Entropy and Uncertainty of Squeezed Quantum Open Systems

We define the entropy S and uncertainty function of a squeezed system interacting with a thermal bath, and study how they change in time by following the evolution of the reduced density matrix in the influence functional formalism. As examples, we calculate the entropy of two exactly solvable squeezed systems: an inverted harmonic oscillator and a scalar field mode evolving in an inflationary universe. For the inverted oscillator with weak coupling to the bath, at both high and low temperatures, $S\to r$, where r is the squeeze parameter. In the de Sitter case, at high temperatures, $S\to (1-c)r$ where $c = \gamma_0/H$, $\gamma_0$ being the coupling to the bath and H the Hubble constant. These three cases confirm previous results based on more ad hoc prescriptions for calculating entropy. But at low temperatures, the de Sitter entropy $S\to (1/2-c)r$ is noticeably different. This result obtained from a more rigorous approach, shows that factors usually ignored by the conventional approaches, i.e., the nature of the environment and the coupling strength betwen the system and the environment, are important

Prediction of a deletion copy number variant by a dense SNP panel

<p>Abstract</p> <p>Background</p> <p>A newly recognized type of genetic variation, Copy Number Variation (CNV), is detected in mammalian genomes, e.g. the cattle genome. This form of variation can potentially cause phenotypic variation. Our objective was to determine whether dense SNP (single nucleotide polymorphisms) panels can capture the genetic variation due to a simple bi-allelic CNV, with the prospect of including the effect of such structural variations into genomic predictions.</p> <p>Methods</p> <p>A deletion type CNV on bovine chromosome 6 was predicted from its neighboring SNP with a multiple regression model. Our dataset consisted of CNV genotypes of 1,682 cows, along with 100 surrounding SNP genotypes. A prediction model was fitted considering 10 to 100 surrounding SNP and the accuracy obtained directly from the model was confirmed by cross-validation.</p> <p>Results and conclusions</p> <p>The accuracy of prediction increased with an increasing number of SNP in the model and the predicted accuracies were similar to those obtained by cross-validation. A substantial increase in accuracy was observed when the number of SNP increased from 10 to 50 but thereafter the increase was smaller, reaching the highest accuracy (0.94) with 100 surrounding SNP. Thus, we conclude that the genotype of a deletion type CNV and its putative QTL effect can be predicted with a maximum accuracy of 0.94 from surrounding SNP. This high prediction accuracy suggests that genetic variation due to simple deletion CNV is well captured by dense SNP panels. Since genomic selection relies on the availability of a dense marker panel with markers in close linkage disequilibrium to the QTL in order to predict their genetic values, we also discuss opportunities for genomic selection to predict the effects of CNV by dense SNP panels, when CNV cause variation in quantitative traits.</p

Genetic interaction between two VNTRs in the MAOA gene is associated with the nicotine dependence

Nicotine dependence is an addiction to tobacco products and a global public health concern that in part would be influenced by our genetics. Smokers are reported to have reduced MAOA activity, but the results from genetic associations with this gene have been inconclusive. Two functionally relevant variable number tandem repeat (VNTR) domains, termed uVNTR and dVNTR, in the MAOA gene are well characterized transcriptional regulatory elements. In the present study, we analyzed uVNTR and dVNTR polymorphisms in the MAOA gene in the Vietnamese male population of smokers and non-smokers in order to assess the association of MAOA with the nicotine dependence measured by the Fagerström Test for Nicotine Dependence (FTND). Individual analysis of VNTRs separately identified uVNTR to be associated with the F6 question of the FTND indicating the stronger addiction to nicotine. No associations were found between the dVNTR and smoking behavior. The combination of dVNTR and uVNTR, that predicts low expression of MAOA (10–3 haplotypes), was significantly associated with the higher nicotine dependence (FTND score), longer smoking duration, and more persistent smoking behavior (fewer quit attempts). In conclusion, our study confirms that low MAOA expression is genetically predictive to the higher nicotine dependence

Alternative splicing of leptin receptor overlapping transcript in osteosarcoma

Alternative splicing of RNA is an essential mechanism that increases proteomic diversity in eukaryotic cells. Aberrant alternative splicing is often associated with various human diseases, including cancer. We conducted whole-transcriptome analysis of 18 osteosarcoma bone samples (paired normal—tumor biopsies). Using RNA-seq, we identified statistically significant (FDR <0.05) 26 differentially expressed transcript variants of leptin receptor overlapping transcript (LEPROT) gene. Some of the transcripts were overexpressed in normal cells, whereas others were overexpressed in tumor cells. The function of LEPROT is not completely understood. Herein, we highlight a possible association between OS and aberrant alternative splicing events and its interaction with the expression of LEPROT. We also discuss the role of LEPROT in regulating growth hormone and its receptor, and the relationship with initiation and progression of OS. This research study may help to understand the association of alternative splicing mechanism in OS and in tumorigenesis more generally. Further, LEPROT gene can also be considered as a potential biomarker of osteosarcoma

Inflationary Reheating in Grand Unified Theories

Grand unified theories may display multiply interacting fields with strong coupling dynamics. This poses two new problems: (1) What is the nature of chaotic reheating after inflation, and (2) How is reheating sensitive to the mass spectrum of these theories ? We answer these questions in two interesting limiting cases and demonstrate an increased efficiency of reheating which strongly enhances non-thermal topological defect formation, including monopoles and domain walls. Nevertheless, the large fluctuations may resolve this monopole problem via a modified Dvali-Liu-Vachaspati mechanism in which non-thermal destabilsation of discrete symmetries occurs at reheating.Comment: 4 pages, 5 ps figures - 1 colour, Revtex. Further (colour & 3-D) figures available from http://www.sissa.it/~bassett/reheating/ . Matched to version to appear in Phys. Rev. let

