Research on High-performance and Scalable Data Access in Parallel Big Data Computing

To facilitate big data processing, many dedicated data-intensive storage systems such as Google File System(GFS), Hadoop Distributed File System(HDFS) and Quantcast File System(QFS) have been developed. Currently, the Hadoop Distributed File System(HDFS) [20] is the state-of-art and most popular open-source distributed file system for big data processing. It is widely deployed as the bedrock for many big data processing systems/frameworks, such as the script-based pig system, MPI-based parallel programs, graph processing systems and scala/java-based Spark frameworks. These systems/applications employ parallel processes/executors to speed up data processing within scale-out clusters. Job or task schedulers in parallel big data applications such as mpiBLAST and ParaView can maximize the usage of computing resources such as memory and CPU by tracking resource consumption/availability for task assignment. However, since these schedulers do not take the distributed I/O resources and global data distribution into consideration, the data requests from parallel processes/executors in big data processing will unfortunately be served in an imbalanced fashion on the distributed storage servers. These imbalanced access patterns among storage nodes are caused because a). unlike conventional parallel file system using striping policies to evenly distribute data among storage nodes, data-intensive file systems such as HDFS store each data unit, referred to as chunk or block file, with several copies based on a relative random policy, which can result in an uneven data distribution among storage nodes; b). based on the data retrieval policy in HDFS, the more data a storage node contains, the higher the probability that the storage node could be selected to serve the data. Therefore, on the nodes serving multiple chunk files, the data requests from different processes/executors will compete for shared resources such as hard disk head and network bandwidth. Because of this, the makespan of the entire program could be significantly prolonged and the overall I/O performance will degrade. The first part of my dissertation seeks to address aspects of these problems by creating an I/O middleware system and designing matching-based algorithms to optimize data access in parallel big data processing. To address the problem of remote data movement, we develop an I/O middleware system, called SLAM, which allows MPI-based analysis and visualization programs to benefit from locality read, i.e, each MPI process can access its required data from a local or nearby storage node. This can greatly improve the execution performance by reducing the amount of data movement over network. Furthermore, to address the problem of imbalanced data access, we propose a method called Opass, which models the data read requests that are issued by parallel applications to cluster nodes as a graph data structure where edges weights encode the demands of load capacity. We then employ matching-based algorithms to map processes to data to achieve data access in a balanced fashion. The final part of my dissertation focuses on optimizing sub-dataset analyses in parallel big data processing. Our proposed methods can benefit different analysis applications with various computational requirements and the experiments on different cluster testbeds show their applicability and scalability

Integrating hypertext with information systems through dynamic mapping

This dissertation presents a general hypertext model (GHMI) supporting integration of hypertext and information systems through dynamic mapping. Information systems integrated based on this model benefit from hypertext function-alities (such as linking, backtracking, history, guided tours, annotations, etc.) while preserving their own computation capabilities. Although systems supporting integration of hypertext and interface-oriented information systems do exist in hypertext literature, there is no existing model or system effectively supporting integration of hypertext and computation-oriented information systems. GHMI makes its major contributions by both extending and specifying the well-known Dexter Hypertext Reference Model. GHMI extends the Dexter model to overcome its limitations. GHMI also maps its capabilities to the extended Dexter model with appropriate specifications to meet the requirements of our dynamic mapping environment. The extended Dexter functions apply bridge laws in the hypertext knowledge base to map information system objects and relationships to hypertext constructs at run-time. We have implemented GHMI as a prototype to prove its feasibility

Ectopic thyroid mass in the left lateral neck and anterior mediastinum: a case report

INTRODUCTION: Ectopic thyroid is characterized by the presence of thyroid tissue in a site other than in its usual pretracheal region. It is a rare condition among the thyroid diseases. Dural ectopic thyroid present in the cervical and anterior mediastinal has not been reported. CASE PRESENTATION: A 45-year-old Chinese woman presented with a nonfunctional ectopic thyroid located both in the cervical and anterior mediastinum. The ectopic thyroid was removed under video-assisted thoracoscopic surgery using a transverse neck incision and her postoperative period has been uneventful thus far. CONCLUSIONS: Ectopic thyroid is a rare condition among the thyroid diseases, and its location in the anterior mediastinum is even more uncommon. Less than 15 cases have been reported in the last four decades. This is the first case of ectopic thyroid to appear in both the cervical and anterior mediastinum at same time. Masses in the anterior mediastinal are usually thymoma, lymphoma, pheochromocytoma and germ cell tumors. Ectopic thyroid in this area is quite rare so this case enhances our understanding of the diagnosis of mediastinal masses

