Miracle-dz/UniFAR-FTUs huggingface dataset:
Engineered Vascular Beds Provide Key Signals to Pancreatic Hormone-Producing Cells

The mechanisms underlying early islet graft failure are not entirely clear, but are thought to involve ischemic injury due to delayed vascularization. We hypothesize that blood vessels play an active role in cell-cell communications supporting islet survival and engraftment. To test this hypothesis and to uncouple endothelial cell (EC)-generated signaling stimuli from their nutritional and gas exchange functions, we developed three dimensional (3D) endothelial vessel networks in engineered pancreatic tissues prepared from islets, fibroblasts and ECs. The tri-culture setup, seeded on highly porous biocompatible polymeric scaffolds closely mimics the natural anatomical context of pancreatic vasculature. Enhanced islet survival correlating with formation of functional tube-like endothelial vessels was demonstrated. Addition of foreskin fibroblasts to islet-endothelial cultures promoted tube-like structure formation, which further supported islet survival as well as insulin secretion. Gene expression profiles of EC growth factors, extracellular matrix (ECM), morphogenes and differentiation markers were significantly different in 2D versus 3D culture systems and were further modified upon addition of fibroblasts. Implantation of prevascularized islets into diabetic mice promoted survival, integration and function of the engrafted engineered tissue, supporting the suggested role of ECs in islet survival. These findings present potential strategies for preparation of transplantable islets with increased survival prospects.
Probabilistic Admission Control to Govern Real-Time Systems under Overload

Existing real-time research focuses on how to formulate. model and enforce timeliness guarantees for task sets whose correctness has a temporal aspect. However; the resulting systems often exhibit poor resource utilization due to the resource scheduler reserving more resources than required in order to ensure that admitted schedules can be satisfied under worst case conditions. Weakening the guarantees leads to the known concepts of firm and soft real-time tasks, butt we think the paradigm needs to be shifted further,: reifying efficient utilization. With Quality-Assuring Scheduling (QAS) we presented such an algorithm. However: its practical applicability is restricted to uniform and harmonic periods, due to its complexity for arbitrary periods. To overcome this limitation, we introduce Quality-Rate-Monotonic Scheduling (QRMS), which, although slightly more pessimistic, is less complex compared to QAS. Thee admission control is again based on a probabilistic model to ensure that a requested fraction of jobs is successfully executed. Thus the amount of missed deadlines can be externally controlled, even in sustained overload situations.
Genetic associations with 25-hydroxyvitamin D deficiency in HIV-1-infected youth: fine-mapping for the GC/DBP gene that encodes the vitamin D-binding protein

Serum 25-hydroxyvitamin D [25(OH)D] is often deficient (<12 ng/ml) or insufficient (<20 ng/ml) in youth living with human immunodeficiency virus type 1 infection (YLH). Based on evidence from multiple genome-wide association studies, we hypothesized that genetic factors associated with 25(OH)D deficiency should be readily detectable in YLH even when controlling for other known factors, including use of the antiretroviral drug efavirenz (EFV). Genotyping by bi-directional sequencing targeted 15 single nucleotide polymorphisms (SNPs) at the GC/DBP locus, with a focus on coding and regulatory variants, as well as those repeatedly reported in the literature. Three intronic SNPs (rs222016, rs222020, and rs222029) in a conserved haplotype block had unequivocal association signals (false discovery rate ≤ 0.006). In particular, the minor allele G for rs222020 was highly unfavorable among 192 YLH (99 African–Americans and 93 others), as gauged by relatively low likelihood for 25(OH)D sufficiency at enrollment (odds ratio = 0.31, p = 9.0 × 10-4). In a reduced multivariable model, race, season, latitude, body mass index, exposure to EFV, and rs222020-G were independent factors that collectively accounted for 38% of variance in the log10-transformed 25(OH)D concentration (p < 0.0001). Interaction terms were evident for rs222020-G × season (p < 0.001), latitude × season (especially fall and winter; p < 0.01), and race × EFV use (p = 0.024). Overall, variance in serum 25(OH)D is substantially attributable to multiple factors, but the exact contribution of genetic and non-genetic factors can be obscured by partial overlaps and frequent interactions.
On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain

SCAND3 and KRBA2 are two mammalian proteins originally described as “cellular-integrases” due to sharing of a similar DDE-type integrase domain whose origin and relationship with other recombinases remain unclear. Here we perform phylogenetic analyses of 341 integrase/transposase sequences to reveal that the integrase domain of SCAND3 and KRBA2 derives from the same clade of GINGER2, a superfamily of cut-and-paste transposons widely distributed in insects and other protostomes, but seemingly absent or extinct in vertebrates. Finally, we integrate the results of phylogenetic analyses to the taxonomic distribution of SCAND3 and KRBA2 and their transposon relatives to discuss some of the processes that promoted the emergence of these two chimeric genes during mammalian evolution.
Development of high fidelity liver and kidney phantom organs for use with robotic surgical systems

The development of high fidelity, anthropomorphically shaped physical phantom organs has a great potential to benefit novel robotic surgical systems by acting as a pre-clinical test bed to validate robotic performance. We present a manufacturing process and methodology to create inexpensive, anatomically accurate kidney and liver phantom organs from gelatin gel with Young's moduli and ultrasound (US) attenuation coefficients matched to those of a porcine kidney and liver. The ration of gelatin to water was varied in order to produce eight gelatin gel samples with a Young's modulus ranging from 8.88 kPa to 76.84. Fresh porcine liver and kidney organs were tested ex vivo to determine their Young's moduli and US attenuation coefficients. A 3D printer created an anthropomorphically accurate kidney mold based on x-ray computed tomography images of a human abdomen. The difference between the porcine and gelatin phantom Young's modulus was less than 2.1 kPa for both the kidney and liver. The US attenuation differed at most by 0.577 dB(cm·MHz)-1 when comparing the phantom material to the porcine organs. The volume of anthropomorphically shaped gelatin phantom kidney was within 5% of the volume of the virtual kidney organ which was constructed from x-ray computed tomography. With a total material cost of approximately $0.70 per organ we foresee these organs to be used in a disposable fashion to facilitate the development of novel surgical robotic systems.
Pen + Mid-Air: An Exploration of Mid-Air Gestures to Complement Pen Input on Tablets

In this paper, we report on a series of studies, exploring the potential of pen and mid-air input on tablets. We describe a field study with an early prototype of a drawing application and follow-up inquiries, such as the development and comparison of gesture sets for pen and mid-air input and pen and multi-touch input with users in a lab environment. Overall, our results suggest that pen and mid-air input should be offered to complement traditional pen and multi-touch input on tablets. We illustrate the final user-defined gestures set for pen and mid-air input and discuss how user preferences of mid-air gestures over touch gestures seem to depend on the complexity of operations and the need of additional menus on the screen.
Filtering automated polling traffic in computer network flow data. 268-271

—Detecting polling behaviour in a computer network has two important applications. First, the polling behaviour can be indicative of malware beaconing, where an undetected software virus sends regular communications to a controller. Second, the polling behaviour may not be malicious, and correspond to regular automated update requests permitted by the client; to build models of normal host behaviour for signature-free anomaly detection, this polling behaviour needs to be understood. This article presents a simple Fourier analysis technique for identifying polling behaviour, and focuses on the second application: modelling the normal behaviour of a host, using real data collected from the computer network of Imperial College London.
and Chemotaxis After Trauma 1-Mediated Neutrophil Calcium Mobilization Receptor 4 Suppresses Leukotriene B Inflammatory Chemoreceptor Cross-Talk

