Deca : a garbage collection optimizer for in-memory data processing

In-memory caching of intermediate data and active combining of data in shuffle buffers have been shown to be very effective in minimizing the recomputation and I/O cost in big data processing systems such as Spark and Flink. However, it has also been widely reported that these techniques would create a large amount of long-living data objects in the heap. These generated objects may quickly saturate the garbage collector, especially when handling a large dataset, and hence, limit the scalability of the system. To eliminate this problem, we propose a lifetime-based memory management framework, which, by automatically analyzing the user-defined functions and data types, obtains the expected lifetime of the data objects and then allocates and releases memory space accordingly to minimize the garbage collection overhead. In particular, we present Deca,1 a concrete implementation of our proposal on top of Spark, which transparently decomposes and groups objects with similar lifetimes into byte arrays and releases their space altogether when their lifetimes come to an end. When systems are processing very large data, Deca also provides field-oriented memory pages to ensure high compression efficiency. Extensive experimental studies using both synthetic and real datasets show that, in comparing to Spark, Deca is able to (1) reduce the garbage collection time by up to 99.9%, (2) reduce the memory consumption by up to 46.6% and the storage space by 23.4%, (3) achieve 1.2× to 22.7× speedup in terms of execution time in cases without data spilling and 16× to 41.6× speedup in cases with data spilling, and (4) provide similar performance compared to domain-specific systems

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

The Influence of a Key Indicator k_v on the Diffusion Range of Underwater Oil Spill

As oil spills cause harm to the survival and environment of the ocean, the objective of the present paper is to study the oil migration range using the key indicator kv, which is defined as the ratio of oil spill speed to ocean current speed. The correctness of diffusion models created and estimated for subsea oil spills can be verified by experiments. We also considered the effect of key indicators on the horizontal and vertical dispersion ranges of oil spills. The study’s findings show that, under various kv settings, the horizontal and vertical spreading heights of oil spills both increase as kv rises. When kv is equal, the leakage velocity and water flow velocity increase synchronously, and over time, the horizontal distance and vertical diffusion height of the oil spill gradually increase. In the early stages of an oil spill, when kv = 50, 100, or 150, the vertical spreading velocity will rapidly decrease. The vertical spreading speed of spilled oil increases as kv rises when the water flow rate remains constant. The horizontal migration distance grows as kv decreases when the leakage rate is constant. Fitting curves for the vertical rise height and horizontal spreading distance for the same and various kv settings were also obtained in order to anticipate the migration mode of oil spills. This is critical for dealing with environmental damage caused by maritime oil spills, as well as emergency responses

Evaluation of the electrocardiogram RV5/V6 criteria in the diagnosis of left ventricular hypertrophy in marathon runners

Abstract To assess the value of electrocardiogram (ECG) RV5/V6 criteria for diagnosing left ventricular hypertrophy (LVH) in marathons. A total of 112 marathon runners who met the requirements for “Class A1” events certified by the Chinese Athletics Association in Changzhou City were selected, and their general clinical information was collected. ECG examinations were performed using a Fukuda FX7402 Cardimax Comprehensive Electrocardiograph Automatic Analyser, whereas routine cardiac ultrasound examinations were performed using a Philips EPIQ 7C echocardiography system. Real‐time 3‐dimensional echocardiography (RT‐3DE) was performed to acquire 3‐dimensional images of the left ventricle and to calculate the left ventricular mass index (LVMI). According to the LVMI criteria of the American Society of Echocardiography for the diagnosis of LVH, the participants were divided into an LVMI normal group (n = 96) and an LVH group (n = 16). The correlation between the ECG RV5/V6 criteria and LVH in marathon runners was analysed using multiple linear regression stratified by sex and compared with the Cornell (SV3 + RaVL), modified Cornell (SD + RaVL), Sokolow–Lyon (SV1 + RV5/V6), Peguero–Lo Presti (SD + SV4), SV1, SV3, SV4, and SD criteria. In marathon runners, the ECG parameters SV3 + RaVL, SD + RaVL, SV1 + RV5/V6, SD + SV4, SV3, SD, and RV5/V6 were able to identify LVH (all p < .05). When stratified by sex, linear regression analysis revealed that a significantly higher number of ECG RV5/V6 criteria were evident in the LVH group than in the LVMI normal group (p < .05), both with no adjustment and after initial adjustment (including age and body mass index), as well as after full adjustment (including age, body mass index, interventricular septal thickness, left ventricular end‐diastolic diameter, left ventricular posterior wall thickness, and history of hypertension). Additionally, curve fitting showed that the ECG RV5/V6 values increased with increasing LVMI in marathon runners, exhibiting a nearly linear positive correlation. In conclusions, the ECG RV5/V6 criteria were correlated with LVH in marathon runners