Synthesis and characterisation of polyacrylonitrile and its derived carbon materials

Carbon is a versatile material which is composed of different allotropes, and also come in with different structures. Carbon nanofibres (CNFs) is one dimensional carbon nanomaterials, which have exhibited superior mechanical properties, great specific area, good electrical conductivity, good biocompatibility, and ease of modification. In addition to the lower cost associated to compare with carbon nanotubes (CNTs), CNFs have been attracted in numerous applications, such as reinforcement materials, filtrations, Li-ion battery, supercapacitor as well as tissue engineering, just to list a few. Therefore, it is a great deal to understand the relationship between the fabrication conditions and the characteristics of the resulted CNFs. In this project, electrospun PAN NFs were used as precursor material to fabricate carbon nanofibres. In order to produce CNFs with good morphology, the processing parameters of PAN nanofibres by electrospinning was optimized toward to the morphology at solution concentration of 12 wt%. The optimized processing parameters at given concentration were 16 kV, 14 cm and 1.5 mL/h, which led to the formation of PAN NFs with average fibre diameter of approximately 260 nm. Along with the effect of processing parameter study, the effect of concentration on the morphology was also carried out at optimized processing parameters. It was found that by increasing concentration of PAN solution from 2 to 16%, the resulted PAN transformed from beads only, to beaded fibres and finally to smooth fibres. With further increasing concentration the morphology of smooth fibres remain with increase in the fibre diameter. Electrospun PAN NFs with average fibre of 306 nm was selected to be converted into CNFs by using standard heating procedures, stabilisation in air at 280 °C and carbonization in N2. The effect of carbonization temperature ranging from 500 to 1000 °C was investigated, by using SEM, FTIR, Raman, and Impedance spectroscopy. With increasing carbonization temperature from 500 to 1000 °C, the diameter of NFs was decreased from 260 to 187, associated with loss of almost all functional groups of NFs. It was indicated by Raman results, that the graphitic crystallite size was increased from 2.62 to 5.24 nm, and the activation energy obtained for this growth was 7570 J/mol. Furthermore, impedance results (i.e. Cole-Cole plot) revealed that the electrical characteristic of CNFs transitioned from being insulating to electrically conducting in nature, suggested by the different electrical circuits extracted from Cole-Cole plots with carbonization temperature from 500 to 800 °C. The carbonization on PAN NFs with diameter of ~431nm was carried out by using novel route, microwave plasma enhance chemical vapour deposition (MPECVD) process. To compare with carbonized PAN NFs by using conventional route, MPECVD was not only able to facilitate carbonization process, but more interestingly can form carbon nanowalls (CNWs) grown on the surfaces of carbonized PAN NFs. Suggested by the unique morphology, the potential applications for the resulted carbon fibrous hybrid materials are supercapacitor electrode material, filtrations, and etc., The method developed in this project required one step less, compared with other literature. Therefore, using MPECVD on stabilised PAN NFs is proposed as economical, and straightforward approach towards mass production of carbon fibrous hybrid materials containing CNWs

Signal regulatory protein alpha initiates cachexia through muscle to adipose tissue crosstalk

