Publications by authors named "Andrew R Jones"

111 Publications

A snapshot of human leukocyte antigen (HLA) diversity using data from the Allele Frequency Net Database.

Hum Immunol 2021 Jul 21;82(7):496-504. Epub 2020 Oct 21.

Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.

The extensive allelic variability observed in several genes related to the immune response and its significance in different areas including transplantation, disease association studies, diversity in human populations, among many others, has led the scientific community to analyse these variants among individuals. Serving as an electronic data warehouse, the Allele Frequency Net Database (AFND, http://www.allelefrequencies.net) contains data on the frequency of immune related genes and their corresponding alleles from more than 1700 worldwide population samples covering more than ten million unrelated individuals. The collection of population data sets available in AFND encompasses different polymorphic regions including the highly-polymorphic human leukocyte antigen (HLA) system for which more than 1200 populations are available. In this article, we provide an insight of the high diversity found in the HLA region by examining population data sets stored in AFND, as well as a description of the available data sets for further analyses.
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http://dx.doi.org/10.1016/j.humimm.2020.10.004DOI Listing
July 2021

Soil organic carbon is significantly associated with the pore geometry, microbial diversity and enzyme activity of the macro-aggregates under different land uses.

Sci Total Environ 2021 Jul 8;778:146286. Epub 2021 Mar 8.

School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia.

Microbial activity strongly influences the stabilization of soil organic matter (SOM), and is affected by the abiotic properties within soil aggregates, which tend to differ between land uses. Here, we assessed the effects of SOM and pore geometry on the diversity and activity of microbial communities within aggregates formed under different land uses (undisturbed, plantation, pasture, and cropping). X-ray micro-computed tomography (μCT) revealed that macro-aggregates (2-8 mm) of undisturbed soils were porous, highly-connected, and had 200% more macro-pores compared with those from pasture and cropping soils. While the macro-aggregates of undisturbed soils had greater soil organic carbon (SOC) contents and N-acetyl β-glucosaminidase, β-glucosidase, and phosphatase activities, those of cropped soils harboured more diverse bacterial communities. Organic carbon was positively associated with the porosity of the macro-aggregates, which was negatively associated with microbial diversity and positively associated with enzyme activity. Thus, the biophysical processes in macro-aggregates may be important for SOC stabilization within the macro-aggregates.
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http://dx.doi.org/10.1016/j.scitotenv.2021.146286DOI Listing
July 2021

A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach.

Front Immunol 2021 26;12:598778. Epub 2021 Feb 26.

School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia.

Emerging infectious diseases (EIDs) caused by viruses are increasing in frequency, causing a high disease burden and mortality world-wide. The COVID-19 pandemic caused by the novel SARS-like coronavirus (SARS-CoV-2) underscores the need to innovate and accelerate the development of effective vaccination strategies against EIDs. Human leukocyte antigen (HLA) molecules play a central role in the immune system by determining the peptide repertoire displayed to the T-cell compartment. Genetic polymorphisms of the HLA system thus confer a strong variability in vaccine-induced immune responses and may complicate the selection of vaccine candidates, because the distribution and frequencies of HLA alleles are highly variable among different ethnic groups. Herein, we build on the emerging paradigm of rational epitope-based vaccine design, by describing an immunoinformatics tool (Predivac-3.0) for proteome-wide T-cell epitope discovery that accounts for ethnic-level variations in immune responsiveness. Predivac-3.0 implements both CD8+ and CD4+ T-cell epitope predictions based on HLA allele frequencies retrieved from the Allele Frequency Net Database. The tool was thoroughly assessed, proving comparable performances (AUC ~0.9) against four state-of-the-art pan-specific immunoinformatics methods capable of population-level analysis (NetMHCPan-4.0, Pickpocket, PSSMHCPan and SMM), as well as a strong accuracy on proteome-wide T-cell epitope predictions for HIV-specific immune responses in the Japanese population. The utility of the method was investigated for the COVID-19 pandemic, by performing T-cell epitope mapping of the SARS-CoV-2 spike glycoprotein according to the ethnic context of the countries where the ChAdOx1 vaccine is currently initiating phase III clinical trials. Potentially immunodominant CD8+ and CD4+ T-cell epitopes and population coverages were predicted for each population (the Epitope Discovery mode), along with optimized sets of broadly recognized (promiscuous) T-cell epitopes maximizing coverage in the target populations (the Epitope Optimization mode). Population-specific epitope-rich regions (T-cell epitope clusters) were further predicted in protein antigens based on combined criteria of epitope density and population coverage. Overall, we conclude that Predivac-3.0 holds potential to contribute in the understanding of ethnic-level variations of vaccine-induced immune responsiveness and to guide the development of epitope-based next-generation vaccines against emerging pathogens, whose geographic distributions and populations in need of vaccinations are often well-defined for regional epidemics.
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http://dx.doi.org/10.3389/fimmu.2021.598778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7952308PMC
March 2021

lcmsWorld: High-Performance 3D Visualization Software for Mass Spectrometry.

J Proteome Res 2021 04 12;20(4):1981-1985. Epub 2021 Mar 12.

Computational Biology Facility, University of Liverpool, Liverpool L69 7ZB, United Kingdom.

