WFA-GPU: gap-affine pairwise read-alignment using GPUs

MOTIVATION

Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long and noisy sequences like those produced by PacBio and Nanopore technologies. The recently proposed wavefront alignment (WFA) algorithm paves the way for more efficient alignment tools, improving time and memory complexity over previous methods. However, high-performance computing (HPC) platforms require efficient parallel algorithms and tools to exploit the computing resources available on modern accelerator-based architectures.

RESULTS

This paper presents WFA-GPU, a GPU (graphics processing unit)-accelerated tool to compute exact gap-affine alignments based on the WFA algorithm. We present the algorithmic adaptations and performance optimizations that allow exploiting the massively parallel capabilities of modern GPU devices to accelerate the alignment computations. In particular, we propose a CPU-GPU co-design capable of performing inter-sequence and intra-sequence parallel sequence alignment, combining a succinct WFA-data representation with an efficient GPU implementation. As a result, we demonstrate that our implementation outperforms the original multi-threaded WFA implementation by up to 4.3× and up to 18.2× when using heuristic methods on long and noisy sequences. Compared to other state-of-the-art tools and libraries, the WFA-GPU is up to 29× faster than other GPU implementations and up to four orders of magnitude faster than other CPU implementations. Furthermore, WFA-GPU is the only GPU solution capable of correctly aligning long reads using a commodity GPU.

AVAILABILITY AND IMPLEMENTATION

WFA-GPU code and documentation are publicly available at https://github.com/quim0/WFA-GPU.

Transcervical carotid artery stenting with flow reversal eliminates emboli during stenting: why does it work and what are the advantages with this approach

Carotid artery stenting (CAS) remains under scrutiny because of the controversial results of major trials that compared it with carotid endarterectomy. However, the question of how the results of carotid stenting are influenced by the access technique and cerebral protection methods has not been properly addressed in any trial. Most unresolved technical weaknesses of transfemoral carotid stenting are related to instrumentation of the arch and proximal supra-aortic trunks, crossing of the carotid lesion without protection, and use of distal filter protection devices of unproven benefit. All these problems can be avoided by using a transcervical approach with carotid flow reversal for protection. The potential advantage of transcervical carotid artery stenting (CAS) is demonstrated by the fact that it can be done in octogenarians without increased morbidity, produces a lower incidence of middle cerebral artery transcranial Doppler (TCD)-detected embolic signals during the procedure, carries a significant reduction in the incidence of ischemic brain infarcts as detected by diffusion weighted magnetic resonance imaging (MRI), when compared to transfemoral stenting with distal filter protection, and can be done with a remarkably low incidence of major adverse events.

Advantages and indications of transcervical carotid artery stenting with carotid flow reversal

AIM

The aim of this Italian prospective registry was to evaluate the applicability and efficacy of the Mo.Ma Device (Invatec, Roncadelle, Italy) for the prevention of cerebral embolization during carotid artery stenting (CAS) in a real world population.

METHODS

In 4 Italian centers, 416 patients (300 men; mean age 71.6+/-9 years) between October 2001 and March 2005 were enrolled in a prospective registry. Two-hundred and sixty-four symptomatic (63.46%) with >50% diameter stenosis and 152 (36.54%) asymptomatic patients with >70% diameter stenosis were included. The Mo.Ma Proximal Flow Blockage Embolic Protection System was used to perform protected CAS, achieving cerebral protection by endovascular clamping of the common carotid artery (CCA) and of the external carotid artery (ECA).

RESULTS

Technical success, defined as the ability to establish protection with the Mo.Ma device and to deploy the stent, was achieved in 412 cases (99.03%). The mean duration of flow blockage was 4.91+/-1.1 min. Transient intolerances to flow blockage were observed in 24 patients (5.76%), but in all cases the procedure was successfully completed. No peri-procedural strokes and deaths were observed. Complications during hospitalization included 16 minor strokes (3.84%), 3 transient ischemic attacks (0.72%), 2 deaths (0.48%) and 1 major stroke (0.24%). This resulted in a cumulative rate at discharge of 4.56% all strokes and deaths, and of 0.72% major strokes and deaths. All the patients underwent thirty-day follow-up. At thirty-day follow-up, there were no deaths and no minor and major strokes, confirming the overall cumulative 4.56% incidence of all strokes and deaths rate, and of 0.72% rate of major strokes and deaths at follow up. In 245 cases (58.89%) there was macroscopic evidence of debris after filtration of the aspirated blood.

