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Neopeptide-based immunotherapy has been recognised as a promising approach for the treatment of cancers. For neopeptides to be recognised by CD8+ T cells and induce an immune response, their binding to human leukocyte antigen class I (HLA-I) molecules is a necessary first step. Most epitope prediction tools thus rely on the prediction of such binding. With the use of mass spectrometry, the scale of naturally presented HLA ligands that could be used to develop such predictors has been expanded. However, there are rarely efforts that focus on the integration of these experimental data with computational algorithms to efficiently develop up-to-date predictors. Here, we present Anthem for accurate HLA-I binding prediction. In particular, we have developed a user-friendly framework to support the development of customisable HLA-I binding prediction models to meet challenges associated with the rapidly increasing availability of large amounts of immunopeptidomic data. Our extensive evaluation, using both independent and experimental datasets shows that Anthem achieves an overall similar or higher area under curve value compared with other contemporary tools. It is anticipated that Anthem will provide a unique opportunity for the non-expert user to analyse and interpret their own in-house or publicly deposited datasets., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

SARS-CoV-2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS-CoV-2, identifying potential T cell epitopes derived from the SARS-CoV-2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS-CoV-2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user-friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide-HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS., (© 2021 Wiley-VCH GmbH.)

HLA-DQ8, a genetic risk factor in type I diabetes (T1D), presents hybrid insulin peptides (HIPs) to autoreactive CD4+ T cells. The abundance of spliced peptides binding to HLA-DQ8 and how they are subsequently recognised by the autoreactive T cell repertoire is unknown. Here we report, the HIP (GQVELGGGNAVEVLK), derived from splicing of insulin and islet amyloid polypeptides, generates a preferred peptide-binding motif for HLA-DQ8. HLA-DQ8-HIP tetramer + T cells from the peripheral blood of a T1D patient are characterised by repeated TRBV5 usage, which matches the TCR bias of CD4+ T cells reactive to the HIP peptide isolated from the pancreatic islets of a patient with T1D. The crystal structure of three TRBV5+ TCR-HLA-DQ8-HIP complexes shows that the TRBV5-encoded TCR β-chain forms a common landing pad on the HLA-DQ8 molecule. The N- and C-termini of the HIP is recognised predominantly by the TCR α-chain and TCR β-chain, respectively, in all three TCR ternary complexes. Accordingly, TRBV5 + TCR recognition of HIP peptides might occur via a 'polarised' mechanism, whereby each chain within the αβTCR heterodimer recognises distinct origins of the spliced peptide presented by HLA-DQ8., (© 2021. The Author(s).)

Mechanisms by which advanced glycation end products (AGEs) contribute to type 1 diabetes (T1D) pathogenesis are poorly understood. Since life-long pharmacotherapy with alagebrium chloride (ALT) slows progression to experimental T1D, we hypothesized that acute ALT therapy delivered prediabetes, may be effective. However, in female, non-obese diabetic (NOD ShiLt ) mice, ALT administered prediabetes (day 50-100) did not protect against experimental T1D. ALT did not decrease circulating AGEs or their precursors. Despite this, pancreatic β-cell function was improved, and insulitis and pancreatic CD45.1 + cell infiltration was reduced. Lymphoid tissues were unaffected. ALT pre-treatment, prior to transfer of primed GC98 CD8 + T cell receptor transgenic T cells, reduced blood glucose concentrations and delayed diabetes, suggesting islet effects rather than immune modulation by ALT. Indeed, ALT did not reduce interferon-γ production by leukocytes from ovalbumin-pre-immunised NOD ShiLt mice and NOD scid recipients given diabetogenic ALT treated NOD splenocytes were not protected against T1D. To elucidate β-cell effects, NOD-derived MIN6N8 β-cell major histocompatibility complex (MHC) Class Ia surface antigens were examined using immunopeptidomics. Overall, no major changes in the immunopeptidome were observed during the various treatments with all peptides exhibiting allele specific consensus binding motifs. As expected, longer MHC Class Ia peptides were captured bound to H-2D b than H-2K b under all conditions. Moreover, more 10-12 mer peptides were isolated from H-2D b after AGE modified bovine serum albumin (AGE-BSA) treatment, compared with bovine serum albumin (BSA) or AGE-BSA+ALT treatment. Proteomics of MIN6N8 cells showed enrichment of processes associated with catabolism, the immune system, cell cycling and presynaptic endocytosis with AGE-BSA compared with BSA treatments. These data show that short-term ALT intervention, given prediabetes, does not arrest experimental T1D but transiently impacts β-cell function.

