Miracle-dz/UniFAR-FTUs huggingface dataset:
Gradient lasso for Cox proportional hazards model

MOTIVATION There has been an increasing interest in expressing a survival phenotype (e.g. time to cancer recurrence or death) or its distribution in terms of a subset of the expression data of a subset of genes. Due to high dimensionality of gene expression data, however, there is a serious problem of collinearity in fitting a prediction model, e.g. Cox's proportional hazards model. To avoid the collinearity problem, several methods based on penalized Cox proportional hazards models have been proposed. However, those methods suffer from severe computational problems, such as slow or even failed convergence, because of high-dimensional matrix inversions required for model fitting. We propose to implement the penalized Cox regression with a lasso penalty via the gradient lasso algorithm that yields faster convergence to the global optimum than do other algorithms. Moreover the gradient lasso algorithm is guaranteed to converge to the optimum under mild regularity conditions. Hence, our gradient lasso algorithm can be a useful tool in developing a prediction model based on high-dimensional covariates including gene expression data. RESULTS Results from simulation studies showed that the prediction model by gradient lasso recovers the prognostic genes. Also results from diffuse large B-cell lymphoma datasets and Norway/Stanford breast cancer dataset indicate that our method is very competitive compared with popular existing methods by Park and Hastie and Goeman in its computational time, prediction and selectivity. AVAILABILITY R package glcoxph is available at http://datamining.dongguk. ac.kr/R/glcoxph.
A Real-Time Pricing Model for Electricity Consumption

The California electric company, i.e., PG&E (Pacific Gas and Electric Co.,), has recently announced its intentions to charge small businesses in the state with dynamic prices for electricity consumption. In this regard, we study a real-time electricity pricing model in the paper and compare it with two static pricing models. We show that real-time pricing outplays static pricing when it comes to jointly maximizing provider and consumer welfare.
SIDS: past, present and future

Despite the large reduction in SIDS mortality, which occurred in the early 1990s following the ‘Back to Sleep’ campaigns, SIDS remains the leading cause of death in the postneonatal age group. This paper describes the position in the 1980s, the contribution of the New Zealand Cot Death Study, what should be recommended and the current research priorities.
Adaptive Output Feedback Control for Mismatched Uncertain Systems: Single Phase Sliding Mode Approach

In this paper, we present a new sliding mode control, only one phase, for mismatched uncertain systems. At the initial time t=0 the switching plane have reached the origin, the plane stops moving and remains fixed. In addition, the sufficient conditions in terms of linear matrix inequalities (LMI) for the existence of a sliding surface guarantee asymptotic stability of the sliding mode dynamics from the beginning time. We have also offered the adaptation laws to calculate the unknown upper bounds of matched uncertainties, and by making use of their updated values, established a class of adaptive output feedback controllers. Finally, a numerical example is used to demonstrate the efficacy on the method.
Mobile edge computing services for dynamic quality of service control

Mobile Edge Computing (MEC) provides cloud computing capabilities in the radio access network. It enables applications that improve user's quality of experience and guarantee maximum utilization of radio network resources. Communication between MEC services and applications is based on Service-oriented Architecture (SOA). In this paper, capabilities for deployment of existing Parlay X Web Services in MEC environment are studied, and a new Web Service that provides access to User equipment-related radio network information is proposed.
Maternal Hyperglycemia Improves Fetal Cardiac Function During Tachycardia-Induced Heart Failure in Pigs

