Next-generation sequencing reveals large connected networks of intra-host HCV variants

Background: Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.Results: Intra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient. The distance between any two variants calculated over the component correlated strongly with nucleotide distances (r = 0.9499; p = 0.0001), a better correlation than the one obtained with Neighbour-Joining trees (r = 0.7624; p = 0.0001). In each patient, components were well separated, with the average distance between (6.53%) being 10 times greater than within each component (0.68%). The ratio of nonsynonymous to synonymous changes was calculated and some patients (6.9%) showed a mixture of networks under strong negative and positive selection. All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes. In vitro sampling showed that 93.02% of components present in the original sample were also found in experimental replicas, with 81.6% of reads found in both. When syringe-sharing transmission events were simulated, 91.2% of all simulated transmission events seeded all components present in the source.Conclusions: Most intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.

Balance-of-payments-constrained growth in Brazil: 1951-2008

The aim of this study is to determine whether Brazil's economic growth has been constrained by the balance of payments in the long run. The question underpinning the analysis can be expressed as follows: Was economic growth in the period 1951-2008 constrained by the balance of payments? To answer this question, the study employs the externally constrained growth methodology developed by Lima and Carvalho (2009), among others. The main statistical method used is vector error correction. The conclusion is that the rate of economic growth in Brazil was restricted by the external sector in the period concerned, validating the theory of balance-of-payments growth constraint with regard to the economic history of Brazil.

Construction and decoding of BCH codes over chain of commutative rings

In this paper, we present a new construction and decoding of BCH codes over certain rings. Thus, for a nonnegative integer t, let A0 ⊂ A1 ⊂···⊂ At−1 ⊂ At be a chain of unitary commutative rings, where each Ai is constructed by the direct product of appropriate Galois rings, and its projection to the fields is K0 ⊂ K1 ⊂···⊂ Kt−1 ⊂ Kt (another chain of unitary commutative rings), where each Ki is made by the direct product of corresponding residue fields of given Galois rings. Also, A∗ i and K∗ i are the groups of units of Ai and Ki, respectively. This correspondence presents a construction technique of generator polynomials of the sequence of Bose, Chaudhuri, and Hocquenghem (BCH) codes possessing entries from A∗ i and K∗ i for each i, where 0 ≤ i ≤ t. By the construction of BCH codes, we are confined to get the best code rate and error correction capability; however, the proposed contribution offers a choice to opt a worthy BCH code concerning code rate and error correction capability. In the second phase, we extend the modified Berlekamp-Massey algorithm for the above chains of unitary commutative local rings in such a way that the error will be corrected of the sequences of codewords from the sequences of BCH codes at once. This process is not much different than the original one, but it deals a sequence of codewords from the sequence of codes over the chain of Galois rings.

Reliable Broadcasting and Streaming of Multimedia Content

This thesis is focused on the study of techniques that allow to have reliable transmission of multimedia content in streaming and broadcasting applications, targeting in particular video content. The design of efficient error-control mechanisms, to enhance video transmission systems reliability, has been addressed considering cross-layer and multi-layer/multi-dimensional channel coding techniques to cope with bit errors as well as packet erasures. Mechanisms for unequal time interleaving have been designed as a viable solution to reduce the impact of errors and erasures by acting on the time diversity of the data flow, thus enhancing robustness against correlated channel impairments. In order to account for the nature of the factors which affect the physical layer channel in the evaluation of FEC schemes performances, an ad-hoc error-event modeling has been devised. In addition, the impact of error correction/protection techniques on the quality perceived by the consumers of video services applications and techniques for objective/subjective quality evaluation have been studied. The applicability and value of the proposed techniques have been tested by considering practical constraints and requirements of real system implementations.

Traffic-Adaptive and Link-Quality-Aware Communication in Wireless Sensor Networks

This paper is a summary of the main contribu- tions of the PhD thesis published in [1]. The main research contributions of the thesis are driven by the research question how to design simple, yet efficient and robust run-time adaptive resource allocation schemes within the commu- nication stack of Wireless Sensor Network (WSN) nodes. The thesis addresses several problem domains with con- tributions on different layers of the WSN communication stack. The main contributions can be summarized as follows: First, a a novel run-time adaptive MAC protocol is intro- duced, which stepwise allocates the power-hungry radio interface in an on-demand manner when the encountered traffic load requires it. Second, the thesis outlines a metho- dology for robust, reliable and accurate software-based energy-estimation, which is calculated at network run- time on the sensor node itself. Third, the thesis evaluates several Forward Error Correction (FEC) strategies to adap- tively allocate the correctional power of Error Correcting Codes (ECCs) to cope with timely and spatially variable bit error rates. Fourth, in the context of TCP-based communi- cations in WSNs, the thesis evaluates distributed caching and local retransmission strategies to overcome the perfor- mance degrading effects of packet corruption and trans- mission failures when transmitting data over multiple hops. The performance of all developed protocols are eval- uated on a self-developed real-world WSN testbed and achieve superior performance over selected existing ap- proaches, especially where traffic load and channel condi- tions are suspect to rapid variations over time.

