Miracle-dz/UniFAR-FTUs huggingface dataset:
Nested Tracking Graphs

Tracking graphs are a well established tool in topological analysis to visualize the evolution of components and their properties over time, i.e., when components appear, disappear, merge, and split. However, tracking graphs are limited to a single level threshold and the graphs may vary substantially even under small changes to the threshold. To examine the evolution of features for varying levels, users have to compare multiple tracking graphs without a direct visual link between them. We propose a novel, interactive, nested graph visualization based on the fact that the tracked superlevel set components for different levels are related to each other through their nesting hierarchy. This approach allows us to set multiple tracking graphs in context to each other and enables users to effectively follow the evolution of components for different levels simultaneously. We demonstrate the effectiveness of our approach on datasets from finite pointset methods, computational fluid dynamics, and cosmology simulations.
TLR-4 Regulates CD8+ T Cell Trapping in the Liver 1

Mammalian TLRs are understood primarily as an activating system for innate and adaptive immunity, but have also been implicated in sensing cellular damage and in promoting intestinal integrity. In this study we show that TLR-4 also controls the in vivo distribution of activated CD8+ T cells. The liver is a site for trapping and apoptosis of activated CD8+ T cells during systemic immune responses, but the reason for this is unknown. In this study we tested the hypothesis that the liver’s constant exposure to endotoxin, derived from commensal bacteria in the gut, acts via TLR-4 to promote activated T cell adhesion. In the absence of TLR-4, the liver was compromised in its ability to sequester activated CD8+ T cells, and there was an inverse correlation between the frequency of activated CD8+ T cells trapped in the liver and their frequency in the circulating pool. Thus, in the absence of any inflammation, TLR-4 ligands play a significant role in the ability of the liver to trap activated CD8+ T cells. This provides a new perspective on the regulation of immune responses by TLR-4 under basal conditions.
Advances in Brief Transfection of Constitutively Active Mitogen-activated Protein / Extracellular Signal-regulated Kinase Kinase Confers Tumorigenic and Metastatic Potentials to NIH 3 T 3 Cells 1

Cellular growth and differentiation are controlled by multiple extracellular signals, many of which activate extracellular signal-regulated kinase (ERK)/mitogen-activated protein (MAP) kinases. Components of the MAP kinase pathways also cause oncogenic transformation in their constitutively active forms. Moreover, expression of activatedras can confer metastatic potential upon some cells. Activation of MAP kinases requires phosphorylation of both Thr and Tyr in the catalytic domain by a family of dual-specificity kinases, called MEKs (MAP kinase/ERK kinase). MEK1 is activated by phosphorylation at Ser 218 and Ser by Raf. Mutation of these two sites to acidic residues, specifically [Asp ], [Asp, Asp], and [Glu, Glu], results in constitutively active MEK1. Using these mutant variants of MEK1, we showed previously that transfection of NIH/3T3 or Swiss 3T3 cells causes morphological transformation and increases growth on soft agar, independent of ERK activity. The transformed cell lines show increased expression of matrix metalloproteinases 2 and 9 and cathepsin L, proteinases that have been implicated in the metastatic process. We tested NIH3T3 cells transfected with the [Asp ] or [Asp, Asp] for metastatic potential after i.v. injection into athymic mice. Parental 3T3 cells formed no tumors grossly or histologically. However, all MEK1 mutant transformants formed macroscopic metastases. Thus, like activated Ras, MEK1 can confer both tumorigenic and metastatic potential upon NIH3T3 cells. These results refine the mechanism through which ras could confer tumorigenic and metastatic potential (i.e., the critical determinants of tumorigenic and metastatic potential are downstream of MEK1).
Thermal and Residual Excited-State Population in a 3D Transmon Qubit.