Complex biological samples, in particular, in proteomics and metabolomics research, are often analyzed using mass spectrometry paired with liquid chromatography or gas chromatography. The chromatography stage adds a third dimension (retention time) to the usual 2D mass spectrometry output (mass/charge, detected ion counts). Experimental results are often discovered by complex computational analysis, but it is not always possible to know if the data has been correctly interpreted. To perform quality-control checks, it can often be helpful to verify the results by manually examining the raw data, and it is typically easier to understand the data in a graphical, rather than numerical, form. 3D graphics hardware is present in most modern computers but is rarely utilized by bioinformatics software, even when the data to be viewed are naturally 3D. lcmsWorld is new software that uses graphics hardware to quickly and smoothly examine and compare LC-MS data. A preprocessing step allows the software to subsequently access any area of the data instantly at multiple levels of detail. The data can then be freely navigated while the software automatically selects, loads, and displays the most appropriate detail. lcmsWorld is open source. Releases, source code, and example data files are available via https://github.com/PGB-LIV/lcmsWorld.
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http://dx.doi.org/10.1021/acs.jproteome.0c00618DOI Listing
April 2021

An OMICs based meta-analysis to support infection state stratification.

Bioinformatics 2021 Feb 9. Epub 2021 Feb 9.

Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom.

Motivation: A fundamental problem for disease treatment is that while antibiotics are a powerful counter to bacteria, they are ineffective against viruses. Often, bacterial and viral infections are confused due to their similar symptoms and lack of rapid diagnostics. With many clinicians relying primarily on symptoms for diagnosis, overuse and misuse of modern antibiotics are rife, contributing to the growing pool of antibiotic resistance. To ensure an individual receives optimal treatment given their disease state and to reduce over-prescription of antibiotics, the host response can in theory be measured quickly to distinguish between the two states. To establish a predictive biomarker panel of disease state (viral/bacterial/no-infection) we conducted a meta-analysis of human blood infection studies using Machine Learning (ML).

Results: We focused on publicly available gene expression data from two widely used platforms, Affymetrix and Illumina microarrays as they represented a significant proportion of the available data. We were able to develop multi-class models with high accuracies with our best model predicting 93% of bacterial and 89% viral samples correctly. To compare the selected features in each of the different technologies, we reverse engineered the underlying molecular regulatory network and explored the neighbourhood of the selected features. The networks highlighted that although on the gene-level the models differed, they contained genes from the same areas of the network. Specifically, this convergence was to pathways including the Type I interferon Signalling Pathway, Chemotaxis, Apoptotic Processes, and Inflammatory/Innate Response.

Availability: Data and code are available on the Gene Expression Omnibus and github.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btab089DOI Listing
February 2021

Temporal modulation of the NF-κB RelA network in response to different types of DNA damage.

Biochem J 2021 02;478(3):533-551

Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.

Different types of DNA damage can initiate phosphorylation-mediated signalling cascades that result in stimulus specific pro- or anti-apoptotic cellular responses. Amongst its many roles, the NF-κB transcription factor RelA is central to these DNA damage response pathways. However, we still lack understanding of the co-ordinated signalling mechanisms that permit different DNA damaging agents to induce distinct cellular outcomes through RelA. Here, we use label-free quantitative phosphoproteomics to examine the temporal effects of exposure of U2OS cells to either etoposide (ETO) or hydroxyurea (HU) by monitoring the phosphorylation status of RelA and its protein binding partners. Although few stimulus-specific differences were identified in the constituents of phosphorylated RelA interactome after exposure to these DNA damaging agents, we observed subtle, but significant, changes in their phosphorylation states, as a function of both type and duration of treatment. The DNA double strand break (DSB)-inducing ETO invoked more rapid, sustained responses than HU, with regulated targets primarily involved in transcription, cell division and canonical DSB repair. Kinase substrate prediction of ETO-regulated phosphosites suggest abrogation of CDK and ERK1 signalling, in addition to the known induction of ATM/ATR. In contrast, HU-induced replicative stress mediated temporally dynamic regulation, with phosphorylated RelA binding partners having roles in rRNA/mRNA processing and translational initiation, many of which contained a 14-3-3ε binding motif, and were putative substrates of the dual specificity kinase CLK1. Our data thus point to differential regulation of key cellular processes and the involvement of distinct signalling pathways in modulating DNA damage-specific functions of RelA.
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http://dx.doi.org/10.1042/BCJ20200627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7886319PMC
February 2021

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.

Structure 2020 11 15;28(11):1259-1268. Epub 2020 Oct 15.

University of Konstanz, Department of Biology, Universitätsstrasse 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.

Cross-linking mass spectrometry (MS) has substantially matured as a method over the past 2 decades through parallel development in multiple labs, demonstrating its applicability to protein structure determination, conformation analysis, and mapping protein interactions in complex mixtures. Cross-linking MS has become a much-appreciated and routinely applied tool, especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Cross-linking MS for which guidelines should be developed as part of a Cross-linking MS standards initiative.
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http://dx.doi.org/10.1016/j.str.2020.09.011DOI Listing
November 2020

Comparing racing performance following arthroscopic surgery of metacarpophalangeal/metatarsophalangeal and carpal joints in Thoroughbred racehorses rehabilitated using conventional and underwater treadmill therapies.

Vet Rec 2020 Oct 23;187(9):355. Epub 2020 Sep 23.

Gail Holmes Equine Orthopedic Research Center, Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA.