BACKGROUND: Muscle wasting from chronic kidney disease (CKD) or from defective insulin signalling results in morbidity and, ultimately, mortality. We have identified an endogenous mediator of insulin resistance, signal regulatory protein alpha (SIRPα), which leads to cachexia in mice and is associated with cachexia in patients with CKD. METHODS: We assessed insulin signalling and mechanisms causing muscle atrophy plus white adipose tissue (WAT) metabolism in mouse models of CKD or acute diabetes (streptozotocin treatment). We then examined these factors in mice with global knockout (KO) of SIRPα and sought mediators of metabolic responses in muscle and adipose tissues of mice with either muscle-specific or adipose tissue-specific KO of SIRPα. Metabolic responses were confirmed in primary cultures of adipose cells. RESULTS: In mice with CKD, SIRPα expression was increased in WAT (three-fold, P \u3c 0.05), and this was associated with precursors of cachexia: \u27pathologic browning\u27, thermogenesis, and a two-fold activation of protein kinase A (P \u3c 0.05 vs. control mice) plus loss of adipose tissue mass. In contrast, mice with SIRPα global KO and CKD or acute diabetes experienced improved insulin signalling and activation of pAkt plus \u27physiologic browning\u27 of WAT. These mice avoided losses of muscle and adipose tissues and experienced a 31% improvement in survival (P \u3c 0.05) than did wild-type mice with CKD. In muscle-specific SIRPα KO mice with CKD, we uncovered that serum SIRPα levels (P \u3c 0.05) were suppressed and were associated with improved insulin signalling both in skeletal muscles and in WAT. These changes were accompanied by physiologic WAT browning. However, in adipose-specific SIRPα KO mice with CKD, levels of serum SIRPα were increased over two-fold (P \u3c 0.05), while muscle losses were minimally inhibited. Clinical implications of SIRPα signalling are suggested by our findings that include increased SIRPα expression in muscle and adipose tissues (P \u3c 0.05 vs. healthy controls) plus higher SIRPα levels in the serum of patients with CKD (2.4-fold, P=0.000017 vs. healthy controls). CONCLUSIONS: Our results show that SIRPα plays an important role as an anti-insulin mediator regulating pathways to cachexia. In muscle-specific SIRPα KO, changes in SIRPα serum levels seem to improve insulin signalling in muscle and WAT, suggesting crosstalk between muscle and adipose tissue. Therefore, targeting SIRPα may prevent cachexia in patients with CKD or acute diabetes

Hydrogen-terminated detonation nanodiamond:impedance spectroscopy and thermal stability studies

In this paper, we investigated the effect of hydrogen termination on the electrical properties and impedance spectra of detonation nanodiamond. The impedance spectra revealed that the hydrogen-termination process increases the electrical conductivity by four orders of magnitude at room temperature. An equivalent circuit has been proposed to correlate with the conduction mechanism. Arrhenius plot showed that there were two different activation energy levels located at 0.089 eV and 0.63 eV between 50 °C and 400 °C. The possible physical mechanism corresponding to these activation energy levels has been discussed. Hydrogen-terminated detonation nanodiamond has been further annealed at different temperatures prior to FTIR and XPS measurements in order to understand their thermal stability. The results demonstrated that the surface oxidization occurred between 100 °C and 150 °C. However, the C-H bonds could partially survive when the temperature reaches 400 °C in air

Towards a comprehensive view of the herpes B virus

Herpes B virus is a biosafety level 4 pathogen and widespread in its natural host species, macaques. Although most infected monkeys show asymptomatic or mild symptoms, human infections with this virus can cause serious neurological symptoms or fatal encephalomyelitis with a high mortality rate. Herpes B virus can be latent in the sensory ganglia of monkeys and humans, often leading to missed diagnoses. Furthermore, the herpes B virus has extensive antigen crossover with HSV, SA8, and HVP-2, causing false-positive results frequently. Timely diagnosis, along with methods with sensitivity and specificity, are urgent for research on the herpes B virus. The lack of a clear understanding of the host invasion and life cycle of the herpes B virus has led to slow progress in the development of effective vaccines and drugs. This review discusses the research progress and problems of the epidemiology of herpes B virus, detection methods and therapy, hoping to inspire further investigation into important factors associated with transmission of herpes B virus in macaques and humans, and arouse the development of effective vaccines or drugs, to promote the establishment of specific pathogen-free (SPF) monkeys and protect humans to effectively avoid herpes B virus infection

Femtosecond laser-induced microstructures on diamond for microfluidic sensing device applications

