Venovenous Extracorporeal Membrane Oxygenation Usage Following Bullet Embolism to the Pulmonary Artery.

Background: Pulmonary artery embolus is a rare complication following gunshot wounds that creates a unique and serious challenge for trauma surgeons. While the majority of bullets that embolize through the vascular system end in the peripheral circulation, approximately one-third enter the central venous circulation. Case Report: We present the case of a bullet embolus to the left pulmonary artery following gunshot wounds to the right chest and the abdomen, with the abdominal ballistic traversing the liver before entering the vena cava and embolizing. The patient's course was complicated by the development of severe acute respiratory distress syndrome that was successfully managed by venovenous extracorporeal membrane oxygenation. Conclusion: Venovenous extracorporeal membrane oxygenation support for severe acute respiratory distress syndrome after bullet embolization to the pulmonary tree and surgical embolectomy is a viable option in appropriately selected patients.

Discrepancies in Mass Shootings and Access to Trauma Care Across the United States, 2014-2018.

INTRODUCTION: The United States has one of the highest rates of gun violence and mass shootings. Timely medical attention in such events is critical. The objective of this study was to assess geographic disparities in mass shootings and access to trauma centers. METHODS: Data for all Level I and II trauma centers were extracted from the American College of Surgeons and the Trauma Center Association of America registries. Mass shooting event data (4+ individuals shot at a single event) were taken from the Gun Violence Archive between 2014 and 2018. RESULTS: A total of 564 trauma centers and 1672 mass shootings were included. Ratios of the number of mass shootings vs trauma centers per state ranged from 0 to 11.0 mass shootings per trauma center. States with the greatest disparity (highest ratio) included Louisiana and New Mexico. CONCLUSION: States in the southern regions of the US experience the greatest disparity due to a high burden of mass shootings with less access to trauma centers. Interventions are needed to increase access to trauma care and reduce mass shootings in these medically underserved areas.

Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication.

BACKGROUND: Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date. RESULTS: Taking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint. CONCLUSIONS: Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.

Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley.

Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.

Wheat Panache: A pangenome graph database representing presence-absence variation across sixteen bread wheat genomes.

Bread wheat (Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence-absence variation (PAV) between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a diverse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate because of the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess PAV between bread wheat genomes.

Graph pangenomes represent more genomic variants than reference genomes. We present a wheat graph pangenome based on 16 public assemblies. We present Wheat Panache, an online visual representation of this graph. Wheat Panache lets users search the graph for presence-absence variants. We also distribute the graph preindexed for Giraffe utilization.

How Did the COVID-19 Pandemic Affect Trauma Volume at an Urban Level I Trauma Center?

INTRODUCTION: The COVID-19 pandemic changed the face of health care worldwide. While the impacts from this catastrophe are still being measured, it is important to understand how this pandemic impacted existing health care systems. As such, the objective of this study was to quantify its effects on trauma volume at an urban Level 1 trauma center in one of the earliest and most significantly affected US cities. METHODS: A retrospective chart review of consecutive trauma patients admitted to a Level 1 trauma center from January 1, 2017 to December 31, 2020 was completed. The total trauma volume in the years prior to the pandemic (2017-2019) was compared to the volume in 2020. These data were then further stratified to compare quarterly volume across all 4 years. RESULTS: A total of 4138 trauma patients were treated in the emergency room throughout 2020 with 4124 seen during 2019, 3774 during 2018, and 3505 during 2017 in the pre-COVID-19 time period. No significant difference in the volume of minor trauma or trauma transfers was observed (P < .05). However, there was a significant increase in the number of major traumas in 2020 as compared to prior years (38.5% vs 35.6%, P < .01) and in the volume of penetrating trauma (29.1% vs 24.0%, P < .01). DISCUSSION: During the COVID-19 outbreak, trauma remained a significant health care concern. This study found an increase in volume of penetrating trauma, specifically gunshot wounds throughout 2020. It remains important to continue to devote resources to trauma patients during the ongoing COVID-19 pandemic.

Does Time to Pelvic Fixation Influence Outcomes in Trauma Patients?

