Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity

A major goal of biomedicine is to understand the function of every gene in the human genome. Loss-of-function mutations can disrupt both copies of a given gene in humans and phenotypic analysis of such 'human knockouts' can provide insight into gene function. Consanguineous unions are more likely to result in offspring carrying homozygous loss-of-function mutations. In Pakistan, consanguinity rates are notably high. Here we sequence the protein-coding regions of 10,503 adult participants in the Pakistan Risk of Myocardial Infarction Study (PROMIS), designed to understand the determinants of cardiometabolic diseases in individuals from South Asia. We identified individuals carrying homozygous predicted loss-of-function (pLoF) mutations, and performed phenotypic analysis involving more than 200 biochemical and disease traits. We enumerated 49,138 rare (<1% minor allele frequency) pLoF mutations. These pLoF mutations are estimated to knock out 1,317 genes, each in at least one participant. Homozygosity for pLoF mutations at PLA2G7 was associated with absent enzymatic activity of soluble lipoprotein-associated phospholipase A2; at CYP2F1, with higher plasma interleukin-8 concentrations; at TREH, with lower concentrations of apoB-containing lipoprotein subfractions; at either A3GALT2 or NRG4, with markedly reduced plasma insulin C-peptide concentrations; and at SLC9A3R1, with mediators of calcium and phosphate signalling. Heterozygous deficiency of APOC3 has been shown to protect against coronary heart disease; we identified APOC3 homozygous pLoF carriers in our cohort. We recruited these human knockouts and challenged them with an oral fat load. Compared with family members lacking the mutation, individuals with APOC3 knocked out displayed marked blunting of the usual post-prandial rise in plasma triglycerides. Overall, these observations provide a roadmap for a 'human knockout project', a systematic effort to understand the phenotypic consequences of complete disruption of genes in humans.D.S. is supported by grants from the National Institutes of Health, the Fogarty International, the Wellcome Trust, the British Heart Foundation, and Pfizer. P.N. is supported by the John S. LaDue Memorial Fellowship in Cardiology from Harvard Medical School. H.-H.W. is supported by a grant from the Samsung Medical Center, Korea (SMO116163). S.K. is supported by the Ofer and Shelly Nemirovsky MGH Research Scholar Award and by grants from the National Institutes of Health (R01HL107816), the Donovan Family Foundation, and Fondation Leducq. Exome sequencing was supported by a grant from the NHGRI (5U54HG003067-11) to S.G. and E.S.L. D.G.M. is supported by a grant from the National Institutes of Health (R01GM104371). J.D. holds a British Heart Foundation Chair, European Research Council Senior Investigator Award, and NIHR Senior Investigator Award. The Cardiovascular Epidemiology Unit at the University of Cambridge, which supported the field work and genotyping of PROMIS, is funded by the UK Medical Research Council, British Heart Foundation, and NIHR Cambridge Biomedical Research Centre ... Fieldwork in the PROMIS study has been supported through funds available to investigators at the Center for Non-Communicable Diseases, Pakistan and the University of Cambridge, UK

Building Secure Web Applications Using Self-Protecting JavaScript

JavaScript has become an intrinsic part of web applications. But it has a dynamic execution nature i.e. any variable in the context of the program can be re-defined and code can be created and execute it on the fly. Malicious or third party script can be injected in to web pages using XSS vulnerabilities to harm the client machines. This thesis work is an empirical study based on the idea of controlling the execution of JavaScript on client-side by modifying the script in way to make it self-protected without browser modification. In this method, security checks are embedded into the web page; to intercept security relevant API calls on JavaScript. The embedding process can be performed at server-side, client-side (web browser) or proxy between the server and client. In this work, we have deployed all the three different architectures to demonstrate that the self-protecting method can enforce security policies to prevent real XSS attacks. For client-side architecture, we play with Greasemonkey for Firefox browser; and we modified an open source web proxy server (WebScarab) to inject security policies into web pages for proxy-based architecture. Web applications conducted in the study include Facebook web applications, several real world documented XSS vulnerability web sites and a sample security critical web application. The study revealed that in the scenario of Facebook application, browser plug-ins are not appropriate for enforcement of policies because policy code is executed after all code in the page executes that make it is not possible for security enforcement. While, on the other hand, script injection using web proxy server and server-side are applicable solutions to enforce policies on client-side. The script injection has been successfully applied using WebScarab on several web applications. Also, the application-specific policies for web application i.e. payment application has been successfully applied using server-side script injection. These policies prevent clients from XMLHttpRequest based reflective attacks by allowing requests only for allowed list of URL’s. The outcome of this study is a self-protected web application and a web proxy server for script injection

