Targeted Protein O-GlcNAcylation Using Bifunctional Small Molecules

Protein O-linked β-N-acetylglucosamine modification (O-GlcNAcylation) plays a crucial role in regulating essential cellular processes. The disruption of the homeostasis of O-GlcNAcylation has been linked to various human diseases, including cancer, diabetes, and neurodegeneration. However, there are limited chemical tools for protein- and site-specific O-GlcNAc modification, rendering the precise study of the O-GlcNAcylation challenging. To address this, we have developed heterobifunctional small molecules, named O-GlcNAcylation TArgeting Chimeras (OGTACs), which enable protein-specific O-GlcNAcylation in living cells. OGTACs promote O-GlcNAcylation of proteins such as BRD4, CK2α, and EZH2 in cellulo by recruiting FKBP12F36V-fused O-GlcNAc transferase (OGT), with temporal, magnitude, and reversible control. Overall, the OGTACs represent a promising approach for inducing protein-specific O-GlcNAcylation, thus enabling functional dissection and offering new directions for O-GlcNAc-targeting therapeutic development.

On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation

Estimating the false discovery rate (FDR) of peptide identifications is a key step in proteomics data analysis, and many methods have been proposed for this purpose. Recently, an entrapment-inspired protocol to validate methods for FDR estimation appeared in articles showcasing new spectral library search tools. That validation approach involves generating incorrect spectral matches by searching spectra from evolutionarily distant organisms (entrapment queries) against the original target search space. Although this approach may appear similar to the solutions using entrapment databases, it represents a distinct conceptual framework whose correctness has not been verified yet. In this viewpoint, we first discussed the background of the entrapment-based validation protocols and then conducted a few simple computational experiments to verify the assumptions behind them. The results reveal that entrapment databases may, in some implementations, be a reasonable choice for validation, while the assumptions underpinning validation protocols based on entrapment queries are likely to be violated in practice. This article also highlights the need for well-designed frameworks for validating FDR estimation methods in proteomics.

Merging Full-Spectrum and Fragment Ion Intensity Predictions from Deep Learning for High-Quality Spectral Libraries

Spectral libraries are useful resources in proteomic data analysis. Recent advances in deep learning allow tandem mass spectra of peptides to be predicted from their amino acid sequences. This enables predicted spectral libraries to be compiled, and searching against such libraries has been shown to improve the sensitivity in peptide identification over conventional sequence database searching. However, current prediction models lack support for longer peptides, and thus far, predicted library searching has only been demonstrated for backbone ion-only spectrum prediction methods. Here, we propose a deep learning-based full-spectrum prediction method to generate predicted spectral libraries for peptide identification. We demonstrated the superiority of using full-spectrum libraries over backbone ion-only prediction approaches in spectral library searching. Furthermore, merging spectra from different prediction models, as a form of ensemble learning, can produce improved spectral libraries, in terms of identification sensitivity. We also show that a hybrid library combining predicted and experimental spectra can lead to 20% more confident identifications over experimental library searching or sequence database searching.

Spectroscape enables real-time query and visualization of a spectral archive in proteomics

In proteomics, spectral archives organize the enormous amounts of publicly available peptide tandem mass spectra by similarity, offering opportunities for error correction and novel discoveries. Here we adapt an indexing algorithm developed by Facebook for organizing online multimedia resources to tandem mass spectra and achieve practically instantaneous retrieval and clustering of approximate nearest neighbors in a large spectral archive. An interactive web-based graphical user interface enables the user to view a query spectrum in its clustered neighborhood, which facilitates contextual validation of peptide identifications and exploration of the dark proteome.

metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering

BACKGROUND

The high diversity and complexity of the microbial community make it a formidable challenge to identify and quantify the large number of proteins expressed in the community. Conventional metaproteomics approaches largely rely on accurate identification of the MS/MS spectra to their corresponding short peptides in the digested samples, followed by protein inference and subsequent taxonomic and functional analysis of the detected proteins. These approaches are dependent on the availability of protein sequence databases derived either from sample-specific metagenomic data or from public repositories. Due to the incompleteness and imperfections of these protein sequence databases, and the preponderance of homologous proteins expressed by different bacterial species in the community, this computational process of peptide identification and protein inference is challenging and error-prone, which hinders the comparison of metaproteomes across multiple samples.

RESULTS

We developed metaSpectraST, an unsupervised and database-independent metaproteomics workflow, which quantitatively profiles and compares metaproteomics samples by clustering experimentally observed MS/MS spectra based on their spectral similarity. We applied metaSpectraST to fecal samples collected from littermates of two different mother mice right after weaning. Quantitative proteome profiles of the microbial communities of different mice were obtained without any peptide-spectrum identification and used to evaluate the overall similarity between samples and highlight any differentiating markers. Compared to the conventional database-dependent metaproteomics analysis, metaSpectraST is more successful in classifying the samples and detecting the subtle microbiome changes of mouse gut microbiomes post-weaning. metaSpectraST could also be used as a tool to select the suitable biological replicates from samples with wide inter-individual variation.

CONCLUSIONS

metaSpectraST enables rapid profiling of metaproteomic samples quantitatively, without the need for constructing the protein sequence database or identification of the MS/MS spectra. It maximally preserves information contained in the experimental MS/MS spectra by clustering all of them first and thus is able to better profile the complex microbial communities and highlight their functional changes, as compared with conventional approaches. tag the videobyte in this section as ESM4 Video Abstract.

Mechanistic Insight into the Inhibitory Activity of Elasnin-Based Coating against Early Marine Biofilms

Marine biofilms are multispecies microbial communities on surfaces that are crucial to the marine environment. They cause marine corrosion, biofouling, and transmission of marine pathogens and thus pose a great threat to public health and the maritime industry. To control marine biofilms, effective and environmentally friendly antibiofilm compounds are highly needed. Elasnin is a potent antibiofilm compound that exhibits high efficiency in inhibiting marine biofilms and biofouling, but its mode of action remains unclear. In the present study, multiomic analysis combined with quorum-sensing assays and in silico study revealed that elasnin acted as a signaling molecule in the microbial community. Elasnin promoted the growth of dominant species in the biofilm but deprived their ability of sensing and responding to environmental changes by disturbing their regulations of the two-component system, i.e., the ATP-binding cassette transport system and the bacterial secretion system. Consequently, biofilm maturation and subsequent biofouler settlement were inhibited. Elasnin also exhibited higher antibiofilm efficiency than dichlorooctylisothiazolinone and had low toxicity potential on the embryos and adults of marine medaka fish. Overall, this study provided molecular and ecological insights into elasnin's mode of action, highlighting its application potential in controlling marine biofilms and the feasibility and advantages of using signal molecules to develop eco-friendly technologies.

Topical corticosteroids for the prevention of severe radiation dermatitis: a systematic review and meta-analysis

PURPOSE

Radiation dermatitis (RD) is a frequently occurring adverse reaction during radiotherapy in cancer patients. While the use of topical corticosteroids (TCs) is common for the treatment of RD, its role in preventing severe reactions remains unclear. This systematic review and meta-analysis aim to evaluate the evidence on the use of TCs as prophylaxis of RD.

