Despite advancements, aortofemoral bypass (AFB) remains the most durable option for aortoiliac occlusive disease. Although runoff has been shown to be associated with AFB patency, the association of ...the Society for Vascular Surgery (SVS) thigh runoff scoring system with patency has not been assessed. The aim of the present study was to evaluate the association between the SVS runoff scoring system and limb-based primary patency after AFB.
Institutional data for patients undergoing AFB with preoperative runoff imaging available from 2000 to 2017 were queried. Runoff scores were assigned according to the presence of occlusive disease in the superficial femoral artery and profunda femoris artery (minimum, 1; maximum, 10) as described by the 1997 SVS reporting standards for lower extremity ischemia. Limb-based patency was the primary endpoint. Kaplan-Meier analysis was used to compare the long-term limb-based patency and freedom from reintervention between limbs with runoff scores ≥6 and those with runoff scores <6. Propensity score-weighted Cox proportional hazards modeling was used to evaluate the association between a runoff score of ≥6 and primary patency loss, controlling for other factors associated with primary patency.
In 161 patients, 316 limbs had undergone revascularization. The mean patient age was 66.7 ± 11.3 years, and 51.6% were women. Most limbs had undergone revascularization for claudication (56.5%). Most (89.4%) had TransAtlantic InterSociety Consensus class D lesions, 27.3% had required suprarenal or higher clamping, and 11.2% had undergone concomitant mesenteric intervention. A femoral outflow adjunct and concurrent lower extremity bypass was required in 41.8% and 2.9% of limbs, respectively. Those with a runoff score of ≥6 had experienced greater rates of 30-day myocardial infarction (11% vs 1%; P = .005), respiratory failure (11% vs 1%; P = .005), and mortality (8% vs 0%; P ≤ .006). The median follow-up period was 4.0 years (interquartile range, 6.5 years). The 1-, 3-, and 5-year primary patency was 94.6% (95% confidence interval CI, 91.9%-97.3%), 89.2% (95% CI, 85.4%-93.2%), and 81.4% (95% CI, 76.0%-87.1%), respectively. The 5-year primary-assisted patency, secondary patency, and freedom from reintervention were 84.9% (95% CI, 79.7%-90.5%), 91.7% (95% CI, 87.3%-96.3%), and 83.3% (95% CI, 78.3%-88.7%), respectively. Patients with a runoff score of ≥6 had lower primary (log-rank P < .01), primary-assisted (P < .01), and secondary patency (P = .01). The factors associated with the loss of primary patency included a high runoff score (runoff score of ≥6: hazard ratio HR, 4.1; 95% CI, 2.1-8.0; P < .01), simultaneous mesenteric endarterectomy (HR, 13.5; 95% CI, 1.9-97.8; P = .01), and chronic kidney disease (HR, 4.6; 95% CI, 1.5-14.6; P = .01). Increasing age (HR, 0.94 per year; 95% CI, 0.91-0.97; P < .01) and hyperlipidemia (HR, 0.44; 95% CI, 0.23-0.85; P = .01) were protective.
The SVS femoral runoff score is an important factor associated with long-term AFB limb patency. Scores of ≥6 portend for worse limb outcomes and a greater incidence of operative complications. The SVS score can be determined from preoperative axial imaging studies and serve as a guide in decision-making and operative planning.
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Pachyonychia congenita (PC) is a rare genodermatosis characterized by focal palmoplantar keratoderma, severe plantar pain and dystrophic nails. Anecdotally, some patients with PC have erythematous ...soles and episodic burning plantar pain, indicative of secondary erythromelalgia. This study aimed to identify the prevalence and genetic predictors of erythromelalgia in PC.
Seasonal influenza vaccination is recommended for patients with cancer despite concerns of disease or treatment-associated immunosuppression. The objective of this study was to evaluate vaccine ...effectiveness (VE) against laboratory-confirmed influenza for patients with cancer.
We conducted an observational test-negative design study of previously diagnosed patients with cancer 18 years of age and older who underwent influenza testing during the 2010-2011 to 2015-2016 influenza seasons in Ontario, Canada. We linked individual-level cancer registry, respiratory virus testing, and health administrative data to identify the study population and outcomes. Vaccination status was determined from physician and pharmacist billing claims. We used multivariable logistic regression to estimate VE, adjusting for age, sex, rurality, income quintile, cancer characteristics, chemotherapy exposure, comorbidities, previous health care use, influenza season, and calendar time.