G protein-coupled chemoattractants recruit neutrophils (PMN) to sites of injury and infection. The leukotrienes (LT) and CXC chemokines (CXC) and their receptors (BLT1/BLT2 and CXCR1/CXCR2) are all known to play roles in these responses. Each system has been studied separately in vitro, but in vivo they act concurrently, and the clinical interactions between the two systems are unstudied. We prospectively studied calcium mobilization and chemotactic responses to LTB 4 in PMN from major trauma patients. The responses of the high afﬁnity BLT1 receptor were suppressed at the 3-day postinjury time point, but recovered by 1 wk. Trauma patients had transient elevations of plasma LT and CXC levels. Functional deﬁcits identical with those in trauma PMN were reproduced in vitro by exposing healthy PMN to CXCs at the elevated plasma concentrations found. Functional responses to LTB 4 were suppressed by cross-talk with CXC and BLT2 receptors that desensitize BLT1. Since the suppression of intracellular calcium mobilization was prominent, we also studied the role of suppressed cell calcium mobilization in the defective chemotactic responses to LTB 4 . We noted that PMN chemotaxis to LTB 4 showed far more dependence on store-operated calcium entry than on the release of cellular calcium stores, and that store-operated calcium responses to BLT1 activation were markedly inhibited during the same time period as was chemotaxis. The intermittent release of inﬂammatory mediators after injury can blunt PMN responses to LTs by suppressing BLT1 as well as downstream calcium entry. Diminished LT receptor activity due to cross-talk with CXC receptors can inhibit PMN recruitment to infective sites. This may predispose injured patients to septic complications. The Journal of Immunology, 2003, 171:
A design approach to socially adaptive lighting environments

Historically light has been a catalyst for social life to emerge. In recent years of lighting research the social effect of light has been underexposed. The environments we occupy on a daily basis are used for a wider variety of activities. Consequently, lighting conditions need to become sensitive to adapt to the variety of activities being performed. We argue that the effect of light on the social relations between people needs to be considered in order to make adaptive lighting environments viable. To design a socially adaptive lighting environment an approach needs to be used that is iterative, experiential and involves multiple users in an actual context. The design process is described in three stages (Interactive Sketching, a Design Experiment and Socially Situated Adaptive Experience); for each stage the aims, the setup, results and lessons learned are provided. In this process an experimental environment is used, named Incubation environment, which is set up as a dining environment and equipped with computer controllable lighting armatures. In the final design stage the Socially Situated Adaptive Experience technique is described and is found a suitable technique to design socially adaptive lighting environments.
Childhood Programs and Practices in the First Decade of Life: Impacts and Implications of the Child-Parent Center Preschool Program

Although significant progress continues in understanding the effects of preschool programs, questions remain about the reliability of long-term impacts for large-scale programs, cost-effectiveness, and the causal mechanisms of change. In this paper, we describe recent findings on the impact of the Child-Parent Center (CPC) preschool program into adulthood and the processes that lead to these effects. Given the program has been run by the Chicago Public Schools for 40 years, the program's consistent evidence of positive effects and high economic returns have significant implications for policy development and modification. The illustrations also show how a confirmatory, theory-driven approach can help advance knowledge in enhancing children's well-being. Key principles of effectiveness are described for promoting enduring effects.
Familial twinning and fertility in Dutch mothers of twins

We studied twinning and fertility indices in mothers with spontaneous monozygotic (MZ) and dizygotic (DZ) twins and in mothers who conceived their twins after the use of assisted reproduction techniques (ART). Participants in this study consisted of 8,222 and 5,505 women with spontaneous DZ and MZ offspring and 4,164 and 250 women with ART DZ and MZ twin pairs, respectively. Women were compared with respect to the number of sibs and offspring, the presence of other relatives with twins and the time it took to conceive the twins. We also compared familial twinning between a younger and an older age group. Women with spontaneous DZ twins more often reported female relatives with twins than those with spontaneous MZ twins. The proportion of DZ versus MZ twin offspring in relatives was also larger in women with spontaneous DZ offspring than in women with MZ offspring. The first group of women reported a shorter time to conceive. Women with ART twins had fewer sibs and offspring and less often reported relatives with twins. We did not observe that DZ twinning was more familial in women who had their twins before age 36 years compared to older women. Familial DZ twinning is clearly present in mothers of spontaneous DZ twins. The mechanisms underlying spontaneous and non‐spontaneous DZ twinning are different and fertility treatment should be taken into account in any study of twinning. Twinning is not more familial in women who have their twins at a younger age. © 2008 Wiley‐Liss, Inc.
A split–merge‐based region‐growing method for fMRI activation detection

