Runtime-Flexible Multi-dimensional Arrays and Views for C++98 and C++0x

Multi-dimensional arrays are among the most fundamental and most useful data structures of all. In C++, excellent template libraries exist for arrays whose dimension is fixed at runtime. Arrays whose dimension can change at runtime have been implemented in C. However, a generic object-oriented C++ implementation of runtime-flexible arrays has so far been missing. In this article, we discuss our new implementation called Marray, a package of class templates that fills this gap. Marray is based on views as an underlying concept. This concept brings some of the flexibility known from script languages such as R and MATLAB to C++. Marray is free both for commercial and non-commercial use and is publicly available from www.andres.sc/marrayComment: Free source code availabl

The Lazy Flipper: MAP Inference in Higher-Order Graphical Models by Depth-limited Exhaustive Search

This article presents a new search algorithm for the NP-hard problem of optimizing functions of binary variables that decompose according to a graphical model. It can be applied to models of any order and structure. The main novelty is a technique to constrain the search space based on the topology of the model. When pursued to the full search depth, the algorithm is guaranteed to converge to a global optimum, passing through a series of monotonously improving local optima that are guaranteed to be optimal within a given and increasing Hamming distance. For a search depth of 1, it specializes to Iterated Conditional Modes. Between these extremes, a useful tradeoff between approximation quality and runtime is established. Experiments on models derived from both illustrative and real problems show that approximations found with limited search depth match or improve those obtained by state-of-the-art methods based on message passing and linear programming.Comment: C++ Source Code available from http://hci.iwr.uni-heidelberg.de/software.ph

How to Extract the Geometry and Topology from Very Large 3D Segmentations

Segmentation is often an essential intermediate step in image analysis. A volume segmentation characterizes the underlying volume image in terms of geometric information--segments, faces between segments, curves in which several faces meet--as well as a topology on these objects. Existing algorithms encode this information in designated data structures, but require that these data structures fit entirely in Random Access Memory (RAM). Today, 3D images with several billion voxels are acquired, e.g. in structural neurobiology. Since these large volumes can no longer be processed with existing methods, we present a new algorithm which performs geometry and topology extraction with a runtime linear in the number of voxels and log-linear in the number of faces and curves. The parallelizable algorithm proceeds in a block-wise fashion and constructs a consistent representation of the entire volume image on the hard drive, making the structure of very large volume segmentations accessible to image analysis. The parallelized C++ source code, free command line tools and MATLAB mex files are avilable from http://hci.iwr.uni-heidelberg.de/software.phpComment: C++ source code, free command line tools and MATLAB mex files are avilable from http://hci.iwr.uni-heidelberg.de/software.ph

Metrizability of spaces of homomorphisms between metric vector spaces

This note tries to give an answer to the following question: Is there a sufficiently rich class of metric vector spaces such that sufficiently large spaces of continuous linear maps between them are metrizable?Comment: 12 pages, no figure, submitted to Journal of Geometry and Physics. Latest version corrected only the misspelling of the author's nam

Increased systemic inflammation is associated with cardiac and vascular dysfunction over the first 12 weeks of antiretroviral therapy among undernourished, HIV-infected adults in Southern Africa.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.INTRODUCTION: Persistent systemic inflammation is associated with mortality among undernourished, HIV-infected adults starting antiretroviral therapy (ART) in sub-Saharan Africa, but the etiology of these deaths is not well understood. We hypothesized that greater systemic inflammation is accompanied by cardiovascular dysfunction over the first 12 weeks of ART. METHODS: In a prospective cohort of 33 undernourished (body mass index <18.5 kg/m2) Zambian adults starting ART, we measured C-reactive protein (CRP), tumor necrosis factor-α receptor 1 (TNF-α R1), and soluble CD163 and CD14 at baseline and 12 weeks. An EndoPAT device measured the reactive hyperemia index (LnRHI; a measure of endothelial responsiveness), peripheral augmentation index (AI; a measure of arterial stiffness), and heart rate variability (HRV; a general marker of autonomic tone and cardiovascular health) at the same time points. We assessed paired changes in inflammation and cardiovascular parameters, and relationships independent of time point (adjusted for age, sex, and CD4+ T-cell count) using linear mixed models. RESULTS: Serum CRP decreased (median change -3.5 mg/l, p=0.02), as did TNF-α R1 (-0.31 ng/ml, p<0.01), over the first 12 weeks of ART. A reduction in TNF-α R1 over 12 weeks was associated with an increase in LnRHI (p=0.03), and a similar inverse relationship was observed for CRP and LnRHI (p=0.07). AI increased in the cohort as a whole over 12 weeks, and a reduction in sCD163 was associated with a rise in the AI score (p=0.04). In the pooled analysis of baseline and 12 week data, high CRP was associated with lower HRV parameters (RMSSD, p=0.01; triangular index, p<0.01), and higher TNF- α R1 accompanied lower HRV (RMSSD, p=0.07; triangular index, p=0.06). CONCLUSIONS: Persistent inflammation was associated with impaired cardiovascular health over the first 12 weeks of HIV treatment among undernourished adults in Africa, suggesting cardiac events may contribute to high mortality in this population.This work was supported by the Vanderbilt Meharry Center for AIDS Research (NIH grant number P30 AI54999); the NIH Fogarty International Center, Office of the Director, National Institutes of Health, National Heart, Blood, and Lung Institute, and National Institute of Mental Health, through the Vanderbilt-Emory-Cornell-Duke Consortium for Global Health Fellows (grant number R25 TW009337); the National Center for Advancing Translational Sciences (CTSA award number UL1TR000445) and the European and Developing Countries Clinical Trials Partnership (grant IP.2009.33011.004)

