Quantum enhanced positioning and clock synchronization

A wide variety of positioning and ranging procedures are based on repeatedly sending electromagnetic pulses through space and measuring their time of arrival. This paper shows that quantum entanglement and squeezing can be employed to overcome the classical power/bandwidth limits on these procedures, enhancing their accuracy. Frequency entangled pulses could be used to construct quantum positioning systems (QPS), to perform clock synchronization, or to do ranging (quantum radar): all of these techniques exhibit a similar enhancement compared with analogous protocols that use classical light. Quantum entanglement and squeezing have been exploited in the context of interferometry, frequency measurements, lithography, and algorithms. Here, the problem of positioning a party (say Alice) with respect to a fixed array of reference points will be analyzed.Comment: 4 pages, 2 figures. Accepted for publication by Natur

Effects of anisotropic interactions on the structure of animal groups

This paper proposes an agent-based model which reproduces different structures of animal groups. The shape and structure of the group is the effect of simple interaction rules among individuals: each animal deploys itself depending on the position of a limited number of close group mates. The proposed model is shown to produce clustered formations, as well as lines and V-like formations. The key factors which trigger the onset of different patterns are argued to be the relative strength of attraction and repulsion forces and, most important, the anisotropy in their application.Comment: 22 pages, 9 figures. Submitted. v1-v4: revised presentation; extended simulations; included technical results. v5: added a few clarification

Integrated photonic quantum gates for polarization qubits

Integrated photonic circuits have a strong potential to perform quantum information processing. Indeed, the ability to manipulate quantum states of light by integrated devices may open new perspectives both for fundamental tests of quantum mechanics and for novel technological applications. However, the technology for handling polarization encoded qubits, the most commonly adopted approach, is still missing in quantum optical circuits. Here we demonstrate the first integrated photonic Controlled-NOT (CNOT) gate for polarization encoded qubits. This result has been enabled by the integration, based on femtosecond laser waveguide writing, of partially polarizing beam splitters on a glass chip. We characterize the logical truth table of the quantum gate demonstrating its high fidelity to the expected one. In addition, we show the ability of this gate to transform separable states into entangled ones and vice versa. Finally, the full accessibility of our device is exploited to carry out a complete characterization of the CNOT gate through a quantum process tomography.Comment: 6 pages, 4 figure

Inferring predominant pathways in cellular models of breast cancer using limited sample proteomic profiling

<p>Abstract</p> <p>Background</p> <p>Molecularly targeted drugs inhibit aberrant signaling within oncogenic pathways. Identifying the predominant pathways at work within a tumor is a key step towards tailoring therapies to the patient. Clinical samples pose significant challenges for proteomic profiling, an attractive approach for identifying predominant pathways. The objective of this study was to determine if information obtained from a limited sample (i.e., a single gel replicate) can provide insight into the predominant pathways in two well-characterized breast cancer models.</p> <p>Methods</p> <p>A comparative proteomic analysis of total cell lysates was obtained from two cellular models of breast cancer, BT474 (HER2+/ER+) and SKBR3 (HER2+/ER-), using two-dimensional electrophoresis and MALDI-TOF mass spectrometry. Protein interaction networks and canonical pathways were extracted from the Ingenuity Pathway Knowledgebase (IPK) based on association with the observed pattern of differentially expressed proteins.</p> <p>Results</p> <p>Of the 304 spots that were picked, 167 protein spots were identified. A threshold of 1.5-fold was used to select 62 proteins used in the analysis. IPK analysis suggested that metabolic pathways were highly associated with protein expression in SKBR3 cells while cell motility pathways were highly associated with BT474 cells. Inferred protein networks were confirmed by observing an up-regulation of IGF-1R and profilin in BT474 and up-regulation of Ras and enolase in SKBR3 using western blot.</p> <p>Conclusion</p> <p>When interpreted in the context of prior information, our results suggest that the overall patterns of differential protein expression obtained from limited samples can still aid in clinical decision making by providing an estimate of the predominant pathways that underpin cellular phenotype.</p

Magnetism and its microscopic origin in iron-based high-temperature superconductors

High-temperature superconductivity in the iron-based materials emerges from, or sometimes coexists with, their metallic or insulating parent compound states. This is surprising since these undoped states display dramatically different antiferromagnetic (AF) spin arrangements and N$\rm \acute{e}$el temperatures. Although there is general consensus that magnetic interactions are important for superconductivity, much is still unknown concerning the microscopic origin of the magnetic states. In this review, progress in this area is summarized, focusing on recent experimental and theoretical results and discussing their microscopic implications. It is concluded that the parent compounds are in a state that is more complex than implied by a simple Fermi surface nesting scenario, and a dual description including both itinerant and localized degrees of freedom is needed to properly describe these fascinating materials.Comment: 14 pages, 4 figures, Review article, accepted for publication in Nature Physic

Knowledge driven decomposition of tumor expression profiles

<p>Abstract</p> <p>Background</p> <p>Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods have been employed to decompose tumor expression profiles into component profiles, hypothetically linked to these events. Interpretation of the resulting data-driven components is often done by post-hoc comparison to, for instance, functional groupings of genes into gene sets. None of the data-driven methods allow the incorporation of that type of knowledge directly into the decomposition.</p> <p>Results</p> <p>We present a linear model which uses knowledge driven, pre-defined components to perform the decomposition. We solve this decomposition model in a constrained linear least squares fashion. From a variety of options, a lasso-based solution to the model performs best in linking single gene perturbation data to mouse data. Moreover, we show the decomposition of expression profiles from human breast cancer samples into single gene perturbation profiles and gene sets that are linked to the hallmarks of cancer. For these breast cancer samples we were able to discern several links between clinical parameters, and the decomposition weights, providing new insights into the biology of these tumors. Lastly, we show that the order in which the Lasso regularization shrinks the weights, unveils consensus patterns within clinical subgroups of the breast cancer samples.</p> <p>Conclusion</p> <p>The proposed lasso-based constrained least squares decomposition provides a stable and relevant relation between samples and knowledge-based components, and is thus a viable alternative to data-driven methods. In addition, the consensus order of component importance within clinical subgroups provides a better molecular characterization of the subtypes.</p

