Factors that influence quality and yield of circulating-free DNA: A systematic review of the methodology literature.

BACKGROUND: Circulating-free DNA (cfDNA) is under investigation as a liquid biopsy of cancer for early detection, monitoring disease progression and therapeutic response. This systematic review of the primary cfDNA literature aims to identify and evaluate factors that influence recovery of cfDNA, and to outline evidence-based recommendations for standardization of methods. METHODS: A search of the Ovid and Cochrane databases was undertaken in May 2018 to obtain relevant literature on cfDNA isolation and quantification. Retrieved titles and abstracts were reviewed by two authors. The factors evaluated include choice of specimen type (plasma or serum); time-to-processing of whole blood; blood specimen tube; centrifugation protocol (speed, time, temperature and number of spins); and methods of cfDNA isolation and quantification. FINDINGS: Of 4,172 articles identified through the database search, 52 proceeded to full-text review and 37 met the criteria for inclusion. A quantitative analysis was not possible, due to significant heterogeneity in methodological approaches between studies. Therefore, included data was tabulated and a textual qualitative synthesis approach was taken. INTERPRETATION: This is the first systematic review of methodological factors that influence recovery and quantification of cfDNA, enabling recommendations to be made that will support standardization of methodological approaches towards development of blood-based cancer tests

China Near Seas Combat Capabilities

The capstone U.S. Defense Department study on the future operational environment declares, China\u27s rise represents the most significant single event on the international horizon since the collapse of the Cold War. Understanding and assessing changes in China\u27s traditionally defensive naval strategy, doctrine, and force structure are of obvious importance to the U.S. Navy (USN) and other Pacific navies concerned with the possible security implications of that rise. This chapter examines the development of the Chinese navy\u27s Houbei (Type 022) fast-attack-craft force and its roles and missions in China\u27s near seas and discusses implications for the U.S. Navy and other navies in the region.https://digital-commons.usnwc.edu/cmsi-red-books/1010/thumbnail.jp

Index and characteristic analysis of partial differential equations

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2000.Includes bibliographical references (leaves 230-238) and index.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Technologies for dynamic simulation of chemical process flowsheets, as implemented in equation-based dynamic simulators,allow solution of fairly sophisticated process models, that include detailed descriptions of physical phenomena along with operating policies and discrete events. Simulation of flowsheet models with this level of detail forms the basis for a wide variety of activities, such as process optimization, startup and shutdown studies, process design, batch policy synthesis, safety interlock validation, and operator training. Technologies that make these activities possible for plant-scale models include sparse linear algebra routines, robust backward difference formula time integration methods, guaranteed state event location algorithms, generation of analytical Jacobian information via automatic differentiation, efficient algorithms for consistent initialization that may also be used to analyze the index of the model equations, automatic index reduction algorithms, and path-constrained dynamic optimization methods. An equation-based dynamic process simulator takes as input the model equations that describe process behavior, along with a description of the operating policy. The input language allows for model decomposition, inheritance, and reuse, which facilitates construction of plant-scale dynamic models. Technologies like the ones mentioned above allow the simulator to then analyze the model for inconsistencies and perform calculations based on dynamic simulation, with a minimum of intervention from the engineer. This reduces both the time and numerical expertise required to perform simulation-based activities. Results, in some cases made possible or economically feasible only by the modeling support provided by a simulator,(cont.) have been impressive. However, these capabilities apply to flowsheet models that consist only of differential-algebraic, or lumped, unit models. Sometimes behavior in a particular unit cannot be adequately described by a lumped formulation, when variation with other independent variables like distance along a PFTR, film coordinate, or polymer chain length are important. In this case, behavior is most naturally modeled with partial differential, or distributed, unit models. Partial differential equations in network flow simulations bring an additional set of mathematical and numerical issues. For a distributed model to bema thematically well-posed, proper initial and boundary conditions must be specified. Boundary condition requirements for nonlinear unit models may change during the course of a dynamic simulation, even in the absence of discrete events. Some distributed models, due to improper formulation or simple transcription errors, may be ill-posed because they do not have a mathematical property called continuous dependence on data. Finally, the model equations must be discretized in the proper manner. This thesis contributes two new analyses of distributed unit models. The first relies on the definition of a differentiation index for partial differential equations developed in this thesis. It is by design a very natural generalization of the differentiation index of differential-algebraic equations.by Wade Steven Martinson.Ph.D

Sea Ice Suppression of CO2 Outgassing in the West Antarctic Peninsula: Implications For The Evolving Southern Ocean Carbon Sink

The Southern Ocean plays an important role in the uptake of atmospheric CO2. In seasonally ice-covered regions, estimates of air-sea exchange remain uncertain in part because of a lack of observations outside the summer season. Here we present new estimates of air-sea CO2 flux in the West Antarctic Peninsula (WAP) from an autonomous mooring on the continental shelf. In summer, the WAP is a sink for atmospheric CO2 followed by a slow return to atmospheric equilibrium in autumn and winter. Outgassing is almost entirely suppressed by ice cover from June through October, resulting in a modest net annual CO2 sink. Model projections indicate sea ice formation will occur later in the season in the coming decades potentially weakening the net oceanic CO2 sink. Interannual variability in the WAP is significant, highlighting the importance of sustained observations of air-sea exchange in this rapidly changing region of the Southern Ocean

Lipid levels in HIV-positive men receiving anti-retroviral therapy are not associated with copy number variation of reverse cholesterol transport pathway genes Genetics

Background: The exacerbation of HIV-1 associated dyslipidemia seen in a subset of patients receiving anti-retroviral therapy suggests that genetic factors put these individuals at greater risk of cardiovascular disease. Single nucleotide polymorphisms (SNPs) within genes of and influencing the reverse cholesterol transport (RCT) pathway are associated with lipid levels but little is known regarding their copy number variation (CNV). This form of quantitative genetic variation has the potential to alter the amount of gene product made, thereby also influencing lipid metabolism. Results: To examine if CNV in RCT pathway genes was associated with altered serum lipid profiles in HIV-positive individuals receiving therapy, we designed a custom multiplex ligation-dependent probe amplification assay to screen 16 RCT genes within a subset of individuals from the Multicenter AIDS Cohort Study who show extreme lipid phenotypes. Verification of CNV was performed using a custom NanoString assay, and the Illumina HT-12 mRNA expression microarray was used to determine the influence of copy number on gene expression. Among the RCT genes, CNV was observed to be extremely rare. The only CNV seen was in the CETP gene, which showed a loss of copy in 1 of the 320 samples (0.3 %) in our study. The genes in our study showed little variation in expression between individuals, and the variation seen was not related to any detected CNV. Conclusions: Whole gene CNV is uncommon in RCT pathway genes, and not a major factor in the development of highly active antiretroviral therapy (HAART) associated dyslipidemia

Relativistic calculations of the lifetimes and hyperfine structure constants in 67^{67}Zn+^{+}

This work presents accurate {\it ab initio} determination of the magnetic dipole (M1) and electric quadrupole (E2) hyperfine structure constants for the ground and a few low-lying excited states in $^{67}$Zn$^{+}$, which is one of the interesting systems in fundamental physics. The coupled-cluster (CC) theory within the relativistic framework has been used here in this calculations. Long standing demands for a relativistic and highly correlated calculations like CC can be able to resolve the disagreements among the lifetime estimations reported previously for a few low-lying states of Zn$^{+}$. The role of different electron correlation effects in the determination of these quantities are discussed and their contributions are presented.Comment: 9 pages, 1 figure. submitted to J. Phys. B Fast Trac