Annealing study of A1/GaSb contact with the use of doppler broadening technique

Using a monoenergetic positron beam, annealing study of the Al/n-GaSb system was performed by monitoring the Doppler broadening of the annihilation radiation as a function of the positron implanting energy. The S-parameter against positron energy data was successfully fitted by a three-layer model (Al/interface/GaSb). The annealing out of the open volume defects in the polycrystalline Al layer was revealed by the decrease in the S-parameter and the increase in the effective diffusion length of the Al layer. For the as-deposited samples, a∼5 nm interfacial region with S-parameter larger than those of the Al overlayer and the bulk was identified. After the 400^ºC annealing, this interfacial region extends to over 40 nm and its S-parameter dramatically drops. This is possibly due to the new phase formation at the interface. Annealing behaviors of SB and L+,B of the GaSb bulk showed the annealing out of positron traps (possibly the VGa-related defect) at 250ºC. However, a further annealing at 400ºC induces the formation of positron traps, which are possibly of another kind of VGa-related defect and the positron shallow trap GaSb antisite.published_or_final_versionProceedings of the 35th Polish Seminar on Positron Annihilation (PSPA), Turawa, Poland, 20-24 September 2004. In Acta Physica Polonica Series A: General Physics, Physics of Condensed Matter, Optics and Quantum Electronics, Atomic and Molecular Physics, Applied Physics, 2005, v. 107 n. 5, p. 874-87

Investigating freeway traffic hypercongestion between an on-ramp and its immediate upstream off-ramp

This paper applies the freeway traffic congestion dynamics proposed in Laval and Leclercq [2010. “Continuum Approximation for Congestion Dynamics Along Freeway Corridors.” Transportation Science 44 (1): 87–97] but with a modified distribution scheme of freeway merging flows to investigation of traffic hypercongestion on a freeway between an on-ramp and its immediate upstream off-ramp. The reason to make this modification is that the original merging scheme of this dynamics is found to possibly give undesired full priority to the traffic from the on-ramp and also occasionally make the resulting flow going through the merge greater than the available capacity. Traffic hypercongestion in this paper refers to a state where speed and flow change in the same direction as density varies. A homogeneous freeway segment chosen for this investigation includes an on-ramp and an off-ramp, which may correspond to a freeway passing by a city or town, with an off-ramp lying upstream towards the city and an on-ramp downstream. The entry flow from the upstream approach of the freeway was fixed and constant within the time horizon while both deterministic and random on-ramp inflow rates were used in this investigation. Then the formation and dissipation of traffic hypercongestion is investigated as on-ramp demand and off-ramp departure profiles vary. The first finding of this investigation is that the density in the hypercongestion area behind the merge never reached the jam density. Second, the hypercongested area continued to grow as long as the sum of the demand from the upstream of the freeway and that from the on-ramp was greater than the available capacity at the merge. Third, as long as the rate of flow leaving from the freeway via the off-ramp was not smaller than the entry flow rates from the on-ramp, no hypercongestion had been observed. In addition, in analysing the numerical results, a series of discussions was carried out to build the linkage between the on- and off-ramp flow profiles and the generated and attracted demand of the city plus its adjacent area the two ramps served for; these discussions suggest that the balanced generated and attracted demand of the city plus its adjacent area can reduce or even remove traffic hypercongestion behind the merge on the chosen freeway segment.postprin

Experimental Measurement of the Berry Curvature from Anomalous Transport

Geometrical properties of energy bands underlie fascinating phenomena in a wide-range of systems, including solid-state materials, ultracold gases and photonics. Most famously, local geometrical characteristics like the Berry curvature can be related to global topological invariants such as those classifying quantum Hall states or topological insulators. Regardless of the band topology, however, any non-zero Berry curvature can have important consequences, such as in the semi-classical evolution of a wave packet. Here, we experimentally demonstrate for the first time that wave packet dynamics can be used to directly map out the Berry curvature. To this end, we use optical pulses in two coupled fibre loops to study the discrete time-evolution of a wave packet in a 1D geometrical "charge" pump, where the Berry curvature leads to an anomalous displacement of the wave packet under pumping. This is both the first direct observation of Berry curvature effects in an optical system, and, more generally, the proof-of-principle demonstration that semi-classical dynamics can serve as a high-resolution tool for mapping out geometrical properties

Exploring 4D Quantum Hall Physics with a 2D Topological Charge Pump

The discovery of topological states of matter has profoundly augmented our understanding of phase transitions in physical systems. Instead of local order parameters, topological phases are described by global topological invariants and are therefore robust against perturbations. A prominent example thereof is the two-dimensional integer quantum Hall effect. It is characterized by the first Chern number which manifests in the quantized Hall response induced by an external electric field. Generalizing the quantum Hall effect to four-dimensional systems leads to the appearance of a novel non-linear Hall response that is quantized as well, but described by a 4D topological invariant - the second Chern number. Here, we report on the first observation of a bulk response with intrinsic 4D topology and the measurement of the associated second Chern number. By implementing a 2D topological charge pump with ultracold bosonic atoms in an angled optical superlattice, we realize a dynamical version of the 4D integer quantum Hall effect. Using a small atom cloud as a local probe, we fully characterize the non-linear response of the system by in-situ imaging and site-resolved band mapping. Our findings pave the way to experimentally probe higher-dimensional quantum Hall systems, where new topological phases with exotic excitations are predicted