Peptide vaccination remains a viable approach to induce T-cell mediated killing of tumors. To identify potential T-cell targets for Triple-Negative Breast Cancer (TNBC) vaccination, we examined the effect of the pro-inflammatory cytokine interferon-γ (IFNγ) on the transcriptome, proteome, and immunopeptidome of the TNBC cell line MDA-MB-231. Using high resolution mass spectrometry, we identified a total of 84,131 peptides from 9,647 source proteins presented by human leukocyte antigen (HLA)-I and HLA-II alleles. Treatment with IFNγ resulted in a remarkable remolding of the immunopeptidome, with only a 34% overlap between untreated and treated cells across the HLA-I immunopeptidome, and expression of HLA-II only detected on treated cells. IFNγ increased the overall number, diversity, and abundance of peptides contained within the immunopeptidome, as well increasing the coverage of individual source antigens. The suite of peptides displayed under conditions of IFNγ treatment included many known tumor associated antigens, with the HLA-II repertoire sampling 17 breast cancer associated antigens absent from those sampled by HLA-I molecules. Quantitative analysis of the transcriptome (10,248 transcripts) and proteome (6,783 proteins) of these cells revealed 229 common proteins and transcripts that were differentially expressed. Most of these represented downstream targets of IFNγ signaling including components of the antigen processing machinery such as tapasin and HLA molecules. However, these changes in protein expression did not explain the dramatic modulation of the immunopeptidome following IFNγ treatment. These results demonstrate the high degree of plasticity in the immunopeptidome of TNBC cells following cytokine stimulation and provide evidence that under pro-inflammatory conditions a greater variety of potential HLA-I and HLA-II vaccine targets are unveiled to the immune system. This has important implications for the development of personalized cancer vaccination strategies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Goncalves, Mullan, Duscharla, Ayala, Croft, Faridi and Purcell.)

Antigen recognition by CD8 + T cells is governed by the pool of peptide antigens presented on the cell surface in the context of HLA class I complexes. Studies have shown not only a high degree of plasticity in the immunopeptidome, but also that a considerable fraction of all presented peptides is generated through proteasome-mediated splicing of noncontiguous regions of proteins to form novel peptide antigens. Here, we used high-resolution mass spectrometry combined with new bioinformatic approaches to characterize the immunopeptidome of melanoma cells in the presence or absence of IFNγ. In total, we identified more than 60,000 peptides from a single patient-derived cell line (LM-MEL-44) and demonstrated that IFNγ induced changes in the peptidome, with an overlap of only approximately 50% between basal and treated cells. Around 6% to 8% of the peptides were identified as cis -spliced peptides, and 2,213 peptides (1,827 linear and 386 cis -spliced peptides) were derived from known melanoma-associated antigens. These peptide antigens were equally distributed between the constitutive- and IFNγ-induced peptidome. We next examined additional HLA-matched patient-derived cell lines to investigate how frequently these peptides were identified and found that a high proportion of both linear and spliced peptides was conserved between individual patient tumors, drawing on data amassing to more than 100,000 peptide sequences. Several of these peptides showed in vitro immunogenicity across multiple patients with melanoma. These observations highlight the breadth and complexity of the repertoire of immunogenic peptides that can be exploited therapeutically and suggest that spliced peptides are a major class of tumor antigens., (©2020 American Association for Cancer Research.)

Purpose: Computational models are widely used during the design and characterization of microwave ablation (MWA) devices, and have been proposed for pretreatment planning. Our objective was to assess three-dimensional (3D) transient temperature and ablation profiles predicted by MWA computational models with temperature profiles measured experimentally using magnetic resonance (MR) thermometry in ex vivo bovine liver., Materials and Methods: We performed MWA in ex vivo tissue under MR guidance using a custom, 2.45 GHz water-cooled applicator. MR thermometry data were acquired for 2 min prior to heating, during 5-10 min microwave exposures, and for 3 min following heating. Fiber-optic temperature sensors were used to validate the accuracy of MR temperature measurements. A total of 13 ablation experiments were conducted using 30-50 W applied power at the applicator input. MWA computational models were implemented using the finite element method, and incorporated temperature-dependent changes in tissue physical properties. Model-predicted ablation zone extents were compared against MRI-derived Arrhenius thermal damage maps using the Dice similarity coefficient (DSC)., Results: Prior to heating, the observed standard deviation of MR temperature data was in the range of 0.3-0.7°C. Mean absolute error between MR temperature measurements and fiber-optic temperature probes during heating was in the range of 0.5-2.8°C. The mean DSC between model-predicted ablation zones and MRI-derived Arrhenius thermal damage maps for 13 experimental set-ups was 0.95. When comparing simulated and experimentally (i.e. using MRI) measured temperatures, the mean absolute error (MAE %) relative to maximum temperature change was in the range 5%-8.5%., Conclusion: We developed a system for characterizing 3D transient temperature and ablation profiles with MR thermometry during MWA in ex vivo liver tissue, and applied the system for experimental validation of MWA computational models., (© 2020 American Association of Physicists in Medicine.)

