Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays

10.1093/nar/gkq040Nucleic Acids Research389e105-NARH

Network of Econophysicists: a weighted network to investigate the development of Econophysics

The development of Econophysics is studied from the perspective of scientific communication networks. Papers in Econophysics published from 1992 to 2003 are collected. Then a weighted and directed network of scientific communication, including collaboration, citation and personal discussion, is constructed. Its static geometrical properties, including degree distribution, weight distribution, weight per degree, and betweenness centrality, give a nice overall description of the research works. The way we introduced here to measure the weight of connections can be used as a general one to construct weighted network.Comment: 6 pages, 7 figure

Computational Fluid Dynamics Simulations at Micro-Scale Stenosis for Microfluidic Thrombosis Model Characterization

Platelet aggregation plays a central role in pathological thrombosis, preventing healthy physiological blood flow within the circulatory system. For decades, it was believed that platelet aggregation was primarily driven by soluble agonists such as thrombin, adenosine diphosphate and thromboxane A2. However, recent experimental findings have unveiled an intriguing but complementary biomechanical mechanism—the shear rate gradients generated from flow disturbance occurring at sites of blood vessel narrowing, otherwise known as stenosis, may rapidly trigger platelet recruitment and subsequent aggregation. In our Nature Materials 2019 paper [1], we employed microfluidic devices which incorporated micro-scale stenoses to elucidate the molecular insights underlying the prothrombotic effect of blood flow disturbance. Nevertheless, the rheological mechanisms associated with this stenotic microfluidic device are poorly characterized. To this end, we developed a computational fluid dynamics (CFD) simulation approach to systematically analyze the hemodynamic influence of bulk flow mechanics and flow medium. Grid sensitivity studies were performed to ensure accurate and reliable results. Interestingly, the peak shear rate was significantly reduced with the device thickness, suggesting that fabrication of microfluidic devices should retain thicknesses greater than 50 µm to avoid unexpected hemodynamic aberration, despite thicker devices raising the cost of materials and processing time of photolithography. Overall, as many groups in the field have designed microfluidic devices to recapitulate the effect of shear rate gradients and investigate platelet aggregation, our numerical simulation study serves as a guideline for rigorous design and fabrication of microfluidic thrombosis models

Sleep education in pediatric residency programs: A cross-cultural look

10.1186/1756-0500-6-130BMC Research Notes61

Brief but Efficient: Acute HIV Infection and the Sexual Transmission of HIV

Background. We examined whether viral dynamics in the genital tract during the natural history of acute human immunodeficiency virus type 1 (HIV-1) infection could explain efficient heterosexual transmission of HIV. Methods. We measured HIV-1 concentration in blood and semen samples from patients with acute and long-term HIV-1 infection. We explored the effect of changes in viral dynamics in semen on the probability of transmission per coital act, using a probabilistic model published elsewhere. Results. Considered over time from infection, semen HIV-1 concentrations, in men with acute infection, increase and decrease in approximate parallel with changes occurring in blood. Modeling suggests that these acute dynamics alone are sufficient to increase probability of heterosexual transmission by 8-10-fold between peak (day 20 after infection, based on the model) and virologic set points (day 54 and later after infection). Depending on the frequency of coitus, men with average semen HIV-1 loads and without sexually transmitted diseases (STDs) would be expected to infect 7%-24% of susceptible female sex partners during the first 2 months of infection. The predicted infection rate would be much higher when either partner has an STD. Conclusions. Empirical biological data strongly support the hypothesis that sexual transmission by acutely infected individuals has a disproportionate effect on the spread of HIV-1 infection. Acute hyperinfectiousness may, in part, explain the current pandemic in heterosexual individual

A dynamic network approach for the study of human phenotypes

The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing correlations obtained from the disease history of more than 30 million patients in a Phenotypic Disease Network (PDN). We present evidence that the structure of the PDN is relevant to the understanding of illness progression by showing that (1) patients develop diseases close in the network to those they already have; (2) the progression of disease along the links of the network is different for patients of different genders and ethnicities; (3) patients diagnosed with diseases which are more highly connected in the PDN tend to die sooner than those affected by less connected diseases; and (4) diseases that tend to be preceded by others in the PDN tend to be more connected than diseases that precede other illnesses, and are associated with higher degrees of mortality. Our findings show that disease progression can be represented and studied using network methods, offering the potential to enhance our understanding of the origin and evolution of human diseases. The dataset introduced here, released concurrently with this publication, represents the largest relational phenotypic resource publicly available to the research community.Comment: 28 pages (double space), 6 figure