Background: Rehabilitation of horses using underwater treadmill therapy has been shown to improve joint range of motion, joint mobility, stride length and proprioceptive parameters with experimental studies. However, studies investigating the prognosis and return to function following rehabilitation are lacking.

Methods: A retrospective study of Thoroughbred racehorses treated with arthroscopic surgery for osteochondral fragments of the metacarpophalangeal (MCP) or metatarsophalangeal (MTP) joints or carpal joints undergoing conventional rehabilitation or underwater treadmill assisted rehabilitation at the same facility were included. The objective of the current study was to investigate if underwater treadmill assisted rehabilitation following arthroscopy in the Thoroughbred racehorse was positively associated with returning to racing, time to return to racing and postoperative racing performance including Beyer Speed Figures.

Results: Surgery was performed on 165 horses on 174 surgical occasions; 70 (40.2 per cent) underwent underwater treadmill rehabilitation, with the remainder undergoing conventional rehabilitation. The time to return to racing was a median of 227 (IQR 185-281) days and 239 (IQR 205-303) days for underwater treadmill and conventional rehabilitation, respectively (P=0.16). Of the horses that raced presurgery, 83 per cent (58/70) of underwater treadmill rehabilitated horses and 61 per cent (63/104) of horses undergoing conventional rehabilitation returned to racing following surgery (P=0.02).

Conclusion: Underwater treadmill rehabilitation is superior in returning a Thoroughbred racehorse to racing following arthroscopic surgery of the carpus and/or MCP/MTP joints.
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http://dx.doi.org/10.1136/vr.105745DOI Listing
October 2020

mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements.

J Proteome Res 2021 01 29;20(1):172-183. Epub 2020 Oct 29.

Department of Population Health Sciences and Bristol Veterinary School, University of Bristol, Bristol BS8 2BN, United Kingdom.

With ever-increasing amounts of data produced by mass spectrometry (MS) proteomics and metabolomics, and the sheer volume of samples now analyzed, the need for a common open format possessing both file size efficiency and faster read/write speeds has become paramount to drive the next generation of data analysis pipelines. The Proteomics Standards Initiative (PSI) has established a clear and precise extensible markup language (XML) representation for data interchange, mzML, receiving substantial uptake; nevertheless, storage and file access efficiency has not been the main focus. We propose an HDF5 file format "mzMLb" that is optimized for both read/write speed and storage of the raw mass spectrometry data. We provide an extensive validation of the write speed, random read speed, and storage size, demonstrating a flexible format that with or without compression is faster than all existing approaches in virtually all cases, while with compression is comparable in size to proprietary vendor file formats. Since our approach uniquely preserves the XML encoding of the metadata, the format implicitly supports future versions of mzML and is straightforward to implement: mzMLb's design adheres to both HDF5 and NetCDF4 standard implementations, which allows it to be easily utilized by third parties due to their widespread programming language support. A reference implementation within the established ProteoWizard toolkit is provided.
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http://dx.doi.org/10.1021/acs.jproteome.0c00192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7871438PMC
January 2021

The Use of Pneumatic Impact Lithotripsy in a Laparoscopic Retrieval Pouch for Removal of Large Cystoliths in Two Female Horses.

J Equine Vet Sci 2020 08 21;91:103125. Epub 2020 May 21.

Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA; San Luis Rey Equine Hospital, Bonsall, CA.

Two mares, aged 15 and 21 years, were examined because of urinary incontinence, intermittent hematuria, and urine scalding. On admission of both horses, physical parameters were within normal limits and urine scalding of the skin at the ventral perineum was noted. Transrectal palpation and cystoscopy revealed a large type I cystolith (>10 cm) with associated hyperemia and focal ulceration of the bladder mucosa. In horse 1, hemogram, serum biochemical analysis, and renal ultrasound were not performed because of owner finances. In horse 2, results from hematological and serum biochemical analysis were unremarkable and renal ultrasonography did not reveal any abnormalities. Pneumatic impact lithotripsy in a laparoscopic retrieval pouch was performed under cystoscopic guidance after caudal epidural anesthesia, with the horses standing and under sedation. A laparoscopic retrieval device was passed alongside a flexible endoscope into the urinary bladder and the cystolith was manipulated into the pouch. A customized single stainless-steel rod scaler attached to an air compressor was used for fragmentation of the cystolith contained within the retrieval pouch. Lithotripsy time was 42 minutes for horse 1 and 31 minutes for horse 2. Both horses were released from hospital the day of surgery. Both horses were continent and voided normal streams of urine for the duration of the follow-up periods of 27 and 19 months for horse 1 and horse 2, respectively. Pneumatic impact lithotripsy in a laparoscopic retrieval pouch provided a time-efficient and minimally invasive surgical treatment option for removal of large cystoliths in mares.
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http://dx.doi.org/10.1016/j.jevs.2020.103125DOI Listing
August 2020

Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics.

Biochem J 2020 07;477(13):2451-2475

Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.

