Ultraaccurate genome sequencing and haplotyping of single human cells.

Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microfluidic reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10-8 and average 500-kb-long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7 Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs

Community Internet of Things as Mobile Infrastructure: Methodological Challenges and Opportunities

From smart devices to homes to cities, Internet of Things (IoT) technologies have become embedded within everyday objects on a global scale. We understand IoT technologies as a form of infrastructure that bridges the gaps between offline spaces and online networks as they track, transmit, and construct digital data from and of the physical world. We examine the social construction of IoT network technologies through their technological design and corporate discourses. In this article, we explore the methodological challenges and opportunities of studying IoT as an emerging network technology. We draw on a case study of a low-power wide-area network (LPWAN), a cost-effective radio frequency network that is designed to connect sensors across long distances. Reflecting on our semi-structured interviews with LPWAN users and advocates, participant observation at conferences about LPWAN, as well as a community-based LPWAN project, we examine the intersections of methods and practices as related to space, data, and infrastructures. We identify three key methodological obstacles involved in studying the social construction of networked technologies that straddle physical and digital environments. These include (a) transcending the invisibility and abstraction of network infrastructures, (b) managing practical and conceptual boundaries to sample key cases and participants, and (c) negotiating competing technospatial imaginaries between participants and researchers. Through our reflection, we demonstrate that these challenges also serve as generative methodological opportunities, extending existing tools to study the ways data connects online and offline spaces

Factors influencing adolescent girls' decision in initiation for human papillomavirus vaccination: A cross-sectional study in Hong Kong

Background: Cervical cancer is one of the common cancers among women worldwide. Despite HPV vaccination being one of the effective preventive measures, it is not included in government vaccination programme in Hong Kong. This study aimed to assess the knowledge of and attitude towards cervical cancer prevention among Chinese adolescent girls in Hong Kong, and to identify factors influencing the initiation of HPV vaccination. Methods: This was a cross-sectional study conducted in Hong Kong during the period of October 2010 to November 2010. A self-administered questionnaire was used, with 1,416 girls from 8 secondary schools completing the questionnaire. Knowledge scores were composited and initiation of HPV vaccination was staged based on stage of change. Analyses were conducted to identify the association of initiation of HPV vaccination with participant's personal and family factors as well as their knowledge and attitude towards cervical cancer prevention. Results: The uptake rate of HPV vaccination was low (7%) with 58% respondents in pre-contemplation and contemplation stage. The survey identified a significant gap in knowledge on cervical cancer prevention. The main channels of information were from media and very few from schools or parents. However, 70% expressed their wishes to have more information on cancer prevention, and 78% stated that they were willing to change their lifestyles if they knew the ways of prevention. Multivariate analysis identified three independent significant factors for initiation of vaccination (action and intention): perceived cancer as terrifying disease, school should provide more information on cancer prevention, and comments from relatives and friends having received the vaccine. The cost of vaccination and socio-economic background were not found to be significant. Conclusions: Public education on cervical cancer needs to be well penetrated into the community for more sharing among friends and relatives. School as setting to provide source of information would facilitate uptake rate of HPV vaccine as students have expressed their wishes that school should provide more information on prevention of cancer. School and community education on cancer prevention would help adolescents to have better understanding of the seriousness of cancer. © 2014 Lee et al.; licensee BioMed Central Ltd.link_to_subscribed_fulltex

An evaluation of Fugu's network deadlock avoidance solution

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.Includes bibliographical references (leaves 82-86).by Victor Lee.M.S

Topics in applied microeconomics : estimating the value of commercial land and testing the efficiency of the U.S. Motor Carrier industry

