Miracle-dz/UniFAR-FTUs huggingface dataset:
The Birmingham–CfA cluster scaling project – II. Mass composition and distribution

We investigate the spatial distribution of the baryonic and non-baryonic mass components in a sample of 66 virialized systems. We have used X-ray measurements to determine the deprojected temperature and density structure of the intergalactic medium and have employed these to map the underlying gravitational potential. In addition, we have measured the deprojected spatial distribution of galaxy luminosity for a subset of this sample, spanning over two decades in mass. With this combined X-ray/optical study, we examine the scaling properties of the baryons and address the issue of mass-to-light (M/L) ratio in groups and clusters of galaxies. We measure a median mass-to-light ratio of 249 h 7 0 (M/L) O . in the rest frame B J band, in good agreement with other measurements based on X-ray determined masses. There is no trend in M/L with X-ray temperature and no significant trend for mass to increase faster than luminosity: M L 1 . 0 8 ′ 0 . 1 2 B J . This implied lack of significant variation in star formation efficiency suggests that gas cooling cannot be greatly enhanced in groups, unless it drops out to form baryonic dark matter. Correspondingly, our results indicate that non-gravitational heating must have played a significant role in establishing the observed departure from self-similarity in low-mass systems. The median baryon fraction for our sample is 0.162 h - 3 / 2 7 0 , which allows us to place an upper limit on the cosmological matter density, Ω m ≤ 0.27 h - 1 7 0 , in good agreement with the latest results from WMAP. We find evidence of a systematic trend towards higher central density concentration in the coolest haloes, indicative of an early formation epoch and consistent with hierarchical formation models.
Blood-based candidate biomarkers of the presence of neuropsychiatric systemic lupus erythematosus in children

Objective To examine select brain-reactive proteins for their usefulness to serve as blood-based biomarkers in the screening for neurocognitive deficits in childhood-onset systemic lupus erythematosus (cSLE-NCD). Methods Patients withcSLE (n=40) were studied longitudinally (month 1; month 18): working memory, psychomotor speed and visuoconstructional ability were assessed using formal neurocognitive testing to determine the presence of cSLE-NCD. Patients also completed the computerised Paediatric Automated Neuropsychological Assessment Metrics. The following brain-reactive proteins were measured in the blood: neutrophil gelatinase associated lipocalin (NGAL), S100B, S100A8/9, antibodies to NR2 glutamate receptor (aNR2-AB), ribosomal-P (aP-AB), glycoprotein-1 (aGP1-AB), and lupus anticoagulant. Results cSLE-NCD was present in 6 of 40 patients at baseline and 4 of 27 patients with 18-month information. aP-AB positivity was more commonly present with cSLE-NCD than without (p=0.05). aP-ABs were negatively associated with performance on tests assessing working memory, psychomotor speed and visuoconstructional ability in using formal neurocognitive testing. There were also significant negative associations between aP-AB, S100A8/9, aNR2-AB, aGP1-AB, and lupus anticoagulant and accuracy rates on select Paediatric Automated Neuropsychological Assessment Metrics subtests (p<0.05). Over time, decline in cognitive performance was more pronounced among patients with higher NGAL and aNR2-AB levels. Combinations of serum levels of S100A8/9, S100B, NGAL, aNR2-AB and aP-AB were able to identify cSLE-NCD (sensitivity: 100%; specificity 76%) in exploratory analysis. Conclusions Select brain-reactive proteins in the blood are associated with cognitive performance and the presence of cSLE-NCD, cross-sectionally and over time. This raises the possibility that testing of these proteins may assist with the screening of cSLE-NCD.
Dense Wide-Baseline Stereo with Varying Illumination and its Application to Face Recognition