Polo-like kinase 4 (PLK4) is the master regulator of centriole duplication in metazoan organisms. Catalytic activity and protein turnover of PLK4 are tightly coupled in human cells, since changes in PLK4 concentration and catalysis have profound effects on centriole duplication and supernumerary centrosomes, which are associated with aneuploidy and cancer. Recently, PLK4 has been targeted with a variety of small molecule kinase inhibitors exemplified by centrinone, which rapidly induces inhibitory effects on PLK4 and leads to on-target centrosome depletion. Despite this, relatively few PLK4 substrates have been identified unequivocally in human cells, and PLK4 signalling outside centriolar networks remains poorly characterised. We report an unbiased mass spectrometry (MS)-based quantitative analysis of cellular protein phosphorylation in stable PLK4-expressing U2OS human cells exposed to centrinone. PLK4 phosphorylation was itself sensitive to brief exposure to the compound, resulting in PLK4 stabilisation. Analysing asynchronous cell populations, we report hundreds of centrinone-regulated cellular phosphoproteins, including centrosomal and cell cycle proteins and a variety of likely 'non-canonical' substrates. Surprisingly, sequence interrogation of ∼300 significantly down-regulated phosphoproteins reveals an extensive network of centrinone-sensitive [Ser/Thr]Pro phosphorylation sequence motifs, which based on our analysis might be either direct or indirect targets of PLK4. In addition, we confirm that NMYC and PTPN12 are PLK4 substrates, both in vitro and in human cells. Our findings suggest that PLK4 catalytic output directly controls the phosphorylation of a diverse set of cellular proteins, including Pro-directed targets that are likely to be important in PLK4-mediated cell signalling.
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http://dx.doi.org/10.1042/BCJ20200309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338032PMC
July 2020

A survey of work-related musculoskeletal disorders associated with performing laparoscopic veterinary surgery.

Authors:
Andrew R E Jones

Vet Surg 2020 Jun 23;49 Suppl 1:O15-O20. Epub 2020 Feb 23.

San Luis Rey Equine Hospital, Bonsall, California.

Objective: To assess the prevalence of work-related musculoskeletal disorders (WRMD) associated with laparoscopy in veterinary surgery.

Study Design: Cross-sectional survey.

Sample Population: Veterinary surgeons who perform laparoscopy.

Methods: Responses were collected with data regarding laparoscopic activities and experience as well as whether the respondents experienced pain as a result of laparoscopy and, if so, additional information on this topic. Variables associated with the risk of experiencing pain were determined by using χ tests and odds ratios (OR).

Results: There were 149 respondents, an estimated 6% response proportion. Forty percent experienced pain that they attributed to the use of laparoscopic instruments during or after laparoscopic surgery. Surgeons who perform laparoscopic surgery frequently (at least monthly) were more likely to experience pain as a result of laparoscopic surgery compared with those who perform laparoscopic surgery infrequently (OR 2.25; 95% confidence interval 1.07-4.75; P = .033). Pain during or after laparoscopic surgery was most often experienced in the neck (81%), back (77%), and shoulders (75%), with 90% of respondents reporting that surgery exacerbated their pain. Fifty-four percent of respondents experienced the pain at home, 64% had taken painkillers for the pain, and 46% had sought other treatment for the pain such as physiotherapy, chiropractic treatment, or seeing a doctor.

Conclusion: Laparoscopic surgery was a potential source of pain in a proportion of surgeons. Surgeons who frequently perform laparoscopic surgery were more likely to experience a WRMD.

Clinical Significance: Work-related musculoskeletal disorders may occur as a result of performing laparoscopic surgery.
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http://dx.doi.org/10.1111/vsu.13400DOI Listing
June 2020

Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles.

PLoS One 2020 6;15(2):e0220754. Epub 2020 Feb 6.

Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.

Introduction: Adverse drug reactions have been linked with HLA alleles in different studies. These HLA proteins play an essential role in the adaptive immune response for the presentation of self and non-self peptides. Anti-thyroid drugs methimazole and propylthiouracil have been associated with drug induced agranulocytosis (severe lower white blood cell count) in patients with B*27:05, B*38:02 and DRB1*08:03 alleles in different populations: Taiwanese, Vietnamese, Han Chinese and Caucasian.

Methods: In this study, informatics methods were used to investigate if any sequence or structural similarities exist between the two associated HLA-B alleles, compared with a set of "control" alleles assumed not be associated, which could help explain the molecular basis of the adverse drug reaction. We demonstrated using MHC Motif Viewer and MHCcluster that the two alleles do not have a propensity to bind similar peptides, and thus at a gross level the structure of the antigen presentation region of the two alleles are not similar. We also performed multiple sequence alignment to identify polymorphisms shared by the risk but not by the control alleles and molecular docking to compare the predicted binding poses of the drug-allele combinations.

Results: Two residues, Cys67 and Thr80, were identified from the multiple sequence alignments to be unique to these risk alleles alone. The molecular docking showed the poses of the risk alleles to favour the F-pocket of the peptide binding groove, close to the Thr80 residue, with the control alleles generally favouring a different pocket. The data are thus suggestive that Thr80 may be a critical residue in HLA-mediated anti-thyroid drug induced agranulocytosis, and thus can guide future research and risk assessment.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220754PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7004376PMC
April 2020

Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools.

Nucleic Acids Res 2020 01;48(D1):D783-D788

Institute of Integrative Biology, University of Liverpool, Biosciences building, Crown Street, Liverpool, L69 7ZB, UK.