Mild hyperthermia has been clinically employed as an adjuvant for radiation/chemotherapy and is under investigation for precise thermally-mediated delivery of cancer therapeutic agents. Magnetic Resonance Imaging (MRI) facilitates non-invasive, real-time spatial thermometry for monitoring and guiding hyperthermia procedures. Long image acquisition time during MR-guided hyperthermia may fail to capture rapid changes in temperature. This may lead to unwanted heating of healthy tissue and/or temperature rise above hyperthermic range. We have developed a block-based compressed sensing approach to reconstruct volumetric MR-derived microwave hyperthermia temperature profiles using a subset of measured data. This algorithm exploits the sparsity of MR images due to the presence of inter- and intra-slice correlation of hyperthermic MR-derived temperature profiles. We have evaluated the performance of our developed algorithm on a phantom and in vivo in mice using previously implemented microwave applicators. This algorithm reconstructs 3D temperature profiles with PSNR of 33 dB - 49 dB in comparison to the original profiles. In summary, this study suggests that microwave hyperthermia induced temperature profiles can be reconstructed using subsamples to reduce MR image acquisition time.

Purpose: To compare the size of the coagulation (CZ) and periablational (PZ) zones created with two commercially available devices in clinical use for radiofrequency (RFA) and microwave ablation (MWA), respectively., Methods: Computer models were used to simulate RFA with a 3-cm Cool-tip applicator and MWA with an Amica-Gen applicator. The Arrhenius model was used to compute the damage index ( Ω ). CZ was considered when Ω  > 4.6 (>99% of damaged cells). Regions with 0.6< Ω  < 2.1 were considered as the PZ (tissue that has undergone moderate sub-ablative hyperthermia). The ratio of PZ volume to CZ volume (PZ/CZ) was regarded as a measure of performance, since a low value implies achieving a large CZ while keeping the PZ small., Results: Ten-min RFA (51 W) created smaller periablational zones than 10-min MWA (11.3 cm 3 vs. 17.2-22.9 cm 3 , for 60-100 W MWA, respectively). Prolonging duration from 5 to 10 min increased the PZ in MWA more than in RFA (2.7 cm 3 for RFA vs. 8.3-11.9 cm 3 for 60-100 W MWA, respectively). PZ/CZ for RFA were relatively high (65-69%), regardless of ablation time, while those for MWA were highly dependent on the duration (increase of up to 25% between 5 and 10 min) and on the applied power (smaller values as power was raised, 102% for 60 W vs. 81% for 100 W, both for 10 min). The lowest PZ/CZ across all settings was 56%, obtained with 100 W-5 min MWA., Conclusions: Although RFA creates smaller periablational zones than MWA, 100 W-5 min MWA provides the lowest PZ/CZ.

Purpose: The objective of this study was to design and characterize a 2.45 GHz microwave hyperthermia applicator for delivering hyperthermia in experimental small animals to 2 - 4 mm diameter targets located 1 - 3 mm from the skin surface, with minimal heating of the surrounding tissue, under 14.1 T MRI real-time monitoring and feedback control., Materials and Methods: An experimentally validated 3D computational model was employed to design and characterize a non-invasive directional water-cooled microwave hyperthermia applicator. We assessed the effects of: reflector geometry, monopole shape, cooling water temperature, and flow rate on spatial-temperature profiles. The system was integrated with real-time MR thermometry and feedback control to monitor and maintain temperature elevations in the range of 4 - 5 °C at 1 - 3 mm from the applicator surface. The quality of heating was quantified by determining the fraction of the target volume heated to the desired temperature, and the extent of heating in non-targeted regions., Results: Model-predicted hyperthermic profiles were in good agreement with experimental measurements (Dice Similarity Coefficient of 0.95 - 0.99). Among the four considered criteria, a reflector aperture angle of 120 °, S-shaped monopole antenna with 0.6 mm displacement, and coolant flow rate of 150 ml/min were selected as the end result of the applicator design. The temperature of circulating water and input power were identified as free variables, allowing considerable flexibility in heating target sizes within varying distances from the applicator surface. 2 - 4 mm diameter targets positioned 1 - 3 mm from the applicator surface were heated to hyperthermic temperatures, with target coverage ratio ranging between 76 - 93 % and 11 - 26 % of non-targeted tissue heated., Conclusion: We have designed an experimental platform for MR-guided hyperthermia, incorporating a microwave applicator integrated with temperature-based feedback control to heat deep-seated targets for experimental studies in small animals.

The amyloid aggregation of peptides and proteins is a hallmark of neurological disorders and type 2 diabetes. Human islet amyloid polypeptide (IAPP), co-secreted with insulin by pancreatic β-cells, plays dual roles in both glycemic control and the pathology of type 2 diabetes. While IAPP can activate the NLRP3 inflammasome and modulate cellular autophagy, apoptosis and extracellular matrix metabolism, no data is available concerning intracellular protein expression upon exposure to the polypeptide. More surprisingly, how intracellular protein expression is modulated by nanoparticle inhibitors of protein aggregation remains entirely unknown. In this study, we first examined the changing proteomes of βTC6, a pancreatic β-cell line, upon exposure to monomeric, oligomeric and fibrillar IAPP, and detailed cellular protein expression rescued by graphene quantum dots (GQDs), an IAPP inhibitor. We found that 29 proteins were significantly dysregulated by the IAPP species, while majority of these proteins were nucleotide-binding proteins. Collectively, our liquid chromatography tandem-mass spectrometry, fluorescence quenching, helium ion microscopy, cytotoxicity and discreet molecular dynamics simulations data revealed a remarkable capacity of GQDs in regulating aberrant protein expression through H-bonding and hydrophobic interactions, pointing to nanomedicine as a new frontier against human amyloid diseases.

