GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies

Background

Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i.e., sequence alignment) to determine the origin of the read. A seed location filter comes into play before alignment, discarding seed locations that alignment would deem a poor match. The ideal seed location filter would discard all poor match locations prior to alignment such that there is no wasted computation on unnecessary alignments.

Results

We propose a novel seed location filtering algorithm, GRIM-Filter, optimized to exploit 3D-stacked memory systems that integrate computation within a logic layer stacked under memory layers, to perform processing-in-memory (PIM). GRIM-Filter quickly filters seed locations by 1) introducing a new representation of coarse-grained segments of the reference genome, and 2) using massively-parallel in-memory operations to identify read presence within each coarse-grained segment. Our evaluations show that for a sequence alignment error tolerance of 0.05, GRIM-Filter 1) reduces the false negative rate of filtering by 5.59x–6.41x, and 2) provides an end-to-end read mapper speedup of 1.81x–3.65x, compared to a state-of-the-art read mapper employing the best previous seed location filtering algorithm.

Conclusion

GRIM-Filter exploits 3D-stacked memory, which enables the efficient use of processing-in-memory, to overcome the memory bandwidth bottleneck in seed location filtering. We show that GRIM-Filter significantly improves the performance of a state-of-the-art read mapper. GRIM-Filter is a universal seed location filter that can be applied to any read mapper. We hope that our results provide inspiration for new works to design other bioinformatics algorithms that take advantage of emerging technologies and new processing paradigms, such as processing-in-memory using 3D-stacked memory devices.

     

The protective effect of fish n-3 fatty acids on cerebral ischemia in rat hippocampus

Reactive oxygen species (ROS) have been implicated in the pathogenesis of cerebral injury after ischemia-reperfusion (I/R). Fish n-3 essential fatty acids (EFA), contain eicosapentaenoic acids (EPA) and docosahexoenoic acids (DHA), exhibit antioxidant properties. DHA is an important component of brain membrane phospholipids and is necessary for the continuity of neuronal functions. EPA prevents platelet aggregation and inhibits the conversion of arachidonic acid into thromboxane A(2) and prostaglandins. They have been suggested to be protective agents against neurological and neuropsychiatric disorders. In this study, the neuroprotective effects of fish n-3 EFA on oxidant-antioxidant systems and number of apoptotic neurons of the hippocampal formation (HF) subjected to cerebral I/R injury was investigated in Sprague-Dawley rats. Six rats were used as control (Group I). Cerebral ischemia was produced by occlusion of both the common carotid arteries combined with hypotension for 45 min, followed by reperfusion for 30 min, in rats either on a standard diet (Group II) or a standard diet plus fish n-3 EFA (Marincap((R)), 0.4 g/kg/day, by gavage) for 14 days (Group III). At the end of procedures, the rats were sacrificed and their brains were removed immediately. The levels of malonedialdehyde (MDA) and nitric oxide (NO) and activities of superoxide dismutase (SOD) and catalase (CAT) were measured in left HF. In addition, the number of apoptotic neurons was counted by terminal transferase dUTP nick end labelling (TUNEL) assay in histological samples of the right HF. We found that SOD activities and MDA levels increased in Group III rats compared with Group II rats. On the other hand, CAT activities and NO levels were found to be decreased in Group III rats compared with Group II rats. Additionally, the number of apoptotic neurons was lower in Group III in comparison with Group II rats. The present findings suggest that fish n-3 EFA could decrease the oxidative status and apoptotic changes in ischemic rat hippocampal formation. Dietary supplementation of n-3 EFA may be beneficial to preserve or ameliorate ischemic cerebral vascular disease.     

Effects of Carbapenem consumption on the prevalence of Acinetobacter infection in intensive care unit patients

Background

The consumption of carbapenems has increased worldwide, together with the increase in resistant gram negative bacilli. Subsequently, the prevalence of carbapenem-resistant Acinetobacter infections has increased rapidly and become a significant problem particularly in intensive care unit patients. The aim of the present study was to evaluate the changes in the prevalence of Acinetobacter infection by restricting the consumption of carbapenems in intensive care unit patients.