The Allele Frequency Net Database (AFND, www.allelefrequencies.net) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex Class I chain related genes (MIC) and a number of cytokine gene polymorphisms in worldwide populations. In the last five years, AFND has become more popular in terms of clinical and scientific usage, with a recent increase in genotyping data as a necessary component of Short Population Report article submissions to another scientific journal. In addition, we have developed a user-friendly desktop application for HLA and KIR genotype/population data submissions. We have also focused on classification of existing and new data into 'gold-silver-bronze' criteria, allowing users to filter and query depending on their needs. Moreover, we have also continued to expand other features, for example focussed on HLA associations with adverse drug reactions. At present, AFND contains >1600 populations from >10 million healthy individuals, making AFND a valuable resource for the analysis of some of the most polymorphic regions in the human genome.
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http://dx.doi.org/10.1093/nar/gkz1029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145554PMC
January 2020

Proteome Bioinformatics Methods for Studying Histidine Phosphorylation.

Methods Mol Biol 2020 ;2077:237-250

Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

In this chapter, we introduce the bioinformatics methods associated with studying histidine phosphorylation (pHis) by LC-MS/MS. We describe methods for converting and preprocessing raw data from MS instruments, the method of searching MS data against a sequence database and scoring the confidence associated with localizing the modification site on the peptide sequence. We also describe methods for performing pathway enrichment once a set of pHis-containing proteins have been identified to understand the putative functions of modified proteins. Several of the methods are relatively straightforward to run but require some theoretical knowledge to optimize parameters and correctly interpret outputs. We also describe some of the theory underpinning statistical considerations, to assist correct usage and interpretation of these bioinformatics methods.
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http://dx.doi.org/10.1007/978-1-4939-9884-5_16DOI Listing
December 2020

VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock.

Gigascience 2019 09;8(9)

Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park Ic2, 146 Brownlow Hill, Liverpool L3 5RF, UK.

Background: Analysing variant antigen gene families on a population scale is a difficult challenge for conventional methods of read mapping and variant calling due to the great variability in sequence, copy number, and genomic loci. In African trypanosomes, hemoparasites of humans and animals, this is complicated by variant antigen repertoires containing hundreds of genes subject to various degrees of sequence recombination.

Findings: We introduce Variant Antigen Profiler (VAPPER), a tool that allows automated analysis of the variant surface glycoprotein repertoires of the most prevalent livestock African trypanosomes. VAPPER produces variant antigen profiles for any isolate of the veterinary pathogens Trypanosoma congolense and Trypanosoma vivax from genomic and transcriptomic sequencing data and delivers publication-ready figures that show how the queried isolate compares with a database of existing strains. VAPPER is implemented in Python. It can be installed to a local Galaxy instance from the ToolShed (https://toolshed.g2.bx.psu.edu/) or locally on a Linux platform via the command line (https://github.com/PGB-LIV/VAPPER). The documentation, requirements, examples, and test data are provided in the Github repository.

Conclusion: By establishing two different, yet comparable methodologies, our approach is the first to allow large-scale analysis of African trypanosome variant antigens, large multi-copy gene families that are otherwise refractory to high-throughput analysis.
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http://dx.doi.org/10.1093/gigascience/giz091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735694PMC
September 2019

Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation.

EMBO J 2019 10 21;38(21):e100847. Epub 2019 Aug 21.

Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

Phosphorylation is a key regulator of protein function under (patho)physiological conditions, and defining site-specific phosphorylation is essential to understand basic and disease biology. In vertebrates, the investigative focus has primarily been on serine, threonine and tyrosine phosphorylation, but mounting evidence suggests that phosphorylation of other "non-canonical" amino acids also regulates critical aspects of cell biology. However, standard methods of phosphoprotein characterisation are largely unsuitable for the analysis of non-canonical phosphorylation due to their relative instability under acidic conditions and/or elevated temperature. Consequently, the complete landscape of phosphorylation remains unexplored. Here, we report an unbiased phosphopeptide enrichment strategy based on strong anion exchange (SAX) chromatography (UPAX), which permits identification of histidine (His), arginine (Arg), lysine (Lys), aspartate (Asp), glutamate (Glu) and cysteine (Cys) phosphorylation sites on human proteins by mass spectrometry-based phosphoproteomics. Remarkably, under basal conditions, and having accounted for false site localisation probabilities, the number of unique non-canonical phosphosites is approximately one-third of the number of observed canonical phosphosites. Our resource reveals the previously unappreciated diversity of protein phosphorylation in human cells, and opens up avenues for high-throughput exploration of non-canonical phosphorylation in all organisms.
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http://dx.doi.org/10.15252/embj.2018100847DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6826212PMC
October 2019

Use of non-contrast-enhanced computed tomography to identify deep digital flexor tendinopathy in horses with lameness: 28 cases (2014-2016).

J Am Vet Med Assoc 2019 Apr;254(7):852-858

Objective: To describe the use of non-contrast-enhanced CT to identify deep digital flexor (DDF) tendinopathy in horses with lameness attributed to pain in regions distal to the metatarsophalangeal or metacarpophalangeal joints.

Design: Retrospective case series.

Animals: 28 client-owned horses.

Procedures: Medical records were searched to identify horses that underwent non-contrast-enhanced CT with or without high-field MRI as part of an evaluation for lameness localized to areas distal to the metacarpophalangeal or metatarsophalangeal joint in ≥ 1 limb. Horses were included in the study if they had ≥ 1 DDF tendon lesion (DDF tendinopathy) identified. Signalment, lameness examination findings and response to perineural anesthesia, imaging modality, anesthetic agents and duration of anesthesia, and imaging findings were recorded. Data were summarized descriptively.

