A Bin-Based Indexing for Scalable Range Join on Genomic Data.

Range-join is an operation for finding overlaps in interval-form genomic data. Range-join is widely used in various genome analysis processes such as annotation, filtering and comparison of variants in whole-genome and exome analysis pipelines. The quadratic complexity of current algorithms with sheer data volume has surged the design challenges. Existing tools have limitations on algorithm efficiency, parallelism, scalability and memory consumption. This paper proposes BIndex, a novel bin-based indexing algorithm and its distributed implementation to attain high throughput range-join processing. BIndex features near-constant search complexity while the inherently parallel data structure facilitates exploitation of parallel computing architectures. Balanced partitioning of dataset further enables scalability on distributed frameworks. The implementation on Message Passing Interface shows upto 933.5x speedup in comparison to state-of-the-art tools. Parallel nature of BIndex further enables GPU-based acceleration with 3.72x speedup than CPU implementations. The add-in modules for Apache Spark provides upto 4.65x speedup than the previously best available tool. BIndex supports wide variety of input and output formats prevalent in bioinformatics community and the algorithm is easily extendable to streaming data in recent Big Data solutions. Furthermore, the index data structure is memory-efficient and consumes upto two orders-of-magnitude lesser RAM, while having no adverse effect on speedup.

Graph Neural Networks for Charged Particle Tracking on FPGAs.

The determination of charged particle trajectories in collisions at the CERN Large Hadron Collider (LHC) is an important but challenging problem, especially in the high interaction density conditions expected during the future high-luminosity phase of the LHC (HL-LHC). Graph neural networks (GNNs) are a type of geometric deep learning algorithm that has successfully been applied to this task by embedding tracker data as a graph-nodes represent hits, while edges represent possible track segments-and classifying the edges as true or fake track segments. However, their study in hardware- or software-based trigger applications has been limited due to their large computational cost. In this paper, we introduce an automated translation workflow, integrated into a broader tool called hls4ml, for converting GNNs into firmware for field-programmable gate arrays (FPGAs). We use this translation tool to implement GNNs for charged particle tracking, trained using the TrackML challenge dataset, on FPGAs with designs targeting different graph sizes, task complexites, and latency/throughput requirements. This work could enable the inclusion of charged particle tracking GNNs at the trigger level for HL-LHC experiments.

The Impact of the Synergistic Effect of Temperature and Air Pollutants on Chronic Lung Diseases in Subtropical Taiwan.

Previous studies have suggested an association between air pollution and lung disease. However, few studies have explored the relationship between chronic lung diseases classified by lung function and environmental parameters. This study aimed to comprehensively investigate the relationship between chronic lung diseases, air pollution, meteorological factors, and anthropometric indices. We conducted a cross-sectional study using the Taiwan Biobank and the Taiwan Air Quality Monitoring Database. A total of 2889 participants were included. We found a V/U-shaped relationship between temperature and air pollutants, with significant effects at both high and low temperatures. In addition, at lower temperatures (<24.6 °C), air pollutants including carbon monoxide (CO) (adjusted OR (aOR):1.78/Log 1 ppb, 95% CI 0.98-3.25; aOR:5.35/Log 1 ppb, 95% CI 2.88-9.94), nitrogen monoxide (NO) (aOR:1.05/ppm, 95% CI 1.01-1.09; aOR:1.11/ppm, 95% CI 1.07-1.15), nitrogen oxides (NOx) (aOR:1.02/ppm, 95% CI 1.00-1.05; aOR:1.06/ppm, 95% CI 1.04-1.08), and sulfur dioxide (SO2) (aOR:1.29/ppm, 95% CI 1.01-1.65; aOR:1.77/ppm, 95% CI 1.36-2.30) were associated with restrictive and mixed lung diseases, respectively. Exposure to CO, NO, NO2, NOx and SO2 significantly affected obstructive and mixed lung disease in southern Taiwan. In conclusion, temperature and air pollution should be considered together when evaluating the impact on chronic lung diseases.