A Probabilistic Analysis of Resilient Reconfigurable Designs

Reconfigurable hardware can be employed to tolerate permanent faults. Hardware components comprising a System-on-Chip can be partitioned into a handful of substitutable units interconnected with reconfigurable wires to allow isolation and replacement of faulty parts. This paper offers a probabilistic analysis of reconfigurable designs estimating for different fault densities the average number of fault-free components that can be constructed as well as the probability to guarantee a particular availability of components. Considering the area overheads of reconfigurability, we evaluate the resilience of various reconfigurable designs with different granularities. Based on this analysis, we conduct a comprehensive design-space exploration to identify the granularity mixes that maximize the fault-tolerance of a system. Our findings reveal that mixing fine-grain logic with a coarse-grain sparing approach tolerates up to 3x more permanent faults than component redundancy and 2x more than any other purely coarse-grain solution. Component redundancy is preferable at low fault densities, while coarse-grain and mixedgrain reconfigurability maximize availability at medium and high fault densities, respectively

Resilient chip multiprocessors with mixed-grained reconfigurability

This article presents a chip multiprocessor (CMP) design that mixes coarse- and fine-grained reconfigurability to increase core availability of safety-critical embedded systems in the presence of hard errors. The authors conducted a comprehensive design-space exploration to identify the granularity mixes that maximize CMP fault tolerance and minimize performance and energy overheads. The authors added fine-grained reconfigurable logic to a coarse-grained sparing approach. Their resulting design can tolerate 3 times more hard errors than core redundancy and 1.5 times more than any other purely coarse-grained solution

A dependable coarse-grain reconfigurable multicore array

© 2014 IEEE. Recent trends in semiconductor technology have dictated the constant reduction of device size. One negative effect stemming from the reduction in size and increased complexity is the reduced device reliability. This paper is centered around the matter of permanent fault tolerance and graceful system degradation in the presence of permanent faults. We take advantage of the natural redundancy of homogeneous multicores following a sparing strategy to reuse functional pipeline stages of faulty cores. This is done by incorporating reconfigurable interconnects next to which the cores of the system are placed, providing the flexibility to redirect the data-flow from the faulty pipeline stages of damaged cores to spare (still) functional ones. Several micro-architectural changes are introduced to decouple the processor stages and allow them to be interchangeable. The proposed approach is a clear departure from previous ones by offering full flexibility as well as highly graceful performance degradation at reasonable costs. More specifically, our coarsegrain faulttolerant multicore array provides up to ×4 better availability compared to a conventional multicore and up to ×2 higher probability to deliver at least one functioning core in high fault densities. For our benchmarks, our design (synthesized for STM 65nm SP technology) incurs a total execution-time overhead for the complete system ranging from ×1.37 to ×3.3 compared to a (baseline) non-fault-tolerant system, depending on the permanent-fault density. The area overhead is 19.5% and the energy consumption, without incorporating any power/energy- saving technique, is estimated on average to be 20.9% higher compared to the baseline, unprotected design

Reducing the performance overhead of resilient CMPs with substitutable resources

Permanent faults on a chip are often tolerated using spare resources. In the past, sparing has been applied to Chip Multiprocessors (CMPs) at various granularities of substitutable units (SUs). Entire processors, pipeline stages or even individual functional units are isolated when faulty and replaced by spare ones using flexible, reconfigurable interconnects. Although spare resources increase systems fault tolerance, the extra delay imposed by the reconfigurable interconnects limits performance. In this paper, we study two options for dealing with this delay: (i) pipelining the reconfigurable interconnects and (ii) scaling down operating frequency. The former keeps a frequency close to the one of the baseline processor, but increases the number of cycles required for executing a program. The latter maintains the number of execution cycles constant, but requires a slower clock. We investigate the above performance tradeoff using an adaptive 4-core CMP design with substitutable pipeline stages. We retrieve post place and route results of different designs running two sets of benchmarks and evaluate their performance. Our experiments indicate that adding reconfigurable interconnects for wiring the SUs of a 4-core CMP pose significant delay increasing the critical path of the design almost by 3.5 times. On the other hand, pipelining the reconfigurable interconnects increases cycle time by 41% and - depending on the processor configuration - reduces performance overhead to 1.4-2.9× the execution time of the baseline

4th Author-Food and Drug Safety Management in Pakistan

Food and drug safety management is critical for public health in Pakistan. This paper reviews the current food and drug safety management system in Pakistan, identifies the challenges, and suggests improvement solutions. The regulatory framework for food and drug safety in Pakistan is the responsibili?ty of several federal and provincial agencies, including the Drug Regulatory Authority of Pakistan (DRAP) for drugs and the Pakistan Standards and Quality Control Authority (PSQCA) for food. However, the system faces sev?eral challenges, including weak regulatory frameworks, a lack of resources, corruption, and a lack of public awareness. The paper suggests solutions such as increased funding and staffing of regulatory agencies, the crackdown on corruption, strengthening of the regulatory framework, and public aware?ness campaigns to promote the importance of food and drug safety. The safety of food and drugs is a critical issue in Pakistan, as it has a direct impact on the health and well-being of its population. Despite significant progress made in recent years, Pakistan still faces significant challenges in ensuring that food and drugs are safe for consumption. This paper examines the cur?rent state of food and drug safety management in Pakistan, including its regu?latory framework, enforcement mechanisms, and challenges. It also provides recommendations for improving food and drug safety management in the country.</p