Results: Bilateral imaging was performed for all horses, irrespective of unilateral or bilateral lameness. Nine of 28 horses underwent both CT and MRI, and all DDF tendon lesions identified by one modality were identified by the other. Of 48 limbs with DDF tendinopathy, 46 (96%) had core lesions and 35 (73%) had dorsal border irregularities. Median anesthesia time for CT and CT followed by MRI was 15 and 110 minutes, respectively.

Conclusions And Clinical Relevance: Results suggested that non-contrast-enhanced CT was useful for identifying DDF tendinopathy in horses with lameness localized to the phalangeal regions, and this was supported by consistency of findings in a subset of horses that underwent MRI. Further research is needed to confirm these results.
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http://dx.doi.org/10.2460/javma.254.7.852DOI Listing
April 2019

A Standing Percutaneous Technique for Proximal Interphalangeal Joint Arthrodesis in Twelve Horses (2014-2017).

Vet Comp Orthop Traumatol 2019 Mar 7;32(2):165-170. Epub 2019 Mar 7.

San Luis Rey Equine Hospital, Bonsall, California, United States.

Objectives:  This report describes the use of a minimally invasive standing pastern arthrodesis technique for the treatment of osteoarthritis in horses and documents its clinical outcome in 12 horses.

Materials And Methods:  Medical records and radiographs of horses diagnosed with proximal interphalangeal joint osteoarthritis that underwent standing pastern arthrodesis using transarticular screws were reviewed. Follow-up information for determination of outcome was obtained via phone interview with the owners.

Results:  Twelve horses (15 limbs) were included in the study. Radiographical findings revealed severe osteoarthritis in 12/15 limbs and moderate osteoarthritis in 3/15 limbs. Follow-up information was available for 11/12 cases (13/15 limbs). Phone surveys with the owners revealed that 8/11 horses were performing at their previous activity level or higher. Two horses remained lame. One horse developed a surgical site infection and was euthanatized. The average time for horses to return to their previous level of activity was 6.5 months (range: 1-18 months).

Clinical Significance:  Stabilization of the proximal interphalangeal joint in horses with moderate-to-severe osteoarthritis can be performed using this minimally invasive standing technique. This procedure can be performed safely and provides a similar outcome when compared with other described techniques.
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http://dx.doi.org/10.1055/s-0039-1677747DOI Listing
March 2019

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.

Anal Chem 2019 03 13;91(5):3302-3310. Epub 2019 Feb 13.

Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB , United Kingdom.

Mass spectrometry (MS) is one of the primary techniques used for large-scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition, and reanalysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative, and the Metabolomics Society, we have created mzTab-M to act as a common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g., LC-MS, GC-MS, DIMS, etc.) and different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.
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http://dx.doi.org/10.1021/acs.analchem.8b04310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660005PMC
March 2019

A minimally invasive surgical technique for ureteral ostioplasty in two fillies with ureteral ectopia.

J Am Vet Med Assoc 2018 Dec;253(11):1467-1472

CASE DESCRIPTION 2 fillies, aged 3 months and 1 month, were examined because of urinary incontinence and urine scalding. CLINICAL FINDINGS In horse 1, ultrasonography did not reveal any structural abnormalities of the kidneys; however, unilateral ureteral ectopia was diagnosed cystoscopically. In horse 2, CT revealed bilateral nephropathy, bilateral distended ureters (up to 3.6 cm in diameter), and bilateral ureteral ectopia. Cystoscopy revealed intramural ureteral ectopia with abnormally caudally positioned ureteral ostia in both horses. TREATMENT AND OUTCOME Ureteral ostioplasty was performed under cystoscopic guidance. Laparoscopic scissors (horse 1) or a vessel-sealing device (horse 2) was introduced, and the tissue separating the intramural portion of the ureter from the urethra and bladder was cut longitudinally in a cranial direction toward the trigone. After surgery, both horses were continent and voided normal streams of urine for the duration of the follow-up periods of 20 and 9 months for horse 1 and horse 2, respectively. CLINICAL RELEVANCE Cystoscopically guided ureteral ostioplasty provided an effective and minimally invasive surgical treatment option for correction of ureteral ectopia in 2 fillies.
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http://dx.doi.org/10.2460/javma.253.11.1467DOI Listing
December 2018

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets.

Mol Cell Proteomics 2019 01 6;18(1):86-98. Epub 2018 Oct 6.

§Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK;. Electronic address:

Rice () is one of the most important worldwide crops. The genome has been available for over 10 years and has undergone several rounds of annotation. We created a comprehensive database of transcripts from 29 public RNA sequencing data sets, officially predicted genes from Ensembl plants, and common contaminants in which to search for protein-level evidence. We re-analyzed nine publicly accessible rice proteomics data sets. In total, we identified 420K peptide spectrum matches from 47K peptides and 8,187 protein groups. 4168 peptides were initially classed as putative novel peptides (not matching official genes). Following a strict filtration scheme to rule out other possible explanations, we discovered 1,584 high confidence novel peptides. The novel peptides were clustered into 692 genomic loci where our results suggest annotation improvements. 80% of the novel peptides had an ortholog match in the curated protein sequence set from at least one other plant species. For the peptides clustering in intergenic regions (and thus potentially new genes), 101 loci were identified, for which 43 had a high-confidence hit for a protein domain. Our results can be displayed as tracks on the Ensembl genome or other browsers supporting Track Hubs, to support re-annotation of the rice genome.
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http://dx.doi.org/10.1074/mcp.RA118.000832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317475PMC
January 2019

Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions.