Remarkable advancements in coherence and control fidelity have been achieved in recent years with cryogenic solid-state qubits. Nonetheless, thermalizing such devices to their milliKelvin environments has remained a long-standing fundamental and technical challenge. In this context, we present a systematic study of the first-excited-state population in a 3D transmon superconducting qubit mounted in a dilution refrigerator with a variable temperature. Using a modified version of the protocol developed by Geerlings et al., we observe the excited-state population to be consistent with a Maxwell-Boltzmann distribution, i.e., a qubit in thermal equilibrium with the refrigerator, over the temperature range 35-150 mK. Below 35 mK, the excited-state population saturates at approximately 0.1%. We verified this result using a flux qubit with ten times stronger coupling to its readout resonator. We conclude that these qubits have effective temperature T(eff)=35 mK. Assuming T(eff) is due solely to hot quasiparticles, the inferred qubit lifetime is 108 μs and in plausible agreement with the measured 80 μs.
An Examination of the Compressive Cyclic Loading Aspects of Damage Tolerance for Polymer Matrix Launch Vehicle Hardware

The issue of fatigue loading of structures composed of composite materials is considered in a requirements document that is currently in place for manned launch vehicles. By taking into account the short lives of these parts, coupled with design considerations, it is demonstrated that the necessary coupon level fatigue data collapse to a static case. Data from a literature review of past studies that examined compressive fatigue loading after impact and data generated from this experimental study are presented to support this finding. In other studies from the literature, a stress amplitude of about 60% of the static compression after impact (CAI) strength was found to exist, below which fatigue had no deleterious effects up to one million cycles. In this study, a stress amplitude of about 80% of the static (CAI) strength was found to exist, below which fatigue had no deleterious effects up to 10,000 cycles. A launch vehicle structure should never experience one cycle above 61.4% of static CAI strength, much less 10,000 at 80%. Despite utilizing severe fatigue amplitude loading in impact damaged coupons, residual strength after fatigue was consistently higher than expected. Unrealistically high fatigue stress amplitudes were needed to fail 5 of 15 specimens, before 10,000 cycles was reached. Since a typical launch vehicle structure, such as the ARES I interstage, only experiences a few cycles near limit load, it is concluded that static CAI strength data will suffice for most launch vehicle structures.
Roles for motility in bacterial–host interactions

The ability to move in a directed manner may confer distinct advantages upon host‐adapted prokaryotes. Potential benefits of motility include increased efficiency of nutrient acquisition, avoidance of toxic substances, the ability to translocate to preferred hosts and access optimal colonization sites within them, and dispersal in the environment during the course of transmission. The costs of motility also may be significant. These include the metabolic burden of synthesizing flagellar components, the energetic expense of fuelling flagellar motors and the presentation of polymeric and highly antigenic targets to the immune system. It is therefore not surprising that synthesis of the motility apparatus is usually subject to strict control. Studies of a variety of bacterial–host interactions demonstrate roles for motility, and its regulation, at points throughout the infectious cycle.
Analytical modeling for the design of a piezoelectric rotating-mode motor

This paper deals with the analytical modeling of a rotating-mode motor. The modeling, based on an equivalent electric circuit, is established by using geometrical and electromechanical parameters for the different parts of the motor. It gives electromechanical characteristics and other useful values for motor design. Numerical simulations and measurements from a real transducer validate the analysis.
Stroke and idiopathic Parkinson's disease: Does a shortage of dopamine offer protection against stroke?

Data on the relationship between idiopathic Parkinson's disease (IPD) and stroke are conflicting. In this study, we examined the frequency of IPD in stroke patients registered in the Maastricht Stroke Registry. With the use of three different search strategies, we found eight individuals with IPD amongst a total of 1,516 stroke patients. We had expected to find approximately 30 IPD patients (relative risk 0.27; 95% confidence interval 0.11–0.53), based on IPD prevalence figures from a Dutch population‐based study. We speculate that dopamine deficiency may protect against ischaemic brain damage, perhaps by reducing the effects of excitotoxicity. Mov. Disord. 16:119–123, 2001. © 2001 Movement Disorder Society.
Divergent Effects of T Cell Costimulation and Inflammatory Cytokine Production on Autoimmune Peripheral Neuropathy Provoked by Aire Deficiency

