John W. Brown
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View article: A randomized trial of a multimodal lifestyle intervention in cancer survivors
A randomized trial of a multimodal lifestyle intervention in cancer survivors Open
Introduction Cancer survivors are often insufficiently physically active, have overweight or obesity, and suboptimal cardiorespiratory fitness. The Small Steps study evaluated a multimodal intervention to address these modifiable risk fact…
View article: Right Atrial Rhabdomyosarcoma; 35-Year Disease-Free Survival Following Radical Resection With Right Internal Thoracic Artery Bypass
Right Atrial Rhabdomyosarcoma; 35-Year Disease-Free Survival Following Radical Resection With Right Internal Thoracic Artery Bypass Open
Cardiac rhabdomyosarcomas (RMS) are rare malignant tumors of the heart with a poor prognosis, even when appropriate treatment regimens are initiated. We present the case of a 12-year-old male who underwent radical resection of a right atri…
View article: <i>REVEILLE2</i> thermosensitive splicing: a molecular basis for the integration of nocturnal temperature information by the Arabidopsis circadian clock
<i>REVEILLE2</i> thermosensitive splicing: a molecular basis for the integration of nocturnal temperature information by the Arabidopsis circadian clock Open
Summary Cold stress is one of the major environmental factors that limit growth and yield of plants. However, it is still not fully understood how plants account for daily temperature fluctuations, nor how these temperature changes are int…
View article: <i>REVEILLE2</i>Thermosensitive Splicing: A Molecular Basis for the Integration of Nocturnal Temperature Information by the Arabidopsis Circadian Clock
<i>REVEILLE2</i>Thermosensitive Splicing: A Molecular Basis for the Integration of Nocturnal Temperature Information by the Arabidopsis Circadian Clock Open
Summary Cold stress is one of the major environmental factors that limit growth and yield of plants. However, it is still not fully understood how plants account for daily temperature fluctuations, nor how these temperature changes are int…
View article: Liposomal bupivacaine reduces opioid requirements following Ravitch repair for pectus excavatum
Liposomal bupivacaine reduces opioid requirements following Ravitch repair for pectus excavatum Open
Background and Aims: The management of post-operative pain after surgical repair of pectus excavatum with the Ravitch procedure is challenging. Although previous studies have compared various methods of pain control in these patients, few …
View article: Perioperative and long‐term outcomes of Ross versus mechanical aortic valve replacement
Perioperative and long‐term outcomes of Ross versus mechanical aortic valve replacement Open
In this mid-term propensity score-matched analysis, the Ross procedure offers similar perioperative outcomes, freedom from reintervention or valve dysfunction as well as overall survival compared to traditional mAVR but without the morbidi…
View article: <scp>BaRTv2</scp> : a highly resolved barley reference transcriptome for accurate transcript‐specific <scp>RNA</scp> ‐seq quantification
<span>BaRTv2</span> : a highly resolved barley reference transcriptome for accurate transcript‐specific <span>RNA</span> ‐seq quantification Open
SUMMARY Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA‐seq data, and enables detailed investigations of tra…
View article: Additional file 1 of A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
Additional file 1 of A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis Open
Additional file 1: Table S1. Plant material for RNA samples for Iso-Seq. Table S2. Read statistics for Iso-seq libraries. Table S3A and B. Number and percentage of splice junctions with sequencing mismatches in positions L1 to L30 for A) u…
View article: An Emergent Nexus between Striae and Thoracic Aortic Dissection
An Emergent Nexus between Striae and Thoracic Aortic Dissection Open
Current approaches to stratify the risk for disease progression in thoracic aortic aneurysm (TAA) lack precision, which hinders clinical decision making. Connective tissue phenotyping of children with TAA previously identified the associat…
View article: Surgical and Transcatheter Pulmonary Valve Replacement: A Single Institution Comparison
Surgical and Transcatheter Pulmonary Valve Replacement: A Single Institution Comparison Open
Background and Hypothesis: Pulmonary valve replacement (PVR) is one of the most commonly performed procedures for patients with congenital heart disease. Transcatheter-based PVR (TPVR) approaches have emerged as alternatives to surgical pu…
View article: Perioperative and Long-Term Outcomes of Ross versus Mechanical Aortic Valve Replacement
Perioperative and Long-Term Outcomes of Ross versus Mechanical Aortic Valve Replacement Open
