Chromosome-level genomes of three key Allium crops and their trait evolution.

Allium crop breeding remains severely hindered due to the lack of high-quality reference genomes. Here we report high-quality chromosome-level genome assemblies for three key Allium crops (Welsh onion, garlic and onion), which are 11.17 Gb, 15.52 Gb and 15.78 Gb in size with the highest recorded contig N50 of 507.27 Mb, 109.82 Mb and 81.66 Mb, respectively. Beyond revealing the genome evolutionary process of Allium species, our pathogen infection experiments and comparative metabolomic and genomic analyses showed that genes encoding enzymes involved in the metabolic pathway of Allium-specific flavor compounds may have evolved from an ancient uncharacterized plant defense system widely existing in many plant lineages but extensively boosted in alliums. Using in situ hybridization and spatial RNA sequencing, we obtained an overview of cell-type categorization and gene expression changes associated with spongy mesophyll cell expansion during onion bulb formation, thus indicating the functional roles of bulb formation genes.

Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta).

In dioecious crops such as Actinidia arguta (kiwiberries), some of the main challenges when breeding for fruit characteristics are the selection of potential male parents and the long juvenile period. Currently, breeding values of male parents are estimated through progeny tests, which makes the breeding of new kiwiberry cultivars time-consuming and costly. The application of best linear unbiased prediction (BLUP) would allow direct estimation of sex-related traits and speed up kiwiberry breeding. In this study, we used a linear mixed model approach to estimate narrow sense heritability for one vine-related trait and five fruit-related traits for two incomplete factorial crossing designs. We obtained BLUPs for all genotypes, taking into consideration whether the relationship was pedigree-based or marker-based. Owing to the high cost of genome sequencing, it is important to understand the effects of different sources of relationship matrices on estimating breeding values across a breeding population. Because of the increasing implementation of genomic selection in crop breeding, we compared the effects of incorporating different sources of information in building relationship matrices and ploidy levels on the accuracy of BLUPs' heritability and predictive ability. As kiwiberries are autotetraploids, multivalent chromosome formation and occasionally double reduction can occur during meiosis, and this can affect the accuracy of prediction. This study innovates the breeding programme of autotetraploid kiwiberries. We demonstrate that the accuracy of BLUPs of male siblings, without phenotypic observations, strongly improved when a tetraploid marker-based relationship matrix was used rather than parental BLUPs and female siblings with phenotypic observations. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01419-8.

Statin therapy is associated with improved perioperative outcomes and long-term mortality following carotid revascularization in the Vascular Quality Initiative.

