SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE". Comments most welcom

Lagrange coded federated learning (L-CoFL) model for Internet of Vehicles

In Internet-of-Vehicles (IoV), smart vehicles can efficiently process various sensing data through federated learning (FL) - a privacy-preserving distributed machine learning (ML) approach that allows collaborative development of the shared ML model without any data exchange. However, traditional FL approaches suffer from poor security against the system noise, e.g., due to low-quality trained data, wireless channel errors, and malicious vehicles generating erroneous results, which affects the accuracy of the developed ML model. To address this problem, we propose a novel FL model based on the concept of Lagrange coded computing (LCC) - a coded distributed computing (CDC) scheme that enables enhancing the system security. In particular, we design the first L-CoFL (Lagrange coded FL) model to improve the accuracy of FL computations in the presence of lowquality trained data and wireless channel errors, and guarantee the system security against malicious vehicles. We apply the proposed L-CoFL model to predict the traffic slowness in IoV and verify the superior performance of our model through extensive simulations

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)

Background: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alterative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC boards to offer ~55 PFLOPS. The CPU-like architecture of MIC allows CPU-based software to be parallelized easily; however, the performance is often inferior to GPU counterparts as an MIC card contains only ~60 cores (while a GPU card typically has over a thousand cores). Results: To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core. By utilizing the 512-bit vector units in the MIC and implementing a new seeding strategy, experiments on aligning 150 bp paired-end reads show that MICA using one MIC card is 4.9 times faster than BWA-MEM (using 6 cores of a top-end CPU), and slightly faster than SOAP3-dp (using a GPU). Furthermore, MICA's simplicity allows very efficient scale-up when multiple MIC cards are used in a node (3 cards give a 14.1-fold speedup over BWA-MEM). Summary: MICA can be readily used by MIC-enabled supercomputers for production purpose. We have tested MICA on Tianhe-2 with 90 WGS samples (17.47 Tera-bases), which can be aligned in an hour using 400 nodes. MICA has impressive performance even though MIC is only in its initial stage of development. Availability and implementation: MICA's source code is freely available at http://sourceforge.net/projects/mica-aligner under GPL v3. Supplementary information: Supplementary information is available as "Additional File 1". Datasets are available at www.bio8.cs.hku.hk/dataset/mica.published_or_final_versio

Intracellular β\u3csub\u3e1\u3c/sub\u3e-Adrenergic Receptors and Organic Cation Transporter 3 Mediate Phospholamban Phosphorylation to Enhance Cardiac Contractility

Rationale: β1ARs (β1-adrenoceptors) exist at intracellular membranes and OCT3 (organic cation transporter 3) mediates norepinephrine entry into cardiomyocytes. However, the functional role of intracellular β1AR in cardiac contractility remains to be elucidated. Objective: Test localization and function of intracellular β1AR on cardiac contractility. Methods and Results: Membrane fractionation, super-resolution imaging, proximity ligation, coimmunoprecipitation, and single-molecule pull-down demonstrated a pool of β1ARs in mouse hearts that were associated with sarco/endoplasmic reticulum Ca2+-ATPase at the sarcoplasmic reticulum (SR). Local PKA (protein kinase A) activation was measured using a PKA biosensor targeted at either the plasma membrane (PM) or SR. Compared with wild-type, myocytes lacking OCT3 (OCT3-KO [OCT3 knockout]) responded identically to the membrane-permeant βAR agonist isoproterenol in PKA activation at both PM and SR. The same was true at the PM for membrane-impermeant norepinephrine, but the SR response to norepinephrine was suppressed in OCT3-KO myocytes. This differential effect was recapitulated in phosphorylation of the SR-pump regulator phospholamban. Similarly, OCT3-KO selectively suppressed calcium transients and contraction responses to norepinephrine but not isoproterenol. Furthermore, sotalol, a membrane-impermeant βAR-blocker, suppressed isoproterenol-induced PKA activation at the PM but permitted PKA activation at the SR, phospholamban phosphorylation, and contractility. Moreover, pretreatment with sotalol in OCT3-KO myocytes prevented norepinephrine-induced PKA activation at both PM and the SR and contractility. Conclusions: Functional β1ARs exists at the SR and is critical for PKA-mediated phosphorylation of phospholamban and cardiac contractility upon catecholamine stimulation. Activation of these intracellular β1ARs requires catecholamine transport via OCT3

Hydrogen Sulfide Mediates K+ and Na+ Homeostasis in the Roots of Salt-Resistant and Salt-Sensitive Poplar Species Subjected to NaCl Stress