We study the problem of dense wide baseline stereo with varying illumination. We are motivated by the problem of face recognition across pose. Stereo matching allows us to compare face images based on physically valid, dense correspondences. We show that the stereo matching cost provides a very robust measure of the similarity of faces that is insensitive to pose variations. We build on the observation that most illumination insensitive local comparisons require the use of relatively large windows. The size of these windows is affected by foreshortening. If we do not account for this effect, we incur misalignments that are systematic and significant and are exacerbated by wide baseline conditions. We present a general formulation of dense wide baseline stereo with varying illumination and provide two methods to solve them. The first method is based on dynamic programming (DP) and fully accounts for the effect of slant. The second method is based on graph cuts (GC) and fully accounts for the effect of both slant and tilt. The GC method finds a global solution using the unary function from the general formulation and a novel smoothness term that encodes surface orientation. Our experiments show that DP dense wide baseline stereo achieves superior performance compared to existing methods in face recognition across pose. The experiments with the GC method show that accounting for both slant and tilt can improve performance in situations with wide baselines and lighting variation. Our formulation can be applied to other more sophisticated window based image comparison methods for stereo.
Space-memory-memory Clos-network switches with in-sequence service

Clos-network switches have attracted a lot of attention because of their modularity and scalability. However, out-of-sequence problems weigh heavily against the application of buffered Clos-network switches. A space-memory-memory (SMM) Clos-network switch is proposed in this study which is able to provide in-sequence service. There are two features in the proposed switch which are different from the previously proposed schemes. First, two-stage load-balanced Birkhoff-von Neumann (LB-BvN) switches are adopted for each second-stage module. Second, no inter-stage matching is needed. The key idea to provide in-order cell delivery in the proposed SMM Clos-network switch is that cells belonging to the same flow will experience the identical delay when passing through the LB-BvN switches at the second stage, and arrive at their destined third-stage module in order. Each switching module operates independently, which makes the proposed SMM Clos-network switch practical to implement in hardware. Simulations show that the proposed switch can achieve high performance under both Bernoulli and Bursty arrival traffic.
Dependence of winter water relations of mature high-elevation Picea engelmannii and Abies lasiocarpa on summer climate.

Water relations of Engelmann spruce (Picea engelmannii Parry) and subalpine fir (Abies lasiocarpa (Hook.) Nutt. ) trees growing at an elevation of 3230 m on Mt. Evans, Colorado, USA, were studied during the winters of 1995-1996 and 1996-1997. During both winters, current-year and 1-year-old shoots were collected weekly and their relative water contents (RWC) determined. Measured meteorological parameters were used in a conifer winter water relations model, WINWAT, to simulate changes in shoot RWC of P. engelmannii and A. lasiocarpa during the winter. The model failed to predict shoot RWCs in 1996-1997 when calibrated with 1995-1996 data. The cold early summer of 1995 inhibited xylem formation, which appears to have caused lower rates of water recharge to the needles during the 1995-1996 winter than during the 1996-1997 winter. We conclude that summer climate strongly affects winter water relations in these subalpine species, and that changes in both summer and winter climate must be considered when predicting future ranges of these species.
The temperature dependence of cell mechanics measured by atomic force microscopy

The cytoskeleton is a complex polymer network that regulates the structural stability of living cells. Although the cytoskeleton plays a key role in many important cell functions, the mechanisms that regulate its mechanical behaviour are poorly understood. Potential mechanisms include the entropic elasticity of cytoskeletal filaments, glassy-like inelastic rearrangements of cross-linking proteins and the activity of contractile molecular motors that sets the tensional stress (prestress) borne by the cytoskeleton filaments. The contribution of these mechanisms can be assessed by studying how cell mechanics depends on temperature. The aim of this work was to elucidate the effect of temperature on cell mechanics using atomic force microscopy. We measured the complex shear modulus (G*) of human alveolar epithelial cells over a wide frequency range (0.1–25.6 Hz) at different temperatures (13–37 °C). In addition, we probed cell prestress by mapping the contractile forces that cells exert on the substrate by means of traction microscopy. To assess the role of actomyosin contraction in the temperature-induced changes in G* and cell prestress, we inhibited the Rho kinase pathway of the myosin light chain phosphorylation with Y-27632. Our results show that with increasing temperature, cells become stiffer and more solid-like. Cell prestress also increases with temperature. Inhibiting actomyosin contraction attenuated the temperature dependence of G* and prestress. We conclude that the dependence of cell mechanics with temperature is dominated by the contractile activity of molecular motors.
The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations

Motivation: The naked mole rat (Heterocephalus glaber) is an exceptionally long-lived and cancer-resistant rodent native to East Africa. Although its genome was previously sequenced, here we report a new assembly sequenced by us with substantially higher N50 values for scaffolds and contigs. Results: We analyzed the annotation of this new improved assembly and identified candidate genomic adaptations which may have contributed to the evolution of the naked mole rat’s extraordinary traits, including in regions of p53, and the hyaluronan receptors CD44 and HMMR (RHAMM). Furthermore, we developed a freely available web portal, the Naked Mole Rat Genome Resource (http://www.naked-mole-rat.org), featuring the data and results of our analysis, to assist researchers interested in the genome and genes of the naked mole rat, and also to facilitate further studies on this fascinating species. Availability and implementation: The Naked Mole Rat Genome Resource is freely available online at http://www.naked-mole-rat.org. This resource is open source and the source code is available at https://github.com/maglab/naked-mole-rat-portal. Contact: jp@senescence.info
The scope of rape: incidence and prevalence of sexual aggression and victimization in a national sample of higher education students.

Because of inadequacies in the methods used to measure sexual assault, national crime statistics, criminal victimization studies, convictions, or incarceration rates fail to reflect the true scope of rape. Studies that have avoided the limitations of these methods have revealed very high rates of overt rape and lesser degrees of sexual aggression. The goal of the present study was to extend previous work to a national basis. The Sexual Experiences Survey was administered to a national sample of 6,159 women and men enrolled in 32 institutions representative of the diversity of higher education settings across the United States. Women's reports of experiencing and men's reports of perpetrating rape, attempted rape, sexual coercion, and sexual contact were obtained, including both the rates of prevalence since age 14 and of incidence during the previous year. The findings support published assertions of high rates of rape and other forms of sexual aggression among large normal populations. Although the results are limited in generalizabil ity to postsecondary students, this group represents 26% of all persons aged 18-24 in the United States. The Federal Bureau of Investigation (FBI) defines rape as "carnal knowledge of a female forcibly and against her consent" and reports that 87,340 such offenses occurred in 1985 (FBI, 1986). However, these figures greatly underestimate the true scope of rape because they are based only on instances reported to police. Government estimates suggest that for every rape reported, 3-10 rapes are committed but not reported (Law Enforcement Assistance Administration [LEAA], 1975). Likewise, it is difficult to obtain realistic estimates of the number of men who perpetrate rape because only a fraction of reported rapes eventually result in conviction (Clark & Lewis, 1977). Victimization studies, such as the annual National Crime Survey (NCS), are the major avenue through which the full extent of the crime is estimated (e.g., Bureau of Justice Statistics [BJS], 1984). In these studies, the residents of a standard sampling area are asked to indicate those crimes of which they or anyone else in their household have been victims during the previous 6 months. These rates are then compared with official crime statistics for the area and the rate of unreported crime is esti
Preparation and Characterization of Nano-Cadmium Ferrite

Nano-hematite (α-Fe2O3) and nano-cadmium ferrite (CdFe2O4) are prepared using template-assisted sol-gel method. The prepared samples are analyzed using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and Mossbauer spectroscopy techniques for structural and microstructural studies. Nano-α-Fe2O3 with particle size ~60 nm is formed at 500°C, while nano-CdFe2O4 with smaller particle size (~40 nm) is formed at 600°C. It is found that with a simple sol-gel process we can prepare nano-CdFe2O4 with better conditions than other methods: pure phase at lower sintering temperature and time (economic point) and of course with a smaller particle size. So, based on the obtained experimental results, a proposed theoretical model is made to explain the link between the use of the sol-gel process and the formation of nano-CdFe2O4 as a pure phase at low temperature. This model is based on a simple magnetostatic interaction between the formed nuclei within the solution leading to the formation of the stable phase at low temperature.
Validation of Rearrangement Break Points Identified by Paired-End Sequencing in Natural Populations of Drosophila melanogaster