OBJECTIVE: Statin therapy is the standard of care for patients with carotid artery stenosis given its proven cardiovascular benefits. However, the impact of statin therapy on outcomes in patients undergoing carotid revascularization in the Vascular Quality Initiative has not yet been evaluated. Therefore, our aim was to investigate the association of statin therapy with outcomes following carotid endarterectomy (CEA), transfemoral carotid artery stenting (tfCAS), and transcarotid artery revascularization (TCAR). METHODS: We identified all patients who underwent CEA, tfCAS, or TCAR in the Vascular Quality Initiative registry from January 2016 to September 2021. To compare outcomes, we stratified patients by procedure type and created 1:1 propensity score-matched cohorts of patients who received no preoperative statin therapy (within 36 hours of procedure) versus those who received preoperative statin therapy. Propensity scores incorporated demographic characteristics, comorbidities, carotid symptom status, preoperative medications, and physician and hospital procedural experience. The primary outcome was a composite end point of in-hospital stroke and/or death. As a secondary analysis, we performed repeat propensity score-matching by postoperative statin use (prescribed at discharge) and assessed 5-year mortality. Relative risks (RR) and hazard ratios (HR) were calculated using log binomial regression and Cox regression, respectively. RESULTS: Among 97,835 CEA, 20,303 tfCAS, and 22,371 TCAR patients, 15%, 17%, and 10% of patients did not receive preoperative statin therapy, respectively. Compared with statin use, no statin use was associated with a higher risk of in-hospital stroke or death among 13,434 matched CEA patients (no statin, 1.7% vs statin, 1.4%; RR, 1.2; 95% confidence interval [CI], 1.02-1.5) and among 2707 matched tfCAS patients (4.8% vs 2.8%; RR, 1.7; 95% CI, 1.3-2.3). However, there was no difference for this outcome by statin use among 2089 matched TCAR patients (1.8% vs 1.6%; RR, 1.1; 95% CI, 0.7-1.8). At 5 years, no statin therapy at discharge was associated with higher 5-year mortality after CEA (15% vs 10%; HR, 1.8; 95% CI, 1.6-2) and tfCAS (18% vs 14%; HR, 1.5; 95% CI, 1.2-1.8), but there was no difference after TCAR (14% vs 11%; HR, 1.3; 95% CI, 0.9-1.8). CONCLUSIONS: Compared with statin use, no statin use was associated with a higher risk of in-hospital stroke or death and 5-year mortality among CEA and tfCAS patients. Although there was no significant difference in outcomes among TCAR patients, this may in part be due to lower statistical power in this cohort. Overall, statin therapy is essential in the short- and long-term management of patients undergoing carotid revascularization. Our findings not only support current Society for Vascular Surgery recommendations for statin therapy in patients undergoing carotid revascularization, but they also highlight an important opportunity for quality improvement.

A COVID-19 Pivot Plan to Resume Elective Surgeries at the Hartford Healthcare Connecticut Orthopaedic Institute.

Background The Connecticut Orthopaedic Institute (COI) conceptualized a Pivot Plan during an elective surgery moratorium at the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic with the goal of planning and executing orthopedic procedures safely. With the resumption of elective surgeries and the continued planning of surgical recovery over the months (and possibly years) to follow, facilities must brace themselves for repeat waves of COVID-19. Thereby, herein we share the Pivot Plan, its implementation process, evaluation of patient safety, and program performance during a pandemic. This could inform the efforts of other institutions seeking to restart non-emergent surgeries during similarly trying times in the future.  Methods The COI formed a multidisciplinary team of leaders that met weekly to design a Pivot Plan and a dashboard to guide the resumption of surgeries and assess the performance of the Pivot Plan. The plan revolved around four domains: safety, space, staff, and supplies. It was implemented in two COI-affiliated facilities: MidState Medical Center (MMC) and St. Vincent's Medical Center (SVMC). Monthly metrics from May to November 2020 were compared to the six-month averages for the pre-pandemic baseline period from September 2019 to February 2020. Results The total number (N) of elective orthopaedic cases prior to the pandemic pre-COVID averaged 372 cases per month for MMC and 197 cases for SVMC. During the pandemic post-COVID, N averaging at 361 for MMC and 243 for SVMC illustrates COI was able to perform elective surgeries amid a worsening pandemic. Same-day (SD) discharge rates for total joint arthroplasty (TJA) pre-COVID averaged 8% for MMC and 3% for SVMC. Post-COVID, the SD average was 16.7% for MMC and 11.4% for SVMC. This data indicates that orthopaedic providers were cognizant of length of stay in order to reduce the risk of in-hospital exposure to COVID-19. The 30-day readmission (30R) rate for TJA pre-COVID averaged 1.4% for MMC and 2.7% for SVMC. A high level of care and follow-up is reflected in a lower average 30R post-COVID, 1.1% for both MMC and SVMC. Transitions for TJA patients to their home settings after surgery also reflect the quality of care and the efficiency of the patient throughput process with necessary precautions in place. Post-COVID, the patient transition to home (T) averaged 98.1% for MMC and 97.5% for SVMC compared to T = 96.8% for MMC and 88% for SVMC pre-COVID. No patients experienced deep vein thrombosis or pulmonary embolism during the time period of the project. Positive COVID-19 diagnosis 23 days after discharge was 0% at MMC and 0.2% at SVMC. Conclusion The COI Pivot Plan was successfully implemented at two different hospitals offering elective orthopaedic surgeries to a varied patient population. The precautions taken by COI were effective in controlling the spread of the SARS-CoV-2 virus while returning to elective orthopaedic surgery. Furthermore, data collected before and after the onset of the COVID-19 pandemic indicated that program performance and quality improved.