This is our response to the Technical Comment by Rolfs et al. where we point out errors in their reanalysis of our data., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet-rich nanofibrils is associated with the pathogeny of type 2 diabetes. Soluble hIAPP is intrinsically disordered with N-terminal residues 8-17 as α-helices. To understand the contribution of the N-terminal helix to the aggregation of full-length hIAPP, here the oligomerization dynamics of the hIAPP fragment 8-20 (hIAPP8-20) are investigated with combined computational and experimental approaches. hIAPP8-20 forms cross-β nanofibrils in silico from isolated helical monomers via the helical oligomers and α-helices to β-sheets transition, as confirmed by transmission electron microscopy, atomic force microscopy, circular dichroism spectroscopy, Fourier transform infrared spectroscopy, and reversed-phase high performance liquid chromatography. The computational results also suggest that the critical nucleus of aggregation corresponds to hexamers, consistent with a recent mass-spectroscopy study of hIAPP8-20 aggregation. hIAPP8-20 oligomers smaller than hexamers are helical and unstable, while the α-to-β transition starts from the hexamers. Converted β-sheet-rich oligomers first form β-barrel structures as intermediates before aggregating into cross-β nanofibrils. This study uncovers a complete picture of hIAPP8-20 peptide oligomerization, aggregation nucleation via conformational conversion, formation of β-barrel intermediates, and assembly of cross-β protofibrils, thereby shedding light on the aggregation of full-length hIAPP, a hallmark of pancreatic beta-cell degeneration., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

CD8 + T cells are essential effectors in antiviral immunity, recognizing short virus-derived peptides presented by MHC class I (pMHCI) on the surface of infected cells. However, the fraction of viral pMHCI on infected cells that are immunogenic has not been shown for any virus. To approach this fundamental question, we used peptide sequencing by high-resolution mass spectrometry to identify more than 170 vaccinia virus pMHCI presented on infected mouse cells. Next, we screened each peptide for immunogenicity in multiple virus-infected mice, revealing a wide range of immunogenicities. A surprisingly high fraction (>80%) of pMHCI were immunogenic in at least one infected mouse, and nearly 40% were immunogenic across more than half of the mice screened. The high number of peptides found to be immunogenic and the distribution of responses across mice give us insight into the specificity of antiviral CD8 + T cell responses., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

Although much has been learned about the fibrillization kinetics, structure and toxicity of amyloid proteins, the properties of amyloid fibrils beyond the saturation phase are often perceived as chemically and biologically inert, despite evidence suggesting otherwise. To fill this knowledge gap, we examined the physical and biological characteristics of human islet amyloid polypeptide (IAPP) fibrils that were aged up to two months. Not only did aging decrease the toxicity of IAPP fibrils, but the fibrils also sequestered fresh IAPP and suppressed their toxicity in an embryonic zebrafish model. The mechanical properties of IAPP fibrils in different aging stages were probed by atomic force microscopy and sonication, which displayed comparable stiffness but age-dependent fragmentation, followed by self-assembly of such fragments into the largest lamellar amyloid structures reported to date. The dynamic structural and toxicity profiles of amyloid fibrils and plaques suggest that they play active, long-term roles in cell degeneration and may be a therapeutic target for amyloid diseases.