A novel optical technology based on 690 nm and 850 nm wavelengths to assist needle thoracostomy.

The sensitivity of pneumothorax diagnosis via handheld ultrasound is low, and there is no equipment suitable for use with life-threatening tension pneumothorax in a prehospital setting. This study proposes a novel technology involving optical fibers and near-infrared spectroscopy to assist in needle thoracostomy decompression. The proposed system via the optical fibers emitted dual wavelengths of 690 and 850 nm, allowing distinction among different layers of tissue in vivo. The fundamental principle is the modified Beer-Lambert law (MBLL) which is the basis of near-infrared tissue spectroscopy. Changes in optical density corresponding to different wavelengths (690 and 850 nm) and hemoglobin parameters (levels of Hb and HbO2) were examined. The Kruskal-Wallis H test was used to compare the differences in parameter estimates among tissue layers; all p-values were < 0.001 relevant to 690 nm and 850 nm. In comparisons of Hb and HbO2 levels relative to those observed in the vein and artery, all p-values were also < 0.001. This study proposes a new optical probe to assist needle thoracostomy in a swine model. Different types of tissue can be identified by changes in optical density and hemoglobin parameters. The aid of the proposed system may yield fewer complications and a higher success rate in needle thoracostomy procedures.

Air Pollution Is Associated with Poor Cognitive Function in Taiwanese Adults.

The issue of air pollution is gaining increasing attention worldwide, and mounting evidence has shown an association between air pollution and cognitive decline. The aim of this study was to investigate the relationships between air pollutants and cognitive impairment using the Mini-Mental State Exam (MMSE) and its sub-domains. In this study, we used data from the Taiwan Biobank combined with detailed daily data on air pollution. Cognitive function was assessed using the MMSE and its five subgroups of cognitive functioning. After multivariable linear regression analysis, a high level of particulate matter with an aerodynamic diameter of ≤2.5 µm (PM2.5), low ozone (O3), high carbon monoxide (CO), high sulfur dioxide (SO2), high nitric oxide (NO), high nitrogen dioxide (NO2), and high nitrogen oxide (NOx) were significantly associated with low total MMSE scores. Further, high SO2 and low O3 were significantly associated with low MMSE G1 scores. Low O3, high CO, high SO2, high NO2, and high NOx were significantly associated with low MMSE G4 scores, and high PM2.5, high particulate matter with an aerodynamic diameter of ≤10 µm (PM10), high SO2, high NO2, and high NOx were significantly associated with low MMSE G5 scores. Our results showed that exposure to different air pollutants may lead to general cognitive decline and impairment of specific domains of cognitive functioning, and O3 may be a protective factor. These findings may be helpful in the development of policies regarding the regulation of air pollution.

Dual-wavelength fiber-optic technique to assist needle cricothyroidotomy.

The traditional needle cricothyroidotomy procedure is performed blindly without any medical equipment. Complications including posterior tracheal wall perforation, accidental vessel puncture, and missed tracheal puncture are reported. Therefore, we proposed a dual-wavelength fiber-optic technique based on the technique of near-infrared spectroscopy to assist operators performing needle cricothyroidotomy in a swine model. We embedded optical fibers in a 16-gauge intravenous needle catheter. Real-time data were displayed on an oscilloscope, and we used the program to analyze the data immediately. The change of optical density corresponding to 690-nm and 850-nm wavelengths and hemoglobin parameters (HbO2 and Hb concentrations) was analyzed immediately using the program in the laptop. Unique and significant optical differences were presented in this experiment. We could easily identify every different tissue by the change of optical density corresponding to 690-nm and 850-nm wavelengths and hemoglobin parameters (HbO2 and Hb concentrations). Statistical method (Kruskal-Wallis H test) was used to compare differences in tissues at each time-point, respectively. The p values in every tissue in optical density change corresponding to 690 nm and 850 nm were all < 0.001. Furthermore, the p values in every tissue in Hb and HbO2 were also all < 0.001. The results were statistically significant. This is the first and novel study to introduce a dual-wavelength embedded fibers into a standard cricothyroidotomy needle. This proposed system might be helpful to provide us real-time information of the advanced needle tip to decrease possible complications.