Background The ideal aortic valve replacement strategy in young- and middle-aged adults remains up for debate. Clinical practice guidelines recommend mechanical prostheses for most patients less than 50 years of age undergoing aortic valve…
View article: BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification
BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification Open
Accurate characterization of splice junctions as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data and enable detailed investigations of transcriptional and…
View article: A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis Open
Background Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single molecule long read sequencing technologies provide improve…
View article: Simulation in coronary artery anastomosis early in cardiothoracic surgical residency training: The Boot Camp experience
Simulation in coronary artery anastomosis early in cardiothoracic surgical residency training: The Boot Camp experience Open
Objective—We evaluated focused training in coronary artery anastomosis with a porcine heart model and portable task station. Methods—At “Boot Camp,” 33 first-year cardiothoracic surgical residents participated in 4-hour coronary anastomosi…
View article: 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists
3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists Open
RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on specialized bioinformati…
View article: TranSuite: a software suite for accurate translation and characterization of transcripts
TranSuite: a software suite for accurate translation and characterization of transcripts Open
Protein translation programs often select the longest open reading frame (ORF) in a transcript leading to numerous inaccurate and mis-annotated ORFs in databases. Unproductive transcript isoforms containing premature termination codons (PT…
View article: Simulation in coronary artery anastomosis early in cardiothoracic surgical residency training: The Boot Camp experience
Simulation in coronary artery anastomosis early in cardiothoracic surgical residency training: The Boot Camp experience Open
We evaluated focused training in coronary artery anastomosis with a porcine heart model and portable task station.
View article: Illuminating the dark side of the human transcriptome with long read transcript sequencing
Illuminating the dark side of the human transcriptome with long read transcript sequencing Open
Background: The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate…
View article: Illuminating the dark side of the human transcriptome with long read transcript sequencing
Illuminating the dark side of the human transcriptome with long read transcript sequencing Open
Background: The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate…
View article: Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis
Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis Open
Nonsense-mediated RNA decay (NMD) is an RNA control mechanism that has also been implicated in the broader regulation of gene expression. Nevertheless, a role for NMD in genome regulation has not yet been fully assessed, partially because …
View article: Illuminating the dark side of the human transcriptome with long read transcript sequencing
Illuminating the dark side of the human transcriptome with long read transcript sequencing Open
Background The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate …
View article: Nonsense mediated RNA decay factor UPF1 is critical for post-transcriptional and translational gene regulation in Arabidopsis
Nonsense mediated RNA decay factor UPF1 is critical for post-transcriptional and translational gene regulation in Arabidopsis Open
Nonsense mediated RNA decay (NMD) is an evolutionary conserved RNA control mechanism that has also been implicated in the broader regulation of gene expression. Nevertheless, a role for NMD in genome regulation has not been fully assessed,…
View article: Revision of New World Cosmorrhyncha Meyrick, 1913 (Lepidoptera: Tortricidae: Olethreutinae), with descriptions of five new species
Revision of New World Cosmorrhyncha Meyrick, 1913 (Lepidoptera: Tortricidae: Olethreutinae), with descriptions of five new species Open
Brown, John W., Razowski, Józef, Timm, Alicia E. (2020): Revision of New World Cosmorrhyncha Meyrick, 1913 (Lepidoptera: Tortricidae: Olethreutinae), with descriptions of five new species. Insecta Mundi 753: 1-21, DOI: 10.5281/zenodo.37029…
View article: The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana Open
The authors were recently made aware of anomalies in Figure 2. Before publication, the image was altered to cover unsightly cracks in the dried radioactive gel.In addition, the figure is a composite of 2 gels that were spliced together bet…
View article: Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane
Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane Open
Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast respon…