Mechanisms of cell competition: Themes and variations

Cell competition is the short-range elimination of slow-dividing cells through apoptosis when confronted with a faster growing population. It is based on the comparison of relative cell fitness between neighboring cells and is a striking example of tissue adaptability that could play a central role in developmental error correction and cancer progression in both Drosophila melanogaster and mammals. Cell competition has led to the discovery of multiple pathways that affect cell fitness and drive cell elimination. The diversity of these pathways could reflect unrelated phenomena, yet recent evidence suggests some common wiring and the existence of a bona fide fitness comparison pathway.

GOCE: assessment of GPS-only gravity field determination

The GOCE satellite was orbiting the Earth in a Sun-synchronous orbit at a very low altitude for more than 4 years. This low orbit and the availability of high-quality data make it worthwhile to assess the contribution of GOCE GPS data to the recovery of both the static and time-variable gravity fields. We use the kinematic positions of the official GOCE precise science orbit (PSO) product to perform gravity field determination using the Celestial Mechanics Approach. The generated gravity field solutions reveal severe systematic errors centered along the geomagnetic equator. Their size is significantly coupled with the ionospheric density and thus generally increasing over the mission period. The systematic errors may be traced back to the kinematic positions of the PSO product and eventually to the ionosphere-free GPS carrier phase observations used for orbit determination. As they cannot be explained by the current higher order ionospheric correction model recommended by the IERS Conventions 2010, an empirical approach is presented by discarding GPS data affected by large ionospheric changes. Such a measure yields a strong reduction of the systematic errors along the geomagnetic equator in the gravity field recovery, and only marginally reduces the set of useable kinematic positions by at maximum 6 % for severe ionosphere conditions. Eventually it is shown that GOCE gravity field solutions based on kinematic positions have a limited sensitivity to the largest annual signal related to land hydrology.

The Time-Series Properties on Housing Prices: A Case Study of the Southern California Market

We examine the time-series relationship between housing prices in eight Southern California metropolitan statistical areas (MSAs). First, we perform cointegration tests of the housing price indexes for the MSAs, finding seven cointegrating vectors. Thus, the evidence suggests that one common trend links the housing prices in these eight MSAs, a purchasing power parity finding for the housing prices in Southern California. Second, we perform temporal Granger causality tests revealing intertwined temporal relationships. The Santa Anna MSA leads the pack in temporally causing housing prices in six of the other seven MSAs, excluding only the San Luis Obispo MSA. The Oxnard MSA experienced the largest number of temporal effects from other MSAs, six of the seven, excluding only Los Angeles. The Santa Barbara MSA proved the most isolated in that it temporally caused housing prices in only two other MSAs (Los Angels and Oxnard) and housing prices in the Santa Anna MSA temporally caused prices in Santa Barbara. Third, we calculate out-of-sample forecasts in each MSA, using various vector autoregressive (VAR) and vector error-correction (VEC) models, as well as Bayesian, spatial, and causality versions of these models with various priors. Different specifications provide superior forecasts in the different MSAs. Finally, we consider the ability of theses time-series models to provide accurate out-of-sample predictions of turning points in housing prices that occurred in 2006:Q4. Recursive forecasts, where the sample is updated each quarter, provide reasonably good forecasts of turning points.

"Ripple Effects" and Forecasting Home Prices in Los Angeles, Las Vegas, and Phoenix

We examine the time-series relationship between housing prices in Los Angeles, Las Vegas, and Phoenix. First, temporal Granger causality tests reveal that Los Angeles housing prices cause housing prices in Las Vegas (directly) and Phoenix (indirectly). In addition, Las Vegas housing prices cause housing prices in Phoenix. Los Angeles housing prices prove exogenous in a temporal sense and Phoenix housing prices do not cause prices in the other two markets. Second, we calculate out-of-sample forecasts in each market, using various vector autoregessive (VAR) and vector error-correction (VEC) models, as well as Bayesian, spatial, and causality versions of these models with various priors. Different specifications provide superior forecasts in the different cities. Finally, we consider the ability of theses time-series models to provide accurate out-of-sample predictions of turning points in housing prices that occurred in 2006:Q4. Recursive forecasts, where the sample is updated each quarter, provide reasonably good forecasts of turning points.

Countervailing Duties in the USA

This paper reveals the characteristics of the ITC's decisions on countervailing duties, which have seldom been studied. The empirical evidences based on time series data show that there is a long run equilibrium relationship between affirmative countervailing decisions and macroeconomic variables such as economic growth rates and import penetration ratios. The error correction models show that there is a unidirectional causality from affirmative countervailing decisions to slower economic growth.