Construction of a high-density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing.

Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa "Hayward," is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis "Red5" reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.

Impact of Frailty on Clinical Outcomes after Carotid Artery Revascularization.

BACKGROUND: Frailty has been increasingly recognized as an important risk factor for vascular procedures. To assess the impact of frailty on clinical outcomes and resource utilization in patients undergoing carotid revascularization using a national cohort. METHODS: The 2005-2017 National Inpatient Sample was used to identify patients who underwent carotid endarterectomy (CEA) or carotid stenting (CAS). Patients were classified as frail using diagnosis codes defined by the Johns Hopkins Adjusted Clinical Groups frailty indicator. Multivariable regression was used to evaluate associations between frailty and in-hospital mortality, postoperative stroke, myocardial infarction (MI), hospitalization costs, and length of stay (LOS). RESULTS: Of 1,426,343 patients undergoing carotid revascularization, 59,158 (4.2%) were identified as frail. Among frail patients, 79.4% underwent CEA and 20.6% underwent CAS. Compared to CEA, a greater proportion of patients undergoing CAS were frail (6.0% vs. 3.8%, P < 0.001). Compared to the nonfrail cohort, frail patients had higher rates of mortality (2.2% vs. 0.5%, P < 0.001), postoperative stroke (2.6% vs. 1.0%, P < 0.001), MI (2.2% vs. 0.8%, P < 0.001), and stroke/death (4.4% vs. 1.4%, P < 0.001). After adjustment, frailty was associated with increased odds of mortality (AOR = 1.59, 95% CI: 1.30-1.80, P < 0.001), stroke (AOR = 1.66, 95% CI: 1.38-1.83 P < 0.001), MI (AOR = 1.51, 95% CI: 1.29-1.72, P < 0.001), and stroke/death (AOR = 1.62, 95% CI: 1.45-1.81, P < 0.001). Furthermore, frailty was associated with increased hospitalization costs (ß = +$5,980, 95% CI: $5,490-$6,470, P < 0.001) and LOS (ß = +2.6 days, 95% CI: 2.4-2.8, P < 0.001). CONCLUSIONS: Frailty is associated with adverse outcomes and greater resource use for those undergoing carotid revascularization. Risk models should include an assessment of frailty to guide management and improve outcomes for these high-risk patients.

QTL Mapping for Resistance to Cankers Induced by Pseudomonas syringae pv. actinidiae (Psa) in a Tetraploid Actinidia chinensis Kiwifruit Population.

Polyploidy is a key driver of significant evolutionary changes in plant species. The genus Actinidia (kiwifruit) exhibits multiple ploidy levels, which contribute to novel fruit traits, high yields and resistance to the canker-causing dieback disease incited by Pseudomonas syringae pv. actinidiae (Psa) biovar 3. However, the genetic mechanism for resistance to Psa observed in polyploid kiwifruit is not yet known. In this study we performed detailed genetic analysis of a tetraploid Actinidia chinensis var. chinensis population derived from a cross between a female parent that exhibits weak tolerance to Psa and a highly Psa-resistant male parent. We used the capture-sequencing approach across the whole kiwifruit genome and generated the first ultra-dense maps in a tetraploid kiwifruit population. We located quantitative trait loci (QTLs) for Psa resistance on these maps. Our approach to QTL mapping is based on the use of identity-by-descent trait mapping, which allowed us to relate the contribution of specific alleles from their respective homologues in the male and female parent, to the control of Psa resistance in the progeny. We identified genes in the diploid reference genome whose function is suggested to be involved in plant defense, which underly the QTLs, including receptor-like kinases. Our study is the first to cast light on the genetics of a polyploid kiwifruit and suggest a plausible mechanism for Psa resistance in this species.

