeostasis. Our current understanding of the hypothalamic-pituitary-adrenal axis physiology in children undergoing cardiopulmonary bypass is very limited due to: (1) very few cortisol time point measurements over long periods (2) difficulties of sampling in low weight babies and (3) the concomitant use of glucocorticoids at anaesthesia induction. This lack of understanding is reflected in a lack of consensus on the utility of glucocorticoids perioperatively in cardiac surgery with the use of cardiopulmonary bypass. METHODS: The Peacock Study is a prospective, two-centre, observational cohort study of 78 children (undergoing cardiopulmonary bypass procedures and non-surgical procedures - split by age/cyanosis) that aims to characterise in detail the hypothalamic-pituitary-adrenal axis physiology of children using the stress model of paediatric cardiac surgery. Also, we aim to correlate cortisol profiles with clinical outcome data. We herein describe the main study design and report the full cortisol profile of one child undergoing heart surgery, thus proving the feasibility of the method. RESULTS: We used an automated, 24-h tissue microdialysis system to measure cortisol and cortisone, every 20 min. We herein report one cortisol profile of a child undergoing heart surgery. Besides, we measured serum cortisol and adrenocorticotrophic hormone at seven-time points for correlation. Tissue concentrations of cortisol increased markedly several hours after the end of surgery. We also noted an increase in the tissue cortisol/cortisone ratio during this response. CONCLUSION: We report for the first time, the use of an automated microdialysis sampling system to evaluate the paediatric adrenal response in children. Changes in cortisol and cortisone could be measured, and the concentration of cortisol in the tissues increased after the end of cardiac surgery. The method has wide application to measure other hormones dynamically and frequently without the limitation of the circulating blood volume. The data from the main study will clarify how these cortisol profiles vary with age, pathology, type of procedure and correlation to clinical outcomes. TRIAL REGISTRATION: ISCRTN registry, number: 982586.

Correction to: The Peacock study: feasibility of the dynamic characterisation of the paediatric hypothalamic-pituitary-adrenal function during and after cardiac surgery.

An amendment to this paper has been published and can be accessed via the original article.

Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics.

The coordination of protein synthesis and degradation regulating protein abundance is a fundamental process in cellular homeostasis. Today, mass spectrometry-based technologies allow determination of endogenous protein turnover on a proteome-wide scale. However, standard dynamic SILAC (Stable Isotope Labeling in Cell Culture) approaches can suffer from missing data across pulse time-points limiting the accuracy of such analysis. This issue is of particular relevance when studying protein stability at the level of proteoforms because often only single peptides distinguish between different protein products of the same gene. To address this shortcoming, we evaluated the merits of combining dynamic SILAC and tandem mass tag (TMT)-labeling of ten pulse time-points in a single experiment. Although the comparison to the standard dynamic SILAC method showed a high concordance of protein turnover rates, the pulsed SILAC-TMT approach yielded more comprehensive data (6000 proteins on average) without missing values. Replicate analysis further established that the same reproducibility of turnover rate determination can be obtained for peptides and proteins facilitating proteoform resolved investigation of protein stability. We provide several examples of differentially turned over splice variants and show that post-translational modifications can affect cellular protein half-lives. For example, N-terminally processed peptides exhibited both faster and slower turnover behavior compared with other peptides of the same protein. In addition, the suspected proteolytic processing of the fusion protein FAU was substantiated by measuring vastly different stabilities of the cleavage products. Furthermore, differential peptide turnover suggested a previously unknown mechanism of activity regulation by post-translational destabilization of cathepsin D as well as the DNA helicase BLM. Finally, our comprehensive data set facilitated a detailed evaluation of the impact of protein properties and functions on protein stability in steady-state cells and uncovered that the high turnover of respiratory chain complex I proteins might be explained by oxidative stress.

ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides.

The analysis of the post-translational modification (PTM) state of proteins using mass spectrometry-based bottom-up proteomic workflows has evolved into a powerful tool for the study of cellular regulatory events that are not directly encoded at the genome level. Besides frequently detected modifications such as phosphorylation, acetylation and ubiquitination, many low abundant or less frequently detected PTMs are known or postulated to serve important regulatory functions. To more broadly understand the LC-MS/MS characteristics of PTMs, we synthesized and analyzed ∼5,000 peptides representing 21 different naturally occurring modifications of lysine, arginine, proline and tyrosine side chains and their unmodified counterparts. The analysis identified changes in retention times, shifts of precursor charge states and differences in search engine scores between modifications. PTM-dependent changes in the fragmentation behavior were evaluated using eleven different fragmentation modes or collision energies. We also systematically investigated the formation of diagnostic ions or neutral losses for all PTMs, confirming 10 known and identifying 5 novel diagnostic ions for lysine modifications. To demonstrate the value of including diagnostic ions in database searching, we reprocessed a public data set of lysine crotonylation and showed that considering the diagnostic ions increases confidence in the identification of the modified peptides. To our knowledge, this constitutes the first broad and systematic analysis of the LC-MS/MS properties of common and rare PTMs using synthetic peptides, leading to direct applicable utility for bottom-up proteomic experiments.