This paper reported a three-dimensional microfluidic channel structure, which was fabricated by Yb:YAG 1026?nm femtosecond laser irradiation on a single-crystalline diamond substrate. The femtosecond laser irradiation energy level was optimized at 100?kHz repetition rate with a sub-500 femtosecond pulse duration. The morphology and topography of the microfluidic channel were characterized by a scanning electron microscope and an atomic force microscope. Raman spectroscopy indicated that the irradiated area was covered by graphitic materials. By comparing the cross-sectional profiles before/after removing the graphitic materials, it could be deduced that the microfluidic channel has an average depth of ~410?nm with periodical ripples perpendicular to the irradiation direction. This work proves the feasibility of using ultra-fast laser inscription technology to fabricate microfluidic channels on biocompatible diamond substrates, which offers a great potential for biomedical sensing applications

Real-time Short Video Recommendation on Mobile Devices

Short video applications have attracted billions of users in recent years, fulfilling their various needs with diverse content. Users usually watch short videos on many topics on mobile devices in a short period of time, and give explicit or implicit feedback very quickly to the short videos they watch. The recommender system needs to perceive users' preferences in real-time in order to satisfy their changing interests. Traditionally, recommender systems deployed at server side return a ranked list of videos for each request from client. Thus it cannot adjust the recommendation results according to the user's real-time feedback before the next request. Due to client-server transmitting latency, it is also unable to make immediate use of users' real-time feedback. However, as users continue to watch videos and feedback, the changing context leads the ranking of the server-side recommendation system inaccurate. In this paper, we propose to deploy a short video recommendation framework on mobile devices to solve these problems. Specifically, we design and deploy a tiny on-device ranking model to enable real-time re-ranking of server-side recommendation results. We improve its prediction accuracy by exploiting users' real-time feedback of watched videos and client-specific real-time features. With more accurate predictions, we further consider interactions among candidate videos, and propose a context-aware re-ranking method based on adaptive beam search. The framework has been deployed on Kuaishou, a billion-user scale short video application, and improved effective view, like and follow by 1.28%, 8.22% and 13.6% respectively.Comment: Accepted by CIKM 2022, 10 page

Propofol EC50 for inducing loss of consciousness in patients under combined epidural-general anesthesia or general anesthesia alone: a randomized double-blind study

BackgroundCombined epidural-general anesthesia (GA + EA) has been recommended as a preferred technique for both thoracic and abdominal surgery. The epidural anesthesia on the general anesthetic (GA) requirements has not been well investigated. Therefore, we conducted the present study to explore the predicted effect-site concentration of propofol (Ceprop) required for achieving the loss of consciousness (LOC) in 50% of patients (EC50) with or without epidural anesthesia.MethodsSixty patients scheduled for gastrectomy were randomized into the GA + EA group or GA alone group to receive general anesthesia alone. Ropivacaine 0.375% was used for epidural anesthesia to achieve a sensory level of T4 or above prior to the induction of general anesthesia. The EC50 of predicted Ceprop for LOC was determined by the up–down sequential method. The consumption of anesthetics, emergence time from anesthesia, and postoperative outcomes were also recorded and compared.ResultsThe EC50 of predicted Ceprop for LOC was lower in the GA + EA group than in the GA alone group [2.97 (95% CI: 2.63–3.31) vs. 3.36 (95% CI: 3.19–3.53) μg mL−1, (p = 0.036)]. The consumption of anesthetics was lower in the GA + EA group than in the GA alone group (propofol: 0.11 ± 0.02 vs. 0.13 ± 0.02 mg kg−1 min−1, p = 0.014; remifentanil: 0.08 ± 0.03 vs. 0.14 ± 0.04 μg kg−1 min−1, p < 0.001). The emergence time was shorter in the GA + EA group than in the GA alone group (16.0 vs. 20.5 min, p = 0.013).ConclusionConcomitant epidural anesthesia reduced by 15% the EC50 of predicted Ceprop for LOC, decreased the consumptions of propofol and remifentanil during maintenance of anesthesia, and fastened recovery from anesthesia.Clinical trial registrationClinicalTrials.gov, identifier: NCT05124704