Impact of Frailty on Clinical and Financial Outcomes Following Minor Lower Extremity Amputation: A Nationwide Analysis.

Frailty has been shown to portend worse outcomes in surgical patients. Our goal was to identify the impact of frailty on outcomes and resource utilization among patients undergoing minor lower extremity amputation in the United States. Using the Nationwide Readmission Database, we identified all adults undergoing a minor amputation between 2010 and 2015, and assessed 90-day outcomes, including readmission, reamputation, mortality, and cumulative hospitalization costs. Frailty was defined by International Classification of Diseases codes consistent with the ten frailty clusters as defined by the Johns Hopkins Adjusted Clinical Group System. Multivariable regression models were developed for risk adjustment. An estimated 302 798 patients (mean age = 61.8 years) were identified, of which 15.2% were categorized as Frail. Before adjustment, frailty was associated with increased rates of readmission (44% vs. 36%, P < .001) and in-hospital mortality (4% vs. 2%, P < .001). Frailty was also associated with increased cumulative costs of care ($39 417 vs. $27 244, P < .001). After risk adjustment, frailty remained an independent predictor of readmission (Adjusted odds ratio [AOR] 1.18, CI 1.14-1.23), in-hospital mortality (AOR 1.48, CI 1.34-1.65), and incremental costs (+$7 646, CI $6927-$8365). Frailty is an independent marker of worse outcomes following minor foot amputation, and may be utilized to direct quality improvement efforts.

Utilizing Advanced Technologies to Augment Pharmacovigilance Systems: Challenges and Opportunities.

There are significant challenges and opportunities in deploying and utilizing advanced information technology (IT) within pharmacovigilance (PV) systems and across the pharmaceutical industry. Various aspects of PV will benefit from automation (e.g., by improving standardization or increasing data quality). Several themes are developed, highlighting the challenges faced, exploring solutions, and assessing the potential for further research. Automation of the workflow for processing of individual case safety reports (ICSRs) is adopted as a use case. This involves a logical progression through a series of steps that when linked together comprise the complete work process required for the effective management of ICSRs. We recognize that the rapid development of new technologies will invariably outpace the regulations applicable to PV systems. Nevertheless, we believe that such systems may be improved by intelligent automation. It is incumbent on the owners of these systems to explore opportunities presented by new technologies with regulators in order to evaluate the applicability, design, deployment, performance, validation and maintenance of advanced technologies to ensure that the PV system continues to be fit for purpose. Proposed approaches to the validation of automated PV systems are presented. A series of definitions and a critical appraisal of important considerations are provided in the form of use cases. We summarize progress made and opportunities for the development of automation of future systems. The overall goal of automation is to provide high quality safety data in the correct format, in context, more quickly, and with less manual effort. This will improve the evidence available for scientific assessment and helps to inform and expedite decisions about the minimization of risks associated with medicines.

Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis).

Pseudomonas syringae pv. actinidiae (Psa) biovar 3, a virulent, canker-inducing pathogen is an economic threat to the kiwifruit (Actinidia spp.) industry worldwide. The commercially grown diploid (2×) A. chinensis var. chinensis is more susceptible to Psa than tetraploid and hexaploid kiwifruit. However information on the genetic loci modulating Psa resistance in kiwifruit is not available. Here we report mapping of quantitative trait loci (QTLs) regulating resistance to Psa in a diploid kiwifruit population, derived from a cross between an elite Psa-susceptible 'Hort16A' and a resistant male breeding parent P1. Using high-density genetic maps and intensive phenotyping, we identified a single QTL for Psa resistance on Linkage Group (LG) 27 of 'Hort16A' revealing 16-19% phenotypic variance and candidate alleles for susceptibility and resistance at this loci. In addition, six minor QTLs were identified in P1 on distinct LGs, exerting 4-9% variance. Resistance in the F1 population is improved by additive effects from 'Hort16A' and P1 QTLs providing evidence that divergent genetic pathways interact to combat the virulent Psa strain. Two different bioassays further identified new QTLs for tissue-specific responses to Psa. The genetic marker at LG27 QTL was further verified for association with Psa resistance in diploid Actinidia chinensis populations. Transcriptome analysis of Psa-resistant and susceptible genotypes in field revealed hallmarks of basal defense and provided candidate RNA-biomarkers for screening for Psa resistance in greenhouse conditions.

