Showing papers by "Kun Tan published in 2016"

ClickNP: Highly Flexible and High Performance Network Processing with Reconfigurable Hardware

Abstract: Highly flexible software network functions (NFs) are crucial components to enable multi-tenancy in the clouds. However, software packet processing on a commodity server has limited capacity and induces high latency. While software NFs could scale out using more servers, doing so adds significant cost. This paper focuses on accelerating NFs with programmable hardware, i.e., FPGA, which is now a mature technology and inexpensive for datacenters. However, FPGA is predominately programmed using low-level hardware description languages (HDLs), which are hard to code and difficult to debug. More importantly, HDLs are almost inaccessible for most software programmers. This paper presents ClickNP, a FPGA-accelerated platform for highly flexible and high-performance NFs with commodity servers. ClickNP is highly flexible as it is completely programmable using high-level C-like languages, and exposes a modular programming abstraction that resembles Click Modular Router. ClickNP is also high performance. Our prototype NFs show that they can process traffic at up to 200 million packets per second with ultra-low latency ($

Impaired imprinted X chromosome inactivation is responsible for the skewed sex ratio following in vitro fertilization.

Abstract: Dynamic epigenetic reprogramming occurs during normal embryonic development at the preimplantation stage. Erroneous epigenetic modifications due to environmental perturbations such as manipulation and culture of embryos during in vitro fertilization (IVF) are linked to various short- or long-term consequences. Among these, the skewed sex ratio, an indicator of reproductive hazards, was reported in bovine and porcine embryos and even human IVF newborns. However, since the first case of sex skewing reported in 1991, the underlying mechanisms remain unclear. We reported herein that sex ratio is skewed in mouse IVF offspring, and this was a result of female-biased peri-implantation developmental defects that were originated from impaired imprinted X chromosome inactivation (iXCI) through reduced ring finger protein 12 (Rnf12)/X-inactive specific transcript (Xist) expression. Compensation of impaired iXCI by overexpression of Rnf12 to up-regulate Xist significantly rescued female-biased developmental defects and corrected sex ratio in IVF offspring. Moreover, supplementation of an epigenetic modulator retinoic acid in embryo culture medium up-regulated Rnf12/Xist expression, improved iXCI, and successfully redeemed the skewed sex ratio to nearly 50% in mouse IVF offspring. Thus, our data show that iXCI is one of the major epigenetic barriers for the developmental competence of female embryos during preimplantation stage, and targeting erroneous epigenetic modifications may provide a potential approach for preventing IVF-associated complications.

Deadlocks in Datacenter Networks: Why Do They Form, and How to Avoid Them

Abstract: Driven by the need for ultra-low latency, high throughput and low CPU overhead, Remote Direct Memory Access (RDMA) is being deployed by many cloud providers To deploy RDMA in Ethernet networks, Priority-based Flow Control (PFC) must be used PFC, however, makes Ethernet networks prone to deadlocks Prior work on deadlock avoidance has focused on {\em necessary} condition for deadlock formation, which leads to rather onerous and expensive solutions for deadlock avoidance In this paper, we investigate {\em sufficient} conditions for deadlock formation, conjecturing that avoiding {\em sufficient} conditions might be less onerous

Fast and cautious: leveraging multi-path diversity for transport loss recovery in data centers

Abstract: To achieve low TCP flow completion time (FCT) in data center networks (DCNs), it is critical and challenging to rapidly recover loss without adding extra congestion. Therefore, in this paper we propose a novel loss recovery approach FUSO that exploits multi-path diversity in DCN for transport loss recovery. In FUSO, when a multi-path transport sender suspects loss on one sub-flow, recovery packets are immediately sent over another sub-flow that is not or less lossy and has spare congestion window slots. FUSO is fast in that it does not need to wait for timeout on the lossy sub-flow, and it is cautious in that it does not violate congestion control algorithm. Testbed experiments and simulations show that FUSO decreases the latency-sensitive flows' 99th percentile FCT by up to ∼82.3% in a 1Gbps testbed, and up to ∼87.9% in a 10Gpbs large-scale simulated network.

IVF affects embryonic development in a sex-biased manner in mice

Abstract: Increasing evidence indicates that IVF (IVF includes in vitro fertilization and culture) embryos and babies are associated with a series of health complications, and some of them show sex-dimorphic patterns. Therefore, we hypothesized that IVF procedures have sex-biased or even sex-specific effects on embryonic and fetal development. Here, we demonstrate that IVF-induced side effects show significant sexual dimorphic patterns from the pre-implantation to the prenatal stage. During the pre-implantation stage, female IVF embryos appear to be more vulnerable to IVF-induced effects, including an increased percentage of apoptosis (7.22 ± 1.94 vs 0.71 ± 0.76, P<0.01), and dysregulated expression of representative sex-dimorphic genes (Xist, Hprt, Pgk1 and Hsp70). During the mid-gestation stage, IVF males had a higher survival rate than IVF females at E13.5 (male:female=1.33:1), accompanied with a female-biased pregnancy loss. In addition, while both IVF males and females had reduced placental vasculogenesis/angiogenesis, the compensatory placental overgrowth was more evident in IVF males. During the late-gestation period, IVF fetuses had a higher sex ratio (male:female=1.48:1) at E19.5, and both male and female IVF placentas showed overgrowth. After birth, IVF males grew faster than their in vivo (IVO) counterparts, while IVF females showed a similar growth pattern with IVO females. The present study provides a new insight into understanding IVF-induced health complications during embryonic and fetal development. By understanding and minimizing these sex-biased effects of the IVF process, the health of IVF-conceived babies may be improved in the future.