Non-invasive micro-test techniques (NMT) were used to analyze NaCl-altered flux profiles of K+, Na+, and H+ in roots and effects of NaHS (a H2S donor) on root ion fluxes in two contrasting poplar species, Populus euphratica (salt-resistant) and Populus popularis (salt-sensitive). Both poplar species displayed a net K+ efflux after exposure to salt shock (100 mM NaCl), as well as after short-term (24 h), and long-term (LT) (5 days) saline treatment (50 mM NaCl, referred to as salt stress). NaHS (50 μM) restricted NaCl-induced K+ efflux in roots irrespective of the duration of salt exposure, but K+ efflux was not pronounced in data collected from the LT salt stress treatment of P. euphratica. The NaCl-induced K+ efflux was inhibited by a K+ channel blocker, tetraethylammonium chloride (TEA) in P. popularis root samples, but K+ loss increased with a specific inhibitor of plasma membrane (PM) H+-ATPase, sodium orthovanadate, in both poplar species under LT salt stress and NaHS treatment. This indicates that NaCl-induced K+ loss was through depolarization-activated K+ channels. NaHS caused increased Na+ efflux and a corresponding increase in H+ influx for poplar roots subjected to both the short- and LT salt stress. The NaHS-enhanced H+ influx was not significant in P. euphratica samples subjected to short term salt stress. Both sodium orthovanadate and amiloride (a Na+/H+ antiporter inhibitor) effectively inhibited the NaHS-augmented Na+ efflux, indicating that the H2S-enhanced Na+ efflux was due to active Na+ exclusion across the PM. We therefore conclude that the beneficial effects of H2S probably arise from upward regulation of the Na+/H+ antiport system (H+ pumps and Na+/H+ antiporters), which promote exchange of Na+ with H+ across the PM and simultaneously restricted the channel-mediated K+ loss that activated by membrane depolarization

Expanding the portfolio of tribo-positive materials: aniline formaldehyde condensates for high charge density triboelectric nanogenerators

The rapid uptake of energy harvesting triboelectric nanogenerators (TENGs) for self-powered electronics requires the development of high-performance tribo-materials capable of providing large power outputs. This work reports on the synthesis and use of aniline formaldehyde resin (AFR) for energy-harvesting applications. The facile, acidic-medium reaction between aniline and formaldehyde produces the aniline-formaldehyde condensate, which upon an in-vacuo high temperature curing step provides smooth AFR films with abundant nitrogen and oxygen surface functional groups which can acquire a tribo-positive charge and thus endow AFR with a significantly higher positive tribo-polarity than the existing state-of-art polyamide-6 (PA6). A TENG comprising of optimized thin-layered AFR against a polytetrafluoroethylene (PTFE) film produced a peak-to-peak voltage of up to ~1,000 V, a current density of ~65 mA m⁻², a transferred charge density of ~200 μC m⁻² and an instantaneous power output (energy pulse) of ~11 W m⁻² (28.1 μJ cycle⁻¹), respectively. The suitability of AFR was further supported through the Kelvin probe force microscopy (KPFM) measurements, which reveal a significantly higher average surface potential value of 1.147 V for AFR as compared to 0.87 V for PA6 and a step-by-step increase of the surface potential with the increase of energy generation cycles. The work not only proposes a novel and scalable mouldable AFR synthesis process but also expands with excellent prospects, the current portfolio of tribo-positive materials for triboelectric energy harvesting applications

Arabidopsis Fatty Acid Desaturase FAD2 Is Required for Salt Tolerance during Seed Germination and Early Seedling Growth

Fatty acid desaturases play important role in plant responses to abiotic stresses. However, their exact function in plant resistance to salt stress is unknown. In this work, we provide the evidence that FAD2, an endoplasmic reticulum localized ω-6 desaturase, is required for salt tolerance in Arabidopsis. Using vacuolar and plasma membrane vesicles prepared from the leaves of wild-type (Col-0) and the loss-of-function Arabidopsis mutant, fad2, which lacks the functional FAD2, we examined the fatty acid composition and Na+-dependent H+ movements of the isolated vesicles. We observed that, when compared to Col-0, the level of vacuolar and plasma membrane polyunsaturation was lower, and the Na+/H+ exchange activity was reduced in vacuolar and plasma membrane vesicles isolated from fad2 mutant. Consistent with the reduced Na+/H+ exchange activity, fad2 accumulated more Na+ in the cytoplasm of root cells, and was more sensitive to salt stress during seed germination and early seedling growth, as indicated by CoroNa-Green staining, net Na+ efflux and salt tolerance analyses. Our results suggest that FAD2 mediated high-level vacuolar and plasma membrane fatty acid desaturation is essential for the proper function of membrane attached Na+/H+ exchangers, and thereby to maintain a low cytosolic Na+ concentration for salt tolerance during seed germination and early seedling growth in Arabidopsis

Treatment of chlorpyrifos manufacturing wastewater by peroxide promoted-catalytic wet air oxidation, struvite precipitation, and biological aerated biofilter

Chlorpyrifos manufacturing wastewater (CMW) is characterized by complex composition, high chemical oxygen demand (COD) concentration, and toxicity. An integrated process comprising of peroxide (H2O2) promoted-catalytic wet air oxidation (PP-CWAO), struvite precipitation, and biological aerated filters (BAF) was constructed to treat CMW at a starting COD of 34000–35000 mg/L, total phosphorus (TP) of 5550–5620 mg/L, and total organophosphorus (TOP) of 4700–4840 mg/L. Firstly, PP-CWAO was used to decompose high concentrations of organic components and convert concentrated and recalcitrant TOP to inorganic phosphate. Copper citrate and ferrous citrate were used as the catalysts of PP-CWAO. Under the optimized conditions, 100% TOP was converted to inorganic phosphate with 95.6% COD removal. Then, the PP-CWAO effluent was subjected to struvite precipitation process for recovering phosphorus. At a molar ratio of Mg2+:NH4+:PO43− = 1.1:1.0:1.0, phosphate removal and recovery reached 97.2%. The effluent of struvite precipitation was further treated by the BAF system. Total removals of 99.0%, 95.2%, 97.3%, 100%, and 98.3% were obtained for COD, total suspended solids, TP, TOP, and chroma, respectively. This hybrid process has proved to be an efficient approach for organophosphate pesticide wastewater treatment and phosphorus reclamation