Thirty-Day Outcomes After Open Revascularization for Acute Mesenteric Ischemia From the American College of Surgeons National Surgical Quality Improvement Program.

BACKGROUND: Open revascularization for acute mesenteric ischemia (AMI) is associated with high perioperative morbidity and mortality; however, results from contemporary studies are varied. Therefore, we evaluated 30-day mortality after open revascularization for AMI and identified preoperative factors associated with mortality. METHODS: We performed a retrospective cohort study of patients in the American College of Surgeons National Surgical Quality Improvement Program database undergoing open mesenteric revascularization for AMI from 2005 to 2017. The primary outcome was 30-day mortality. We used multivariable logistic regression to identify preoperative factors independently associated with 30-day mortality. RESULTS: The study cohort included 918 patients; their median age was 70 years (interquartile range: 59-80 years), 62% were female, and 90% were white. Thirty-day mortality after open revascularization for AMI was 32%, specifically 35% after embolectomy, 31% after thromboendarterectomy, and 28% after mesenteric bypass. Mortality was higher in patients requiring concomitant bowel resection (38% vs. 29%, respectively, P < 0.01). The preoperative factor most strongly associated with 30-day mortality was disseminated cancer (odds ratio = 8.8, 95% confidence interval = 2.4-32, P = 0.001). Other factors independently associated with mortality were renal dysfunction, preoperative intubation, preoperative blood transfusion, diabetes, elevated preoperative international normalized ratio, elevated preoperative white blood cell count, and increasing age. CONCLUSIONS: In this retrospective cohort study using a real-world, nationwide cohort, open revascularization for AMI was associated with high mortality, with nearly one-third of patients dying within 30 days of their operation. The factors identified to be independently associated with 30-day mortality, particularly disseminated cancer, preoperative renal dysfunction, and elevated preoperative WBC count, are an important tool for preoperative risk stratification.

Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids.

During analysis of kiwifruit derived from hybrids between the high vitamin C (ascorbic acid; AsA) species Actinidia eriantha and A. chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis, we performed whole-genome sequencing on pools of hybrid genotypes with either high or low AsA fruit. Pool-GWAS (genome-wide association study) revealed a single Quantitative Trait Locus (QTL) spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis × A. eriantha) × A. chinensis backcross families, showing that the A. eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNA sequencing (RNASEQ). This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harbouring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.

Select type I and type III endoleaks at the completion of fenestrated endovascular aneurysm repair resolve spontaneously.