We identified 26,463 patients with cancer who underwent influenza testing, with 4,320 test-positive cases (16%) and 11,783 (45%) vaccinated. Mean age was 70 years, 52% were male, mean time since diagnosis was 6 years, 69% had solid tumor malignancies, and 23% received active chemotherapy. VE against laboratory-confirmed influenza was 21% (95% CI, 15% to 26%), and VE against laboratory-confirmed influenza hospitalization was 20% (95% CI, 13% to 26%). For patients with solid tumor malignancies, VE was 25% (95% CI, 18% to 31%), compared with 8% (95% CI, -5% to 19%) for patients with hematologic malignancies (
.015). Active chemotherapy usage did not significantly affect VE, especially among patients with solid tumor cancer.
Our results support recommendations for influenza vaccination for patients with cancer. VE was decreased for patients with hematologic malignancies, and there was no significant difference in VE among patients with solid tumor cancer receiving active chemotherapy. Strategies to optimize influenza prevention among patients with cancer are warranted.
The Optical Mapping System discovers structural variants and potentiates sequence assembly of genomes via scaffolding and comparisons that globally validate or correct sequence assemblies. Despite ...its utility, there are few publicly available tools for aligning optical mapping datasets.
Here we present software, named 'Maligner', for the alignment of both single molecule restriction maps (Rmaps) and in silico restriction maps of sequence contigs to a reference. Maligner provides two modes of alignment: an efficient, sensitive dynamic programming implementation that scales to large eukaryotic genomes, and a faster indexed based implementation for finding alignments with unmatched sites in the reference but not the query. We compare our software to other publicly available tools on Rmap datasets and show that Maligner finds more correct alignments in comparable runtime. Lastly, we introduce the M-Score statistic for normalizing alignment scores across restriction maps and demonstrate its utility for selecting high quality alignments.
The Maligner software is written in C ++ and is available at https://github.com/LeeMendelowitz/maligner under the GNU General Public License.
mpop@umiacs.umd.edu.
Pulsed-field gel electrophoresis Herschleb, Jill; Ananiev, Gene; Schwartz, David C
Nature protocols,
03/2007, Volume:
2, Issue:
3
Journal Article
Peer reviewed
This protocol describes pulsed-field gel electrophoresis (PFGE), a method developed for separation of large DNA molecules. Whereas standard DNA gel electrophoresis commonly resolves fragments up to ...approximately 50 kb in size, PFGE fractionates DNA molecules up to 10 Mb. The mechanism driving these separations exploits the fact that very large DNA molecules unravel and "snake" through a gel matrix, and such electrophoretic trajectories are perturbed in a size-dependent manner by carefully oriented electrical pulses. PFGE has enabled the rapid genomic analysis of microbes and mammalian cells, and motivated development of large-insert cloning systems such as bacterial and yeast artificial chromosomes. As such, this protocol includes descriptions of two types of PFGE instrumentation (not commercially available), along with detailed instructions for their operation. Additionally, this protocol provides basic instructions for the preparation of intact chromosomal DNA from several types of organisms. PFGE takes 2-3 days, excluding sample preparation.
Variation in genome structure is an important source of human genetic polymorphism: It affects a large proportion of the genome and has a variety of phenotypic consequences relevant to health and ...disease. In spite of this, human genome structure variation is incompletely characterized due to a lack of approaches for discovering a broad range of structural variants in a global, comprehensive fashion. We addressed this gap with Optical Mapping, a high-throughput, high-resolution single-molecule system for studying genome structure. We used Optical Mapping to create genome-wide restriction maps of a complete hydatidiform mole and three lymphoblast-derived cell lines, and we validated the approach by demonstrating a strong concordance with existing methods. We also describe thousands of new variants with sizes ranging from kb to Mb.
Maize is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as ...sorghum, wheat, and rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC) was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize genomic sequence, new sequence-based genetic markers, and an optical map, we dynamically picked a minimum tiling path (MTP) of 16,910 bacterial artificial chromosome (BAC) and fosmid clones that were used by the MGSC to sequence the maize genome. The final MTP resulted in a significantly improved physical map that reduced the number of contigs from 721 to 435, incorporated a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2,120 Mb (93%) of the 2,300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2,103.4 Mb (99.2% of the 2,120 Mb physical map). More importantly, 336 contigs, comprising 94.0% of the physical map ( approximately 1,993 Mb), were ordered and oriented. Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP) of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1).
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