CONCLUSIONS

This Italian multicenter registry confirms and further supports the efficacy and applicability of the endovascular clamping concept with proximal flow blockage in a broad patient series. Results match favorably with current available studies on carotid stenting with cerebral protection.

Low molecular weight heparin versus oral anticoagulants in the long-term treatment of deep venous thrombosis

PURPOSE

The purpose of this study was to evaluate whether low molecular weight heparin (LMWH) could be equal or more effective than conventional oral anticoagulants (OAs) in the long-term treatment of deep venous thrombosis (DVT).

METHODS

One hundred fifty-eight patients with symptomatic DVT of the lower limbs confirmed by means of duplex ultrasound scan were randomized to receive 3 to 6 months' treatment with nadroparine calcium or acenocoumarol. Quantitative and qualitative duplex scan scoring systems were used to study the evolution of thrombosis in both groups at 1, 3, 6, and 12 months.

RESULTS

During the 12-month surveillance period, two (2.5%) of the 81 patients who received LMWH and seven (9%) of the 77 patients who received OAs had recurrence of venous thrombosis (not significant). In the LMWH group no cases of major bleeding were found, and four cases (5.2%) occurred in the OA group (not significant). The mortality rate was nine (11.1%) in the LMWH group and 7.8% in the OA group (not significant). The quantitative mean duplex scan score decreased in both groups during the follow-up and had statistical significance after long-term LMWH treatment on iliofemoral DVT (1, 3, 6, and 12 months), femoropopliteal DVT (1-3 months), and infrapopliteal DVT (first month). Duplex scan evaluation showed that the rate of venous recanalization significantly increased in the common femoral vein at 6 and at 12 months and during each point of follow-up in the superficial and popliteal veins in the LMWH group. Reflux was significantly less frequent in communicating veins after LMWH treatment (17.9% vs 32.2% in the OA group). The reflux rates in the superficial (22.4% in the LMWH group, 30.6% in OA group) and deep (13.4% vs 17.7%) venous system showed no significant differences between groups.

CONCLUSIONS

The unmonitored subcutaneous administration of nadroparine in fixed daily doses was more effective than oral acenocoumarol with laboratory control adjustment in achieving recanalization of leg thrombi. With nadroparine, there was less late valvular communicating vein insufficiency, and it was at least as efficacious and safe as oral anticoagulants after long-term administration. These results suggest that LMWHs may therefore represent a real therapeutic advance in the long-term management of DVT.

The role of cholesterol accumulation in prosthetic vascular graft anastomotic intimal hyperplasia

PURPOSE

To demonstrate that modulation of plasma cholesterol concentrations affects prosthetic vascular graft anastomotic intimal hyperplasia (AIH), aortic grafts were examined histologically and biochemically in 41 rabbits.

METHODS

Twenty-seven rabbits were fed standard rabbit diet, whereas 14 were fed cholesterol-supplemented diet to induce hypercholesterolemia.

RESULTS

A smooth muscle cell proliferative response, similar to AIH in humans, was seen equally at the proximal and distal anastomoses. However, surface area and thickness of AIH were significantly greater in rabbits with hypercholesterolemia. Anastomotic tissue cholesterol concentrations were fifteenfold higher in rabbits with hypercholesterolemia than in rabbits with normal cholesterol concentrations and anastomotic cholesterol concentrations were fivefold higher than in the aorta away from the graft in rabbits with hypercholesterolemia. Preferential deposition of radioiodinated dilactitol tyramine coupled to low-density lipoproteins, but not albumin, was demonstrated in anastomotic areas and grafts of rabbits with normal cholesterol concentrations as well. Surface area and thickness of AIH correlated closely with plasma and tissue cholesterol concentrations.

CONCLUSIONS

Oxidized products of lipoproteins have been shown to stimulate production of growth factors that cause smooth muscle cell proliferation, migration, and synthetic function. It is likely they play an important part in prosthetic vascular graft AIH, similar to their role in atherogenesis.