Nuclear spin conversion of water inside fullerene cages detected by low-temperature nuclear magnetic resonance

The water-endofullerene H2O@C60 provides a unique chemical system in which freely rotating water molecules are confined inside homogeneous and symmetrical carbon cages. The spin conversion between the ortho and para species of the endohedral H2O was studied in the solid phase by low-temperature nuclear magnetic resonance. The experimental data are consistent with a second-order kinetics, indicating a bimolecular spin conversion process. Numerical simulations suggest the simultaneous presence of a spin di↵usion process allowing neighbouring ortho and para molecules to exchange their angular momenta. Cross-polarization experiments found no evidence that the spin conversion of the endohedral H2O molecules is catalysed by 13C nuclei present in the cages

Effects of carrier injection profile on low noise thin Al0.85Ga0.15As0.56Sb0.44 avalanche photodiodes

Avalanche photodiodes (APDs) with thin avalanche regions have shown low excess noise characteristics and high gain-bandwidth products, so they are suited for long-haul optical communications. In this work, we investigated how carrier injection profile affects the avalanche gain and excess noise factors of Al0.85Ga0.15As0.56Sb0.44 (lattice-matched to InP substrates) p-i-n and n-i-p diodes with total depletion widths of 145-240 nm. Different carrier injection profiles were achieved by using light with wavelengths of 420, 543 and 633nm. For p-i-n diodes, shorter wavelength light produces higher avalanche gains for a given reverse bias and lower excess noise factors at a given gain, compared to longer wavelength light. Thus, using 420 nm light on the p-i-n diodes, corresponding to pure electron injection conditions, gave the highest gain and lowest excess noise. In n-i-p diodes, pure hole injection yields significantly lower gain and higher excess noise, compared to mixed carrier injection. These show that the electron ionization coefficient, α, is higher than the hole ionization coefficient, β. Using pure electron injection, excess noise factor characteristics with effective ionization ratios, keff, of 0.08-0.1 were obtained. This is significantly lower than those of InP and In0.52Al0.48As, the commonly used avalanche materials combined with In0.53Ga0.47As absorber. The data reported in this paper is available from the ORDA digital repository (DOI: 10.15131/shef. DATA: 5787318)

Simulation of the CMS Resistive Plate Chambers

The Resistive Plate Chamber (RPC) muon subsystem contributes significantly to the formation of the trigger decision and reconstruction of the muon trajectory parameters. Simulation of the RPC response is a crucial part of the entire CMS Monte Carlo software and directly influences the final physical results. An algorithm based on the parametrization of RPC efficiency, noise, cluster size and timing for every strip has been developed. Experimental data obtained from cosmic and proton-proton collisions at $\sqrt{s}=7$ TeV have been used for determination of the parameters. A dedicated validation procedure has been developed. A good agreement between the simulated and experimental data has been achieved.Comment: to be published in JINS

Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices

BACKGROUND: Protein-protein interactions are critical for cellular functions. Recently developed computational approaches for predicting protein-protein interactions utilize co-evolutionary information of the interacting partners, e.g., correlations between distance matrices, where each matrix stores the pairwise distances between a protein and its orthologs from a group of reference genomes. RESULTS: We proposed a novel, simple method to account for some of the intra-matrix correlations in improving the prediction accuracy. Specifically, the phylogenetic species tree of the reference genomes is used as a guide tree for hierarchical clustering of the orthologous proteins. The distances between these clusters, derived from the original pairwise distance matrix using the Neighbor Joining algorithm, form intermediate distance matrices, which are then transformed and concatenated into a super phylogenetic vector. A support vector machine is trained and tested on pairs of proteins, represented as super phylogenetic vectors, whose interactions are known. The performance, measured as ROC score in cross validation experiments, shows significant improvement of our method (ROC score 0.8446) over that of using Pearson correlations (0.6587). CONCLUSION: We have shown that the phylogenetic tree can be used as a guide to extract intra-matrix correlations in the distance matrices of orthologous proteins, where these correlations are represented as intermediate distance matrices of the ancestral orthologous proteins. Both the unsupervised and supervised learning paradigms benefit from the explicit inclusion of these intermediate distance matrices, and particularly so in the latter case, which offers a better balance between sensitivity and specificity in the prediction of protein-protein interactions