Several recent studies have focused on the evolution of recently duplicated genes in Drosophila. Currently, however, little is known about the evolutionary forces acting upon duplications that are segregating in natural populations. We used a high-throughput, paired-end sequencing platform (Illumina) to identify structural variants in a population sample of African D. melanogaster. Polymerase chain reaction and sequencing confirmation of duplications detected by multiple, independent paired-ends showed that paired-end sequencing reliably uncovered the break points of structural rearrangements and allowed us to identify a number of tandem duplications segregating within a natural population. Our confirmation experiments show that rates of confirmation are very high, even at modest coverage. Our results also compare well with previous studies using microarrays (Emerson J, Cardoso-Moreira M, Borevitz JO, Long M. 2008. Natural selection shapes genome wide patterns of copy-number polymorphism in Drosophila melanogaster. Science. 320:1629–1631. and Dopman EB, Hartl DL. 2007. A portrait of copy-number polymorphism in Drosophila melanogaster. Proc Natl Acad Sci U S A. 104:19920–19925.), which both gives us confidence in the results of this study as well as confirms previous microarray results. We were also able to identify whole-gene duplications, such as a novel duplication of Or22a, an olfactory receptor, and identify copy-number differences in genes previously known to be under positive selection, like Cyp6g1, which confers resistance to dichlorodiphenyltrichloroethane. Several “hot spots” of duplications were detected in this study, which indicate that particular regions of the genome may be more prone to generating duplications. Finally, population frequency analysis of confirmed events also showed an excess of rare variants in our population, which indicates that duplications segregating in the population may be deleterious and ultimately destined to be lost from the population.
Identification of Features Regulating OST1 Kinase Activity and OST1 Function in Guard Cells1[W]

The phytohormone abscisic acid (ABA) mediates drought responses in plants and, in particular, triggers stomatal closure. Snf1-related kinase 2 (SnRK2) proteins from several plant species have been implicated in ABA-signaling pathways. In Arabidopsis (Arabidopsis thaliana) guard cells, OPEN STOMATA 1 (OST1)/SRK2E/SnRK2-6 is a critical positive regulator of ABA signal transduction. A better understanding of the mechanisms responsible for SnRK2 protein kinase activation is thus a major goal toward understanding ABA signal transduction. Here, we report successful purification of OST1 produced in Escherichia coli: The protein is active and autophosphorylates. Using mass spectrometry, we identified five target residues of autophosphorylation in recombinant OST1. Sequence analysis delineates two conserved boxes located in the carboxy-terminal moiety of OST1 after the catalytic domain: the SnRK2-specific box (glutamine-303 to proline-318) and the ABA-specific box (leucine-333 to methionine-362). Site-directed mutagenesis and serial deletions reveal that serine (Ser)-175 in the activation loop and the SnRK2-specific box are critical for the activity of recombinant OST1 kinase. Targeted expression of variants of OST1 kinase in guard cells uncovered additional features that are critical for OST1 function in ABA signaling, although not required for OST1 kinase activity: Ser-7, Ser-18, and Ser-29 and the ABA-specific box. Ser-7, Ser-18, Ser-29, and Ser-43 represent putative targets for regulatory phosphorylation and the ABA-specific box may be a target for the binding of signaling partners in guard cells.
Noninvasive Assessment of Hypoxia in Rabbit Advanced Atherosclerosis Using 18F-fluoromisonidazole Positron Emission Tomographic Imaging