OBJECTIVE: The Society for Vascular Surgery reporting standards for endovascular aneurysm repair (EVAR) consider the presence of a type I or type III endoleak a technical failure. However, the nature and implications of these endoleaks in fenestrated EVAR (FEVAR) are not well understood. METHODS: We performed a single-center retrospective review of 53 patients who underwent FEVAR with the Zenith Fenestrated AAA Endovascular Graft (Cook Medical, Bloomington, Ind) from 2013 to 2018. We excluded one patient without contrast-enhanced postoperative imaging who was lost to follow-up after discharge. Small, slow, type I and type III endoleaks on completion angiography were routinely observed. We identified patients with completion type I or type III endoleaks by angiography review and characterized endoleak type, location, and rate of resolution on initial postoperative imaging. RESULTS: Fifty-two patients were included; mean age was 75 ± 8 years, 75% were male, and 91% were white. Of 146 visceral vessels (100 renal arteries and 46 superior mesenteric arteries), 145 (99%) were preserved with 103 fenestrations and 43 scallops; 102 (70%) target vessels were stented. After implantation of all device components, 31 patients (60%) had evidence of type I or type III endoleak. Twelve patients (39%) underwent further intervention at the index procedure, and three endoleaks resolved completely. Twenty-eight patients (54%) had a type I or type III endoleak on completion angiography. There were no differences between patients with and without completion endoleaks in baseline demographics, graft design, neck anatomy, or proportion of cases performed within the instructions for use of the device. Perioperative mortality was 1.9%. On initial postoperative imaging, 27 of 28 (96%) endoleaks resolved spontaneously. One small, persistent type IA or type III endoleak was identified on postoperative day 27 and was observed. This endoleak had resolved completely on computed tomography angiography 6 months postoperatively. In patients without a completion endoleak, one type IA endoleak secondary to graft infolding was discovered on postoperative imaging and was successfully treated with placement of endoanchors and Palmaz stent. Median follow-up was 269 days. No additional type I or type III endoleaks were identified in any patient for the duration of follow-up. CONCLUSIONS: Whereas completion type I and type III endoleaks are common after FEVAR with the ZFEN device, nearly all of these endoleaks resolve spontaneously by the initial postoperative imaging. These results suggest that select completion endoleaks after FEVAR with the ZFEN device do not require intervention at the index procedure.

Modelling the transport of shipborne per- and polyfluoroalkyl substances (PFAS) in the coastal environment.

Per- and polyfluoroalkyl substances (PFAS) are presently essential ingredients in aqueous film forming foam (AFFF) used for fire-fighting, but are also pervasive environmental contaminants. The use and subsequent release and transport of AFFF in the ocean environment from marine vessels has not been studied to date. A numerical model (Delft3D) was rigorously calibrated and validated for the hydrodynamics, and used to predict the transport of PFAS released instantaneously into a large harbour (Halifax Harbour, Nova Scotia) that is representative of coastal environments in eastern Canada and other parts of the world. The numerical model results indicate that PFAS released in the presence of strong winds and waves during a storm will travel up to 31 km in 2 days, approximately 40% farther than PFAS release during a time period dominated by tidal currents with light winds and small waves (<1 m). After a 10 day simulation, PFAS levels from release sites in the Inner Harbour were higher (40-60 µg/L) compared to PFAS levels from the Outer Harbour release site which had decreased to low levels (<1 µg/L) during a non-storm period. Along shorelines within the Harbour, PFAS concentrations remained elevated after 12 h (40-500 µg/L) and 48 h (2-300 µg/L). These concentrations are within the range of PFAS guidance values for recreational water use. The methods described here are relevant to studies of PFAS dispersion and transport in other coastal areas, and could be used to determine best practices for applications of AFFF in the coastal environment.

Vascular fellow and resident experience performing infrapopliteal revascularization with endovascular procedures and vein bypass during training.

OBJECTIVE: Endovascular aneurysm repair has led to a significant reduction in vascular trainee experience in the surgical treatment of aortic aneurysms. We sought to evaluate whether the vascular training paradigm or the "endovascular first" approach to lower extremity vascular disease has had a similar effect on trainee experience with infrapopliteal endovascular therapy and vein bypass. METHODS: Deidentified data were provided by the Vascular Surgery Board on the number of procedures performed by each 2014 fellowship and residency (0 + 5) graduate during training. Data were analyzed using parametric and nonparametric methods, where appropriate. RESULTS: Of 125 trainees (109 fellows, 16 residents), 33 (27%) performed 10 or fewer infrapopliteal vein bypasses and 37 (29%) performed 10 or fewer infrapopliteal endovascular procedures during their training. Eleven trainees (9%) performed 10 or fewer of both procedures. There was a positive correlation between number of infrapopliteal vein bypass and endovascular procedures performed (r = 0.19; P = .03). There was no difference between fellows and residents in the mean number of bypass operations performed during training (17.3 vs 19.1; P = .50; range, 0-53). However, residents performed more infrapopliteal endovascular procedures than fellows did (median, 29 vs 16; P = .03; range, 0-128). CONCLUSIONS: More than one in four graduates of both training paradigms finish with a low number of infrapopliteal bypasses and endovascular interventions. The number of these procedures needed for proficiency is not known. Vascular surgery training programs should critically evaluate the number of infrapopliteal procedures required to achieve proficiency.