Background—Fetal tachycardia often leads to cardiac failure, which in experimental settings can be prevented by direct fetal glucose-insulin administration. In this study, we hypothesize that similar effects can be obtained indirectly by inducing maternal hyperglycemia. Methods and Results—Systolic and diastolic indices (dP/dtmax and &tgr;) of left ventricular function were measured by use of high-fidelity catheters during 180 minutes of aggressive atrial pacing (≈300 bpm) in 12 preterm porcine fetuses. In 6 fetuses, maternal hyperglycemia (15 mmol/L) was induced for the last 120 minutes of pacing. The remaining fetuses served as controls. Glucose, insulin, and free fatty acid levels were determined, as was fetal myocardial glycogen content. Maternal glucose infusion led to significant fetal hyperglycemia and hyperinsulinemia but did not change the inherently low fetal levels of free fatty acids. There were no differences between groups with regard to dP/dtmax (1025±226 and 1037±207 mm Hg, P=NS) and &tgr; (20.6±2.0 and 21.4±1.6 ms, P=NS) at baseline (100%). During the 180 minutes of pacing, systolic function (dP/dtmax) and diastolic function (&tgr;) deteriorated more in the control group than in the hyperglycemic group (P<0.001 for both). At 180 minutes, dP/dtmax was 62±18% of baseline in controls and 85±11% in hyperglycemic fetuses (P=0.03), and &tgr; was 117±12% and 98±4%, respectively (P=0.004). Conclusions—Induced maternal hyperglycemia improves fetal cardiac function during fetal tachycardia and suggests a possible additional therapeutic option to improve the function of the failing fetal heart before or during antiarrhythmic therapy. The findings may be relevant in fetal heart failure in general.
The Impact of Sterilization Method on Wear in Knee Arthroplasty

Sterilization by gamma irradiation in air has been shown to have the potential to accelerate the oxidation of polyethylene components resulting in reduced mechanical properties. In the hip, it has been reported that the occurrence of delamination and cracking in retrieved bearings is significantly different when comparing components sterilized with gamma irradiation in air with components sterilized with ethylene oxide. Using a collection of 1635 retrieved polyethylene knee bearings, this study pursues a similar comparison of sterilization method with clinical wear in the knee. It confirms that retrieved polyethylene knee components that were gamma irradiated in air have a high incidence of delamination and cracking, leading at times to complete wear through of the bearing. Knee components sterilized with ethylene oxide showed no evidence of fatigue damage even after in vivo durations in excess of 15 years.
Selective Activation of the c-Jun NH2-terminal Protein Kinase Signaling Pathway by Stimulatory KIR in the Absence of KARAP/DAP12 in CD4+ T Cells

Activation of CD4+ T cells is governed by interplay between stimulatory and inhibitory receptors; predominance of stimulatory signals favors autoimmune reactions. In patients with rheumatoid arthritis, expression of the critical costimulatory molecule, CD28, is frequently lost. Instead, CD4+CD28null T cells express killer immunoglobulin-like receptors (KIRs) with a preferential expression of the stimulatory receptor, CD158j. The frequency of CD4+CD28null T cells in rheumatoid arthritis (RA) correlates with the risk for more severe disease. Moreover, the KIR2DS2 gene, which encodes for CD158j, is a genetic risk factor for rheumatoid vasculitis. CD158j signals through the adaptor molecule, KARAP/DAP12, to positively regulate cytotoxic activity in NK cells. However, the majority of CD4+CD28null T cell clones lacked the expression of KARAP/DAP12. Despite the absence of KARAP/DAP12, CD158j was functional and augmented interferon-γ production after T cell receptor stimulation. Cross-linking of CD158j resulted in selective phosphorylation of c-Jun NH2-terminal protein kinase (JNK) and its upstream kinase, MKK4 that led to the expression of ATF-2 and c-Jun, all in the absence of extracellular signal–regulated kinase (ERK)1/2 phosphorylation. Mutation of the lysine residue within the transmembrane domain of CD158j abolished JNK activation, suggesting that an alternate adaptor molecule was being used. CD4+CD28null T cells expressed DAP10 and inhibition of phosphatidylinositol 3-kinase, which acts downstream of DAP10, inhibited JNK activation; however, no interaction of DAP10 with CD158j could be detected. Our data suggest that CD158j in T cells functions as a costimulatory molecule through the JNK pathway independent of KARAP/DAP12 and DAP10. Costimulation by CD158j may contribute to the autoreactivity of CD4+CD28null T cells in RA.
Embedding of fluorescent dyes into polyelectrolyte capsules for remote destruction of the capsule shell by laser irradiation