The Pan London Emergency Cardiac Surgery service blueprint.

The authors share their experience of managing the cardiac surgery services across London during the challenging Covid-19 pandemic. The Pan London Emergency Cardiac Surgery Service model could serve as a blueprint to design policies applicable to other surgical specialities and parts of the UK and worldwide.

Investigation of In-Situ Carbon Coated LiFePO4 as a Superior Cathode Material for Lithium Ion Batteries.

In the present study, we have developed a simple and cost-effective approach for the synthesis of carbon coated LiFePO4 wherein different carbon precursors were used to find out the suitable precursor for carbon coating. Initially, the appropriate amount of Li, Fe, and P precursors and carbon source (glucose/sucrose/fructose) were dissolved in ethanol solution followed by hydrothermal treatment at 180 °C to obtain carbon coated LiFePO4. The structure and morphological analysis of In-Situ carbon coated LiFePO4 revealed the formation of thin and homogeneous carbon layer on crystalline single-phase LiFePO4 particles with fructose used as carbon precursor. Raman analysis confirms the presence of more ordered graphitic carbon and the ID/IG ratio is 1.01, 0.69 and 0.87 for C-LFP-S, C-LFP-F and C-LFP-G respectively, indicating that fructose assisted In-Situ carbon coating leads to the formation of more ordered carbon coating on LiFePO4 with high graphitization degree in comparison with carbon coating by glucose and sucrose. HR-TEM results revealed the presence of uniform carbon distribution, which encapsulates the crystalline LiFePO4 particles forming a core-shell structure in the presence of fructose as carbon precursor. C-LFP-S delivered a capacity of 125 mAh/g at 0.1 C rate but then due to non-uniform carbon layer distribution, the capacity faded out completely when tested at higher C-rates. Whereas C-LFP-F delivered a discharge capacity of 98 mAh/g at 0.1 C and 48 mAh/g at 1 C, which is promising compared to the LiFePO4 carbon coated using sucrose and glucose. It is concluded that LiFePO4 carbon coated using monosacrides as carbon precursors showed better electro-chemical performance in terms of capacity and cyclic stability when compared to LiFePO4 carbon coated using dissacrides, attributing that uniform, thin layer, and highly ordered graphitic carbon coverage on nano sized LiFePO4 particles greatly reduces the polarization resistance and hence improving the electrochemical performance of C-LFP-F.

Intratumor MAPK and PI3K signaling pathway heterogeneity in glioblastoma tissue correlates with CREB signaling and distinct target gene signatures.

Limitations in discovering useful tumor biomarkers and drug targets is not only due to patient-to-patient differences but also due to intratumor heterogeneity. Heterogeneity arises due to the genetic and epigenetic variation of tumor cells in response to microenvironmental interactions and cytotoxic therapy. We explored specific signaling pathway activation in glioblastoma (GBM) by investigating the intratumor activation of the MAPK and PI3K pathways. We present data demonstrating a striking preponderance for mutual exclusivity of MAPK and PI3K activation in GBM tissue, where MAPK activation correlates with proliferation and transcription factor CREB activation and PI3K activation correlates with CD44 expression. Bioinformatic analysis of signaling and CREB-regulated target genes supports the immunohistochemical data, showing that the MAPK-CREB activation correlates with proliferative regions. In-silico analysis suggests that MAPK-CREB signaling activates a pro-inflammatory molecular signature and correlates with a mesenchymal GBM subtype profile, while PI3K-CREB activation correlates with the proneural GBM subtype and a tumor cell invasive gene signature. Overall, the data suggests the existence of intratumor subtype heterogeneity in GBM and that using combinations of both MAPK and PI3K drug inhibitors is necessary for effective targeted therapy.

PROCAL: A Set of 40 Peptide Standards for Retention Time Indexing, Column Performance Monitoring, and Collision Energy Calibration.

Beyond specific applications, such as the relative or absolute quantification of peptides in targeted proteomic experiments, synthetic spike-in peptides are not yet systematically used as internal standards in bottom-up proteomics. A number of retention time standards have been reported that enable chromatographic aligning of multiple LC-MS/MS experiments. However, only few peptides are typically included in such sets limiting the analytical parameters that can be monitored. Here, we describe PROCAL (ProteomeTools Calibration Standard), a set of 40 synthetic peptides that span the entire hydrophobicity range of tryptic digests, enabling not only accurate determination of retention time indices but also monitoring of chromatographic separation performance over time. The fragmentation characteristics of the peptides can also be used to calibrate and compare collision energies between mass spectrometers. The sequences of all selected peptides do not occur in any natural protein, thus eliminating the need for stable isotope labeling. We anticipate that this set of peptides will be useful for multiple purposes in individual laboratories but also aiding the transfer of data acquisition and analysis methods between laboratories, notably the use of spectral libraries.