Amyloid fibrils generally display chirality, a feature which has rarely been exploited in the development of therapeutics against amyloid diseases. This study reports, for the first time, the use of mesoscopic chiral silica nanoribbons against the in vivo amyloidogenesis of human islet amyloid polypeptide (IAPP), the peptide whose aggregation is implicated in type 2 diabetes. The thioflavin T assay and transmission electron microscopy show accelerated IAPP fibrillization through elimination of the nucleation phase and shortening of the elongation phase by the nanostructures. Coarse-grained simulations offer complementary molecular insights into the acceleration of amyloid aggregation through their nonspecific binding and directional seeding with the nanostructures. This accelerated IAPP fibrillization translates to reduced toxicity, especially for the right-handed silica nanoribbons, as revealed by cell viability, helium ion microscopy, as well as zebrafish embryo survival, developmental, and behavioral assays. This study has implicated the potential of employing chiral nanotechnologies against the mesoscopic enantioselectivity of amyloid proteins and their associated diseases., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The diversity of peptides displayed by class I human leukocyte antigen (HLA) plays an essential role in T cell immunity. The peptide repertoire is extended by various posttranslational modifications, including proteasomal splicing of peptide fragments from distinct regions of an antigen to form nongenomically templated cis-spliced sequences. Previously, it has been suggested that a fraction of the immunopeptidome constitutes such cis-spliced peptides; however, because of computational limitations, it has not been possible to assess whether trans-spliced peptides (i.e., the fusion of peptide segments from distinct antigens) are also bound and presented by HLA molecules, and if so, in what proportion. Here, we have developed and applied a bioinformatic workflow and demonstrated that trans-spliced peptides are presented by HLA-I, and their abundance challenges current models of proteasomal splicing that predict cis-splicing as the most probable outcome. These trans-spliced peptides display canonical HLA-binding sequence features and are as frequently identified as cis-spliced peptides found bound to a number of different HLA-A and HLA-B allotypes. Structural analysis reveals that the junction between spliced peptides is highly solvent exposed and likely to participate in T cell receptor interactions. These results highlight the unanticipated diversity of the immunopeptidome and have important implications for autoimmunity, vaccine design, and immunotherapy., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Introduction: Our immune system discriminates self from non-self by examining the peptide cargo of human leukocyte antigen (HLA) molecules displayed on the cell surface. Successful recognition of HLA-bound non-self peptides can induce T cell responses leading to, for example, the destruction of infected cells. Today, largely due to advances in technology, we have an unprecedented capability to identify the nature of these presented peptides and unravel the true complexity of antigen presentation. Areas covered: In addition to conventional linear peptides, HLA molecules also present post-translationally modified sequences comprising a wealth of chemical and structural modifications, including a novel class of noncontiguous spliced peptides. This review focuses on these emerging themes in antigen presentation and how mass spectrometry in particular has contributed to a new view of the antigenic landscape that is presented to the immune system. Expert Commentary: Advances in the sensitivity of mass spectrometers and use of hybrid fragmentation technologies will provide more information-rich spectra of HLA bound peptides leading to more definitive identification of T cell epitopes. Coupled with improvements in sample preparation and new informatics workflows, studies will access novel classes of peptide antigen and allow interrogation of rare and clinically relevant samples.

Thermal ablation of the endometrial lining of the uterus is a minimally-invasive technique for treatment of menorrhagia. We have previously presented a 915 MHz microwave triangular loop antenna for endometrial ablation. Uterine fibroids are benign pelvic tumors, of considerably different water content compared to normal uterus, and may change the shape of the uterus. Collectively, these changes introduced by fibroids may alter the pattern of microwave endometrial ablation. In this study, we have investigated the effect of 1 - 3 cm diameter uterine fibroids in different locations around the uterine cavity on ablation profiles following 60 W, 150 s microwave exposure with a loop antenna. Our computational model predicts ablation zone extents within 1 ± 0.8 of ablation zones observed in experiments in ex vivo tissue. The maximum change in simulated ablation depths due to the presence of fibroids was 1.1 mm. In summary, this simulation study suggests that 1 - 3 cm diameter uterine fibroids can be expected to have minimal impact on the extent of microwave endometrial ablation patterns.

Purpose: Integrating small-animal experimental hyperthermia instrumentation with magnetic resonance imaging (MRI) affords real-time monitoring of spatial temperature profiles. This study reports on the development and preliminary in vivo characterisation of a 2.45 GHz microwave hyperthermia system for pre-clinical small animal investigations, integrated within a 14 T ultra-high-field MRI scanner., Materials and Methods: The presented system incorporates a 3.5 mm (OD) directional microwave hyperthermia antenna, positioned adjacent to the small-animal target, radiating microwave energy for localised heating of subcutaneous tumours. The applicator is integrated within the 30 mm bore of the MRI system. 3D electromagnetic and biothermal simulations were implemented to characterise hyperthermia profiles from the directional microwave antenna. Experiments in tissue mimicking phantoms were performed to assess hyperthermia profiles and validate MR thermometry against fibre-optic temperature measurements. The feasibility of delivering in vivo hyperthermia exposures to subcutaneous 4T1 tumours in experimental mice under simultaneous MR thermometry guidance was assessed., Results: Simulations and experiments in tissue mimicking phantoms demonstrated the feasibility of heating 21-982 mm 3 targets with 8-12 W input power. Minimal susceptibility and electrical artefacts introduced by the hyperthermia applicator were observed on MR imaging. MR thermometry was in excellent agreement with fibre-optic temperatures measurements (max. discrepancy ≤0.6 °C). Heating experiments with the reported system demonstrated the feasibility of heating subcutaneous tumours in vivo with simultaneous MR thermometry., Conclusions: A platform for small-animal hyperthermia investigations under ultra-high-field MR thermometry was developed and applied to heating subcutaneous tumours in vivo.

Immunopeptidomics employs the use of mass spectrometry to identify and quantify peptides presented on the surface of cells by major histocompatibility complex (MHC; human leukocyte antigen [HLA], in humans) molecules, an essential component of adaptive immunity. Currently, immunopeptidomics follows the same or similar workflows as the more established field of shotgun proteomics, yet inherent differences between these two fields create significant drawbacks for the former. In this viewpoint, we would like to highlight such technical issues and provide suggestions for novel workflows that would increase peptide sequencing coverage, depth, and confidence, collectively enhancing the capabilities of the field of immunopeptidomics., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Herbal oils have been widely used in Iran as medicinal compounds dating back to thousands of years in Iran. Chamomile oil is widely used as an example of traditional oil. We remade chamomile oils and tried to modify it with current knowledge and facilities. Six types of oil (traditional and modified) were prepared. Microbial limit tests and physicochemical tests were performed on them. Also, principal component analysis, hierarchical cluster analysis, and partial least squares discriminant analysis were done on the spectral data of attenuated total reflectance-infrared in order to obtain insight based on classification pattern of the samples. The results show that we can use modified versions of the chamomile oils (modified Clevenger-type apparatus method and microwave method) with the same content of traditional ones and with less microbial contaminations and better physicochemical properties.