METHODS

A systematic search was conducted using OVID MedLine, Embase, and Cochrane databases (between 1946 and 2023) to identify studies examining TC use in the prevention of severe RD. Statistical analysis was completed using RevMan 5.4 to calculate pooled effect sizes and 95% confidence intervals. Forest plots were then developed using a random effects model.

RESULTS

Ten RCTs with a total of 1041 patients met the inclusion criteria. Six studies reported on mometasone furoate (MF) and four studies reported on betamethasone. Both TCs were associated with a significant improvement in the prevention of moist desquamation [OR = 0.34, 95% CI [0.25, 0.47], p < 0.00001], but betamethasone was found to be more effective than MF [OR = 0.29, 95% CI [0.18, 0.46], p < 0.00001 and OR = 0.39, 95% CI [0.25, 0.61], p < 0.0001, respectively]. A similar finding was seen in reducing the development of grade 2 or higher RD according to the Radiation Therapy Oncology Group scale.

CONCLUSIONS

The current evidence supports the use of TCs in preventing severe reactions of RD. Both MF and betamethasone were found to be effective; however, betamethasone, a higher potency TC, is more effective despite MF being more commonly reported in literature.

Pterosin sesquiterpenoids from Pteris laeta Wall. ex Ettingsh. protect cells from glutamate excitotoxicity by modulating mitochondrial signals

ETHNOPHARMACOLOGICAL RELEVANCE

The genus Pteris (Pteridaceae) has been used as a traditional herb for a long time. In particular, Pteris laeta Wall. ex Ettingsh. has been widely used in traditional Chinese medicine to treat nervous system diseases and some pterosin sesquiterpenes from Pteris show neuroprotective activity, but their underlying molecular mechanisms remain elusive. Therefore, to investigate the neuroprotective activity and working mechanism of pterosin sesquiterpenes from P. laeta Wall. ex Ettingsh. will provide a better understanding and guidance in using P. laeta Wall. ex Ettingsh. as a traditional Chinese medicine.

AIM OF THE STUDY

We aim to develop effective treatments for neurodegenerative diseases from pterosin sesquiterpenes by evaluating their neuroprotective activity and investigating their working mechanisms.

MATERIALS AND METHODS

Primary screening on the glutamate-induced excitotoxicity cell model was assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) assay. Fluorescent-activated cell sorting (FACS) was used to analyze the activation level of glutamate receptors and mitochondria membrane potential after treatment. Transcriptomics and proteomics analysis was performed to identify possible targets of pterosin B. The key pathways were enriched by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis through the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The core targets were visualized by a protein-protein interaction network using STRING. The mRNA and protein expressions were evaluated using real-time quantitative polymerase chain reaction (Q-PCR) and western blot, respectively. Immunocytochemistry was performed to monitor mitochondrial and apoptotic proteins. Cellular reactive oxygen species (ROS) were measured by ROS assay, and Ca²⁺ was stained with Fluo-4 AM to quantify intracellular Ca²⁺ levels.

RESULTS

We found pterosin B from Pteris laeta Wall. ex Ettingsh. showed significant neuroprotective activity against glutamate excitotoxicity, enhancing cell viability from 43.8% to 105% (p-value: <0.0001). We demonstrated that pterosin B worked on the downstream signaling pathways of glutamate excitotoxicity rather than directly blocking the activation of glutamate receptors. Pterosin B restored mitochondria membrane potentials, alleviated intracellular calcium overload from 107.4% to 95.47% (p-value: 0.0006), eliminated cellular ROS by 36.55% (p-value: 0.0143), and partially secured cells from LPS-induced inflammation by increasing cell survival from 46.75% to 58.5% (p-value: 0.0114). Notably, pterosin B enhanced the expression of nuclear factor-erythroid factor 2-related factor 2 (NRF2) and heme oxygenase-1 (HO-1) by 2.86-fold (p-value: 0.0006) and 4.24-fold (p-value: 0.0012), and down-regulated Kelch-like ECH-associated protein 1 (KEAP1) expression by 2.5-fold (p-value: 0.0107), indicating that it possibly promotes mitochondrial biogenesis and mitophagy to maintain mitochondria quality control and homeostasis, and ultimately inhibits apoptotic cell death.

CONCLUSIONS

Our work revealed that pterosin B protected cells from glutamate excitotoxicity by targeting the downstream mitochondrial signals, making it a valuable candidate for developing potential therapeutic agents in treating neurodegenerative diseases.

Prevention of radiation dermatitis with skin hygiene and washing: a systematic review and meta-analysis

PURPOSE

This systematic review and meta-analysis aims to evaluate the effects of washing in patients receiving radiotherapy (RT) on radiation dermatitis (RD) severity.

METHODS

A literature search was performed using Ovid MEDLINE, Embase, and Cochrane databases between January 1, 1946, and January 31, 2023. Four randomized controlled trials (RCTs) studying the effects of washing with or without soap on RD were identified. A meta-analysis was conducted for clinician-reported outcomes using RevMan 5.4 and a narrative synthesis for patient-reported outcomes due to a lack of reported data amenable to quantitative comparison in accordance with the Synthesis Without Meta-analysis (SWiM) guidelines. The Cochrane Risk of bias (RoB2) and Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) criteria were used to assess risk of bias and certainty of evidence, respectively.

RESULTS

Two RCTs met the inclusion criteria for meta-analysis. Washing with or without soap significantly reduced the incidence of severe RD (OR: 0.32, 95% CI: 0.19-0.55, p < 0.01) and moist desquamation (OR: 0.25, 95% CI: 0.12-0.52, p < 0.01). Two of four trials found an association between washing and reduced itching score (p = 0.38). Pain score was not found to be significantly different with or without washing in any of the four studies (p = 0.07). The two studies that assessed burn scores did not detect any difference between the washing group versus no washing group (p = 0.25). Washing was associated with improved quality of life (QoL) measures in one study.

CONCLUSION

Washing with or without soap during RT resulted in less severe RD and less moist desquamation. Given the QoL benefits of washing, it should be advocated as part of routine skin care during RT.

MASCC clinical practice guidelines for the prevention and management of acute radiation dermatitis: part 1) systematic review

Acute radiation dermatitis (ARD) commonly develops in cancer patients undergoing radiotherapy and is often characterized by erythema, desquamation, and pain. A systematic review was conducted to summarize the current evidence on interventions for the prevention and management of ARD. Databases were searched from 1946 to September 2020 to identify all original studies that evaluated an intervention for the prevention or management of ARD, with an updated search conducted in January 2023. A total of 235 original studies were included in this review, including 149 randomized controlled trials (RCTs). Most interventions could not be recommended due to a low quality of evidence, lack of supporting evidence, or conflicting findings across multiple trials. Photobiomodulation therapy, Mepitel® film, mometasone furoate, betamethasone, olive oil, and oral enzyme mixtures showed promising results across multiple RCTs. Recommendations could not be made solely based on the published evidence due to limited high-quality evidence. As such, Delphi consensus recommendations will be reported in a separate publication.

Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics

One of the chief objectives in mass spectrometry-based peptide identification in proteomics is the statistical validation of top-scoring peptide-spectrum matches (PSMs) in the form of false discovery rate (FDR) estimation. Existing methods construct a null model that captures the characteristics of incorrect target PSMs to estimate the FDR, most often with the help of decoys. Decoy-based methods, however, increase the computational cost and rely on the difficult-to-verify assumption that decoy PSMs constitute a sufficient and representative sample of the population of possible incorrect target PSMs. On the other hand, the possibility of FDR estimation assisted by the plentiful non-top-scoring PSMs, which are almost always incorrect, has been scarcely explored. In this work, we propose a novel decoy-free procedure for developing null models for top-scoring PSMs using the transformed e-value (TEV) score and the distributions of non-top-scoring target PSMs. The method relies on a theoretically derivable relationship between the parameters of the distributions of lower-order statistics of the TEV score and a necessary empirical optimization to fit a single parameter to actual data. The framework was tested on multiple different data sets and two search engines. We present evidence that our method is comparable to and occasionally outperforms popular decoy-free and decoy-based methods in FDR estimation.

Photobiomodulation therapy for the prevention of acute radiation dermatitis: a systematic review and meta-analysis

PURPOSE

Approximately 95% of patients undergoing radiotherapy (RT) experience radiation dermatitis (RD). Evidence has suggested that photobiomodulation therapy (PBMT) can stimulate skin renewal and minimize RD. The aim of the present paper was to investigate the efficacy of PBMT in RD prevention through a comprehensive literature review.

METHODS

A literature search of Ovid MEDLINE, Embase, and Cochrane databases was conducted from 1980 to March 2021 to identify RCT on the use of PBMT for RD prevention. Forest plots were developed using RevMan software to quantitatively compare data between studies.

RESULTS

Five papers were identified: four in breast and one in head and neck cancer patients. Patients receiving PBMT experienced less severe RD than the control groups after 40 Gray (Gy) of RT (grade 3 toxicity: Odds Ratio (OR): 0.57, 95% CI 0.14-2.22, p = 0.42) and at the end of RT (grade 0 + 1 vs. 2 + 3 toxicity: OR: 0.28, 95% CI 0.15-0.53, p < 0.0001). RT interruptions due to RD severity were more frequent in the control group (OR: 0.81, 95% CI 0.10-6.58, p = 0.85).

CONCLUSION

Preventive PBMT may be protective against the development of severe grades of RD and reduce the frequency of RT interruptions. Larger sample sizes and other cancer sites at-risk of RD should be evaluated in future studies to confirm the true efficacy of PBMT, also in preventing the onset of RD and to finalize a standardized protocol to optimize the technique. At present, starting PBMT when RT starts is recommendable, as well as performing 2 to 3 laser sessions weekly.

Barrier Films and Dressings for the Prevention of Acute Radiation Dermatitis: A Systematic Review and Meta-Analysis

PURPOSE

This systematic review and meta-analysis aimed to evaluate the efficacy of barrier films and dressings in preventing acute radiation dermatitis (RD).

METHODS

OVID Medline, Embase, and Cochrane databases were searched from 1946 to September 2020 to identify randomized controlled trials on the use of barrier films or dressings to prevent RD. For comparable outcomes between studies, pooled effect sizes and 95% confidence intervals (CI) were calculated using the random effects analysis in RevMan 5.4.

RESULTS

Fourteen and 11 studies were included in the qualitative and quantitative analyses, respectively. Five types of barrier films used for RD were identified: Hydrofilm, StrataXRT®, Mepitel® Film, 3 M™ Cavilon™ No-Sting Barrier Film, and silver leaf nylon dressing. Hydrofilm and Mepitel Film significantly reduced the development of RD grade ≥ 2 in breast and head and neck cancer patients (RR 0.32, 95%CI 0.19, 0.56, p < 0.0001; RR 0.21, 95%CI 0.05, 0.89, p = 0.03, resp.). Moreover, Hydrofilm had a beneficial effect on patient-reported outcomes (PROs) (SMD -0.75, 95%CI -1.2, -0.29, p = 0.001). The meta-analyses on the other barrier films did not show any significant effect.

CONCLUSION

This review and meta-analysis demonstrated that Hydrofilm and Mepitel Film could effectively reduce RD severity and improve PROs. The evidence is generally weak for all the studies on barrier films and dressings due to a limited study number, high risk of bias, small sample sizes, and minimal comparable outcome measures. It's potential has been proven, but future research in this field is recommended to confirm the efficacy of these products and assess real-world feasibility.

Topical non-steroidal agents for the prevention of radiation dermatitis: a systematic review and meta-analysis

PURPOSE

Radiation dermatitis (RD) is a common side effect of radiation therapy, affecting a majority of breast and head and neck cancer patients with a negative impact on quality of life. Currently, no consensus exists regarding the prevention of RD.

METHODS

PubMed, Embase and Cochrane databases (1946 to December 2022) were searched using PRISMA guidelines to identify randomized controlled trials (RCTs) that investigated the use of topical non-steroidal agents in the prevention of RD in patients undergoing radiotherapy.

RESULTS

A total of six RCTs were included, comprising 627 patients. Among the topical non-steroidal agents analyzed, only the use of Biafine® in breast cancer patients was significant in preventing grade 4 and 3 + RD as classified by the Radiation Therapy Oncology group (RTOG) scale (OR = 0.07, 95% CI 0.01-0.63, p = 0.02, and OR 0.11, 95% CI 0.03-0.41, p < 0.01, respectively). The remaining agents (trolamine alone and hyaluronic acid/hyaluronan) did not significantly prevent the occurrence of RD.

CONCLUSION

The results of this systematic review and meta-analysis indicate that Biafine® can prevent grade 3 + RD in breast cancer patients. The use of trolamine and hyaluronic acid does not significantly affect the incidence of RD.

Comparative proteomic analysis reveals the different hepatotoxic mechanisms of human hepatocytes exposed to silver nanoparticles

Silver nanoparticles (AgNPs), which have been used extensively in consuming products and eventually released into the natural environment, have aroused concerns recently because of their potentially harmful effects on human beings following various routes of exposure. As the liver is one of the largest accumulation and deposition sites of circulatory AgNPs, it is important to evaluate the hepatotoxicity induced by AgNPs. However, the acting mechanisms of AgNPs-induced hepatotoxicity are still elusive to a great extent. Herein, we investigated the hepatotoxic effects of AgNPs using a comparative proteomics approach. First, we evaluated the cytotoxicity of different-sized AgNPs and found that the cancerous liver cells were generally more sensitive than the normal liver cells. Next, proteomics results suggested that HepG2 and L02 cells showed distinct adaptive responses upon AgNPs exposure. HepG2 cells respond to stresses by adapting energy metabolism, upregulating metallothionein expression and increasing the expression of antioxidants, while L02 cells protect themselves by increasing DNA repair and macro-autophagy. Besides, mitochondrial ROS has been identified as one of the causes of AgNPs-induced hepatotoxicity. Collectively, our results revealed that hepatic cancer cells and normal cells cope with AgNPs in notably different pathways, providing new insights into mechanisms underlying AgNPs-induced hepatotoxicity. DATA AVAILABILITY: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Deutsch et al. (2020)) via the PRIDE (Perez-Riverol et al. (2019)) partner repository with the dataset identifier PXD029511.