A Melting Curve-Based Multiplex RT-qPCR Assay for Simultaneous Detection of Four Human Coronaviruses

Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 are common respiratory viruses associated with acute respiratory infection. They have a global distribution. Rapid and accurate diagnosis of HCoV infection is important for the management and treatment of hospitalized patients with HCoV infection. Here, we developed a melting curve-based multiplex RT-qPCR assay for simultaneous detection of the four HCoVs. In the assay, SYTO 9 was used to replace SYBR Green I as the fluorescent dye, and GC-modified primers were designed to improve the melting temperature (Tm) of the specific amplicon. The four HCoVs were clearly distinguished by characteristic melting peaks in melting curve analysis. The detection sensitivity of the assay was 3 × 102 copies for HCoV-OC43, and 3 × 101 copies for HCoV-NL63, HCoV-229E and HCoV-HKU1 per 30 μL reaction. Clinical evaluation and sequencing confirmation demonstrated that the assay was specific and reliable. The assay represents a sensitive and reliable method for diagnosis of HCoV infection in clinical samples

Potential role of Cyr61 induced degeneration of human Müller cells in diabetic retinopathy.

The degeneration of Müller cells has been recognized to involve in the pathogenesis of diabetic retinopathy. However, the mechanism is not yet clear. This study is to explore the potential role of Cyr61, a secreted signaling protein in extracellular matrix, in inducing human Müller cell degeneration in diabetic retinopathy (DR). Twenty patients with proliferative diabetic retinopathy (PDR) and twelve non-diabetic patients were recruited for this study. Vitreous fluid was collected during vitrectomy surgery for Cyr61 ELISA. Human Müller cell line MIO-M1 were cultured to be subconfluent, and then treated with glucose (0-20 mM) or Cyr61 (0-300 ng/ml). Cyr61 expression induced by increasing concentrations of glucose was evaluated by RT-qPCR and Western blot. Effects of Cyr61 on Müller cells viability, migration and apoptosis were observed by MTT assay, Transwell assay, and TUNEL assay. Vitreous Cyr61 levels were observed to be 8-fold higher in patients with PDR (3576.92 ± 1574.58 pg/mL), compared with non-diabetic controls (436.14 ± 130.69 pg/mL). Interestingly, the active PDR group was significantly higher than the quiescent PDR group (P<0.01). In retinal Müller cells culture, high glucose significantly and dose-dependently elevated Cyr61 expression at both mRNA and protein levels. Cyr61 at high concentrations dose-dependently inhibited the viability and migration of Müller cells. TUNEL assay further revealed that high concentration of Cyr61 significantly promoted the cell apoptosis. In conclusion, these findings demonstrated for the first time that the expression of Cyr61 was elevated by high glucose in Müller cells, and Cyr61 inhibited cell viability and migration while induced apoptosis, suggesting the potential role of Cyr61 in Müller cell degeneration. The elevated Cyr61 levels in vitreous fluid of PDR patients further support its role in diabetic retinopathy (DR)