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

BACKGROUND: Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. RESULTS: A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. CONCLUSIONS: Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Quantification of free sugars, fructan, pungency and sweetness indices in onion populations by FT-MIR spectroscopy.

BACKGROUND: To facilitate faster phenotyping of onions (Allium cepa L.), Fourier-transform mid infrared (FT-MIR) spectroscopy with partial least squares (PLS) regression modelling was evaluated for the determination of pungency (pyruvate), sweetness (free sugars) and fructan in juice samples (n = 605) expressed from bulbs from breeding populations. RESULTS: Fourier-transform infrared (FTIR) spectra (range 1700-900 cm-1 ) were obtained from droplets (30 µL) of unprocessed juice. Goodness-of-fit (r2 ) and prediction errors (standard error of cross validation) for optimal PLS models were: soluble solids (0.997, 0.1 °Brix), pyruvate [0.825, 0.8 µmol g-1 fresh weight (FW)], fructan (0.98, 1.9 mg g-1 FW), glucose (0.941, 1.1 mg g-1 FW), fructose (0.967, 1.0 mg g-1 FW) and sucrose (0.919, 1.7 mg g-1 FW). FTIR models for industry sweetness indices based on glucose or sucrose equivalents were also developed. Because of its very low concentration (0.8-12 µmol g-1 FW) relative to other compounds, pyruvate was the weakest model developed. Fructan could be determined spectroscopically without the need for enzymatic digestion. CONCLUSIONS: All of the chemometric models developed are acceptable for screening purposes. Those for soluble solids, fructan and fructose are also suitable for routine analysis. FT-MIR can therefore be utilised for the simultaneous determination of pungency, sweetness and fructan in this crop. © 2018 Society of Chemical Industry.

LDL-cholesterol Predicts a First CHD Event in Senior Citizens, Especially So in Those With Elevated Lipoprotein(a): Dubbo Study of the Elderly.

OBJECTIVE: The analysis was designed to explore the combined effects of LDL-cholesterol and lipoprotein(a) (Lp(a)) in predicting incident coronary heart disease (CHD) in senior citizens without prior CHD. METHODS: This is a prospective cohort study in Dubbo NSW which has followed 2805 men and women 60 years and older for 16 years since 1988-1989. Subjects with prior CHD (n=607) were excluded from this analysis. Incident CHD events were identified by hospital record linkage. The contributions of LDL and Lp(a) to CHD events and their combined effects were evaluated in proportional hazards regression models. RESULTS: There were 689 CHD events over 16 years in a cohort of 2198 men and women without prior CHD. LDL-cholesterol (corrected for cholesterol content of Lp(a)) and Lp(a) modelled in quartile categories each independently predicted CHD, but exclusively in Quartile 4 (Q4) for each parameter. Using the combination of LDL Q1 and Lp(a) Q1 as a reference group, LDL Q4 (>4.90mmol/L) most clearly predicted CHD in combination with Lp(a) Q4 (>276mg/L), hazard ratio 1.95 (95%CI 1.31-2.90). CONCLUSION: The present findings may have important practical implications in clinical management. If Lp(a) is assessed in senior citizens without prior CHD and found to be genuinely low, elevated LDL-cholesterol may not require active intervention.