Methods

This study was conducted between May 1, 2011 and February 28, 2013. The amount of carbapenem consumption and the number of patients with multi-drug resistant Acinetobacter baumannii (MDRAB) isolates during the study period were retrospectively obtained from the records of the patients, who were hospitalized in the intensive care unit. The study period was divided into two periods named as: Carbapenem non-restricted period (CNRP) and carbapenem-restricted period (CRP). During CNRP, no restrictions were made on the use of carbapenems. During CRP, the use of carbapenems was not allowed if there was an alternative to carbapenems. Primary Endpoint: MDRAB infection after ICU admission. The definition of nosocomial infections related to Acinetobacter spp. was based on the criteria of the Center for Disease Control (CDC). The correlation between the amount of carbapenem consumption and the number of infections with MDRAB strains between the two periods were evaluated.

Results

During the study period, a total of 1822 patients’ (1053 patients in CNRP and 769 patients in CRP) records were evaluated retrospectively. A total of 10.82 defined daily dose (DDD/100 ICU days) of anti-pseudomonal carbapenem were used in CNRP, and this figure decreased to 6.95 DDD/100 ICU days in CRP. In the 8-month CNRP, 42 (3.98%) MDRAB-related nosocomial infections were detected, and 14 (1.82%) infections were detected in CRP (p?=?0.012).

Conclusion

The prevalence of MDRAB strains isolated in the CNRP was 2.24-fold higher than the prevalence in the CRP. The prevalence of Acinetobacter infections can be reduced by taking strict isolation measures as well as by implementing good antibiotics usage policy.     

A Stochastic Model Correctly Predicts Changes in Budding Yeast Cell Cycle Dynamics upon Periodic Expression of CLN2

In this study, we focus on a recent stochastic budding yeast cell cycle model. First, we estimate the model parameters using extensive data sets: phenotypes of 110 genetic strains, single cell statistics of wild type and cln3 strains. Optimization of stochastic model parameters is achieved by an automated algorithm we recently used for a deterministic cell cycle model. Next, in order to test the predictive ability of the stochastic model, we focus on a recent experimental study in which forced periodic expression of CLN2 cyclin (driven by MET3 promoter in cln3 background) has been used to synchronize budding yeast cell colonies. We demonstrate that the model correctly predicts the experimentally observed synchronization levels and cell cycle statistics of mother and daughter cells under various experimental conditions (numerical data that is not enforced in parameter optimization), in addition to correctly predicting the qualitative changes in size control due to forced CLN2 expression. Our model also generates a novel prediction: under frequent CLN2 expression pulses, G1 phase duration is bimodal among small-born cells. These cells originate from daughters with extended budded periods due to size control during the budded period. This novel prediction and the experimental trends captured by the model illustrate the interplay between cell cycle dynamics, synchronization of cell colonies, and size control in budding yeast.     

Role of hemoglobin oxygenation in the modulation of red blood cell mechanical properties by nitric oxide

It has been previously demonstrated that both externally generated and internally synthesized nitric oxide (NO) can affect red blood cell (RBC) deformability. Further studies have shown that the RBC has active NO synthesizing mechanisms and that these mechanisms may play role in maintaining normal RBC mechanical properties. However, hemoglobin within the RBC is known to be a potent scavenger of NO; oxy-hemoglobin scavenges NO faster than deoxy-hemoglobin via the dioxygenation reaction to nitrate. The present study aimed at investigating the role of hemoglobin oxygenation in the modulation of RBC rheologic behavior by NO. Human blood was obtained from healthy volunteers, anticoagulated with sodium heparin (15 IU/mL), and the hematocrit was adjusted to 0.4 L/L by adding or removing autologous plasma. Several two mL aliquots of blood were equilibrated at room temperature (22 ± 2 °C) with moisturized air or 100% nitrogen by a membrane gas exchanger, The NO donor sodium nitroprusside (SNP), at a concentration range of 10^?7–10^?4 M, was added to the equilibrated aliquots which were maintained under the same conditions for an additional 60 min. The effect of the non-specific NOS inhibitor l-NAME was also tested at a concentration of 10^?3 M. RBC deformability was measured using an ektacytometer with an environment corresponding to that used for the prior incubation (i.e., oxygenated or deoxygenated). Our results indicate an improvement of RBC deformability with the NO donor SNP that was much more pronounced in the deoxygenated aliquots. SNP also had a more pronounced effect on RBC aggregation for deoxygenated RBC. Conversely, l-NAME had no effect on deoxygenated blood but resulted in impaired deformability, with no change in aggregation for oxygenated blood. These findings can be explained by a differential behavior of hemoglobin under oxygenated and deoxygenated conditions; the influence of oxygen partial pressure on NOS activity may also play a role. It is therefore critical to consider the oxygenation state of intracellular hemoglobin while studying the role of NO as a regulator of RBC mechanical properties.     