Natural and miscellaneous agents for the prevention of acute radiation dermatitis: a systematic review and meta-analysis

PURPOSE

This systematic review and meta-analysis aimed to evaluate the available literature describing the efficacy of natural and miscellaneous agents in preventing acute radiation dermatitis (RD) in cancer patients.

METHODS

OVID MedLine, Embase, and Cochrane literature databases were searched from 1946 to January 2023 for randomized controlled trials studying the use of natural and miscellaneous agents to prevent RD. RevMan 5.4 was used for the meta-analysis to calculate the pooled effect sizes and 95% confidence intervals (CI) using the random effects analysis.

RESULTS

For the systematic review and meta-analysis, 19 and 16 studies were included, respectively. Of the five studied natural products (aloe vera, oral enzymes, olive oil, calendula, and curcumin), only oral enzymes and olive oil significantly reduced the incidence of Radiation Therapy Oncology Group grade 2⁺ (RR: 0.42, 95%CI 0.30-0.58, p < 0.00001, RR: 0.66, 95% CI 0.51-0.85, p = 0.001, resp.). The oral enzymes also reduced the grade 3⁺ RD incidence (RR: 0.18, 95%CI 0.06-0.55, p = 0.003). The other agents demonstrated no significant effect.

CONCLUSION

This review and meta-analysis on natural and miscellaneous agents in preventing RD in cancer patients demonstrated that oral enzymes and olive oil prevented RD severity. However, evidence supporting natural agents to prevent RD is inconsistent, mainly because of low studies numbers, low-quality study designs, and small sample sizes. Therefore, concrete conclusions cannot be made. Research on (new) natural or miscellaneous agents should focus on a randomized controlled double-blinded study design with a large patient population, a higher consistency in research methods, and clinician- and patient-reported outcomes.

Layer- and cell-type-specific differences in neural activity in mouse barrel cortex during a whisker detection task

To address the question which neocortical layers and cell types are important for the perception of a sensory stimulus, we performed multielectrode recordings in the barrel cortex of head-fixed mice performing a single-whisker go/no-go detection task with vibrotactile stimuli of differing intensities. We found that behavioral detection probability decreased gradually over the course of each session, which was well explained by a signal detection theory-based model that posits stable psychometric sensitivity and a variable decision criterion updated after each reinforcement, reflecting decreasing motivation. Analysis of multiunit activity demonstrated highest neurometric sensitivity in layer 4, which was achieved within only 30 ms after stimulus onset. At the level of single neurons, we observed substantial heterogeneity of neurometric sensitivity within and across layers, ranging from nonresponsiveness to approaching or even exceeding psychometric sensitivity. In all cortical layers, putative inhibitory interneurons on average proffered higher neurometric sensitivity than putative excitatory neurons. In infragranular layers, neurons increasing firing rate in response to stimulation featured higher sensitivities than neurons decreasing firing rate. Offline machine-learning-based analysis of videos of behavioral sessions showed that mice performed better when not moving, which at the neuronal level, was reflected by increased stimulus-evoked firing rates.

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.

Nontargeted metabolomics reveals differences in the metabolite profiling among methicillin-resistant and methicillin-susceptible Staphylococcus aureus in response to antibiotics

Staphylococcus aureus (S. aureus) causes infections and can be fatal. In the long-term struggle against antibiotics, S. aureus has acquired resistance toward antibiotics and become more difficult to kill. Metabolomics could directly reflect the responses of S. aureus toward antibiotics, which is effective for studying the resistance mechanism of S. aureus. In this study, based on a nontargeted metabolic figure printing technique, the metabolome of a pair of isogenic methicillin-susceptible and resistant S. aureus strains ATCC25923 (MSSA) and ATCC43300 (MRSA) treated with or without oxacillin was characterized. 7 and 29 significantly changed metabolites in MRSA and MSSA were identified by combined accurate mass and mass fragmentation analysis. Pathway enrichment analysis suggested that DNA repair and flavin biosynthesis are the universal pathways of both MSSA and MRSA under antibiotic stress. MRSA systematically and effectively fights against oxacillin through precise control of energy production, PBP2a substrate biosynthesis and antioxidant function. In contrast, MSSA lacks effective defense pathways against oxacillin. The different metabolome responses of MSSA and MRSA toward antibiotics provide us with new insights into how S. aureus develops antibiotic resistance.

ODP519 Thyroid Cyst Grows E. coli

Background

Thyroid abscesses are extremely rare, representing less than 1% of all thyroiddiseases. The thyroid gland is very robust against infections due to its vastlymphatic drainage, dual blood supply, encapsulation, and iodine concentration. Immunocompromised patients are at greater risk of developing thyroid abscesses. 1 Case: A 51-year-old female presented to her primary care provider with acute onset ofpainful right neck mass with associated cough, hoarseness, fever, and fatigue. She was seen by an Otolaryngologist who aspirated 6 cc of brown purulentmaterial from a suspected thyroid mass. The thyroid fluid was sent for culture,and she was empirically started on Augmentin. CT neck demonstrated a cysticlesion of the right thyroid gland, retropharyngeal edema, and mass effect withleftward deviation of the larynx and trachea without airway obstruction. Due tothese findings, the patient was admitted to the hospital where initial two setsof blood cultures were negative but repeat blood cultures revealed 2 of 2positive for E. coli. Thyroid cyst fluid also grew E. coli. Urine culture hadno growth. She was found to have a suppressed TSH of 0.24 uIU/mL, elevated free T4 of 1.80 ng/dL, and suppressed total T3 of 0.52 ng/mL. Previous TSH was within normal limits, 0.82 uIU/mL. The suppressed TSH and suppressed T3 were thought to be secondary to euthyroid sick syndrome. She was maintained onCeftriaxone while admitted and discharged on Ciprofloxacin. Pathology from theright thyroid cyst revealed acute inflammatory cells only consistent with anabscess, negative for malignancy. The patient elected to undergo a righthemithyroidectomy with isthmusectomy.

Discussion

Thyroiditis is defined as inflammation of the thyroid gland and has a variety ofetiologies. Suppurative thyroiditis, which includes thyroid abscess as in thiscase we have described, is an infrequent cause of thyroiditis. It is usuallycaused by hematogenous spread or direct inoculation of a pathogen. Treatmentincludes systemic antibiotics targeting the causative organism; although thegold standard remains surgical drainage. Surgical management is the mainstay ofmanaging patients with thyroid abscesses. 2 References: 1 Sharma, R., McManus, C., Kuo, J. (2020). MON-485 Thyroid Abscess in a Healthy 22 Year Old Female. Journal of the Endocrine Society, 4(1), A792-A793. https://academic.oup.com/jes/article/4/Supplement_1/MON-485/5832886 2 Singh, G., Jaiswal R., Gulati, N.,Granieri, E. (2019). A case of idiopathic thyroid abscess caused by Escherichia coli. Journal of Community Hospital Internal Medicine Perspectives. 9(2): 159-161. https://europepmc.org/article/MED/31044048

Presentation: No date and time listed

Fluorescent Imaging and Sorting of High-Lipid-Content Strains of Green Algae by Using an Aggregation-Induced Emission Luminogen

Microalgae-based biofuels are receiving attention at the environmental, economic, and social levels because they are clean, renewable, and quickly produced. The green algae Chlorella vulgaris has been extensively studied in research laboratories and the biofuel industry as a model organism to increase lipid production to be cost-effective in commercial production. In this work, we utilized a lipid-droplet-specific luminogen with aggregation-induced emission (AIE) characteristics to increase the lipid production of C. vulgaris by fluorescent imaging and sorting of those algal cells with large and rich lipid droplets for subculturing. The AIE-active TPA-A enabled real-time monitoring of the size and number of lipid droplets in C. vulgaris during their growth period so that we can identify the best time for harvesting. Furthermore, the algae cells with high lipid content were identified and collected for subculturing by the technique of fluorescence-activated cell sorting (FACS). The lipid production in the generation of two successive selections was almost doubled compared to the generation with natural selection. This work demonstrated that the technologies of AIE and FACS could be applied together to improve the production of a third-generation biofuel.