Four-dimensional ultrafast electron microscopy of phase transitions

Reported here is direct imaging (and diffraction) by using 4D ultrafast electron microscopy (UEM) with combined spatial and temporal resolutions. In the first phase of UEM, it was possible to obtain snapshot images by using timed, single-electron packets; each packet is free of space–charge effects. Here, we demonstrate the ability to obtain sequences of snapshots ("movies") with atomic-scale spatial resolution and ultrashort temporal resolution. Specifically, it is shown that ultrafast metal–insulator phase transitions can be studied with these achieved spatial and temporal resolutions. The diffraction (atomic scale) and images (nanometer scale) we obtained manifest the structural phase transition with its characteristic hysteresis, and the time scale involved (100 fs) is now studied by directly monitoring coordinates of the atoms themselves

Effects on mortality of a nutritional intervention for malnourished HIV-infected adults referred for antiretroviral therapy: a randomised controlled trial.

Malnourished HIV-infected African adults are at high risk of early mortality after starting antiretroviral therapy (ART). We hypothesized that short-course, high-dose vitamin and mineral supplementation in lipid nutritional supplements would decrease mortality

From Wasting to Obesity: The Contribution of Nutritional Status to Immune Activation in HIV Infection.

The impact of human immunodeficiency virus (HIV) infection on innate and adaptive immune activation occurs in the context of host factors, which serve to augment or dampen the physiologic response to the virus. Independent of HIV infection, nutritional status, particularly body composition, affects innate immune activation through a variety of conditions, including reduced mucosal barrier defenses and microbiome dysbiosis in malnutrition and the proinflammatory contribution of adipocytes and stromal vascular cells in obesity. Similarly, T-cell activation, proliferation, and cytokine expression are reduced in the setting of malnutrition and increased in obesity, potentially due to adipokine regulatory mechanisms restraining energy-avid adaptive immunity in times of starvation and exerting a paradoxical effect in overnutrition. The response to HIV infection is situated within these complex interactions between host nutritional health and immunologic function, which contribute to the varied phenotypes of immune activation among HIV-infected patients across a spectrum from malnutrition to obesity

Nutritional status is the major factor affecting grip strength of African HIV patients before and during antiretroviral treatment.

: Low grip strength is a marker of frailty and a risk factor for mortality among HIV patients and other populations. We investigated factors associated with grip strength in malnourished HIV patients at referral to ART, and at 12 weeks and 2-3 years after starting ART. : The study involved HIV-infected Zambian and Tanzanian participants recruited to the NUSTART trial when malnourished (body mass index &lt;18.5 kg/m(2) ) and requiring ART. The relationship of grip strength to nutritional, infectious and demographic factors was assessed by multivariable linear regression at referral for ART (n=1742) and after 12 weeks (n=778) and 2-3 years of ART (n=273). : In analyses controlled only for sex, age and height, most nutrition and infection-related variables were associated with grip strength. However, in multivariable analyses, consistent associations were seen for fat-free mass index, mid-upper arm circumference, haemoglobin and systolic blood pressure, and a variable association with fat mass index in men. C-reactive protein and CD4 count had limited independent effects on grip strength, while receiving tuberculosis treatment was associated with weaker grip strength. : In this population of originally malnourished HIV patients, poor grip strength was more strongly and independently associated with nutritional than with infection and inflammation variables. Programmes to improve health and survival of HIV patients should incorporate nutritional assessment and management and could use grip strength as a functional indicator of improving nutrition. This article is protected by copyright. All rights reserved.<br/

Electronic structure of REREAuMg and REREAgMg (RERE = Eu, Gd, Yb)

We have investigated the electronic structure of the equiatomic EuAuMg, GdAuMg, YbAuMg and GdAgMg intermetallics using x-ray photoelectron spectroscopy. The spectra revealed that the Yb and Eu are divalent while the Gd is trivalent. The spectral weight in the vicinity of the Fermi level is dominated by the mix of Mg $s$, Au/Ag $sp$ and $RE$ $spd$ bands, and not by the $RE$ $4f$. We also found that the Au and Ag $d$ bands are extraordinarily narrow, as if the noble metal atoms were impurities submerged in a low density $sp$ metal host. The experimental results were compared with band structure calculations, and we found good agreement provided that the spin-orbit interaction in the Au an Ag $d$ bands is included and correlation effects in an open $4f$ shell are accounted for using the local density approximation + Hubbard $U$ scheme. Nevertheless, limitations of such a mean-field scheme to explain excitation spectra are also evident.Comment: 4 pages, 3 figures, Brief Repor