Chronic inflammatory demyelinating polyneuropathy results from autoimmune destruction of the peripheral nervous system and is a component of the multiorgan autoimmunity syndrome that results from Aire gene mutations in humans. In parallel, peripheral nervous system autoimmunity resembling chronic inflammatory demyelinating polyneuropathy develops spontaneously in NOD mice with a partial loss of Aire function (NOD.AireGW/+ mice) and is a T cell–mediated disease. In this study, we analyze how key aspects of T cell activation and function modulate disease development in Aire-deficient mice. We show that genetic ablation of the Th1 cytokine IFN-γ completely prevents clinical and electrophysiological evidence of neuropathy in NOD.AireGW/+ mice. IFN-γ deficiency is associated with absence of immune infiltration and decreased expression of the T cell chemoattractant IP-10 in sciatic nerves. Thus, IFN-γ is absolutely required for the development of autoimmune peripheral neuropathy in NOD.AireGW/+ mice. Because IFN-γ secretion is enhanced by B7-CD28 costimulation of T cells, we sought to determine the effects of these costimulatory molecules on neuropathy development. Surprisingly, B7-2 deficiency accelerated neuropathy development in NOD.AireGW/+ mice, and Ab blockade of both B7-1 and B7-2 resulted in fulminant, early-onset neuropathy. Thus, in contrast to IFN-γ, B7-2 alone and B7-1/B7-2 in combination function to ameliorate neuropathy development in NOD.AireGW/+ mice. Together, these findings reveal distinct and opposing effects of the T cell costimulatory pathway and IFN-γ production on the pathogenesis of autoimmune peripheral neuropathy.
Exclusive Ubiquitination and Sumoylation on Overlapping Lysine Residues Mediate NF-κB Activation by the Human T-Cell Leukemia VirusTax Oncoprotein

ABSTRACT The transcription factor NF-κB is critical for the induction of cancer, including adult T-cell leukemia, which is linked to infection by human T-cell leukemia virus type 1 and the expression of its regulatory protein Tax. Although activation of the NF-κB pathway by Tax involves its interaction with the regulatory subunit of the IκB kinase (IKK) complex, NEMO/IKKγ, the mechanism by which Tax activates specific cellular genes in the nucleus remains unknown. Here, we demonstrate that the attachment of SUMO-1 to Tax regulates its localization in nuclear bodies and the recruitment of both the RelA subunit of NF-κB and free IKKγ in these nuclear structures. However, this sumoylation step is not sufficient for the activation of the NF-κB pathway by Tax. This activity requires the prior ubiquitination and colocalization of ubiquitinated Tax with IKK complexes in the cytoplasm and the subsequent migration of the RelA subunit of NF-κB to the nucleus. Thus, the ubiquitination and sumoylation of Tax function in concert to result in the migration of RelA to the nucleus and its accumulation with IKKγ in nuclear bodies for activation of gene expression. These modifications may result in targets for the treatment of adult T-cell leukemia.
Hematopoietic stem cell transplantation in sickle cell disease: patient selection and special considerations

Hematopoietic stem cell transplantation remains the only curative treatment currently in use for patients with sickle cell disease (SCD). The first successful hematopoietic stem cell transplantation was performed in 1984. To date, approximately 1,200 transplants have been reported. Given the high prevalence of this disorder in Africa, and its emergence in the developed world through immigration, this number is relatively small. There are many reasons for this; primary among them are the availability of a donor, the risks associated with this complex procedure, and the cost and availability of resources in the developing world. Of these, it is fair to say that the risks associated with the procedure have steadily decreased to the point where, if currently performed in a center with experience using a matched sibling donor, overall survival is close to 100% and event-free survival is over 90%. While there is little controversy around offering hematopoietic stem cell transplantation to symptomatic SCD patients with a matched sibling donor, there is much debate surrounding the use of this modality in “less severe” patients. An overview of the current state of our understanding of the pathology and treatment of SCD is important to show that our current strategy is not having the desired impact on survival of homozygous SCD patients, and should be changed to significantly impact the small proportion of these patients who have matched siblings and could be cured, especially those without overt clinical manifestations. Both patient families and providers must be made to understand the progressive nature of SCD, and should be encouraged to screen full siblings of patients with homozygous SCD for their potential to be donors. Matched siblings should be referred to an experienced transplant center for evaluation and counseling. In this review, we will discuss the rationale for these opinions and make recommendations for patient selection.
Ranking Highlights in Personal Videos by Analyzing Edited Videos