Daily movements and home range of Eastern Hermann's Tortoise,Testudo hermanni boettgeri (Reptilia: Testudines)

Understanding the movements of animals in the wild is critical for providing important information regarding their conservation and management. With this aim in mind, we studied a population of Testudo hermanni in their natural habitat using micro GPS devices. Additionally, using VHF transmitters we tracked six individuals (four females and two males) from May to August 2015. The overall home range size varied from 813 and 123,567 m². Home range size did not differ significantly between males and females, and was also independent of the size of the individual (expressed as straight carapace length). Individual movements were confined to short distances (males 25.7 m; females 18.5 m). Activity levels were highest in July and August for males and May and July for females.     

Particle simulation on the Cell BE architecture

This paper presents two parallel formulations for the Barnes-Hut algorithm on the Cell architecture, which differ in tree distribution and construction phases of the algorithm. In the initial parallelization, the domains are dynamically partitioned and assigned to the synergistic processing elements (SPEs), and SPEs construct local trees of the sub-domains in parallel. The enhanced parallelization scheme provides better clustering of the particles by sequentially constructing the global tree of the entire work space in the power processing element (PPE) and by partitioning the tree into sub-trees that can fit in the Local Store. SPEs operate on the sub-tree data and construct local trees in parallel. Our experimental evaluation indicates that this application performs much faster on the Cell BE compared to the Intel Xeon based system. Specifically, our first and second methods on the Cell BE outperform Intel Xeon by a factor of 5.8 and 7.1 for 8192 particles, respectively.     

Asymmetrically reliable caches for multicore architectures under performance and energy constraints

Cache structures in a multicore system are more vulnerable to soft errors due to high transistor density. Protecting all caches unselectively has notable overhead on performance and energy consumption. In this study, we propose asymmetrically reliable caches to supply reliability need of the system using sufficient additional hardware under the performance and energy constraints. In our framework, a chip multiprocessor is composed of a high reliability core which has ECC protection, and a set of low reliability cores which have no protection on their data caches. Between two types of cores, there is also a middle-level reliability core which has only parity check. Application threads are mapped on the different cores in terms of reliability based on their critical data usage. The experimental results for selected applications show that our proposed techniques improve reliability with considerable performance and energy overhead on the average compared to traditional unsafe caches.     

Time course of hemorheological alterations after heavy anaerobic exercise in untrained human subjects.

The time course of hemorheological alterations was investigated after heavy anaerobic exercise in untrained male human subjects. The Wingate protocol was performed by each subject, and blood lactate, red blood cell (RBC) deformability and aggregation, white blood cell (WBC) activation, and several hematological parameters were investigated during 24 h after the exercise and compared with preexercise values. Compared with the preexercise value, blood lactate level was found to be approximately 10-fold higher immediately after the exercise. There was a transient, significant increment of RBC and WBC counts immediately after exercise that was followed by a decrement of RBC count. There was a second increase of WBC count, accompanied with increased percentages of granulocytes and granulocyte activation, starting 45 min after exercise. RBC deformability was found to be impaired immediately after exercise and remained reduced for at least 12 h; RBC aggregation was also found to be decreased after exercise, with the onset of this decrease delayed by 30 min. The results of this study indicate that a single bout of heavy anaerobic exercise may induce significant hemorheological deterioration lasting for up to 12 h and thus suggest the need to consider such effects in individuals with impaired cardiovascular function.