Tom Smith
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View article: Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro
Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro Open
Industrial and agricultural chemicals such as pesticides are often considered to have restricted biological activity. Yet, there are concerns regarding their broader toxicity range and impact on human gut microbiota. Here we report a syste…
View article: Kittiwakes nesting on offshore oil and gas infrastructure: An emerging and under‐recorded phenomenon
Kittiwakes nesting on offshore oil and gas infrastructure: An emerging and under‐recorded phenomenon Open
Black‐legged kittiwake ( Rissa tridactyla ) populations are in decline globally, including in Britain and Ireland, which support internationally important numbers. Although kittiwakes typically nest on coastal cliffs, they are known to col…
View article: Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging
Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging Open
Electron cryomicroscopy (cryo-EM) allows high-resolution spatial visualization of biological specimens, however, it is challenging to chemically identify densities observed in cryo-EM. To overcome this, we combined cryo-EM with chemical im…
View article: Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy
Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy Open
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated due to their degree of redundancy and extensive modifications. As such, no tRNA-Seq method has become well established, while various approaches …
View article: Off-purpose activity of industrial and agricultural chemicals against human gut bacteria
Off-purpose activity of industrial and agricultural chemicals against human gut bacteria Open
Contamination by industrial and agricultural chemicals like pesticides are a cause of great concern due to the risk to human and environmental health. While these chemicals are often considered to have restricted activity and are labelled …
View article: Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy
Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy Open
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated due to their degree of redundancy and extensive modifications. As such, no tRNA-Seq method has become well established, while various approaches …
View article: Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy
Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy Open
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated by their degree of redundancy and extensive modifications. As such, no tRNA-Seq method has become well established, while various approaches have…
View article: Author response: Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy
Author response: Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy Open
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated by their degree of redundancy and extensive modifications. As such, no tRNA-Seq method has become well established, while various approaches have…
View article: Reviewer #2 (Public Review): Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy
Reviewer #2 (Public Review): Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy Open
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated by their degree of redundancy and extensive modifications. As such, no tRNA-Seq method has become well established, while various approaches have…
View article: Reviewer #1 (Public Review): Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy
Reviewer #1 (Public Review): Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy Open
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated by their degree of redundancy and extensive modifications. As such, no tRNA-Seq method has become well established, while various approaches have…
View article: Bacterial isolate chemical responses data
Bacterial isolate chemical responses data Open
Dataset of growth responses of bacterial isolates to mixtures of chemical stressors. Data present:tidy-data.csv - raw growth curves, OD600 readings recorded at hourly time intervals.spline_fits.csv - results of fitting spline curves to the…
View article: Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy
Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy Open
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated due to their degree of redundancy and extensive modifications. As such, no tRNA-Seq method has become well established, while various approaches …
View article: Supplementary Data Tables from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study
Supplementary Data Tables from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study Open
Supplementary Data Table S1: general characterisctic of the different cohorts of patients Supplementary Data Table S2: characterisctic of Population A Supplementary Data Table S3: characterisctic of Population B Supplementary Data Table S4…
View article: Supplementary Data from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study
Supplementary Data from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study Open
Supplementary Data Figure S1. Determination of IgLV3-21 positivity by real-time PCR. Supplementary Data Figure S2: CLL-OS analysis including only CLL-related deaths. Supplementary Data Figure S3. Validation of the poor prognosis associated…
View article: Data from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study
Data from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study Open
Purpose: Unmutated (UM) immunoglobulin heavy chain variable region (IgHV) status or IgHV3-21 gene usage is associated with poor prognosis in chronic lymphocytic leukemia (CLL) patients. Interestingly, IgHV3-21 is often co-expressed with li…
View article: Supplementary Data from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study
Supplementary Data from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study Open
Supplementary Data Figure S1. Determination of IgLV3-21 positivity by real-time PCR. Supplementary Data Figure S2: CLL-OS analysis including only CLL-related deaths. Supplementary Data Figure S3. Validation of the poor prognosis associated…
View article: Supplementary Data Tables from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study
Supplementary Data Tables from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study Open
Supplementary Data Table S1: general characterisctic of the different cohorts of patients Supplementary Data Table S2: characterisctic of Population A Supplementary Data Table S3: characterisctic of Population B Supplementary Data Table S4…
View article: Data from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study
Data from The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study Open
Purpose: Unmutated (UM) immunoglobulin heavy chain variable region (IgHV) status or IgHV3-21 gene usage is associated with poor prognosis in chronic lymphocytic leukemia (CLL) patients. Interestingly, IgHV3-21 is often co-expressed with li…
View article: Margin Variance Analysis for Informing Customer Engagement Strategy
Margin Variance Analysis for Informing Customer Engagement Strategy Open
A margin variance analysis measures the sources of difference in gross margins between pieces of business within a larger set of business. When the piece of business is defined as the the total sales to an individual customer over a period…
View article: Operation of a TCA cycle subnetwork in the mammalian nucleus
Operation of a TCA cycle subnetwork in the mammalian nucleus Open
Nucleic acid and histone modifications critically depend on the tricarboxylic acid (TCA) cycle for substrates and cofactors. Although a few TCA cycle enzymes have been reported in the nucleus, the corresponding pathways are considered to o…
View article: 327 To Fuse or Not to Fuse: The Elderly Patient with Lumbar Stenosis and Low-Grade Spondylolisthesis. Systematic Review and Meta-Analysis of Randomised Controlled Trials
327 To Fuse or Not to Fuse: The Elderly Patient with Lumbar Stenosis and Low-Grade Spondylolisthesis. Systematic Review and Meta-Analysis of Randomised Controlled Trials Open
Aim The optimum surgical intervention for elderly patients with lumbar spinal stenosis(LSS) and low-grade degenerative-spondylolisthesis(LGDS) has been extensively debated. We conducted a systematic review and meta-analysis of randomised-c…
View article: Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments
Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments Open
Tandem mass tags (TMTs) enable simple and accurate quantitative proteomics for multiplexed samples by relative quantification of tag reporter ions. Orbitrap quantification of reporter ions has been associated with a characteristic notch re…
View article: A system-wide quantitative map of RNA and protein subcellular localisation dynamics
A system-wide quantitative map of RNA and protein subcellular localisation dynamics Open
Existing methods to analyse RNA localisation are constrained to specific RNAs or subcellular niches, precluding the cell-wide mapping of RNA. We present Localisation of RNA (LoRNA), which maps, at once, RNAs to membranous (nucleus, ER and …
View article: Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments
Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments Open
Tandem mass tags (TMT) enable simple and accurate quantitative proteomics for multiplexed samples by relative quantification of tag reporter ions. Orbitrap™ quantification of reporter ions has been associated with a characteristic notch re…
View article: Provenance metadata for statistical data: An introduction to Structured Data Transformation Language (SDTL)
Provenance metadata for statistical data: An introduction to Structured Data Transformation Language (SDTL) Open
Structured Data Transformation Language (SDTL) provides structured, machine actionable representations of data transformation commands found in statistical analysis software. The Continuous Capture of Metadata for Statistical Data Project …
View article: Automating the Capture of Data Transformation Metadata from Statistical Analysis Software
Automating the Capture of Data Transformation Metadata from Statistical Analysis Software Open
The C2Metadata (“Continuous Capture of Metadata for Statistical Data”) Project automates one of the most burdensome aspects of documenting the provenance of research data: describing data transformations performed by statistical software. …