BACKGROUND: Pelvic fractures cause significant morbidity in the trauma population. Many factors influence time to fracture fixation. No previous study has determined the optimal time window for pelvic fixation. METHODS: A retrospective review of trauma patients with pelvic fractures from 2016 to 2020 was performed. Patients were stratified into EARLY and LATE groups, by time to fixation within 3 days or greater than 3 days whether from admission or from completion of a life-saving procedure. Unpaired Student's t-test and Fisher's exact test were performed with multiple linear regression for variables with P < .2 on univariate analysis. RESULTS: 287 patients were identified with a median fixation time of 3 days. There was no significant difference in demographics, incidence of preceding life-saving procedure, angioembolization, or mechanism of injury in the 2 groups (P > .05). Length of stay in the EARLY group was significantly reduced at 11.9 +/- .7 days compared to 18.0 +/-1.2 days in the LATE group (P < .001). There was no significant difference in rates of ventilator-associated pneumonia, deep vein thrombosis, pulmonary embolism (PE), acute kidney injury (AKI), pressure ulcer, or acute respiratory distress syndrome (ARDS) (P > .05). There were significantly more SSIs (surgical site infections) in the LATE group. After multiple linear regression adjusting for covariates of age and ISS, the difference in hospital LOS was 5.5 days (95% CI -8.0 to -3.1, P < .001). DISCUSSION: Fixation of traumatic pelvic fractures within 3 days reduced LOS. Prospective multi-center studies will help identify additional factors to decrease time to surgery and improve patient outcomes.

Lessons Learned From an Early Hotspot During the COVID-19 Pandemic.

The Covid-19 pandemic has provided challenges for surgical residency programs demanding fluid decision making focused on providing care for our patients, maintaining an educational environment, and protecting the well-being of our residents. This brief report summarizes the impact of the impact on our residency programs clinical care and education. We have identified opportunities to improve our program using videoconferencing, managing recruitment, and maintaining a satisfactory caseload to ensure the highest possible quality of surgical education.

Compression of the Right Atrium and Inferior Vena Cava from an Extrahepatic Biloma Following Liver Trauma.

A 26-year-old male presented to a Level 1 trauma center following a motorcycle crash. Workup of his injuries demonstrated a grade 5 liver laceration with active extravasation, grade 5 kidney laceration, right apical pneumothorax, and a sternal fracture. The patient underwent hepatic artery embolization with interventional radiology (IR) followed by an exploratory laparotomy, liver packing, and small bowel resection with primary anastomosis. Four days post-op, the patient developed dyspnea, tachycardia, and decreasing oxygen saturation. Computed tomography pulmonary angiography demonstrated perihepatic fluid compressing the right atrium and inferior vena cava. Percutaneous perihepatic drain placement with aspiration of 700 mL bilious fluid resulted in immediate resolution of the compression. He subsequently underwent endoscopic retrograde cholangiopancreatography (ERCP) with stenting of the ampulla nine days later. The patient was discharged ten days post-ERCP with oral amoxicillin/clavulanic acid for polymicrobial coverage and follow-up with gastroenterology and IR for stent removal and drain maintenance.

Gastroduodenal Artery Pseudoaneurysm Causing Obstructive Jaundice.

Background: Visceral artery aneurysms and pseudoaneurysms are uncommon phenomena with a high mortality rate in cases of rupture. These rare vascular pathologies are usually asymptomatic and are therefore generally discovered incidentally on computed tomography or magnetic resonance imaging examination. Current therapeutic options have trended toward a minimally invasive approach because of evolving endovascular treatment options, with open operations typically reserved for cases of intraabdominal hemorrhage. Case Report: We describe a case of gastroduodenal artery pseudoaneurysm manifesting as obstructive jaundice and pancreatitis because of extrahepatic compression of the common bile duct and pancreatic duct by mass effect. Open repair was ultimately required secondary to arterial anatomy that was not amenable to any endovascular treatment approach. Conclusion: While endovascular options are the preferred treatment modality for visceral artery aneurysms and pseudo-aneurysms, some cases require definitive open repair for a variety of reasons, including unsuitable anatomy.

BarleyVarDB: a database of barley genomic variation.