Effects of seismic devices on transverse responses of piers in the Sutong Bridge

The Sutong Bridge in China opened to traffic in 2008, and is an arterial connection between the cities of Nantong and Suzhou. It is a cable-stayed bridge with a main span of 1,088 m. Due to a tight construction schedule and lack of suitable seismic devices at the time, fixed supports were installed between the piers and the girder in the transverse direction. As a result, significant transverse seismic forces could occur in the piers and foundations, especially during a return period of a 2500-year earthquake. Therefore, the piers, foundations and fixed bearings had to be designed extraordinarily strong. However, when larger earthquakes occur, the bearings, piers and foundations are still vulnerable. The recent rapid developments in seismic technology and the performance-based design approach offer a better opportunity to optimize the transverse seismic design for the Sutong Bridge piers. The optimized design can be applied to the Sutong Bridge (as a retrofit), as well as other bridges. Seismic design alternatives utilizing viscous fluid dampers (VFD), or friction pendulum sliding bearings (FPSB), or transverse yielding metallic dampers (TYMD) are thoroughly studied in this work, and the results are compared with those from the current condition with fixed transverse supports and a hypothetical condition in which only sliding bearings are provided on top of the piers (the girder can move “freely” in the transverse direction during the earthquake, except for frictional forces of the sliding bearings). Parametric analyses were performed to optimize the design of these proposed seismic devices. From the comparison of the peak bridge responses in these configurations, it was found that both VFD and TYMD are very effective in the reduction of transverse seismic forces in piers, while at the same time keeping the relative transverse displacements between piers and the box girder within acceptable limits. However, compared to VFD, TYMD do not interact with the longitudinal displacements of the girder, and have simpler details and lower initial and maintenance costs. Although the use of FPSB can also reduce seismic forces, it generally causes the transverse relative displacements to be higher than acceptable limits

Genetic determinants of co-accessible chromatin regions in activated T cells across humans.

Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression

Sleep quality in middle-aged and elderly Chinese: distribution, associated factors and associations with cardio-metabolic risk factors

Background Poor sleep quality has been associated with increased risk of heart disease, diabetes and mortality. However, limited information exists on the distribution and determinants of sleep quality and its associations with cardio-metabolic risk factors in Chinese populations. We aimed to evaluate this in the current study. Methods A cross-sectional survey conducted in 2005 of 1,458 men and 1,831 women aged 50–70 years from urban and rural areas of Beijing and Shanghai. Using a questionnaire, sleep quality was measured in levels of well, common and poor. Comprehensive measures of socio-demographical and health factors and biomarkers of cardio-metabolic disease were recorded. These were evaluated in association with sleep quality using logistic regression models. Results Half of the population reported good sleep quality. After adjusting for potential confounders, women and Beijing residents had almost half the probability to report good sleep quality. Good physical and mental health (good levels of self-rated health (OR 2.48; 95%CI 2.08 to 2.96) and no depression (OR 4.05; 95%CI 3.12 to 5.26)) related to an increased chance of reporting good sleep quality, whereas short sleep duration (<7 hrs OR 0.10; 95%CI 0.07 to 0.14)) decreased it substantially. There were significant associations between levels of sleep quality and concentrations of plasma insulin, total and LDL cholesterol, and index of insulin resistance. Conclusion Levels of good sleep quality in middle-age and elderly Chinese were low. Gender, geographical location, self-rated health, depression and sleep quantity were major factors associated with sleep quality. Prospective studies are required to distil the factors that determine sleep quality and the effects that sleep patterns exert on cardio-metabolic health

Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined

The serum vaspin levels are reduced in Japanese chronic hemodialysis patients

Background: Visceral adipose tissue-derived serine proteinase inhibitor (vaspin) is an adipokine identified in genetically obese rats that correlates with insulin resistance and obesity in humans. Recently, we found that 7% of the Japanese population with the minor allele sequence (A) of rs77060950 exhibit higher levels of serum vaspin. We therefore evaluated the serum vaspin levels in Japanese chronic hemodialysis patients. Methods: Healthy Japanese control volunteers (control; n = 95, 49.9 +/- 6.91 years) and Japanese patients undergoing hemodialysis therapy (HD; n = 138, 51.4 +/- 10.5 years) were enrolled in this study, and serum samples were subjected to the human vaspin RIA system. Results: The measurement of the serum vaspin levels demonstrated that a fraction of control subjects (n = 5) and HD patients (n = 11) exhibited much higher levels (> 10 ng/ml; Vaspin(High) group), while the rest of the population exhibited lower levels (< 3 ng/ml; Vaspin(Low) group). By comparing the patients in the Vaspin(Low) group, the serum vaspin levels were found to be significantly higher in the control subjects (0.87 +/- 0.24 ng/ml) than in the HD patients (0.32 +/- 0.15 ng/ml) (p < 0.0001). In the stepwise regression analyses, the serum creatinine and triglyceride levels were found to be independently and significantly associated with the vaspin concentrations in all subjects. Conclusions: The creatinine levels are negatively correlated with the serum vaspin levels and were significantly reduced in the Japanese HD patients in the Vaspin(Low) group

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/