Background—Hypoxia is an important microenvironmental factor influencing atherosclerosis progression by inducing foam-cell formation, metabolic adaptation of infiltrated macrophages, and plaque neovascularization. Therefore, imaging plaque hypoxia could serve as a marker of lesions at risk. Methods and Results—Advanced aortic atherosclerosis was induced in 18 rabbits by atherogenic diet and double balloon endothelial denudation. Animals underwent 18F-fluoromisonidazole positron emission tomographic and 18F-fluorodeoxyglucose positron emission tomographic imaging after 6 to 8 months (atherosclerosis induction) and 12 to 16 months (progression) of diet initiation. Four rabbits fed standard chow served as controls. Radiotracer uptake of the abdominal aorta was measured using standardized uptake values. After imaging, plaque hypoxia (pimonidazole), macrophages (RAM-11), neovessels (CD31), and hypoxia-inducible factor-1&agr; were assessed by immunohistochemistry.18F-fluoromisonidazole uptake increased with time on diet (standardized uptake value mean, 0.10±0.01 in nonatherosclerotic animals versus 0.20±0.03 [P=0.002] at induction and 0.25±0.03 [P<0.001] at progression). Ex vivo positron emission tomographic imaging corroborated the 18F-fluoromisonidazole uptake by the aorta of atherosclerotic rabbits. 18F-fluorodeoxyglucose uptake also augmented in atherosclerotic animals, with an standardized uptake value mean of 0.43±0.02 at induction versus 0.35±0.02 in nonatherosclerotic animals (P=0.031) and no further increase at progression. By immunohistochemistry, hypoxia was mainly located in the macrophage-rich areas within the atheromatous core, whereas the macrophages close to the lumen were hypoxia-negative. Intraplaque neovessels were found predominantly in macrophage-rich hypoxic regions (pimonidazole+/hypoxia-inducible factor-1&agr;+/RAM-11+). Conclusions—Plaque hypoxia increases with disease progression and is present in macrophage-rich areas associated with neovascularization. 18F-fluoromisonidazole positron emission tomographic imaging emerges as a new tool for the detection of atherosclerotic lesions.
Simple Adaptive Mosaic Effects

We present an algorithm that creates a mosaic effect for an image in an adaptive and automatic fashion. The algorithm is automatic because it does not need user intervention, except for the choice of a couple of parameters. The algorithm is adaptive because it creates tiles whose sizes are adapted to the features of the image. This is achieved by using a centroidal Voronoi diagram with a density function that emphasizes image features.
An efficient, variational non-parametric model of tumour induced brain deformation to aid non-diffeomorphic image registration

In the present work we propose a novel, efficient strategy for modelling tumour induced brain deformation as a prior for non-rigid image registration in non-diffeomorphic registration problems seen in serial or cross-population brain tumour imaging studies. Here, the presence of pathology dramatically alters the morphological and textural appearance of the anatomical structures under consideration and by that induces changes in topology in the considered images rendering the registration problem non-diffeomorphic. In the present work we extend on a model of tumour induced brain deformation that has been formulated as a parametric optimisation problem and translate it to a non-parametric model, for which efficient solution strategies are available. More precisely, we exploit the fact that diffusive regularisation can efficiently be approximated via successive Gaussian convolution. To generate diffeomorphic deformation patterns, a regridding strategy is employed. The resulting (point-wise) regularity of the mapping allows for accounting for mass preservation during deformation. Numerical experiments demonstrate the flexible control of the deformation pattern. A qualitative comparison to imaging data substantiates the potential of the proposed model. The generic variational framework makes this model generally applicable for an integration into any non-parametric image registration algorithm. The discussed implementation makes it particularly suited for demons-type registration approaches.
Effect of Breast Cancer Resistance Protein (Bcrp/Abcg2) on the Disposition of Phytoestrogens

The effect of breast cancer resistance protein (Bcrp/Abcg2) on the disposition of the phytoestrogens daidzein, genistein, and coumestrol was investigated using Bcrp-/- mice. Expression of the genes for either mouse Bcrp or human BCRP in MDCK II cells induced apically directed transport of the three phytoestrogens, whereas their transcellular transport was identical in mock and LLC-PK1 cells expressing mouse Mdr1a. After oral administration, the plasma levels of daidzein and genistein were increased in Bcrp-/- mice, but only a minimal change was observed for coumestrol. At steady state, tissue-to-plasma concentration ratios of the three phytoestrogens in the brain and testis of wild-type mice were very small and similar to those of [14C]inulin, whereas those were significantly increased in the brain and testis of Bcrp-/- mice. The largest increases were observed with genistein (9.2- and 5.8-fold in the brain and testis, respectively). The distributions of genistein in the epididymis and fetus, but not the ovary, were also increased in Bcrp-/- mice. The Bcrp protein was localized in the luminal membrane of the endothelial cells in the testis and the body of the epididymis and in both the luminal and abluminal side of ducts in the head of the epididymis. These results suggest that Bcrp limits the oral availability and distribution into the brain and testis, epididymis, and fetus of phytoestrogens.