Dynamic integrated analysis of DNA methylation and gene expression profiles in in vivo and in vitro fertilized mouse post-implantation extraembryonic and placental tissues

Abstract: Study hypothesis How does in vitro fertilization (IVF) alter promoter DNA methylation patterns and its subsequent effects on gene expression profiles during placentation in mice? Study finding IVF-induced alterations in promoter DNA methylation might have functional consequences in a number of biological processes and functions during IVF placentation, including actin cytoskeleton organization, hematopoiesis, vasculogenesis, energy metabolism and nutrient transport. What is known already During post-implantation embryonic development, both embryonic and extraembryonic tissues undergo de novo DNA methylation, thereby establishing a global DNA methylation pattern, and influencing gene expression profiles. Embryonic and placental tissues of IVF conceptuses can have aberrant morphology and functions, resulting in adverse pregnancy outcomes such as pregnancy loss, low birthweight, and long-term health effects. To date, the IVF-induced global profiling of DNA methylation alterations, and their functional consequences on aberrant gene expression profiles in IVF placentas have not been systematically studied. Study design, samples/materials, methods Institute for Cancer Research mice (6 week-old females and 8-9 week-old males) were used to generate in vivo fertilization (IVO) and IVF blastocysts. After either IVO and development (IVO group as control) or in vitro fertilization and culture (IVF group), blastocysts were collected and transferred to pseudo-pregnant recipient mice. Extraembryonic (ectoplacental cone and extraembryonic ectoderm) and placental tissues from both groups were sampled at embryonic day (E) 7.5 (IVO, n = 822; IVF, n = 795) and E10.5 (IVO, n = 324; IVF, n = 278), respectively. The collected extraembryonic (E7.5) and placental tissues (E10.5) were then used for high-throughput RNA sequencing (RNA-seq) and methylated DNA immunoprecipitation sequencing (MeDIP-seq). The main dysfunctions indicated by bioinformatic analyses were further validated using molecular detection, and morphometric and phenotypic analyses. Main results and the role of chance Dynamic functional profiling of high-throughput data, together with molecular detection, and morphometric and phenotypic analyses, showed that differentially expressed genes dysregulated by DNA methylation were functionally involved in: (i) actin cytoskeleton disorganization in IVF extraembryonic tissues, which may impair allantois or chorion formation, and chorioallantoic fusion; (ii) disturbed hematopoiesis and vasculogenesis, which may lead to abnormal placenta labyrinth formation and thereby impairing nutrition transport in IVF placentas; (iii) dysregulated energy and amino acid metabolism, which may cause placental dysfunctions, leading to delayed embryonic development or even lethality; (iv) disrupted genetic information processing, which can further influence gene transcriptional and translational processes. Limitations, reasons for caution Findings in mouse placental tissues may not be fully representative of human placentas. Further studies are necessary to confirm these findings and determine their clinical significance. Wider implications of the findings Our study is the first to provide the genome-wide analysis of gene expression dysregulation caused by DNA methylation during IVF placentation. Systematic understanding of the molecular mechanisms implicated in IVF placentation can be useful for the improvement of existing assisted conception systems to prevent these IVF-associated safety concerns. Study funding and competing interests This work was supported by grants from the National Natural Science Foundation of China (No. 31472092), and the National High-Tech R&D Program (Nos. 2011|AA100303, 2013AA102506). There was no conflict of interest.

Downregulation of miR-199a-5p Disrupts the Developmental Potential of In Vitro-Fertilized Mouse Blastocysts

Abstract: Although in vitro fertilization (IVF), one of the most effective and successful assisted reproductive technologies, is widely used for treating infertility and in animal breeding, increasing evidence indicates that IVF offspring are linked to various short- or long-term consequences. Erroneous epigenetic modifications induced by IVF are suspected of contributing to these consequences. Among these epigenetic modifications, microRNAs may affect embryo implantation and early postimplantation development. Here, we performed comparative microRNA profiling between in vivo-fertilized (IVO group) and in vitro-fertilized (IVF group) mouse embryos at Embryonic Day 3.5 (E3.5) and E7.5. Our dynamic analyses showed that the dysregulated microRNAs were mainly associated with the regulation of genes involved in carcinogenesis, genetic information processing, glucose metabolism, cytoskeleton organization, and neurogenesis. Further analysis showed that miR-199a-5p was consistently downregulated in IVF embryos compared with their IVO counterparts. Through gain- and loss-of-function experiments, we demonstrated that IVF-induced downregulation of miR-199a-5p results in a higher glycolytic rate and lower developmental potential of IVF blastocysts, including cell lineage misallocation and lower fetal survival post implantation. Therefore, preventing downregulation of miR-199a-5p may become an effective strategy for improving the development of IVF peri-implantation embryos in the future.