Quantile regression forests for individualized surgery scheduling

Determining the optimal surgical case start times is a challenging stochastic optimization problem that shares a key feature with many other healthcare operations problems. Namely, successful problem solutions require using a vast array of available historical data to create distributions that accurately capture a case duration's uncertainty for integration into an optimization model. Distribution fitting is the conventional approach to generate these distributions, but it can only employ a limited, aggregate portion of the detailed patient features available in Electronic Medical Records systems today. If all the available information can be taken advantage of, then distributions individualized to every case can be constructed whose precision would support higher quality solutions in the presence of uncertainty. Our individualized stochastic optimization framework shows how the quantile regression forest (QRF) method predicts individualized distributions that are integrable into sample-average approximation, robust optimization, and distributionally robust optimization models for problems like surgery scheduling. In this paper, we present some related theoretical performance guarantees for each formulation. Numerically, we also study our approach's benefits relative to three other traditional models using data from Memorial Sloan Kettering Cancer Center in New York, NY, USA.

Mode of action of elasnin as biofilm formation eradicator of methicillin-resistant Staphylococcus aureus

Biofilm is made up of microbes and their extracellular matrix, making microorganisms highly tolerant, resistant, and resilient to a wide range of antimicrobials. Biofilm treatment with conventional antimicrobial agents can accelerate the evolution and spread of resistance due to the reduced efficacy and increased gene transfer and differentiation within biofilms. Therefore, effective biofilm-targeting compounds are currently highly sought after. In the present study, we identified elasnin as a potent biofilm-targeting compound against methicillin-resistant Staphylococcus aureus (MRSA). Elasnin effectively inhibited biofilm formation and especially eradicated the pre-formed biofilms of MRSA with low cytotoxicity and low risk of resistance development and retains its activity in a chronic wound biofilms model. A comprehensive mechanistic study using multi-omics and confocal and scanning electron microscopy revealed that elasnin induced the biofilm matrix destruction in a time-dependent manner and interfered with the cell division during the exponential phase, primarily by repressing the expression of virulence factors. Cells released from the elasnin-treated biofilms exhibited a defective appearance and became more sensitive to beta-lactam antibiotic penicillin G. Through gene overexpression and deletion assay, we discovered the key role of sarZ during elasnin-induced biofilm eradication. Overall, the present study identified elasnin as a potent biofilm eradicator against MRSA that harbors potential to be developed for biofilm removal and chronic wound treatment, and provided new insights into the molecular targets for biofilm eradication in MRSA.

Proteome profiling of evolved methicillin-resistant Staphylococcus aureus strains with distinct daptomycin tolerance and resistance phenotypes

Methicillin-resistant Staphylococcus aureus (MRSA) is a highly dangerous pathogen, and daptomycin has been increasingly used to treat its infections in clinics. Recently, several groups have shown that tolerance and resistance of microbes can evolve rapidly under cyclic antibiotic exposure. We have previously shown that the same tolerance and resistance development occurs in MRSA treated with daptomycin in an adaptive laboratory evolution (ALE) experiment. In the present study, we performed proteomic analysis to compare six daptomycin-tolerant and resistant MRSA strains that were evolved from the same ancestral strain. The strain with a higher tolerance level than the others had the most different proteome and response to antibiotic treatment, resembling those observed in persister cells, which are small subpopulations of bacteria that survive lethal antibiotics treatment. By comparing the proteome changes across strains with similar phenotypes, we identified the key proteins that play important roles in daptomycin tolerance and resistance in MRSA. We selected two candidates to be confirmed by gene overexpression analysis. Overexpression of EcsA1 and FabG, which were up-regulated in all of the tolerant evolved strains, led to increased daptomycin tolerance in wild-type MRSA. The proteomics data also suggested that cell wall modulations were implicated in both resistance and tolerance, but in different ways. While the resistant strains had peptidoglycan changes and a more positive surface charge to directly repel daptomycin, the tolerant strains possessed different cell wall changes that do not involve the peptidoglycan nor alterations of the surface charge. Overall, our study showed the differential proteome profiles among multiple tolerant and resistant strains, pinpointed the key proteins for the two phenotypes and revealed the differences in cell wall modulations between the daptomycin-tolerant/resistant strains.

Proteomining-Based Elucidation of Natural Product Biosynthetic Pathways in Streptomyces

The genus Streptomyces is known to harbor numerous biosynthetic gene clusters (BGCs) of potential utility in synthetic biology applications. However, it is often difficult to link uncharacterized BGCs with the secondary metabolites they produce. Proteomining refers to the strategy of identifying active BGCs by correlating changes in protein expression with the production of secondary metabolites of interest. In this study, we devised a shotgun proteomics-based workflow to identify active BGCs during fermentation when a variety of compounds are being produced. Mycelia harvested during the non-producing growth phase served as the background. Proteins that were differentially expressed were clustered based on the proximity of the genes in the genome to highlight active BGCs systematically from label-free quantitative proteomics data. Our software tool is easy-to-use and requires only 1 point of comparison where natural product biosynthesis was significantly different. We tested our proteomining clustering method on three Streptomyces species producing different compounds. In Streptomyces coelicolor A3(2), we detected the BGCs of calcium-dependent antibiotic, actinorhodin, undecylprodigiosin, and coelimycin P1. In Streptomyces chrestomyceticus BCC24770, 7 BGCs were identified. Among them, we independently re-discovered the type II PKS for albofungin production previously identified by genome mining and tedious heterologous expression experiments. In Streptomyces tenebrarius, 5 BGCs were detected, including the known apramycin and tobramycin BGC as well as a newly discovered caerulomycin A BGC in this species. The production of caerulomycin A was confirmed by LC-MS and the inactivation of the caerulomycin A BGC surprisingly had a significant impact on the secondary metabolite regulation of S. tenebrarius. In conclusion, we developed an unbiased, high throughput proteomics-based method to complement genome mining methods for the identification of biosynthetic pathways in Streptomyces sp.