We introduce a hybrid method for functional magnetic resonance imaging (fMRI) activation detection based on the well‐developed split–merge and region‐growing techniques. The proposed method includes conjoining both of the spatio‐temporal priors inherent in split–merge and the prior information afforded by the hypothesis‐led component of region selection. Compared to the fuzzy c‐means clustering analysis, this method avoids making assumptions about the number of clusters and the computation complexity is reduced markedly. We evaluated the effectiveness of the proposed method in comparison with the general linear model and the fuzzy c‐means clustering method conducted on simulated and in vivo datasets. Experimental results show that our method successfully detected expected activated regions and has advantages over the other two methods. Hum. Brain Mapping 22:271–279, 2004. © 2004 Wiley‐Liss, Inc.
Solubilization of Membrane Proteins into Functional Lipid‐Bilayer Nanodiscs Using a Diisobutylene/Maleic Acid Copolymer

Abstract Once removed from their natural environment, membrane proteins depend on membrane‐mimetic systems to retain their native structures and functions. To this end, lipid‐bilayer nanodiscs that are bounded by scaffold proteins or amphiphilic polymers such as styrene/maleic acid (SMA) copolymers have been introduced as alternatives to detergent micelles and liposomes for in vitro membrane‐protein research. Herein, we show that an alternating diisobutylene/maleic acid (DIBMA) copolymer shows equal performance to SMA in solubilizing phospholipids, stabilizes an integral membrane enzyme in functional bilayer nanodiscs, and extracts proteins of various sizes directly from cellular membranes. Unlike aromatic SMA, aliphatic DIBMA has only a mild effect on lipid acyl‐chain order, does not interfere with optical spectroscopy in the far‐UV range, and does not precipitate in the presence of low millimolar concentrations of divalent cations.
The independent components of characters are 'strokes'

What are the natural features of handwritten characters and how to arrive at them automatically? We apply independent components analysis on handwritten characters. Independent components analysis extracts the underlying statistically independent signals from a mixture of them. We expect strokes to be the independent components of handwritten characters. Our findings show that stroke-like features emerge as a result of the analysis confirming the above intuition. This finding is significant since it gives automatic procedures for extracting stroke-like features from multilingual character data sets. We use these features for handwritten digit recognition using a very simple classifier. The classifier is chosen to be simple so that the quality of the input feature set can be evaluated. The recognition results indicate that the features arrived at by independent component analysis are useful.
Reconstructing fully-resolved trees from triplet cover distances

It is a classical result that any finite tree with positively weighted edges, and without vertices of degree 2, is uniquely determined by the weighted path distance between each pair of leaves. Moreover, it is possible for a (small) strict subset L of leaf pairs to suffice for reconstructing the tree and its edge weights, given just the distances between the leaf pairs in L. It is known that any set L with this property for a tree in which all interior vertices have degree 3 must form a cover for T {that is, for each interior vertex v of T, L must contain a pair of leaves from each pair of the three components of T v. Here we provide a partial converse of this result by showing that if a set L of leaf pairs forms a cover of a certain type for such a tree T then T and its edge weights can be uniquely determined from the distances between the pairs of leaves in L. Moreover, there is a polynomial-time algorithm for achieving this reconstruction. The result establishes a special case of a recent question concerning `triplet covers', and is relevant to a problem arising in evolutionary genomics.
A Cell-Based Reporter Gene Assay for Determining Induction of CYP3A4 in a High-Volume System