Polyelectrolyte capsules were modified by different types of fluorescent dyes and their optical properties were investigated. Three methods of encapsulation were used: dye adsorption onto the porous core, change of the solvent and embedding into the polyelectrolyte shell. Suspension of capsules with Rhodamine 6G molecules in the shell was irradiated by laser beam with wavelength corresponded with the absorption band for the dye molecule. Measurements of the capsules size distribution before and after laser irradiation showed that the capsules were destroyed by laser radiation.
EgoNet identifies differential ego-modules and pathways related to prednisolone resistance in childhood acute lymphoblastic leukemia

ABSTRACT Purpose: To extract feature ego-modules and pathways in childhood acute lymphoblastic leukemia (ALL) resistant to prednisolone treatment, and further to explore the mechanisms behind prednisolone resistance. Materials and methods: EgoNet algorithm was used to identify candidate ego-network modules, mainly via constructing differential co-expression network (DCN); selecting ego genes; collecting ego-network modules; refining candidate modules. Afterwards, statistical significance was calculated for these candidate modules. Biological functions of differential ego-network modules were identified using Reactome database. To verify this proposed method can lead to truly positive findings in clinical settings, support vector machine (SVM) was utilized to compute the AUC values for each significant pathway using 3-fold cross-validation method. To predict the reliability of our findings, another established method (attract) was used to identify the differential attractor modules using the same microarray profile. Results: After eliminating the modules with classification accuracy < 0.9 and node number < 15, only ego-network module 30 was eligible. After significance calculation, module 30 was significant. Module 30 was enriched in APC/C-mediated degradation of cell cycle proteins. The AUC for the significant pathway of APC/C-mediated degradation of cell cycle proteins was 0.915. Although the attract method obtained more modules, the module identified by our proposed method owned more gene nodes, and had more classification ability (AUC = 0.915). Conclusion: One differential ego-network module identified in childhood ALL resistance to prednisolone based on DCN and EgoNet, might be helpful to reveal the mechanisms underlying prednisolone resistance in childhood ALL.
DISTRIBUTING STEREOSCOPIC SCIENTIFIC VISUALISATION ACROSS THE GRID

An architecture that allows stereoscopic scientific visualisation to be distributed across the grid is presented. As the quantity of data generated by scientists increases so does the need for tools to analyse and interpret that data: visualisation is one such tool. The architecture presented allows resources distributed across the grid to be brought together and allows scientists to build effective stereoscopic visualisations that can provide insight and help in the understanding of the data being analysed.
Tissue‐specific and Developmental Expression of Pituitary Adenylate Cyclase‐activating Polypeptide (PACAP) Receptors in Rat Brain

The two forms of pituitary adenylate cyclase‐activating polypeptide, PACAP27 and PACAP38, are novel members of the vasoactive intestinal peptide (VIP)/secretin/glucagon family of peptides. PACAP receptors that are positively coupled to adenylate cyclase and phospholipase C have been recently identified. We examined the expression of PACAP receptors in the rat cortex, hippocampus, cerebellum and hypothalamus during postnatal development. Functional studies revealed PACAP stimulation of cAMP formation in all the brain areas examined and [3H]inositol monophosphate ([3H]insP) accumulation only in the cerebellum and hypothalamus. Throughout development, the efficacy of PACAP in stimulating cAMP formation slightly increased in the cortex and hypothalamus and decreased in the hippocampus and cerebellum; PACAP stimulation of [3H]lnsP formation decreased in the cerebellum and remained steady in the hypothalamus. The effects of PACAP27 and PACAP38 on cAMP levels and inositol phospholipid hydrolysis were dose‐dependent between 1 and 100 nM. In the same brain areas, treatment with VIP increased cAMP formation at doses greater than 100 nM and failed to affect [3H]lnsP content, thus suggesting the existence of type‐l PACAP receptors. The reverse transcription polymerase chain reaction (RT‐PCR) was used to analyse the mRNA expression of type‐l PACAP receptor splice variants. PACAP receptor gene expression in the central nervous system was regulated in a developmental‐ and tissue‐specific manner. The PACAP‐R transcript was detected in all the brain areas examined whereas PACAP‐R‐hop mRNA occurred only in the cerebellum and hypothalamus. The different expression profiles and functional properties of PACAP receptors in the developing rat brain suggest an involvement of PACAP in histogenesis, maturation and neurotransmission.
Mitochondrial Protection by Resveratrol