Cost of TB prevention and treatment in the Philippines in 2017

BACKGROUND: The Philippines aims to accelerate TB reduction through the provision of universally accessible and affordable services. The objectives of this paper are to estimate the costs of TB services and interventions using a health systems´ perspective, and to explore cost differences in service delivery via primary care facilities or hospitals.METHODS: Data were collected from a multi-stage stratified random sampling of 28 facilities in accordance with Global Health Cost Consortium costing standards and analysis tools. Unit costs (in US$) estimated using top-down (TD) and bottom-up (BU) approaches, are summarised following Value TB reporting standards and by broad facility type.RESULTS: Cost of delivering 32 TB services and eight interventions varied by costing method and delivery platform. Average BU costs ranged from US$0.38 for treatment support visits, US$2.5 for BCG vaccination, US$19.48 for the Xpert^® MTB/RIF test to US$3,677 for MDR-TB treatment using the long regimen. Delivering TB care in hospitals was generally more costly than in primary care facilities, except for TB prevention in children and MDR-TB treatment using the long regimen.CONCLUSION: Comprehensive costing data for TB care in the Philippines are now available to aid in the design, planning, and prioritisation of delivery models to End TB.

Proteomics and Transcriptomics Uncover Key Processes for Elasnin Tolerance in Methicillin-Resistant Staphylococcus aureus

Elasnin is a new antibiofilm compound that was recently reported to have excellent activity against methicillin-resistant Staphylococcus aureus (MRSA) biofilms. In this study, we established that elasnin also has antibacterial activity against growing S. aureus planktonic cells. To explore elasnin's potential as an antibiotic, we applied adaptive laboratory evolution (ALE) and produced evolved strains with elevated elasnin tolerance. Interestingly, they were more sensitive toward daptomycin and lysostaphin. Whole-genome sequencing revealed that all of the evolved strains possessed a single point mutation in a putative phosphate transport regulator. Subsequently, they exhibited increased intracellular phosphate (Pi) and polyphosphate levels. Inhibition of the phosphate transport regulator gene changed the phenotype of the wild type to one resembling those observed in the evolved strains. Proteomics and transcriptomics analyses showed that elasnin treatment resulted in the downregulation of many proteins related to cell division and cell wall synthesis, which is important for the survival of growing exponential-phase cells. Other downregulated processes and factors were fatty acid metabolism, glycolysis, the two-component system, RNA degradation, and ribosomal proteins. Most importantly, transport proteins and proteins involved in oxidative phosphorylation and the phosphotransferase system were more upregulated in the evolved strain than in the ancestral strain, indicating that they are important for elasnin tolerance. Overall, this study showed that elasnin has antibacterial activity against growing S. aureus cells and revealed the altered processes due to elasnin treatment and those associated with its tolerance. IMPORTANCE Besides the excellent antibiofilm properties of elasnin, we discovered that it can also kill growing methicillin-resistant Staphylococcus aureus (MRSA) planktonic cells. We subjected MRSA cells to an in vitro evolution experiment, and the resulting evolved strains exhibited increased elasnin tolerance, reduced growth rate, loss of pigmentation, and an increased proportion of small-colony formation, and they became more sensitive toward daptomycin and lysostaphin. Through multiomics analysis, we uncovered the affected processes in growing S. aureus planktonic cells following elasnin treatment, including the downregulation of cell wall synthesis, cell division, and some genes/proteins for the two-component system. These findings suggest that elasnin suppressed processes important for the cells' survival and adaptation to environmental stresses, making it an ideal drug adjuvant candidate. Overall, our study provides new insights into the mechanism of elasnin in S. aureus planktonic cells and pointed out the potential application of elasnin in clinics.

Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens

Antibiotic resistance, the ability of a microbial pathogen to evade the effects of antibiotics thereby allowing them to grow under elevated drug concentrations, is an alarming health problem worldwide and has attracted the attention of scientists for decades. On the other hand, the clinical importance of persistence and tolerance as alternative mechanisms for pathogens to survive prolonged lethal antibiotic doses has recently become increasingly appreciated. Persisters and high-tolerance populations are thought to cause the relapse of infectious diseases, and provide opportunities for the pathogens to evolve resistance during the course of antibiotic therapy. Although proteomics and other omics methodology have long been employed to study resistance, its applications in studying persistence and tolerance are still limited. However, due to the growing interest in the topic and recent progress in method developments to study them, there have been some proteomic studies that yield fresh insights into the phenomenon of persistence and tolerance. Combined with the studies on resistance, these collectively guide us to novel molecular targets for the potential drugs for the control of these dangerous pathogens. In this review, we surveyed previous proteomic studies to investigate resistance, persistence, and tolerance mechanisms, and discussed emerging experimental strategies for studying these phenotypes with a combination of adaptive laboratory evolution and high-throughput proteomics. This article is protected by copyright. All rights reserved.

Common Decoy Distributions Simplify False Discovery Rate Estimation in Shotgun Proteomics

In shotgun proteomics, false discovery rate (FDR) estimation is a necessary step to ensure the quality of accepted peptide-spectrum matches (PSMs) from a database search. Popular statistical validation tools for FDR control tend to rely on target-decoy searching to build empirical, dataset-specific models, which often leads to inaccurate FDR estimates. In this paper, we propose a new approach named common decoy distribution (CDD) to FDR estimation using the idea of a fixed empirical null score distribution derived from millions of peptide tandem mass spectra. To demonstrate the viability of CDD, its stability with respect to noise and the presence of unexpected peptide modifications was evaluated. PeptideProphet-based implementation of CDD was benchmarked against decoy-based PeptideProphet, and both methods exhibited similar accuracy of FDR estimates and retrieval of correct PSMs. The finding of this study calls for a re-evaluation of the necessity of dataset-specific target-decoy searches and illustrates the potential of Big Data approaches for statistical analysis in proteomics.

Fully Integrated On-line strategy for Highly Sensitive Proteome Profiling of 10-500 Mammalian Cells

Recent development in proteomic sample preparation using nanofluidic devices has made single-cell proteome profiling possible. However, these nanofluidic devices require special expertise and costly nanopipetting instruments. They are also specially...

Colchicine use in patients with COVID-19: A systematic review and meta-analysis

INTRODUCTION

Colchicine may inhibit inflammasome signaling and reduce proinflammatory cytokines, a purported mechanism of COVID-19 pneumonia. The aim of this systematic review and meta-analysis is to report on the state of the current literature on the use of colchicine in COVID-19 and to investigate the reported clinical outcomes in COVID-19 patients by colchicine usage.

METHODS

The literature was searched from January 2019 through January 28, 2021. References were screened to identify studies that reported the effect of colchicine usage on COVID-19 outcomes including mortality, intensive care unit (ICU) admissions, or mechanical ventilation. Studies were meta-analyzed for mortality by the subgroup of trial design (RCT vs observational) and ICU status. Studies reporting an risk ratio (RR), odds ratio (OR) and hazard ratio (HR) were analyzed separately.

RESULTS

Eight studies, reporting on 16,248 patients, were included in this review. The Recovery trial reported equivalent mortality between colchicine and non-colchicine users. Across the other studies, patients who received colchicine had a lower risk of mortality-HR of 0.25 (95% CI: 0.09, 0.66) and OR of 0.22 (95% CI: 0.09, 0.57). There was no statistical difference in risk of ICU admissions between patients with COVID-19 who received colchicine and those who did not-OR of 0.26 (95% CI: 0.06, 1.09).