Measurement of GSTP1 promoter methylation in body fluids may complement PSA screening: a meta-analysis

Background: Prostate-specific antigen (PSA) screening has low specificity. Assessment of methylation status in body fluids may complement PSA screening if the test has high specificity. Method: The purpose of this study was to conduct a meta-analysis of the sensitivity and specificity for prostate cancer detection of glutathione-s-transferase–π (GSTP1) methylation in body fluids (plasma, serum, whole blood, urine, ejaculate, and prostatic secretions). We conducted a comprehensive literature search on Medline (Pubmed). We included studies if they met all four of the following criteria: (1) measurement of DNA methylation in body fluids; (2) a case-control or case-only design; (3) publication in an English journal; and (4) adult subjects. Reviewers conducted data extraction independently using a standardised protocol. Twenty-two studies were finally included in this paper. Primer sequences and methylation method in each study were summarised and evaluated using meta-analyses. This paper represents a unique cross-disciplinary approach to molecular epidemiology. Results: The pooled specificity of GSTP1 promoter methylation measured in plasma, serum, and urine samples from negative-biopsy controls was 0.89 (95% CI, 0.80–0.95). Stratified analyses consistently showed a high specificity across different sample types and methylation methods (include both primer sequences and location). The pooled sensitivity was 0.52 (95% CI, 0.40–0.64). Conclusions: The pooled specificity of GSTP1 promoter methylation measures in plasma, serum, and urine was excellent and much higher than the specificity of PSA. The sensitivity of GSTP1 was modest, no higher than that of PSA. These results suggest that measurement of GSTP1 promoter methylation in plasma, serum, or urine samples may complement PSA screening for prostate cancer diagnosis

Recombination and positive selection identified in complete genome sequences of Japanese encephalitis virus

The mosquito-borne Japanese encephalitis virus (JEV) causes encephalitis in man but not in pigs. Complete genomes of a human, mosquito and pig isolate from outbreaks in 1982 and 1985 in Thailand were sequenced with the aim of identifying determinants of virulence that may explain the differences in outcomes of JEV infection between pigs and man. Phylogenetic analysis revealed that five of these isolates belonged to genotype I, but the 1982 mosquito isolate belonged to genotype III. There was no evidence of recombination among the Thai isolates, but there were phylogenetic signals suggestive of recombination in a 1994 Korean isolate (K94P05). Two sites of the genome under positive selection were identified: codons 996 and 2296 (amino acids 175 of the non-structural protein NS1 and 24 of NS4B, respectively). A structurally significant substitution was seen at NS4B position 24 of the human isolate compared with the mosquito and pig isolates from the 1985 outbreak in Thailand. The potential importance of the two sites in the evolution and ecology of JEV merits further investigation

Ultrasonographic median nerve cross-section areas measured by 8-point "inching test" for idiopathic carpal tunnel syndrome: a correlation of nerve conduction study severity and duration of clinical symptoms

<p>Abstract</p> <p>Background</p> <p>Incremental palmar stimulation of the median nerve sensory conduction at the wrist, the "inching test", provides an assessment with reference to segments proximal and distal to the entrapment. This study used high-resolution ultrasonography (US) to measure the median nerve's cross-section areas (CSAs) like the "inching test" and to correlate with the nerve conduction study (NCS) severity and duration of carpal tunnel syndrome (CTS).</p> <p>Methods</p> <p>Two hundred and twelve (212) "CTS-hands" from 135 CTS patients and 50 asymptomatic hands ("A-hands") from 25 control individuals were enrolled. The median nerve CSAs were measured at the 8-point marked as <it>i</it>4, <it>i</it>3, <it>i</it>2, <it>i</it>1, <it>w</it>, <it>o</it>1, <it>o</it>2, and <it>0</it>3 in inching test. The NCS severities were classified into six groups based on motor and sensory responses (i.e., negative, minimal, mild, moderate, severe, and extreme). Results of US studies were compared in terms of NCS severity and duration of clinical CTS symptoms.</p> <p>Results</p> <p>There was significantly larger CSA of the NCS negative group of "CTS-hands" than of "A-hands". The cut-off values of the CSAs of the NCS negative CTS group were 12.5 mm², 11.5 mm²and 10.1 mm²at the inlet, wrist crease, and outlet, respectively. Of the 212 "CTS-hands", 32 were NCS negative while 40 had minimal, 43 mild, 85 moderate, 10 severe, and two extreme NCS severities. The CSAs of "CTS-hands" positively correlated with different NCS severities and with the duration of CTS symptoms. By duration of clinical symptoms, 12 of the 212 "CTS-hands" were in the 1 month group; 82 in >1 month and ≤12 months group, and 118 in >12 months group. In "inching test", segments <it>i</it>4-<it>i</it>3 and <it>i</it>3-<it>i</it>2 were the most common "positive-site". The corresponding CSAs measured at <it>i</it>4 and <it>i</it>3, but not at <it>i</it>2, were significantly larger than those measured at points that were not "positive-site".</p> <p>Conclusions</p> <p>Using the 8-point measurement of the median nerve CSA from inlet to outlet similar to the "inching test" has positive correlations with NCS severity and duration of CTS clinical symptoms, and can provide more information on anatomic changes. Combined NCS and US studies using the 8-point measurement may have a higher positive rate than NCS alone for diagnosing CTS.</p