Objective: Some of the adverse effects of aspirin including peptic ulcers, gastrointestinal bleeding and aspirin resistance compelled researchers to find a suitable alternative with fewer adverse effects. In this clinical trial, we aimed to find the effective antiplatelet dose of garlic., Materials and Methods: This randomized controlled clinical trial (RCT) was conducted on 62 healthy volunteers of 20-50 years old. All volunteers used 80 mg aspirin per day for 1 week and at the end of this time, platelet aggregation (PA) induced by 4 agonists acting in aggregation pathway including adenosinediphosphate (20 μmol/l), epinephrine (20 μmol/l), collagen(0.19 mg/ ml) and arachidonic acid (0.5mg/ ml) was measured by Light Transmittance Aggregometry (LTA) in all participants. After one month washout period, volunteers were randomized into 3 groups and each received 1, 2 or 3 garlic tablets (1250 mg) a day for 1 month. After one month, PA was examined in all groups., Results: The mean ±SD of the age of all volunteers was 28.60 ± 9.00 years. In addition, 52.00 % of our volunteers were male and 48.00% of them were female. Garlic tablet didnot have significant effect on PA at any dose. However, 30% of volunteers in the group that used 3 garlic tablets/day reported adverse effect (i.e. bleeding). No significant association between sex, age and PA was observed., Conclusion: In this study, we were unable to determine the effective anti-platelet dose of garlic which that could be equal to that of aspirin anti-platelet activity, as assessed LTA method.

Dissatisfaction from sexual relationships can result in deprivation as well as problems, such as depression, anxiety, and destruction of family's mental health. One hundred twenty-five women (18 to 40 years) who suffered from hypoactive sexual desire disorder were divided into Elaeagnus angustifolia flower (4.5 g g daily for 35 days), sildenafil citrate tablet (50 mg for 4 weeks), and control groups. The study data were collected using the Female Sexual Function Index and Spielberger's questionnaire and measurement of thyroid-stimulating hormone and prolactin hormone. In the Elaeagnus angustifolia group, the mean score of state and trait anxiety decreased after the intervention. In the sildenafil citrate group also, the mean score of state anxiety decreased from 22.15 ± 4.98 to 20.1 ± 5.15 (P = .001) and that of trait anxiety decreased from 23.07 ± 4.44 to 21.55 ± 4.82 (P = .002) after the intervention. Consumption of sildenafil citrate tablet was effective in reduction of the mean score of anxiety resulting from sexual dysfunction., (© The Author(s) 2015.)

We present the first standardized HLA peptidomics dataset generated by the immunopeptidomics community. The dataset is composed of native HLA class I peptides as well as synthetic HLA class II peptides that were acquired in data-dependent acquisition mode using multiple types of mass spectrometers. All laboratories used the spiked-in landmark iRT peptides for retention time normalization and data analysis. The mass spectrometric data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001872. The generated data were used to build HLA allele-specific peptide spectral and assay libraries, which were stored in the SWATHAtlas database. Data presented here are described in more detail in the original eLife article entitled 'An open-source computational and data resource to analyze digital maps of immunopeptidomes'.

Effective tissue hemostasis in periapical surgical site is important in the procedures. Plants with large amount of tannins may act as a local hemostatic agent. We aimed to compare the hemostatic effect of the extract of Quercus persica with one of the common hemostatic material used in periapical surgery. Six standardized bone holes were prepared in the calvaria of 5 Burgundy rabbits. Two hemostatic medicaments were tested for their hemostatic effect and were compared with control defects: Group 1, cotton pellet soaked in 15.5% ferric sulfate solution; Group 2, cotton pellet soaked in pure ethanolic extract of Q. persica. Bleeding score between the groups was compared. The ferric sulfate group exhibited significantly less bleeding than the other 2 groups. Q. persica was found to cause more hemostasis than the control group at 4 and 5 minutes but there were no significant differences between normal saline and Q. persica extract in bleeding control., (© The Author(s) 2015.)

Persian or Russian olive (Elaeagnus angustifolia L.), from the family Elaeagnaceae, is a nitrogen-fixing thorny shrub extensively used in traditional medicine to alleviate pain and treat rheumatoid arthritis, osteoarthritis, gastrointestinal problems, fever, and asthma. The current review has tried to give a concise overview of the phytochemistry and pharmacological properties of the plant from published data. Accordingly, published English literatures on Elaeagnus angustifolia were gathered from popular databases such as PubMed, Scopus, Web of Science, and ScienceDirect up to 31 December 2015. In accordance with traditional and ethnopharmacological uses, different extracts of E. angustifolia have been known for their antioxidant, anti-inflammatory, anti-nociceptive, antimicrobial, muscle relaxant, anti-ulcer and wound-healing capabilities. Additionally, cardioprotective, antitumor and anti-mutagenic effects of the herb have been demonstrated by current assessments. Despite numerous experimental studies, there is a notable lack of profound and comprehensive clinical trials as well as critical research on E. angustifolia toxicity and teratogenicity. With reference to various pharmacological effects based on experimental and animal investigation, it is worthy to mention a frame for respective clinical studies in further studies.

