A Study of Application-awareness in Software-defined Data Center Networks

A data center (DC) has been a fundamental infrastructure for academia and industry for many years. Applications in DC have diverse requirements on communication. There are huge demands on data center network (DCN) control frameworks (CFs) for coordinating communication traffic. Simultaneously satisfying all demands is difficult and inefficient using existing traditional network devices and protocols. Recently, the agile software-defined Networking (SDN) is introduced to DCN for speeding up the development of the DCNCF. Application-awareness preserves the application semantics including the collective goals of communications. Previous works have illustrated that application-aware DCNCFs can much more efficiently allocate network resources by explicitly considering applications needs. A transfer application task level application-aware software-defined DCNCF (SDDCNCF) for OpenFlow software-defined DCN (SDDCN) for big data exchange is designed. The SDDCNCF achieves application-aware load balancing, short average transfer application task completion time, and high link utilization. The SDDCNCF is immediately deployable on SDDCN which consists of OpenFlow 1.3 switches. The Big Data Research Integration with Cyberinfrastructure for LSU (BIC-LSU) project adopts the SDDCNCF to construct a 40Gb/s high-speed storage area network to efficiently transfer big data for accelerating big data related researches at Louisiana State University. On the basis of the success of BIC-LSU, a coflow level application-aware SD- DCNCF for OpenFlow-based storage area networks, MinCOF, is designed. MinCOF incorporates all desirable features of existing coflow scheduling and routing frame- works and requires minimal changes on hosts. To avoid the architectural limitation of the OpenFlow SDN implementation, a coflow level application-aware SDDCNCF using fast packet processing library, Coflourish, is designed. Coflourish exploits congestion feedback assistances from SDN switches in the DCN to schedule coflows and can smoothly co-exist with arbitrary applications in a shared DCN. Coflourish is implemented using the fast packet processing library on an SDN switch, Open vSwitch with DPDK. Simulation and experiment results indicate that Coflourish effectively shortens average application completion time

Reliable Detection of Paternal SNPs within Deletion Breakpoints for Non-Invasive Prenatal Exclusion of Homozygous α0-Thalassemia in Maternal Plasma

Reliable detection of large deletions from cell-free fetal DNA (cffDNA) in maternal plasma is challenging, especially when both parents have the same deletion owing to a lack of specific markers for fetal genotyping. In order to evaluate the efficacy of a non-invasive prenatal diagnosis (NIPD) test to exclude α-thalassemia major that uses SNPs linked to the normal paternal α-globin allele, we established a novel protocol to reliably detect paternal SNPs within the (−−SEA) breakpoints and performed evaluation of the diagnostic potential of the protocol in a total of 67 pregnancies, in whom plasma samples were collected prior to invasive obstetrics procedures in southern China. A group of nine SNPs identified within the deletion breakpoints were scanned to select the informative SNPs in each of the 67 couples DNA by multiplex PCR based mini-sequencing technique. The paternally inherited SNP allele from cffDNA was detected by allele specific real-time PCR. A protocol for reliable detection of paternal SNPs within the (−−SEA) breakpoints was established and evaluation of the diagnostic potential of the protocol was performed in a total of 67 pregnancies. In 97% of the couples one or more different SNPs within the deletion breakpoint occurred between paternal and maternal alleles. Homozygosity for the (−−SEA) deletion was accurately excluded in 33 out of 67 (49.3%, 95% CI, 25.4–78.6%) pregnancies through the implementation of the protocol. Protocol was completely concordant with the traditional reference methods, except for two cases that exhibited uncertain results due to sample hemolysis. This method could be used as a routine NIPD test to exclude gross fetal deletions in α-thalassemia major, and could further be employed to test for other diseases due to gene deletion

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

An Effective Distributed GHSOM Algorithm for Unsupervised Clustering on Big Data

基於屬性相似度將樣本進行分群的技術已經被廣泛應用在許多領域，如模式識別，特徵提取和惡意行為偵測。由於此技術的重要性，很多人已經將各種分群技術利用分散式框架進行再製，例如K-means搭配Hadoop在Apache Mahout平台上。由於K-means需要預先定義分群數量，而自組織映射圖（SOM）需要預先定義圖的大小，所以能夠自動將樣本依照樣本間的變化容差進行分群的GHSOM（增長層次自組織映射圖）就提供了一個很棒的非監督學習方法用來針對某些資訊不完整的資料。然而，GHSOM目前並不是一個分散式的演算法，這就限制了其在大數據資料的應用上。在本篇論文中，我們提出了一種新的分散式GHSOM演算法。我們使用Scala的Actor Model來實現GHSOM的分散式系統，我們將GHSOM演算法中的水平擴增以及垂直擴增交由Actor來處理並顯示出顯著的性能提升。為了評估我們所提出的方法，我們收集並分析了數千個惡意程式在現實生活中的執行行為，並通過在數百萬個樣本上進行非監督分群後推導出惡意程式行為的檢測規則來顯示其性能的改進、規則有效性以及實踐中的潛在用法。Clustering techniques that group samples based on their attribute similarity have been widely used in many fields such as pattern recognition, feature extraction and malicious behavior characterization. Due to its importance, various clustering techniques have been developed with distributed frameworks such as K-means with Hadoop in Apache Mahout for scalable computation. While K-means requires the number of clusters and self organizing maps (SOM) requires the map size to be given, the technique of GHSOM (growing hierarchical self organizing maps) that clusters samples dynamically to satisfy the requirement on tolerance of variation between samples, poses an attractive unsupervised learning solution for data that have limited information to decide the number of clusters in advance. However it is not scalable with sequential computation, which limits its applications on big data. In this paper, we present a novel distributed algorithm on GHSOM. We take advantage of parallel computation with scala actor model for GHSOM construction, distributing vertical and horizontal expansion tasks to actors and showing significant performance improvement. To evaluate the presented approach, we collect and analyze execution behaviors of thousands of malware in real life and derive detection rules with the presented unsupervised clustering on millions samples, showing its performance improvement, rule effectiveness and potential usage in practice