4th Author-Traffic Problems in Dhaka City Causes, Effects, and Solutions (Case Study to Develop a Business Model)

Dhaka, the capital city of Bangladesh, is facing a severe traffic problem due to the rapid growth of the city’s population and inadequate transportation infrastructure. This year, the total number of working hours lost on Dhaka’s roads has surpassed eight million per day, a significant increase compared to the five million working hours lost daily in 2017. This paper presents a comprehensive analysis of Dhaka’s traffic problem, examining the underlying causes and their implications. The analysis process involves an examination of the existing literature and data related to Dhaka’s traffic problem. The paper evaluates the historical development of the city’s transportation infrastructure and urban planning policies to understand how they have contributed to the current situation. The study also analyzes the socioeconomic factors that drive private vehicle ownership and usage in Dhaka. The lack of public transportation and the unregulated growth of private vehicles are major contributors to Dhaka’s traffic congestion. Additionally, poor road infrastructure and traffic management exacerbate the problem, leading to increased air pollution and economic costs. The paper presents a detailed analysis of these factors and their impact on the city. The paper also evaluates potential solutions to the problem, including the expansion of public transportation, the improvement of road infrastructure, the promotion of alternative modes of transport, and the implementation of better traffic management strategies. The study found that a combination of these solutions could effectively address Dhaka’s traffic problem. However, the success of these solutions requires political will and financial investment. In conclusion, the paper high?lights the urgency of addressing Dhaka’s traffic problem and emphasizes the need for comprehensive and sustainable solutions. The study provides policymakers and researchers with a framework for understanding and addressing the traffic problem in Dhaka, contributing to the ongoing discussion on how to improve the quality of life for the city’s residents.</p

Apolipoprotein(a) isoform size, lipoprotein(a) concentration, and coronary artery disease: a mendelian randomisation analysis.

BACKGROUND: The lipoprotein(a) pathway is a causal factor in coronary heart disease. We used a genetic approach to distinguish the relevance of two distinct components of this pathway, apolipoprotein(a) isoform size and circulating lipoprotein(a) concentration, to coronary heart disease. METHODS: In this mendelian randomisation study, we measured lipoprotein(a) concentration and determined apolipoprotein(a) isoform size with a genetic method (kringle IV type 2 [KIV2] repeats in the LPA gene) and a serum-based electrophoretic assay in patients and controls (frequency matched for age and sex) from the Pakistan Risk of Myocardial Infarction Study (PROMIS). We calculated odds ratios (ORs) for myocardial infarction per 1-SD difference in either LPA KIV2 repeats or lipoprotein(a) concentration. In a genome-wide analysis of up to 17 503 participants in PROMIS, we identified genetic variants associated with either apolipoprotein(a) isoform size or lipoprotein(a) concentration. Using a mendelian randomisation study design and genetic data on 60 801 patients with coronary heart disease and 123 504 controls from the CARDIoGRAMplusC4D consortium, we calculated ORs for myocardial infarction with variants that produced similar differences in either apolipoprotein(a) isoform size in serum or lipoprotein(a) concentration. Finally, we compared phenotypic versus genotypic ORs to estimate whether apolipoprotein(a) isoform size, lipoprotein(a) concentration, or both were causally associated with coronary heart disease. FINDINGS: The PROMIS cohort included 9015 patients with acute myocardial infarction and 8629 matched controls. In participants for whom KIV2 repeat and lipoprotein(a) data were available, the OR for myocardial infarction was 0·93 (95% CI 0·90-0·97; p<0·0001) per 1-SD increment in LPA KIV2 repeats after adjustment for lipoprotein(a) concentration and conventional lipid concentrations. The OR for myocardial infarction was 1·10 (1·05-1·14; p<0·0001) per 1-SD increment in lipoprotein(a) concentration, after adjustment for LPA KIV2 repeats and conventional lipids. Genome-wide analysis identified rs2457564 as a variant associated with smaller apolipoprotein(a) isoform size, but not lipoprotein(a) concentration, and rs3777392 as a variant associated with lipoprotein(a) concentration, but not apolipoprotein(a) isoform size. In 60 801 patients with coronary heart disease and 123 504 controls, OR for myocardial infarction was 0·96 (0·94-0·98; p<0·0001) per 1-SD increment in apolipoprotein(a) protein isoform size in serum due to rs2457564, which was directionally concordant with the OR observed in PROMIS for a similar change. The OR for myocardial infarction was 1·27 (1·07-1·50; p=0·007) per 1-SD increment in lipoprotein(a) concentration due to rs3777392, which was directionally concordant with the OR observed for a similar change in PROMIS. INTERPRETATION: Human genetic data suggest that both smaller apolipoprotein(a) isoform size and increased lipoprotein(a) concentration are independent and causal risk factors for coronary heart disease. Lipoprotein(a)-lowering interventions could be preferentially effective in reducing the risk of coronary heart disease in individuals with smaller apolipoprotein(a) isoforms. FUNDING: British Heart Foundation, US National Institutes of Health, Fogarty International Center, Wellcome Trust, UK Medical Research Council, UK National Institute for Health Research, and Pfizer