Mol Immunol 2018 09 18;101:488-499. Epub 2018 Aug 18.

Institute of Integrative Biology, University of Liverpool, Liverpool, UK. Electronic address:

Adverse drug reactions have been linked with genetic polymorphisms in HLA genes in numerous different studies. HLA proteins have an essential role in the presentation of self and non-self peptides, as part of the adaptive immune response. Amongst the associated drugs-allele combinations, anti-HIV drug Abacavir has been shown to be associated with the HLA-B*57:01 allele, and anti-epilepsy drug Carbamazepine with B*15:02, in both cases likely following the altered peptide repertoire model of interaction. Under this model, the drug binds directly to the antigen presentation region, causing different self peptides to be presented, which trigger an unwanted immune response. There is growing interest in searching for evidence supporting this model for other ADRs using bioinformatics techniques. In this study, in silico docking was used to assess the utility and reliability of well-known docking programs when addressing these challenging HLA-drug situations. The overall aim was to address the uncertainty of docking programs giving different results by completing a detailed comparative study of docking software, grounded in the MHC-ligand experimental structural data - for Abacavir and to a lesser extent Carbamazepine - in order to assess their performance. Four docking programs: SwissDock, ROSIE, AutoDock Vina and AutoDockFR, were used to investigate if each software could accurately dock the Abacavir back into the crystal structure for the protein arising from the known risk allele, and if they were able to distinguish between the HLA-associated and non-HLA-associated (control) alleles. The impact of using homology models on the docking performance and how using different parameters, such as including receptor flexibility, affected the docking performance were also investigated to simulate the approach where a crystal structure for a given HLA allele may be unavailable. The programs that were best able to predict the binding position of Abacavir were then used to recreate the docking seen for Carbamazepine with B*15:02 and controls alleles. It was found that the programs investigated were sometimes able to correctly predict the binding mode of Abacavir with B*57:01 but not always. Each of the software packages that were assessed could predict the binding of Abacavir and Carbamazepine within the correct sub-pocket and, with the exception of ROSIE, was able to correctly distinguish between risk and control alleles. We found that docking to homology models could produce poorer quality predictions, especially when sequence differences impact the architecture of predicted binding pockets. Caution must therefore be used as inaccurate structures may lead to erroneous docking predictions. Incorporating receptor flexibility was found to negatively affect the docking performance for the examples investigated. Taken together, our findings help characterise the potential but also the limitations of computational prediction of drug-HLA interactions. These docking techniques should therefore always be used with care and alongside other methods of investigation, in order to be able to draw strong conclusions from the given results.
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http://dx.doi.org/10.1016/j.molimm.2018.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6148408PMC
September 2018

Does pre-operative anxiety and/or depression affect patient outcome after primary knee replacement arthroplasty?

Knee 2018 Dec 16;25(6):1238-1246. Epub 2018 Aug 16.

Morriston Hospital, Swansea, United Kingdom of Great Britain and Northern Ireland.

Background: Chronic pain is associated with psychological distress, most commonly manifested as anxiety and/or depression.

Methods: In order to investigate the effect of such distress on outcome from knee arthroplasty, we prospectively investigated the anxiety and depression levels of 104 patients undergoing a total of 107 primary knee arthroplasty procedures and the outcomes they achieved pre-operatively and at six weeks, one year and seven years post-operatively. The Hospital Anxiety and Depression Scale was used to record psychological status. Oxford Knee Score and American Knee Society Score were used to record functional outcomes.

Results: Forty-four percent (47/107) of the patients had an abnormal pre-operative anxiety and/or depression score. Mean anxiety and depression scores improved at six weeks and one year of follow-up, but then deteriorated slightly at seven years, albeit not back to baseline. Knee scores showed similar patterns over time. Regardless of pre-operative psychological status, mean AKSS Knee scores improved at six weeks and further improved at one year post-op. They then showed slight deterioration at seven years, but remained significantly better than pre-op.

Conclusions: Psychological distress is common in our patients pre-operatively. Improvements in knee pain and function as a result of surgery correlate well with lower levels of psychological distress post-operatively. Knee replacement surgery positively influences all of the outcome measures studied rather than recovery being negatively influenced by pre-operative states. Knee replacement arthroplasty is not contra-indicated by pre-operative psychological distress. Successful knee replacement improves knee pain and function, as well as symptoms of anxiety and depression. These improvements persist for many years after the surgery.
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http://dx.doi.org/10.1016/j.knee.2018.07.011DOI Listing
December 2018

Allele Frequency Net Database.

Methods Mol Biol 2018 ;1802:49-62

Transplant Immunology Laboratory, Royal Liverpool and Broadgreen University Hospital, Liverpool, UK.

The allele frequency net database (AFND, http://www.allelefrequencies.net ) is an online web-based repository that contains information on the frequencies of immune-related genes and their corresponding alleles in worldwide human populations. At present, the system contains data from 1505 populations in more than ten million individuals on the frequency of genes from different polymorphic regions including data for the human leukocyte antigens (HLA) system. This resource has been widely used in a variety of contexts such as histocompatibility, immunology, epidemiology, pharmacogenetics, and population genetics, among many others. In this chapter, we present some of the more commonly used searching mechanisms and some of the most recent developments included in AFND.
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http://dx.doi.org/10.1007/978-1-4939-8546-3_4DOI Listing
March 2019

Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants.