We present a fully automatic system for ranking domain-specific highlights in unconstrained personal videos by analyzing online edited videos. A novel latent linear ranking model is proposed to handle noisy training data harvested online. Specifically, given a targeted domain such as “surfing,” our system mines the YouTube database to find pairs of raw and their corresponding edited videos. Leveraging the assumption that an edited video is more likely to contain highlights than the trimmed parts of the raw video, we obtain pair-wise ranking constraints to train our model. The learning task is challenging due to the amount of noise and variation in the mined data. Hence, a latent loss function is incorporated to mitigate the issues caused by the noise. We efficiently learn the latent model on a large number of videos (about 870 min in total) using a novel EM-like procedure. Our latent ranking model outperforms its classification counterpart and is fairly competitive compared with a fully supervised ranking system that requires labels from Amazon Mechanical Turk. We further show that a state-of-the-art audio feature mel-frequency cepstral coefficients is inferior to a state-of-the-art visual feature. By combining both audio-visual features, we obtain the best performance in dog activity, surfing, skating, and viral video domains. Finally, we show that impressive highlights can be detected without additional human supervision for seven domains (i.e., skating, surfing, skiing, gymnastics, parkour, dog activity, and viral video) in unconstrained personal videos.
The foamability of low-melt-strength linear polypropylene with nanoclay and coupling agent

In this work, the feasibility of producing microcellular foam by using homopolymer linear polypropylene with an melt flow index of 18 g/10 min, a high melt flow index coupling agent (G3003, melt flow index of 380 g/min), and different nanoclay (Cloisite 20A) content was investigated. A twin-screw extruder was used to prepare the nanocomposite compounds, and an X-ray diffraction machine was used to characterize the intercalation and exfoliation of nanoclay within the matrix. A rheology test was undertaken to investigate the melt shear viscosity of the samples. A single-screw extruder was employed to produce foam by using 5% supercritical CO2 at various die temperatures. Scanning electron microscopy was used to explore the morphology of the foamed samples, and cell density was calculated by scanning electron microscopy images. Density measurement data was used to calculate the expansion ratio of the foamed samples. Extrusion foaming produced foams with high expansion ratios of about 20 and a high cell density of about 108−9 cells/cm3. The crystallinity behavior of the foamed and unfoamed linear polypropylene and linear polypropylene nanocomposites was also investigated. A high-pressure differential scanning calorimetry was used to investigate the dependency of crystallization behavior on high pressure CO2.
The Time Dimension in Conceptual Modelling 1 The Time Dimension in Conceptual Modelling

In recent years there has been a growing interest in the explicit introduction of time modelling in a conceptual schema. This has come about as as a result of the relaisation that realisation that the development of large information systems is becoming increasingly more difficult as user requirements become broader and more sophisticated. Arguably the most critical activity in the development of a large data-intensive information system is that of requirements capture and specification. The effectiveness of such a specification depends largely on the ability of the chosen conceptual model to represent the problem domain in such a way so as to permit natural and rigorous descriptions within a methodological framework. The explicit representation of time in a conceptual model plays a major role in achieving this effectiveness. This paper examines the ontology and properties of time in the context of information systems and conceptual modelling. In particular, a critical set of ontological assumptions about time are examined which in turn give rise to the way different paradigms deal with time modelling at the conceptual level. The paper describes and critically evaluates nine contemporary approaches to the specification and use of time in information systems. The Time Dimension in Conceptual Modelling 2
Explaining the energetic AGN outburst of MS 0735+7421 with massive slow jets