CONCLUSION

Colchicine may reduce the risk of mortality in individuals with COVID-19. Further prospective investigation may further determine the efficacy of colchicine as treatment in COVID-19 patients in various care settings of the disease, including post-hospitalization and long-term care.

ClusterSheep: A Graphics Processing Unit-Accelerated Software Tool for Large-Scale Clustering of Tandem Mass Spectra from Shotgun Proteomics

Modern shotgun proteomics experiments generate gigabytes of spectra every hour, only a fraction of which were utilized to form biological conclusions. Instead of being stored as flat files in public data repositories, this large amount of data can be better organized to facilitate data reuse. Clustering these spectra by similarity can be helpful in building high-quality spectral libraries, correcting identification errors, and highlighting frequently observed but unidentified spectra. However, large-scale clustering is time-consuming. Here, we present ClusterSheep, a method utilizing Graphics Processing Units (GPUs) to accelerate the process. Unlike previously proposed algorithms for this purpose, our method performs true pairwise comparison of all spectra within a precursor mass-to-charge ratio tolerance, thereby preserving the full cluster structures. ClusterSheep was benchmarked against previously reported clustering tools, MS-Cluster, MaRaCluster, and msCRUSH. The software tool also functions as an interactive visualization tool with a persistent state, enabling the user to explore the resulting clusters visually and retrieve the clustering results as desired.

Mass spectrometry-based multi-omics analysis reveals the thermogenetic regulation of herbal medicine in rat model of yeast-induced fever

ETHNOPHARMACOLOGICAL RELEVANCE

In the principle of traditional Chinese medicine (TCM), clinical usage is based on drug attributes of the herbal medicine. The cold and hot properties of TCM are classified accordingly to their pharmacological effects, such as temperature change. Herbal medicine has been used as food supplements in our daily life, and the thermogenetic regulation is one of their primary applications. However, the underlying mechanism of "cold" or "hot" stimulating effect of herbal medicine has not been fully identified.

AIM OF THE STUDY

Thermogenetic regulation and classification of herbal medicine of hot/cold herbs were determined by rat model of yeast-induced fever.

MATERIALS AND METHODS

Here, a novel method in classifying and characterizing cold- and hot-herbal medicines was established by analyses of mass spectrometry (MS)-based metabolomics and lipidomics from the serum of herbal extract-treated rats. The yeast-induced inflammatory rats were used as the model system, which were subjected to the treatments of cold- or hot-herbal medicine.

RESULTS

The multi-omics approach identified the clustering of metabolites from cold and hot herb-treated rat serum by using partial least squares discriminant analysis (PLS-DA), and which subsequently identified that the 8-h treatment was the metabolic perturbation point of herb-mediated thermogenesis. Meanwhile, the levels of identified metabolites in the serum, i.e. lysoPE, lysoPC and carnitine, showed a positive relationship with the regulation of body temperature; while the levels of amino acid, fatty acid and bile acid were contrary correlated with the temperature change. In addition, the differential expressed metabolites were subjected to pathway enrichment and network analyses in revealing the possible action mechanism of herbal medicines in relating to thermogenetic regulation.

CONCLUSION

The developed MS-based omics provides a new insight in characterizing the properties of cold/hot herbal medicine.

Measurement-based care educational programmes for clinical trainees in mental healthcare: a scoping review protocol

INTRODUCTION

Measurement-based care (MBC) represents the approach of regularly using symptom rating scales to guide patient care decisions in mental healthcare. MBC is an effective, feasible and acceptable approach to enhance clinical outcomes in various disciplines, including medicine, psychology, social work and psychotherapy. Yet, it is infrequently used by clinicians, potentially due to limited education for care providers. The objective of this scoping review is to survey the characteristics of MBC educational programmes for undergraduate, graduate and postgraduate clinical trainees in mental healthcare.

METHODS AND ANALYSIS

Using database-tailored search strategies, we plan on searching Medline, PsycINFO, Embase, CINAHL and Cochrane Central for relevant studies. Thereafter, we will analyse the selected studies to extract information on the delivery of educational programmes, the clinical and educational outcomes of these programmes, and the potential enablers and barriers to MBC education. In this paper, we articulate the protocol for this scoping review.

ETHICS AND DISSEMINATION

This scoping review does not require research ethics approval. The findings from this scoping review will be incorporated into the creation of a novel MBC curriculum and handbook. Results will be disseminated at appropriate national or international conferences, as well as in a peer-reviewed journal publication.

Comparative proteomic investigation of multiple methicillin-resistant Staphylococcus aureus strains generated through adaptive laboratory evolution

Recent discoveries indicate that tolerance and resistance could rapidly evolve in bacterial populations under intermittent antibiotic treatment. In the present study, we applied antibiotic combinations in laboratory experiments to generate novel methicillin-resistant Staphylococcus aureus strains with distinct phenotypes (tolerance, resistance, and suppressed tolerance), and compared their proteome profiles to uncover the adaptation mechanisms. While the tolerant strains have very different proteomes than the susceptible ancestral strain, the resistant strain largely resembles the ancestral in terms of their proteomes. Our proteomics data and other assays support the connection between the detected mutations to the observed phenotypes, confirming the general understanding of tolerance and resistance mechanisms. While resistance directly counteracts the action mechanism of the antibiotic, tolerance involves complex substantial changes in the cells' biological process to achieve survival advantages. Overall, this study provides insights into the existence of diverse evolutionary pathways for tolerance and resistance development under different treatment scenarios.

Optimal sampled phase-only hologram (OSPOH)

A sampled phase-only hologram (SPOH) is the phase component of the hologram of an object image with pixels being sampled with a periodic grid-cross pattern. The reconstructed image of a SPOH is a sparse image with abundant empty voids and degradation in sharpness and contrast. In this paper we proposed a method based on a new sampling scheme, together with stochastic binary search (SBS), to obtain an optimal sampling lattice that can be applied to generate phase-only holograms with enhanced reconstructed image. Experimental results show that with our proposed method, the fidelity and quality of the reconstructed image are increased.

Universal Spectrum Identifier for mass spectra

Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USI enables greater transparency of spectral evidence, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.

Does Cathodal vs. Sham Transcranial Direct Current Stimulation Over Contralesional Motor Cortex Enhance Upper Limb Motor Recovery Post-stroke? A Systematic Review and Meta-analysis

Background: During recovery from stroke, the contralesional motor cortex (M1) may undergo maladaptive changes that contribute to impaired interhemispheric inhibition (IHI). Transcranial direct current stimulation (tDCS) with the cathode over contralesional M1 may inhibit this maladaptive plasticity, normalize IHI, and enhance motor recovery.

Objective: The objective of this systematic review and meta-analysis was to evaluate available evidence to determine whether cathodal tDCS on contralesional M1 enhances motor re-learning or recovery post-stroke more than sham tDCS.

Methods: We searched OVID Medline, Embase, and the Cochrane Central Register of Controlled Trials for participants with stroke (>1 week post-onset) with motor impairment and who received cathodal or sham tDCS to contralesional M1 for one or more sessions. The outcomes included a change in any clinically validated assessment of physical function, activity, or participation, or a change in a movement performance variable (e.g., time, accuracy). A meta-analysis was performed by pooling five randomized controlled trials (RCTs) and comparing the change in Fugl–Meyer upper extremity scores between cathodal and sham tDCS groups.