DEVELOPMENT OF NOVEL METHODS TO MINIMIZE THE IMPACT OF SEQUENCING ERRORS IN THE NEXT-GENERATION SEQUENCING DATA ANALYSIS

Next-generation sequencing (NGS) technology has become a prominent tool in biological and biomedical research. However, NGS data analysis, such as de novo assembly, mapping and variants detection is far from maturity, and the high sequencing error-rate is one of the major problems. . To minimize the impact of sequencing errors, we developed a highly robust and efficient method, MTM, to correct the errors in NGS reads. We demonstrated the effectiveness of MTM on both single-cell data with highly non-uniform coverage and normal data with uniformly high coverage, reflecting that MTM’s performance does not rely on the coverage of the sequencing reads. MTM was also compared with Hammer and Quake, the best methods for correcting non-uniform and uniform data respectively. For non-uniform data, MTM outperformed both Hammer and Quake. For uniform data, MTM showed better performance than Quake and comparable results to Hammer. By making better error correction with MTM, the quality of downstream analysis, such as mapping and SNP detection, was improved. SNP calling is a major application of NGS technologies. However, the existence of sequencing errors complicates this process, especially for the low coverage (

(Table 1) Gas tie points used to correlate NorthGRIP and Vostol records

North Atlantic sediment records (MD95-2042), Greenland (Greenland Ice Core Project (GRIP)) and Antarctica (Byrd and Vostok) ice core climate records have been synchronized over marine isotopic stage 3 (MIS 3) (64 to 24 kyr B.P.) (Shackleton et al., 2000). The resulting common timescale suggested that MD95-2042 d18Obenthic fluctuations were synchronous with temperature changes in Antarctica (dDice or d18Oice records). In order to assess the persistency of this result we have used here the recent Greenland NorthGRIP ice core covering the last glacial inception. We transfer the Antarctic Vostok GT4 timescale to NorthGRIP d18Oice and MD95-2042 d18Oplanktonic records and precisely quantify all the relative timing uncertainties. During the rapid warming of Dansgaard-Oeschger 24, MD95-2042 d18Obenthic decrease is in phase with d18Oplanktonic decrease and therefore with NorthGRIP temperature increase, but it takes place 1700 ± 1100 years after the Antarctic warming. Thus the present study reveals that the results obtained previously for MIS 3 cannot be generalized and demonstrates the need to improve common chronologies for marine and polar archives.

Tab. 1: U-Pb analyses of zircons from rock samples in MT. Newton and Cumpston Massif, East Antarctica

We present new U-Pb zircon (SHRIMP) data on rocks from Mt Newton and Cumpston Massif in the southern Prince Charles Mountains. Our data demonstrate that Mt Newton was affected by a newly proposed Palaeoproterozoic "Newton" Orogeny at c. 2100-2200 Ma. Sedimentation, felsic volcanism (c. 2200 Ma), metamorphism and folding, followed by granite intrusion (c. 2100 Ma), suggest development of a trough or aulacogene in the area during the early Palaeoproterozoic. An orthogneiss from Cumpston Massif yielded an age of c. 3180 Ma for granitic protolith emplacement, which is in good agreement with many U-Pb zircon ages from similar rocks in the southern Mawson Escarpment. A syn- to late-tectonic muscovite-bearing pegmatite from Cumpston Massif yielded a c. 2500 Ma date of emplacement, which indicates early Palaeoproterozoic activity in this block, probably in response to a tectono-magmatic episode in the Lambert Terrane bordering the Ruker Terrane in the northeast. The correlation of tectono-magmatic events in both the Ruker and Lambert terranes of the southern Prince Charles Mountains provides evidence for their common evolution during the Proterozoic.

Shipborne ocean color remote sensing

In this paper, modernized shipborne procedures are presented to collect and process above-water radiometry for remote sensing applications. A setup of five radiometers and a bidirectional camera system, which provides panoramic sea surface and sky images, is proposed for the collection of high-resolution radiometric quantities. Images from the camera system can be used to determine sky state and potential glint, whitecaps, or foam contamination. A peak in the observed remote sensing reflectance RRS spectra between 750-780 nm was typically found in spectra with relatively high surface reflected glint (SRG), which suggests this waveband could be a useful SRG indicator. Simplified steps for computing uncertainties in SRG corrected RRS are proposed and discussed. The potential of utilizing "unweighted multimodel averaging," which is the average of four or more common SRG correction models, is examined to determine the best approximation RRS. This best approximation RRS provides an estimate of RRS based on various SRG correction models established using radiative transfer simulations and field investigations. Applying the average RRS provides a measure of the inherent uncertainties or biases that result from a user subjectively choosing any one SRG correction model. Comparisons between inherent and apparent optical property derived observations were used to assess the robustness of the SRG multimodel averaging ap- proach. Correlations among the standard SRG models were completed to determine the degree of association or similarities between the SRG models. Results suggest that the choice of glint models strongly affects derived RRS values and can also influence the blue to green band ratios used for modeling biogeochemical parameters such as for chlorophyll a. The objective here is to present a uniform and traceable methodology for determining ship- borne RRS measurements and its associated errors due to glint correction and to ensure the direct comparability of these measurements in future investigations. We encourage the ocean color community to publish radiometric field measurements with matching and complete metadata in open access repositories.