Assessing the inducibility of CYP3A4 by various xenobiotics can predict potential drug interactions. In the present investigation, human hepatoma cells were stably integrated with either the CYP3A4 enhancer region and a luciferase reporter gene or the CYP3A4-luciferase construct and the human pregnane X receptor (PXR). Several colonies containing one to three copies of luciferase per cell were identified by Southern blot analysis. Those transformants producing high luciferase activity in response to rifampicin were used to standardize a 96-well plate screening system with minimal inter- and intraplate variability. Standardization also consisted of assessing viability of cells cultured in medium containing various serum concentrations. In cells maintained for 48 h in medium with less than 5% serum, a significant (p < 0.01) decline was observed in viability accompanied by altered induction. A defined serum-free medium also produced less viable cells but did not alter the inductive response. Treatment of transformants with various concentrations of rifampicin produced a dose-response curve with maximal induction at 10 μM (5.6 ± 0.18- and 2.1 ± 0.3-fold above dimethyl sulfoxide (DMSO)-treated cells in transformants with and without PXR, respectively). Of additional agents examined for their ability to induce CYP3A4, omeprazole (200 μM) was the most potent inducer (12.8 ± 1.9- and 2.4 ± 0.2-fold above DMSO-treated cells in transformants with and without PXR, respectively). Mifepristone and mevastatin produced modest induction (∼3-fold) in the cell line containing exogenous PXR, but produced less than 1.2-fold increases in cells lacking PXR. Thus, only potent inducers can be identified in the cell line without PXR. In contrast, cells containing the receptor can be used to rank CYP3A4 induction. Because a high volume of chemicals can be readily and accurately screened for their ability to induce CYP3A4 with this format, such a system could be valuable in the initial stages of preclinical drug development.
The Clusters Ages Experiment (CASE). II. The Eclipsing Blue Straggler OGLEGC 228 in the Globular Cluster 47 Tuc

We use photometric and spectroscopic observations of the eclipsing binary OGLEGC 228 (V228) to derive the masses, radii, and luminosities of the component stars. Based on measured systemic velocity, proper motion, and distance, the system is a blue straggler member of the globular cluster 47 Tuc. Our analysis shows that V228 is a semidetached Algol. We obtain M = 1.512 ± 0.022 M⊙, R = 1.357 ± 0.019 R⊙, and L = 7.02 ± 0.050 L⊙ for the hotter and more luminous primary component and M = 0.200 ± 0.007 M⊙, R = 1.238 ± 0.013 R⊙, and L = 1.57 ± 0.09 L⊙ for the Roche lobe-filling secondary.
Approximating Revenue-Maximizing Combinatorial Auctions

Designing revenue-maximizing combinatorial auctions (CAs) is a recognized open problem in mechanism design. It is unsolved even for two bidders and two items for sale. Rather than attempting to characterize the optimal auction, we focus on designing approximations (suboptimal auction mechanisms which yield high revenue). Our approximations belong to the family of virtual valuations combinatorial auctions (VVCA). VVCA is a Vickrey-Clarke-Groves (VCG) mechanism run on virtual valuations that are linear transformations of the bidders' real valuations. We pursue two approaches to constructing approximately optimal CAs. The first is to construct a VVCA with worst-case and average-case performance guarantees. We give a logarithmic approximation auction for basic important special cases of the problem: 1) limited supply of items on sale with additive valuations and 2) unlimited supply. The second approach is to search the parameter space of VVCAs in order to obtain high-revenue mechanisms for the general problem. We introduce a series of increasingly sophisticated algorithms that use economic insights to guide the search and thus reduce the computational complexity. Our experiments demonstrate that in many cases these algorithms perform almost as well as the optimal VVCA, yield a substantial increase in revenue over the VCG mechanism and drastically outperform the straightforward algorithms in run-time.
A Core/Periphery Perspective on Individual Creative Performance: Social Networks and Cinematic Achievements in the Hollywood Film Industry

The paper advances a relational perspective to studying creativity at the individual level. Building on social network theory and techniques, we examine the role of social networks in shaping individuals’ ability to generate a creative outcome. More specifically, we argue that individuals who occupy an intermediate position between the core and the periphery of their social system are in a favorable position to achieve creative results. In addition, the benefits accrued through an individual’s intermediate core/periphery position can also be observed at the team level, when the same individual works in a team whose members come from both ends of the core/periphery continuum. We situate the analysis and test our hypotheses within the context of the Hollywood motion picture industry, which we trace over the period 1992–2003. The theoretical implications of the results are discussed.