Barley (Hordeum vulgare L.) is one of the first domesticated grain crops and represents the fourth most important cereal source for human and animal consumption. BarleyVarDB is a database of barley genomic variation. It can be publicly accessible through the website at http://146.118.64.11/BarleyVar. This database mainly provides three sets of information. First, there are 57 754 224 single nuclear polymorphisms (SNPs) and 3 600 663 insertions or deletions (InDels) included in BarleyVarDB, which were identified from high-coverage whole genome sequencing of 21 barley germplasm, including 8 wild barley accessions from 3 barley evolutionary original centers and 13 barley landraces from different continents. Second, it uses the latest barley genome reference and its annotation information publicly accessible, which has been achieved by the International Barley Genome Sequencing Consortium (IBSC). Third, 522 212 whole genome-wide microsatellites/simple sequence repeats (SSRs) were also included in this database, which were identified in the reference barley pseudo-molecular genome sequence. Additionally, several useful web-based applications are provided including JBrowse, BLAST and Primer3. Users can design PCR primers to asses polymorphic variants deposited in this database and use a user-friendly interface for accessing the barley reference genome. We envisage that the BarleyVarDB will benefit the barley genetic research community by providing access to all publicly available barley genomic variation information and barley reference genome as well as providing them with an ultra-high density of SNP and InDel markers for molecular breeding and identification of functional genes with important agronomic traits in barley. Database URL: http://146.118.64.11/BarleyVar.

Genomic Analysis of Circulating Tumor DNA Using a Melanoma-Specific UltraSEEK Oncogene Panel.

The analysis of circulating tumor DNA provides a minimally invasive molecular interrogation that has the potential to guide treatment selection and disease monitoring. Here, the authors evaluated a custom UltraSEEK melanoma panel for the MassARRAY system, probing for 61 mutations over 13 genes. The analytical sensitivity and clinical accuracy of the UltraSEEK melanoma panel was compared with droplet digital PCR. The blinded analysis of 68 mutations detected in 48 plasma samples from stage IV melanoma patients revealed a concordance of 88% between the two platforms. Further comparison of both methods for the detection of BRAF V600E mutations in 77 plasma samples demonstrated a Cohen's κ of 0.826 (bias-corrected and accelerated 95% CI, 0.669-0.946). These results indicate that the UltraSEEK melanoma panel is as sensitive as droplet digital PCR for the detection of circulating tumor DNA in this cohort of patients but highlight the need for detected variants to be confirmed orthogonally to mitigate any false-positive results. The MassARRAY system enables rapid and sensitive genotyping for the detection of multiple melanoma-associated mutations in plasma.

The pseudogenes of barley.

Pseudogenes have a reputation of being 'evolutionary relics' or 'junk DNA'. While they are well characterized in mammals, studies in more complex plant genomes have so far been hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high-quality genome reference assembly available for a Triticeae crop, we conducted a whole-genome assessment of pseudogenes on the barley genome. We identified, characterized and classified 89 440 gene fragments and pseudogenes scattered along the chromosomes, with occasional hotspots and higher densities at the chromosome ends. Full-length pseudogenes (11 015) have preferentially retained their exon-intron structure. Retrotransposition of processed mRNAs only plays a marginal role in their creation. However, the distribution of retroposed pseudogenes reflects the Rabl configuration of barley chromosomes and thus hints at founding mechanisms. While parent genes related to the defense-response were found to be under-represented in cultivated barley, we detected several defense-related pseudogenes in wild barley accessions. The percentage of transcriptionally active pseudogenes is 7.2%, and these may potentially adopt new regulatory roles.The barley genome is rich in pseudogenes and small gene fragments mainly located towards chromosome tips or as tandemly repeated units. Our results indicate non-random duplication and pseudogenization preferences and improve our understanding of the dynamics of gene birth and death in large plant genomes and the mechanisms that lead to evolutionary innovations.

Plant Proteogenomics: Improvements to the Grapevine Genome Annotation.

Grapevine is an important perennial fruit to the wine industry, and has implications for the health industry with some causative agents proven to reduce heart disease. Since the sequencing and assembly of grapevine cultivar Pinot Noir, several studies have contributed to its genome annotation. This new study further contributes toward genome annotation efforts by conducting a proteogenomics analysis using the latest genome annotation from CRIBI, legacy proteomics dataset from cultivar Cabernet Sauvignon and a large RNA-seq dataset. A total of 341 novel annotation events are identified consisting of five frame-shifts, 37 translated UTRs, 15 exon boundaries, one novel splice, nine novel exons, 159 gene boundaries, 112 reverse strands, and one novel gene event in 213 genes and 323 proteins. From this proteogenomics evidence, the Augustus gene prediction tool predicted 52 novel and revised genes (54 protein isoforms), 11 genes of which are associated with key traits such as stress tolerance and floral and fruity wine characteristics. This study also highlights a likely over-assembly with the genome, particularly on chromosome 7.

Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome.

The genome of the cattle tick Rhipicephalus microplus, an ectoparasite with global distribution, is estimated to be 7.1Gbp in length and consists of approximately 70% repetitive DNA. We report the draft assembly of a tick genome that utilized a hybrid sequencing and assembly approach to capture the repetitive fractions of the genome. Our hybrid approach produced an assembly consisting of 2.0Gbp represented in 195,170 scaffolds with a N50 of 60,284bp. The Rmi v2.0 assembly is 51.46% repetitive with a large fraction of unclassified repeats, short interspersed elements, long interspersed elements and long terminal repeats. We identified 38,827 putative R. microplus gene loci, of which 24,758 were protein coding genes (≥100 amino acids). OrthoMCL comparative analysis against 11 selected species including insects and vertebrates identified 10,835 and 3,423 protein coding gene loci that are unique to R. microplus or common to both R. microplus and Ixodes scapularis ticks, respectively. We identified 191 microRNA loci, of which 168 have similarity to known miRNAs and 23 represent novel miRNA families. We identified the genomic loci of several highly divergent R. microplus esterases with sequence similarity to acetylcholinesterase. Additionally we report the finding of a novel cytochrome P450 CYP41 homolog that shows similar protein folding structures to known CYP41 proteins known to be involved in acaricide resistance.

A chromosome conformation capture ordered sequence of the barley genome.

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. 'Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

High-throughput parallel proteogenomics: a bacterial case study.

In recent years, a new paradigm for genome annotation has emerged, termed "proteogenomics," that leverages peptide MS to annotate a genome. This is achieved by mapping peptides to a six-frame translation of a genome, including available splice databases, which may suggest refinements to gene models. Using this approach, it is possible to refine gene regions such as exon boundaries, novel genes, gene boundaries, frame shifts, reverse strands, translated UTRs, and novel splice junctions. One of the challenges of proteogenomics is how best to (1) tackle assigning confidence to any resulting annotation and (2) apply these gene model refinements, either through manual annotation or through an automated process via training gene prediction tools. This is not a straightforward process, as many gene prediction tools have their defined suitability for niche genomes (either eukaryotic or prokaryotic) trained on and refined with model organisms such as Arabidopsis thaliana and Escherichia coli, and varying degrees of features that can leverage the use of external evidence. In this study, we outline a suitable approach toward preprocessing mass spectra and optimizing the MS/MS search for a given dataset. We also discuss future challenges, which continue to pose a problem in the field of proteogenomics, and better strategies to successfully tackle them with, using existing tools. We use Bradyrhizobium diazoefficiens (Nitrogen-fixing bacteria), with a 9.1 Mb genome as a case study, utilizing the latest in second-generation proteogenomics tools with multiple gene models for cross-validation of proteogenomics annotations.

Applying polygenic risk scores to postpartum depression.

The etiology of major depressive disorder (MDD) is likely to be heterogeneous, but postpartum depression (PPD) is hypothesized to represent a more homogenous subset of MDD. We use genome-wide SNP data to explore this hypothesis. We assembled a total cohort of 1,420 self-report cases of PPD and 9,473 controls with genome-wide genotypes from Australia, The Netherlands, Sweden and the UK. We estimated the total variance attributable to genotyped variants. We used association results from the Psychiatric Genomics Consortia (PGC) of bipolar disorder (BPD) and MDD to create polygenic scores in PPD and related MDD data sets to estimate the genetic overlap between the disorders. We estimated that the percentage of variance on the liability scale explained by common genetic variants to be 0.22 with a standard error of 0.12, p = 0.02. The proportion of variance (R (2)) from a logistic regression of PPD case/control status in all four cohorts on a SNP profile score weighted by PGC-BPD association results was small (0.1 %) but significant (p = 0.004) indicating a genetic overlap between BPD and PPD. The results were highly significant in the Australian and Dutch cohorts (R (2) > 1.1 %, p < 0.008), where the majority of cases met criteria for MDD. The genetic overlap between BPD and MDD was not significant in larger Australian and Dutch MDD case/control cohorts after excluding PPD cases (R (2) = 0.06 %, p = 0.08), despite the larger MDD group affording more power. Our results suggest an empirical genetic evidence for a more important shared genetic etiology between BPD and PPD than between BPD and MDD.