By conducting axisymmetrical hydrodynamical numerical simulations (2.5 dimensional code) we show that slow, massive, wide jets can reproduce the morphology of the huge X-ray deficient bubble pair in the cluster of galaxies MS 0735+7421. The total energy of the jets, composed of the energy in the bubble pair and in the shock wave, is constrained by observations conducted by McNamara et al. to be ~10 62 erg. We show that two opposite jets that are active for ~100Myr, each with a launching half opening angle of α ≃ 70°, an initial velocity of v j ~ 0.1 c and a total mass loss rate of the two jets of M 2j ~ 100 M ⊙ yr -1 can account for the observed morphology. Rapidly precessing narrow jets can be used instead of wide jets. In our model the cluster suffered from a cooling catastrophe ~100Myr ago. Most of the mass that cooled,~10 10 M ⊙ , was expelled back to the intracluster medium by the active galactic nuclei activity and is inside the bubbles now,~1 per cent formed stars and~1 per cent of the cold gas was accreted by the central black hole and was the source of the outburst energy. This type of activity is similar to that expected to occur in galaxy formation.
The Potential Impact of Animal Science Research on Global Maternal and Child Nutrition and Health: A Landscape Review12

High among the challenges facing mankind as the world population rapidly expands toward 9 billion people by 2050 is the technological development and implementation of sustainable agriculture and food systems to supply abundant and wholesome nutrition. In many low-income societies, women and children are the most vulnerable to food insecurity, and it is unequivocal that quality nutrition during the first 1000 d of life postconception can be transformative in establishing a robust, lifelong developmental trajectory. With the desire to catalyze disruptive advancements in global maternal and child health, this landscape review was commissioned by the Bill & Melinda Gates Foundation to examine the nutritional and managerial practices used within the food-animal agricultural system that may have relevance to the challenges faced by global human health. The landscape was categorized into a framework spanning 1) preconception, 2) gestation and pregnancy, 3) lactation and suckling, and 4) postweaning and toddler phases. Twelve key findings are outlined, wherein research within the discipline of animal sciences stands to inform the global health community and in some cases identifies gaps in knowledge in which further research is merited. Notable among the findings were 1) the quantitative importance of essential fatty acid and amino acid nutrition in reproductive health, 2) the suggested application of the ideal protein concept for improving the amino acid nutrition of mothers and children, 3) the prospect of using dietary phytase to improve the bioavailability of trace minerals in plant and vegetable-based diets, and 4) nutritional interventions to mitigate environmental enteropathy. The desired outcome of this review was to identify potential interventions that may be worthy of consideration. Better appreciation of the close linkage between human health, medicine, and agriculture will identify opportunities that will enable faster and more efficient innovations in global maternal and child health.
Poor physical function in elderly women in low-level aged care is related to muscle strength rather than to measures of sarcopenia

Purpose: To determine the prevalence of sarcopenia and investigate relationships among body composition, muscle strength, and physical function in elderly women in low-level aged care. Subjects and methods: Sixty-three ambulatory women (mean age 86 years) participated in this cross-sectional study where body composition was determined by dual energy X-ray absorptiometry (DXA); ankle, knee, and hip strength by the Nicholas Manual Muscle Tester; and physical function by ‘timed up and go’ (TUG) and walking speed (WS) over 6 meters. Body composition data from a female reference group (n = 62, mean age 29 years) provided cut-off values for defining sarcopenia. Results: Elderly women had higher body mass index (P < 0.001), lower lean mass (P < 0.001), and higher fat mass (P < 0.01) than the young reference group. Only a small proportion (3.2%) had absolute sarcopenia (defined by appendicular skeletal muscle mass/height squared) whereas 37% had relative sarcopenia class II (defined by percentage skeletal muscle mass). Scores for TUG and WS indicated relatively poor physical function, yet these measures were not associated with muscle mass or indices of sarcopenia. In multivariate analysis, only hip abductor strength predicted both TUG and WS (both P = 0.01). Conclusion: Hip strength is a more important indicator of physical functioning than lean mass. Measurement of hip strength may therefore be a useful screening tool to detect those at risk of functional decline and requirement for additional care. Further longitudinal studies with a range of other strength measures are warranted.