Results: Eleven studies met the inclusion criteria. Qualitatively, four out of five cross-over design studies and three out of six RCTs reported a significant effect of cathodal vs. sham tDCS. In the quantitative synthesis, cathodal tDCS (n = 65) did not significantly reduce motor impairment compared to sham tDCS (n = 67; standardized mean difference = 0.33, z = 1.79, p = 0.07) with a little observed heterogeneity (I² = 5%).

Conclusions: The effects of cathodal tDCS to contralesional M1 on motor recovery are small and consistent. There may be sub-populations that may respond to this approach; however, further research with larger cohorts is required.

Evolution of Bacterial Tolerance Under Antibiotic Treatment and Its Implications on the Development of Resistance

Recent laboratory evolution studies have shown that upon repetitive antibiotic treatments, bacterial populations will adapt and eventually became tolerant and resistant to the drug. Drug tolerance rapidly evolves upon frequent, intermittent antibiotic treatments, and such emerging drug tolerance seems to be specific to the treatment conditions, complicating clinical practice. Moreover, it has been shown that tolerance often promotes the development of resistance, which further reinforces the need of clinical diagnostics for antibiotic tolerance to reduce the occurrence of acquired resistance. Here, we discuss the laboratory evolution studies that were performed to track the development of tolerance in bacterial populations, and highlight the urgency of developing a comprehensive knowledge base of various tolerance phenotypes and their detection in clinics. Finally, we propose future directions for basic research in this growing field.

Diagnostic Imaging Modalities to Assess Treatment Response of Bone Metastasis in Patients Receiving Palliative Radiotherapy: A Scoping Review of the Literature

PURPOSE

Several studies have used objective radiologic data to assess the effect of palliative radiotherapy on tumor burden. The purpose of this literature review was to survey the various metrics that have been used to quantify bone tumor response to palliative radiotherapy by radiographical means and to determine whether any of these metrics were associated with clinical palliative outcomes.

METHODS

In accordance with PRISMA extension for Scoping Reviews guidelines, a literature search Ovid Medline and OldMedline from 1946 to February 6, 2019, Embase Classic/Embase from 1947 to 2019 week 5, and Cochrane Central Register of Controlled Trials February 2019 to extract articles related to quantified radiologic evaluation of bone metastases following palliative radiotherapy. Imaging modality, quantification metric, and association between imaging modality and clinical response were recorded.

RESULTS

Fourteen articles selected for full-text review utilized computed tomography (10 studies), fluorodeoxyglucose-positron emission tomography (3 studies), magnetic resonance imaging (1 study), diffusion-weighted magnetic resonance imaging (3 studies), and X-ray (1 study) imaging modalities. Variables assessed included tumor volume regression, bone density, metabolic activity, and signal intensity. Studies differed both in the type of imaging modality used and metric derived to quantify the radiologic findings. Fifty percent of the included studies aimed to identify a relationship between a quantified radiologic metric and clinical palliative response. Of these studies, 86% reported a correlation.

CONCLUSION

Quantified radiologic metrics can provide an objective measure of response to palliative radiotherapy and may be useful in predicting clinical palliative response. More studies are needed to validate these metrics and develop a standardized protocol for radiologic evaluation that can be implemented into a clinical workflow.

Prediction of breast cancer-related outcomes with the Edmonton Symptom Assessment Scale: A literature review

PURPOSE

The Edmonton Symptom Assessment Scale (ESAS) is a validated tool used in patients with varied cancer diagnoses to measure patient symptoms. The present manuscript will review the literature assessing the ability of the ESAS to predict patient-related outcomes in breast cancer patients.

METHODS

A literature search was conducted of Cochrane Central Register of Controlled Trials databases, Ovid MEDLINE, and Embase for English articles that investigated the use of predictive modelling with the ESAS in the breast cancer population. Study type, publication year, sample size, patient demographics, predicted outcomes, and strongest predictive factors/symptoms were summarized for each study.

RESULTS

A total of nine articles were included in this review. Five articles used the ESAS in predictive models to determine patient time to death. ESAS was also used to predict emergency department visits, determine symptoms associated with decreased quality of life, and generate a Health Utility Score. Lack of appetite was the most common ESAS symptom, as it was reported in five studies to be associated with decreased survival. In four of the nine articles, an additional survey investigating physical functioning was used in combination with ESAS to strengthen the predictive models.

CONCLUSIONS

Included studies support the use of ESAS in predictive models, particularly for predicting survival. Using the ESAS as a predictive tool allows for more accurate time to death predictions, potentially improving symptom management and preventing overtreatment of palliative patients near the end of life.

Modeling the likely economic cost of non-adherence to TB medicines in the Philippines

SETTING: The Philippines has a population of over 90 million people and is one of the 22 highest TB burden countries in the world.OBJECTIVE: To understand the economic cost of non-adherence to TB medicines due to loss to follow up and stock-outs in the Philippines.DESIGN: Data were collected on the economic costs of non-adherence to TB medicines and a model was developed to show those costs under different scenarios.RESULTS: The model showed that as many as 1958 and 233 persons are likely to have died as a result of DS-TB and MDR-TB loss to follow up, respectively, and 588 persons are likely to have died as a result of TB medicine stock outs. The related economic impact in each case is likely have been to be as much as US$72.2 million, US$13.4 million and US$21.0 million, respectively.CONCLUSION: The economic costs of non-adherence to TB medicines due to loss to follow-up and stock-outs represent a significant economic burden for the country and it is likely that the cost of addressing these problems would be much less than this burden and, therefore, a wise investment.

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.

The impact of smoking on adjuvant breast cancer radiation treatment: A systematic review

BACKGROUND

The influence of cigarette smoking on cancer risk has been well-studied. Similarly, exposure to ionizing radiation from radiotherapy (RT) can produce detrimental effects on an individual's health. In patients administered RT, there has been an observed relationship in other primary carcinomas. The purpose of this systematic review was to summarize the influence of cigarette smoking on outcomes post adjuvant RT in breast cancer patients.

METHODS

OVID Medline, Cochrane and Embase were searched and 1893 articles were identified. A total of 71 articles were included in the review. Study type, published year and sample size, age, systemic therapies, RT techniques and treatment side effects were collected if available.

RESULTS

The review found 198 different outcomes which fell into 7 categories and similar outcomes were recorded. 40% of skin reaction outcomes, 50% of cardiovascular outcomes, 71% of reconstruction outcomes, 29% of pulmonary function outcomes, 33% of mortality outcomes and 42% of secondary recurrence outcomes reported significant differences between smokers and non-smokers. None of the articles reported non-smokers to have a higher risk than smokers.

CONCLUSION

Cigarette smoking can pose a higher risk of post-treatment complications that can influence an individual's quality of life, survival rate and/or recurrence risk. This review further assessed the impact of smoking on various patient outcomes and side-effects in the adjuvant breast RT setting. The information provided in this review suggest that smoking cessation programs would help educate patients to understand their risks of being a current or former smoker when undergoing RT.