Air Pollutants Interaction and Gender Difference on Bone Mineral Density T-Score in Taiwanese Adults.

Osteoporosis is defined as a systemic skeletal disease characterized by a reduction in bone mass and microarchitectural deterioration of bone tissue. Previous studies have reported associations between air pollution and lower bone mineral density; however, few studies have investigated the association between air pollution and osteoporosis. In this study, we combined two databases, the first including 5000 individuals registered in the Taiwan Biobank, and the second containing detailed daily data on air pollution. After multivariable adjustments, ozone (O3) (unstandardized coefficient ß, 0.015; p = 0.008) was significantly positively associated with T-score, whereas carbon monoxide (CO) (unstandardized coefficient ß, -0.809; p < 0.001), sulfur dioxide (SO2) (unstandardized coefficient ß, -0.050; p = 0.005), nitric oxide (NO) (unstandardized coefficient ß, -0.040; p < 0.001), nitrogen dioxide (NO2) (unstandardized coefficient ß, -0.023; p < 0.001), and nitrogen oxide (NOx) (unstandardized coefficient ß, -0.017; p < 0.001) were significantly negatively associated with T-score. The interactions between CO and NOx (p = 0.001) and SO2 and NO2 (p = 0.004) on T-score were statistically significant. An increase in exposure to CO, NO and NOx was associated with a faster decline in T-score in the female participants compared to the male participants. In addition, an increase in O3 was associated with a faster increase in T-score in the female participants compared to the male participants. In conclusion, the air pollutants CO, SO2, NO, NO2, and NOx were associated with osteoporosis. In addition, there were interaction and synergetic effects between CO and NOx and SO2 and NO2 on T-score. We also observed differences in the associations between air pollutants and T-score between the female and male participants.

A Novel Smart Assistance System for Blood Vessel Approaching: A Technical Report Based on Oximetry.

In clinical practice, the catheter has to be placed at an accurate position during anesthesia administration. However, effectively guiding the catheter to the accurate position in deeper tissues can be difficult for an inexperienced practitioner. We aimed to address the current issues associated with catheter placement using a novel smart assistance system for blood vessel catheter placement. We used a hollow introducer needle embedded with dual wavelength (690 and 850 nm) optical fibers to advance the tip into the subclavian vessels in anesthetized piglets. The results showed average optical density changes, and the difference between the absorption spectra and hemoglobin concentrations of different tissue components effectively identified different tissues (p < 0.05). The radial basis function neural network (RBFNN) technique was applied to distinguish tissue components (the F-measure value and accuracy were 93.02% and 94%, respectively). Finally, animal experiments were designed to validate the performance of the proposed system. Using this system based on oximetry, we easily navigated the needle tip to the target vessel. Based on the experimental results, the proposed system could effectively distinguish different tissue layers of the animals.

Towards High Performance Data Analytic on Heterogeneous Many-core Systems: A Study on Bayesian Sequential Partitioning.

Bayesian Sequential Partitioning (BSP) is a statistically effective density estimation method to comprehend the characteristics of a high dimensional data space. The intensive computation of the statistical model and the counting of enormous data have caused serious design challenges for BSP to handle the growing volume of the data. This paper proposes a high performance design of BSP by leveraging a heterogeneous CPU/GPGPU system that consists of a host CPU and a K80 GPGPU. A series of techniques, on both data structures and execution management policies, is implemented to extensively exploit the computation capability of the heterogeneous many-core system and alleviate system bottlenecks. When compared with a parallel design on a high-end CPU, the proposed techniques achieve 48x average runtime enhancement while the maximum speedup can reach 78.76x.