Ethnopharmacological Relevance: This study provides ethnopharmacological knowledge of traditional herbal healers from Shiraz and Fasa in Fars region (Iran) for treatment of diabetes mellitus., Materials and Methods: Field surveys were carried out during September 2013-February 2014 in Shiraz and Fasa. The data were collected through structured questionnaire in Persian. All plant species recorded for the treatment of diabetes mellitus were sampled. Samples were identified by a botanist and obtained a voucher specimens number and deposited in the Shiraz School of Pharmacy Herbarium. The information such as scientific name, family, local name, medicinal use(s), parts used and preparation method were provided. Literature review on available data about antidiabetic effect of the addressed plant species was done to highlight gaps in current knowledge and propose the next steps., Results: In total, 50 informants were interviewed. Totally 39 plant species were recommended by herbal healers, of which 28 are native to Iran. The most recommended plants for diabetes were Trigonella foenum-graecam (28 Attars), Securigera securidaca (22 Attars), Vaccinium arctostaphylos (18 Attars). The most abundant families were Fabaceae, Asteraceae, Lamiaceae and Apiaceae. Plant parts used were mainly seeds, flowers, leaves and fruits. The most usual preparation methods were decoction, powder and distillation. Around 44% of all reported plants for diabetes are also in use for obesity management, Conclusions: This study provided ethnopharmacological knowledge from Fars region in Iran for a specific disease and we have introduced important plant species which are recommended by local herbal healers for diabetes mellitus. For 23% of reported plants, clinical studies approved antidiabetic properties and for 61%, animal studies approved antidiabetic activity., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)

Ethnopharmacological Relevance: Kidney stones are one of the most common disorders of the urinary tract and cause a great deal of morbidity and economic loss. Because of the side effects and costs of current interventional procedures, researchers are interested in finding medicinal therapies. In this regard, some reports have focused on traditional medicines as a drug discovery resource. Iranian scholars in the medieval era recommended Lapis judaicus for the prevention and treatment of kidney stones. The present study assessed the efficacy and safety of Lapis judaicus on the size of calcium kidney stones and some related biochemical factors in blood and urine., Materials and Methods: Sixty patients with kidney stone disease were included in this double-blind randomized clinical study. Thirty patients received 2g of Lapis judaicus powder in hard capsules per day for 10 weeks, and another 30 patients received a placebo for the same period. Ultrasonography was performed on patients, and blood and urine samples were collected before and after the study to evaluate the efficacy and safety of Lapis judaicus in calcium kidney stone patients., Results: The size of the kidney stones was reduced significantly (p<0.001) in the drug group. In 9 patients from the drug group, the stone was completely dissolved. Moreover, urine calcium concentration and specific gravity were reduced and urine magnesium was increased (p<0.05). Lapis judaicus did not affect BUN, creatinine, ALT, or AST., Conclusion: Contrary to the placebo group, the size of kidney stones was reduced significantly in the treatment group after oral administration of Lapis judaicus. This preliminary study confirms traditional knowledge of the efficacy and safety of Lapis judaicus in kidney stone diseases and suggests a new method to treat calcium kidney stones. Further detailed in vitro and in vivo studies aimed at discovering the mechanism of action of Lapis judaicus and clinical studies involving a larger population of patients will be necessary to fully explain and confirm the results obtained in the present study., (Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.)

Background: Orgasmic disorder can create a feeling of deprivation and failure and provide mental problems, incompatibility and marital discord. This study aimed to compare the effects of Elaeagnus angustifolia flower extract and sildenafil citrate on female orgasmic disorder in women in 2013., Methods: In this randomized clinical trial, 125 women between 18-40 years old who suffered from orgasmic disorder were divided into three E. angustifolia, sildenafil citrate and control groups. The data were gathered using Female Sexual Function Index and through measurement of TSH and prolactin. The first intervention group had to consume 4.5 gr E. angustifolia extract in two divided doses for 35 days and the second one had to use 50 mg sildenafil citrate tablets for 4 weeks one hour before their sexual relationship. However, the control group had to consume the placebo. The data were analyzed using paired t-test, one-way ANOVA, and Bonferroni posthoc test and p<0.05 was considered significant., Results: The frequency of orgasmic disorder before the intervention was 41.5%, 40.5%, and 57.1% in E. angustifolia, sildenafil citrate, and control groups, respectively (p=0.23). However, these measures were respectively 29.3%, 16.7%, and 50% after the intervention (p=0.004). A significant difference between the two groups regarding sexual satisfaction after the intervention (p=0.003) compared to the beginning of the study (p=0.356). Besides, the highest reduction of changes after the intervention (58.82%) was observed in the sildenafil citrate group., Conclusion: Both E. angustifolia extract and sildenafil citrate were effective in reduction of the frequency of orgasmic disorder in women.

Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).

The manner by which genotype and environment affect complex phenotypes is one of the fundamental questions in biology. In this study, we quantified the transcriptome--a subset of the metabolome--and, using targeted proteomics, quantified a subset of the liver proteome from 40 strains of the BXD mouse genetic reference population on two diverse diets. We discovered dozens of transcript, protein, and metabolite QTLs, several of which linked to metabolic phenotypes. Most prominently, Dhtkd1 was identified as a primary regulator of 2-aminoadipate, explaining variance in fasted glucose and diabetes status in both mice and humans. These integrated molecular profiles also allowed further characterization of complex pathways, particularly the mitochondrial unfolded protein response (UPR(mt)). UPR(mt) shows strikingly variant responses at the transcript and protein level that are remarkably conserved among C. elegans, mice, and humans. Overall, these examples demonstrate the value of an integrated multilayered omics approach to characterize complex metabolic phenotypes., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Sphygmology is a 2000-year-old method that is still used in some traditional medicine systems, mainly Iranian, Chinese and Ayurveda. Ibn Sina is one of the most popular physicians in the history of Sphygmology, who had made great contributions to this method, but few meticulous studies have been made on his concepts. In this article, his standpoints on Pulsology are studied. Ibn Sina has mentioned 10 parameters for pulse palpation, and 13 compound pulses, as well. Besides, some pulse patterns applicable for differentiating similar diseases have been introduced. Nowadays some concepts on pulse patterns, such as pulse change in sleep and pregnancy have been studied; but unfortunately many of the ideas on Pulsology have not yet been examined. Sphygmology, as an accessible and inexpensive means, having a substantial diagnosis yield, has been accepted by the people since its rise, and its development over centuries ago. Although some new instruments have been innovated, which can measure different parameters of pulse, yet sphygmology can be one of the most commonly usable diagnostic methods in future, not only applicable by cardiologists but also by all the physicians.

Ibn-Sina (commonly known as Avicenna) is one of the most famous and influential scientists in the history of medicine. The Canon of Medicine, which is his most celebrated book in medicine, presents a summary of all the medical knowledge of his time. Ibn-Sina wrote a complete section about kidney calculi in his book. Totally, 65 herbal, 8 animal, and 4 mineral medicines are mentioned in the Canon of Medicine as beneficial drugs for dissolving, expelling, and preventing kidney calculi. Ibn-Sina introduced very advanced drug designing based on drug delivery, targeting the organ, deposition in the site of action, pain control, wound healing, clearance after action, and supporting the organ. Using Ibn-Sina's ideas help scientists to choose better drugs with a historical background to reduce the cost of therapies and research projects.

Pistacia terebinthus L. smoke has been used traditionally in Iran as disinfectant and air purifier. Smoke was collected by a simple method, and the chemical constituents and antimicrobial activity of the smoke were analyzed. The chemical constituents of the smoke were alpha-pinene (65.1%), limonene (11.5%) and allo-ocimene (2.8%). The non polar phase of smoke noticeably inhibited the growth of different microorganisms. MIC test shows that non polar fraction of smoke can inhibit the growth of some bacteria. The results indicating that the properties of the smoke as a flavoring and preservative agent could be a potential subject for future studies., (Copyright (c) 2010 Elsevier B.V. All rights reserved.)

All through time, humans have used smoke of medicinal plants to cure illness. To the best of our knowledge, the ethnopharmacological aspects of natural products' smoke for therapy and health care have not been studied. Mono- and multi-ingredient herbal and non-herbal remedies administered as smoke from 50 countries across the 5 continents are reviewed. Most of the 265 plant species of mono-ingredient remedies studied belong to Asteraceae (10.6%), followed by Solanaceae (10.2%), Fabaceae (9.8%) and Apiaceae (5.3%). The most frequent medical indications for medicinal smoke are pulmonary (23.5%), neurological (21.8%) and dermatological (8.1%). Other uses of smoke are not exactly medical but beneficial to health, and include smoke as a preservative or a repellent and the social use of smoke. The three main methods for administering smoke are inhalation, which accounts for 71.5% of the indications; smoke directed at a specific organ or body part, which accounts for 24.5%; ambient smoke (passive smoking), which makes up the remaining 4.0%. Whereas inhalation is typically used in the treatment of pulmonary and neurological disorders and directed smoke in localized situations, such as dermatological and genito-urinary disorders, ambient smoke is not directed at the body at all but used as an air purifier. The advantages of smoke-based remedies are rapid delivery to the brain, more efficient absorption by the body and lower costs of production. This review highlights the fact that not enough is known about medicinal smoke and that a lot of natural products have potential for use as medicine in the smoke form. Furthermore, this review argues in favor of medicinal smoke extended use in modern medicine as a form of drug delivery and as a promising source of new active natural ingredients.