J Proteomics 2018 06 11;181:152-159. Epub 2018 Apr 11.

Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK. Electronic address:

Phosphorylation is one of the most prevalent post-translational modifications and plays a key role in regulating cellular processes. We carried out a bioinformatics analysis of pre-existing phosphoproteomics data, to profile two model species representing the largest subclasses in flowering plants the dicot Arabidopsis thaliana and the monocot Oryza sativa, to understand the extent to which phosphorylation signaling and function is conserved across evolutionary divergent plants. We identified 6537 phosphopeptides from 3189 phosphoproteins in Arabidopsis and 2307 phosphopeptides from 1613 phosphoproteins in rice. We identified phosphorylation motifs, finding nineteen pS motifs and two pT motifs shared in rice and Arabidopsis. The majority of shared motif-containing proteins were mapped to the same biological processes with similar patterns of fold enrichment, indicating high functional conservation. We also identified shared patterns of crosstalk between phosphoserines with enrichment for motifs pSXpS, pSXXpS and pSXXXpS, where X is any amino acid. Lastly, our results identified several pairs of motifs that are significantly enriched to co-occur in Arabidopsis proteins, indicating cross-talk between different sites, but this was not observed in rice.

Significance: Our results demonstrate that there are evolutionary conserved mechanisms of phosphorylation-mediated signaling in plants, via analysis of high-throughput phosphorylation proteomics data from key monocot and dicot species: rice and Arabidposis thaliana. The results also suggest that there is increased crosstalk between phosphorylation sites in A. thaliana compared with rice. The results are important for our general understanding of cell signaling in plants, and the ability to use A. thaliana as a general model for plant biology.
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http://dx.doi.org/10.1016/j.jprot.2018.04.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5971217PMC
June 2018

phpMs: A PHP-Based Mass Spectrometry Utilities Library.

J Proteome Res 2018 03 13;17(3):1309-1313. Epub 2018 Feb 13.

Department of Functional and Comparative Genomics, Institute of Integrated Biology, University of Liverpool , Liverpool, L69 7ZB, United Kingdom.

The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .
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http://dx.doi.org/10.1021/acs.jproteome.7b00783DOI Listing
March 2018

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.

Genome Biol 2018 01 31;19(1):12. Epub 2018 Jan 31.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry-based proteomics data with genomics and transcriptomics information in proteogenomics studies. proBAM and proBed are adaptations of the well-defined, widely used file formats SAM/BAM and BED, respectively, and both have been extended to meet the specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtools and Bedtools, and several widely used genome browsers, can already be used to manipulate and visualize these formats "out-of-the-box." We also highlight that a number of specific additional software tools, properly supporting the proteomics information available in these formats, are now available providing functionalities such as file generation, file conversion, and data analysis. All the related documentation, including the detailed file format specifications and example files, are accessible at http://www.psidev.info/probam and at http://www.psidev.info/probed .
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http://dx.doi.org/10.1186/s13059-017-1377-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793360PMC
January 2018

The Instruments and Capabilities of the (MinXSS) CubeSats.

Sol Phys 2018 23;293(2):21. Epub 2018 Jan 23.

5NASA Goddard Space Flight Center, Code 671.0, Greenbelt, MD USA.

The (MinXSS) CubeSat is the first solar science oriented CubeSat mission flown for the NASA Science Mission Directorate, with the main objective of measuring the solar soft X-ray (SXR) flux and a science goal of determining its influence on Earth's ionosphere and thermosphere. These observations can also be used to investigate solar quiescent, active region, and flare properties. The MinXSS X-ray instruments consist of a spectrometer, called X123, with a nominal 0.15 keV full-width at half-maximum (FWHM) resolution at 5.9 keV and a broadband X-ray photometer, called XP. Both instruments are designed to obtain measurements from 0.5 - 30 keV at a nominal time cadence of 10 s. A description of the MinXSS instruments, performance capabilities, and relation to the (GOES) 0.1 - 0.8 nm flux is given in this article. Early MinXSS results demonstrate the capability of measuring variations of the solar spectral soft X-ray (SXR) flux between 0.8 - 12 keV from at least GOES A5-M5 ( ) levels and of inferring physical properties (temperature and emission measure) from the MinXSS data alone. Moreover, coronal elemental abundances can be inferred, specifically for Fe, Ca, Si, Mg, S, Ar, and Ni, when the count rate is sufficiently high at each elemental spectral feature. Additionally, temperature response curves and emission measure loci demonstrate the MinXSS sensitivity to plasma emission at different temperatures. MinXSS observations coupled with those from other solar observatories can help address some of the most compelling questions in solar coronal physics. Finally, simultaneous observations by MinXSS and the (RHESSI) can provide the most spectrally complete soft X-ray solar flare photon flux measurements to date.
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http://dx.doi.org/10.1007/s11207-018-1243-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6566308PMC
January 2018

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

Anal Chem 2018 01 14;90(1):649-656. Epub 2017 Dec 14.

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K.

NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.
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http://dx.doi.org/10.1021/acs.analchem.7b02795DOI Listing
January 2018