Client as a first-class citizen: Practical user-centric network MIMO clustering

Abstract: Recent advances have demonstrated the potential of network MIMO (netMIMO), which combines a practical number of distributed antennas as a virtual netMIMO AP (nAP) to improve spatial multiplexing of an WLAN. Existing solutions, however, either simply cluster nearby antennas as static nAPs, or dynamically cluster antennas on a per-packet basis so as to maximize the sum rate of the scheduled clients. To strike the balance between the above two extremes, in this paper, we present the design, implementation and evaluation of FlexNEMO, a practical two-phase netMIMO clustering system. Unlike previous per-packet clustering approaches, FlexNEMO only clusters antennas when client distribution and traffic pattern change, as a result being more practical to be implemented. A medium access control protocol is then designed to allow the clients at the center of nAPs to have a higher probability to gain access opportunities, but still ensure long-term fairness among clients. By combining on-demand clustering and priority-based access control, FlexNEMO not only improves antenna utilization, but also optimizes the channel condition for every individual client. We evaluated our design via both testbed experiments on USRPs and trace-driven emulations. The results demonstrate that FlexNEMO can deliver 94.7% and 93.7% throughput gains over static antenna clustering in a 4-antenna testbed and 16-antenna emulation, respectively.

CoSchd: Coordinated Scheduling With Channel and Load Awareness for Alleviating Cellular Congestion

Abstract: Although cellular networks can be provisioned according to the peak demand, they usually experience large fluctuations in both channel conditions and traffic load level. Scheduling with both channel and load awareness allows us to exploit the delay tolerance of data traffic to alleviate network congestion, and thus reduce the peak. However, solving the optimal scheduling problem leads to a large-scale Markov decision process (MDP) with extremely high complexity. In this paper, we propose a scalable and distributed approach to this problem, called Coordinated Scheduling (CoSchd). CoSchd decomposes the large-scale MDP problem into many individual MDP problems, each of which can be solved independently by each user under a limited amount of coordination signals from the base station (BS). We show that CoSchd is close to optimal when the number of users becomes large. Furthermore, we propose an approximation of CoSchd that iteratively updates the scheduling policy based on online measurements. Simulation results demonstrate that exploiting channel and load awareness with CoSchd can effectively alleviate cellular network congestion.

Smart and Secure: Preserving Privacy in Untrusted Home Routers

Abstract: Recently, wireless home routers increasingly become smart. While these smart routers provide rich functionalities to users, they also raise security concerns. Since a smart home router may process and store personal data for users, once compromised, these sensitive information will be exposed. Unfortunately, current operating systems on home routers are far from secure. As a consequence, users are facing a difficult tradeoff between functionality and privacy risks. This paper attacks this dilemma with a novel SEAL architecture for home routers. SEAL leverages the ARM TrustZone technology to divide a conventional router OS (i.e., Linux) in a non-secure/normal world. All sensitive user data are shielded from the normal world using encryption. Modules (called applets) that process the sensitive data are located in a secure world and confined in secure sandboxes provided by a tiny secure OS. We report the system design of SEAL and our preliminary implementation and evaluation results.

Method for improving development quality of in vitro fertilization female embryos after implantation

Abstract: The invention provides a method for improving development quality of in vitro fertilization (IVF) female embryos after implantation and correcting sex ratio of IFV embryos. The method comprises: transferring mouse fertilized embryos obtained by IVF technology into a culture solution added with low-dose retinoic acid (RA) for short-term culturing, a female specific apparent modification event (namely x-chromosomal inactivation) in early development of IFV embryos is established normally so that an abnormal development ratio of mouse IFV female embryos after implantation is reduced and the mouse IVF birth sex ratio imbalance problem is finally corrected. In addition, the method is successfully applied in a bovine IVF system, effectively increasing development rate of bovine IFV female blastulas and correcting the sex ratio of bovine IFV blastulas. The RA in the invention is used as a fallopian tube to widely express an endogenous active matter, this matter is suitably added in the IVF system with endogenous ingredients not blindly added, and application safety is greatly ensured.

Remote router request relaying

Abstract: Various systems and methods for relaying remote a request are described herein In one example, a method includes receiving a request at a public website to access a private router The method can also include authenticating the request via an authentication service Furthermore, the method can include providing access to the private router via the public website upon authentication