Analysis of the Expression of Repetitive DNA Elements in Osteosarcoma

Osteosarcoma (OS) is a rare malignant bone tumor. It affects mostly young persons and has poor outcome with the present treatment. No improvement was observed since the introduction of chemotherapy. The better understanding of osteosarcoma development could indicate better management strategy. Repetitive DNA elements were found to play a role in cancer mechanism especially in epithelial tumors but not yet analyzed in osteosarcoma. We conducted the study to analyse the expression profile of repetitive elements (RE) in osteosarcoma. Methods: Fresh bone paired (tumor and normal bone) samples were obtained from excised parts of tumors of 18 patients with osteosarcoma. We performed sequencing of RNA extracted from 36 samples (18 tumor tissues and 18 normal bone for controls), mapped raw reads to the human genome and identified the REs. EdgeR package was used to analyse the difference in expression of REs between osteosarcoma and normal bone. Results: 82 REs were found differentially expressed (FDR < 0.05) between osteosarcoma and normal bone. Out of all significantly changed REs, 35 were upregulated and 47 were downregulated. HERVs (THE1C-int, LTR5, MER57F and MER87B) and satellite elements (HSATII, ALR-alpha) were the most significantly differential expressed elements between osteosarcoma and normal tissues. These results suggest significant impact of REs in the osteosarcoma. The role of REs should be further studied to understand the mechanism they have in the genesis of osteosarcoma

Thermal Particle Creation in Cosmological Spacetimes: A Stochastic Approach

The stochastic method based on the influence functional formalism introduced in an earlier paper to treat particle creation in near-uniformly accelerated detectors and collapsing masses is applied here to treat thermal and near-thermal radiance in certain types of cosmological expansions. It is indicated how the appearance of thermal radiance in different cosmological spacetimes and in the two apparently distinct classes of black hole and cosmological spacetimes can be understood under a unifying conceptual and methodological framework.Comment: 17 pages, revtex (aps, eqsecnum), submitted to PRD, April 199

BEC Collapse and Dynamical Squeezing of Vacuum Fluctuations

We analyze the phenomena of Bose Novae, as described by Donley et al [Nature 412, 295 (2001)], by focusing on the behavior of excitations or fluctuations above the condensate, as driven by the dynamics of the condensate (rather than the dynamics of the condensate alone or the kinetics of the atoms). The dynamics of the condensate squeezes and amplifies the quantum excitations, mixing the positive and negative frequency components of their wave functions thereby creating particles which appear as bursts and jets. By analyzing the changing amplitude and particle content of these excitations, our simple physical picture (based on a test field approximation) explains well the overall features of the Bose Novae phenomena and provide excellent quantitative fits with experimental data on several aspects, such as the scaling behavior of the collapse time and the amount of particles in the jet. The predictions of the bursts at this level of approximation is less than satisfactory but may be improved on by including the backreaction of the excitations on the condensate. The mechanism behind the dominant effect -- parametric amplification of vacuum fluctuations and freezing of modes outside of horizon -- is similar to that of cosmological particle creation and structure formation in a rapid quench (which is fundamentally different from Hawking radiation in black holes). This shows that BEC dynamics is a promising venue for doing `laboratory cosmology'.Comment: Latex 36 pages, 6 figure

Entropy and Uncertainty of Squeezed Quantum Open Systems

We define the entropy S and uncertainty function of a squeezed system interacting with a thermal bath, and study how they change in time by following the evolution of the reduced density matrix in the influence functional formalism. As examples, we calculate the entropy of two exactly solvable squeezed systems: an inverted harmonic oscillator and a scalar field mode evolving in an inflationary universe. For the inverted oscillator with weak coupling to the bath, at both high and low temperatures, $S\to r$, where r is the squeeze parameter. In the de Sitter case, at high temperatures, $S\to (1-c)r$ where $c = \gamma_0/H$, $\gamma_0$ being the coupling to the bath and H the Hubble constant. These three cases confirm previous results based on more ad hoc prescriptions for calculating entropy. But at low temperatures, the de Sitter entropy $S\to (1/2-c)r$ is noticeably different. This result, obtained from a more rigorous approach, shows that factors usually ignored by the conventional approaches, i.e., the nature of the environment and the coupling strength betwen the system and the environment, are important.Comment: 36 pages, epsfig, 2 in-text figures include

Global supply-chain effects of COVID-19 control measures

Countries have sought to stop the spread of coronavirus disease 2019 (COVID-19) by severely restricting travel and in-person commercial activities. Here, we analyse the supply-chain effects of a set of idealized lockdown scenarios, using the latest global trade modelling framework. We find that supply-chain losses that are related to initial COVID-19 lockdowns are largely dependent on the number of countries imposing restrictions and that losses are more sensitive to the duration of a lockdown than its strictness. However, a longer containment that can eradicate the disease imposes a smaller loss than shorter ones. Earlier, stricter and shorter lockdowns can minimize overall losses. A ‘go-slow’ approach to lifting restrictions may reduce overall damages if it avoids the need for further lockdowns. Regardless of the strategy, the complexity of global supply chains will magnify losses beyond the direct effects of COVID-19. Thus, pandemic control is a public good that requires collective efforts and support to lower-capacity countries