Probucol reduces the cellularity of aortic intimal thickening at anastomotic regions adjacent to prosthetic grafts in cholesterol-fed rabbits

Intimal hyperplasia is a persistent problem after implantation of prosthetic grafts. Although the mechanisms underlying this hyperplastic response are unknown, it has been proposed that such responses may be due to chronic vascular injury similar to that of atherogenesis. Thus, the role of oxidation was explored using the potent antioxidant drug probucol. Adult New Zealand White rabbits fed a modestly (0.25%) cholesterol-enriched diet had a polytetrafluoroethylene prosthetic graft placed into the lower aorta. After the grafting procedure, a group of 11 rabbits was placed on the cholesterol-enriched diet supplemented with 1% wt/wt probucol while a control group of 10 rabbits was placed on the cholesterol-enriched diet alone. The rabbits were maintained for a further 10 weeks before histological examination of the area surrounding the graft. Although administration of probucol did not significantly alter the dimensions of lesions at the anastomotic sites, the drug promoted striking histological changes in the surrounding tissue. Both groups of rabbits had a similar intimal hyperplastic response of the aortic tissue surrounding the graft. The vascular lesions present in the perigraft region of the control group consisted of a normal-appearing media but a thickened intima. The thickened intima contained numerous smooth muscle cells in a network of extracellular matrix. Regions in the neointima that were rich in smooth muscle cells exhibited modest staining for proliferating cell nuclear antigen. A few macrophages were present in the control group as determined by immunostaining with the monoclonal antibody RAM-11. In contrast, administration of probucol led to a marked reduction in the presence of RAM-11-staining macrophages.(ABSTRACT TRUNCATED AT 250 WORDS)

Sequential abdominal reexploration with the zipper technique

Frequently, several multiple abdominal reexplorations are needed in patients with acute necrotizing hemorrhagic pancreatitis (ANP) or with persistent intraabdominal sepsis (PIAS). Residual undrained necrotic and septic foci lead to multiple organ failure. To provide wide-open drainage of the abdominal cavity, since 1985 we have performed sequential abdominal reexploration with the zipper technique (SARZT) in 24 patients. Apache II score was used to evaluate expected mortality. In the pancreatic necrosis group, with a mean Apache II score of 31, the expected and the observed mortality were 70% and 29%, respectively. In the PIAS group, with a mean Apache II score of 30, the expected and observed mortality were 60 and 28%, respectively. These results are attributed to the sequential reexploration of the abdominal cavity that permits excision and drainage of necrotic and septic foci.

Extensive disobliteration of the aorto-iliac and common femoral arteries using the LeVeen plaque cracker

In 1978 LeVeen et al. described an original technique for extended aortobifemoral disobliteration using a retroperitoneal approach. This technique was introduced to Europe by Widdershoven and Willekens in 1977 and was adopted in Belgium by Suy and Nevelsteen in 1982 and in Spain by Cuesta and Bengoechea in 1984. A group of 228 patients treated by the LeVeen's method from 1982 to 1987 were followed-up for a mean of 21 months (1-54). Disabling claudication (66%) or more advanced ischaemia (34%) was the indication for treatment. An aorto-bifemoral endarterectomy was performed in 124 patients. Aorto-biiliac endarterectomy in 39, unilateral aortofemoral endarterectomy with a contralateral aorto-iliac endarterectomy in 17 and unilateral iliofemoral endarterectomy in 48 cases. There were seven postoperative deaths (3%) and an early thrombectomy had to be performed in 8 patients. There were 14 late deaths. Occlusion occurred in 11 patients giving a 3-year-patency rate of 97%. There were no late complications related to the technique. It is concluded that disobliteration using the LeVeen technique compares well with prosthetic grafting. Since this method does not require the use of foreign material the patient is protected from the complications sometimes seen after the insertion of prosthetic grafts.

Extensive endarterectomy of the aorta, common and external iliac arteries, and common femoral arteries by a modified Le Veen method

It has been 8 years since Le Veen et al. described a new method of disobliteration of the distal aorta and iliac arteries. Since then no further reports have appeared in the literature. During the past 2 1/2 years we have treated 23 patients with severe ischemia of the lower limbs, caused in most cases by severe and multilevel arterial occlusions (types II and III), which included the infrarenal aorta, common and external iliac arteries, and common femoral arteries, with the method of Le Veen et al. with some modifications in the technique. A satisfactory revascularization was obtained in all patients. Similarly, there were no operative deaths or morbidity and no early or late arterial occlusions. We conclude that this method of arterial disobliteration has certain advantages over the much more widely used bypass grafting, deserves an extensive trial, and could in the future become a well-accepted procedure to treat extensive occlusions of the distal aorta, common and external iliac arteries, and common femoral arteries.