This thesis consists of two essays on applied microeconomics issues. The first essay presents a hedonic price econometric model of vacant commercial land. The second essay presents cost frontier analysis on the industry and firm's performance of the U.S. Motor Carrier industry. Our hedonic price econometric model includes two new developments in estimating land values in a multicentric urban area First, two composite indexes of market accessibility and highway accessibility are developed to account for the impacts of different characteristics of different regional nodes on land value at a particular site. Second, we use nonlinear least squares to estimate the decay parameters of the accessibility indexes within the model. We found that market accessibility is the dominant land value determinant. The estimated market accessibility decay parameter is different in value from the ones that are commonly assumed in hedonic models. The effect of access to highway interchanges is insignificant. Corner lots are of higher value. Finally, under Seattle's zoning policy, zoning classification of neighborhood commercial and community commercial land does not have significant effect on land value. The second essay uses the stochastic cost frontiers to analyze the performance of the U.S. motor carrier industry in the pre- and post-MCA periods. The average industry inefficiencies were between 14 and 27 percent during studied period. Our results indicate that the deregulation has no impact on industry efficiency. After a short adjustment period, the average industry inefficiency in the post-MCA years falls back to its pre-MCA level of around 14 to 16 percent. We analyzed the firm-specific inefficiencies by tobit regression. Our result shows that union firms are 1.5 and 4 percent less efficient than non-union firms in the pre- and post-MCA years, respectively. Firms located in the southern region are relatively efficient and the ones in the northern regions are relatively inefficient. Our result supports Stigler's Survivor Principle that survivor firms are relatively efficient

Active Site Chemistry of the NADPH-Dependent:7-Cyano-7-Deazaguanine (PreQ0) Nitrile Oxidoreductase, an Enzyme involved in Queuosine Biosynthesis

Queuosine (Q) is a modified nucleoside found at the wobble position of bacterial and eukaryotic transfer RNAs (tRNAs) that are specific for the amino acids tyrosine, histidine, aspartate and asparagine. A recently discovered enzyme in the biosynthetic pathway of Q, the NADPH-dependent 7-cyano-7-deazaguanine oxidoreductase (QueF), carries out the two-fold, four-electron reduction of Q precursor preQ0 to preQ1 and represents the first example of the enzymatic conversion of the nitrile functional group to an amine. Presented herein are kinetic, spectroscopic, mutational, biophysical, and isotope labeling studies directed at the elucidation of the chemical and kinetic mechanisms of this new class of protein. Steady-state kinetic analysis using a NADPH-linked continuous assay provided the kinetic parameters Km(NADPH) = 19 ± 2 μM and kcat = 0.69 ± 0.02 min-1. To determine the kinetic parameters of preQ0, a fluorescence assay that was used to follow the formation of NADP+ as an alkaline degradation product was optimized, and this method gave the kinetic constants Km (preQ0) = 0.237 ± 0.045 μM, and k cat = 0.66 ± 0.04 min-1. Titrations of enzyme with preQ0, inactivation and protection studies with iodoacetamide, and site-directed mutagenesis of a conserved cysteine residue (Cys55 in Bacillus subtilis), followed by the biochemical and biophysical analysis of the resulting protein products suggest covalent catalysis is employed by QueF, with Cys55 serving as the catalytic nucleophile to form a covalent thioimide adduct. The mechanism of hydride transfer from NADPH to preQ0 was addressed using isotope labeling studies. The data obtained from 1 H-NMR, ESI-MS and steady-state kinetic analysis of QueF suggests that the protein promotes the stereospecific transfer of the pro-R hydride of NADPH. Mutational and kinetic studies are also described for the substitution of a conserved glutamate (Glu97 in B. subtilis). As evidenced by 25-fold to 280-fold increases in Km (preQ 0) values, the results show this residue is critical for preQ0 recognition and binding. In addition, the kinetics revealed 13-fold to 20-fold decreases in kcat, suggesting substitution of Glu97 also impacts chemistry at the active site. These data provide insights into the active-site chemistry of the QueF mediated nitrile reduction and a chemical mechanism consistent with our results is proposed

Mediatization of Social Space and the Case of Uber Drivers

Digital data have become a form of “objectivation”, which affect how we construct social knowledge and organize social space (Couldry & Hepp, 2017). The workplace is one sphere that is increasingly datafied. This study explores how Uber drivers, a form of digitally-enabled service workers, contribute to the normalization of the social production of space through their interpretative practices of digital data in an online forum. Drawing on Uber’s corporate discourse and an Uber driver online forum, we analyze two facets of the Uber app and drivers’ mediated experiences: (1) the quantification and discipline of drivers’ performance through Uber’s rating system and (2) the coordination of spatial movement through location-related metrics. We argue that the underlying workings of the Uber app premediate expectations of service encounters and spatial movement. Uber drivers meanwhile develop practices which respond to and circumvent their own data contributions to the system. Drivers’ practices, we argue, are largely in compliance with the calculative logics set by Uber. The article addresses implications of Uber drivers’ practices for the reproduction of social space and power-relations in digitally-enabled service work and the gig economy