Trimodal Mixed Mode Chromatography That Enables Efficient Offline Two-Dimensional Peptide Fractionation for Proteome Analysis.

Offline two-dimensional chromatography is a common means to achieve deep proteome coverage. To reduce sample complexity and dynamic range and to utilize mass spectrometer (MS) time efficiently, high chromatographic resolution of and good orthogonality between the two dimensions are needed. Ion exchange and high pH reversed phase chromatography are often used for this purpose. However, the former requires desalting to be MS-compatible, and the latter requires fraction pooling to create orthogonality. Here, we report an alternative first-dimension separation technique using a commercial trimodal phase incorporating polar embedded reversed phase, weak anion exchange, and strong cation exchange material. The column is capable of retaining polar and nonpolar peptides alike without noticeable breakthrough. It allows separating ordinary and TMT-labeled peptides under mild acidic conditions using an acetonitrile gradient. The direct MS compatibility of solvents and good orthogonality to online coupled C18 columns enable a straightforward workflow without fraction pooling and desalting while showing comparable performance to the other techniques. The method scales from low to high microgram sample quantity and is amenable to full automation. To demonstrate practical utility, we analyzed the proteomes of 10 human pancreatic cancer cell lines to a depth of >8,700 quantified proteins.

Over-expression of miR-31 or loss of KCNMA1 leads to increased cisplatin resistance in ovarian cancer cells.

Ovarian cancers have a high mortality rate; this is in part due to resistance to the platinum-based compounds used in chemotherapy. In this paper, we assess the role of microRNA-31 in the development of chemoresistance to cisplatin. We used previous data from microarray experiments to identify potential microRNAs (miRNAs) involved in chemoresistance. The functional significance of these microRNAs was tested using miRNA mimics. We used RNA-seq to identify pathways and genes de-regulated in the resistant cell line and then determined their role using RNAi. Analysis of publically available datasets reveals the potential clinical significance. Our data show that miR-31 is increased, whilst potassium channel calcium activated large conductance subfamily M alpha, member 1 (KCNMA1), a subunit of calcium-regulated big potassium (BK) channels, is reduced in resistant ovarian cells. Over-expression of miR-31 increased resistance, as did knockdown of KCNMA1 or inhibition of BK channels. This suggests that these genes directly modulate cisplatin response. Our data also suggest that miR-31 represses KCNMA1 expression. Comparing the levels of miR-31 and KCNMA1 to cisplatin resistance in the NCI60 panel or chemoresistance in cohorts of ovarian cancer tumours reveals correlations that support a role for these genes in vitro and in vivo. Here we show that miR-31 and KCNMA1 are involved in mediating cisplatin resistance in ovarian cancer. Our data gives a new insight into the potential mechanisms to therapeutically target in cisplatin resistance common to ovarian cancer.

Development of a novel carbon-coating strategy for producing core-shell structured carbon coated LiFePO4 for an improved Li-ion battery performance.

In the present study, LiFePO4 (LFP) has been synthesized using a flame spray pyrolysis unit followed by carbon coating on LFP using a novel strategy of dehydration assisted polymerization process (DAP) in order to improve its electronic conductivity. Characterization studies revealed the presence of a pure LFP structure and the formation of a thin, uniform and graphitic carbon layer with a thickness of 6-8 nm on the surface of the LFP. A carbon coated LFP with 3 wt% of carbon, using a DAP process, delivered a specific capacity of 167 mA h g-1 at a 0.1C rate, whereas LFP carbon coated by a carbothermal process (CLFP-C) delivered a capacity of 145 mA h g-1 at 0.1C. Further carbon coated LFP by the DAP exhibited a good rate capability and cyclic stability. The enhanced electrochemical performance of C-LFP by DAP is attributed to the presence of a uniform, thin and ordered graphitic carbon layer with a core-shell structure, which greatly increased the electronic conductivity of LFP and thereby showed an improved electro-chemical performance. Interestingly, the developed carbon coating process has been extended to synthesize a bulk quantity (0.5 kg) of carbon coated LFP under optimized experimental conditions as a part of up-scaling and the resulting material electro-chemical performance has been evaluated and compared with commercial electrode materials. Bulk C-LFP showed a capacity of 131 mA h g-1 and 87 mA h g-1 at a rate of 1C and at 10C, respectively, illustrating that the developed DAP process greatly improved the electrochemical performance of LFP in terms of rate capability and cyclic stability, not only during the lab scale synthesis but also during the large scale synthesis. Benchmark studies concluded that the electro-chemical performance of C-LFP by DAP is comparable with that of TODA LFP and better than that of UNTPL LFP. The DAP process developed in the present study can be extended to other electrode materials as well.