Mitochondrial dysfunction and oxidative stress are thought to play important roles in mammalian aging. Resveratrol is a plant-derived polyphenol that exerts diverse antiaging activities, mimicking some of the molecular and functional effects of dietary restriction. This review focuses on the molecular mechanisms underlying the mitochondrial protective effects of resveratrol, which could be exploited for the prevention or amelioration of age-related diseases in the elderly.
GPR56 Functions Together with α3β1 Integrin in Regulating Cerebral Cortical Development

Loss of function mutations in GPR56, which encodes a G protein-coupled receptor, cause a specific human brain malformation called bilateral frontoparietal polymicrogyria (BFPP). Studies from BFPP postmortem brain tissue and Gpr56 knockout mice have previously showed that GPR56 deletion leads to breaches in the pial basement membrane (BM) and neuronal ectopias during cerebral cortical development. Since α3β1 integrin also plays a role in pial BM assembly and maintenance, we evaluated whether it functions together with GPR56 in regulating the same developmental process. We reveal that loss of α3 integrin enhances the cortical phenotype associated with Gpr56 deletion, and that neuronal overmigration through a breached pial BM occurs earlier in double knockout than in Gpr56 single knockout mice. These observations provide compelling evidence of the synergism of GPR56 and α3β1 integrin in regulating the development of cerebral cortex.
Enabling functional validation of virtual cars through Natural Interaction metaphors

Natural Interaction in virtual environments is a key requirement for the virtual validation of functional aspects in automotive product development processes. Natural Interaction is the metaphor people encounter in reality: the direct manipulation of objects by their hands. To enable this kind of Natural Interaction, we propose a pseudo-physical metaphor that is both plausible enough to provide realistic interaction and robust enough to meet the needs of industrial applications. Our analysis of the most common types of objects in typical automotive scenarios guided the development of a set of refined grasping heuristics to support robust finger-based interaction of multiple hands and users. The objects' behavior in reaction to the users' finger motions is based on pseudo-physical simulations, which also take various types of constrained objects into account. In dealing with real-world scenarios, we had to introduce the concept of Normal Proxies, which extend objects with appropriate normals for improved grasp detection and grasp stability. An expert review revealed that our interaction metaphors allow for an intuitive and reliable assessment of several functionalities of objects found in a car interior.
P‐239: Synthesis and Photoluminescence Properties of Tb3+‐Doped Lanthanide Orthophosphates (La1−xGdx)0.94Tb0.06PO4 (0.5≤x≤1.0)

The photoluminescence properties of the (La1−xGdx)0.94Tb0. 06PO4 (0.5≤x≤1.0) phosphors synthesized by ultrasonic spray pyrolysis were investigated under VUV irradiation. In order to understand the effect of Gd addition on the photoluminescence properties, we obtained the excitation and emission spectra of the (La1−xGdx)0.94Tb0. 06PO4 phosphors with various Gd contents. Annealed (La1−xGdx)0.94Tb0. 06PO4 phosphors showed a smooth, regular, and spherical morphology. The XRD spectra of the (La1−xGdx)0.94Tb0. 06PO4 showed the solid solutions of the constituent lanthanide phosphates, which crystallized in a monoclinic monazite. The XRD peaks shifted slightly toward higher angles with increasing Gd content, indicating that the lattice parameter slightly decreased with an increase in Gd content. The phosphors emitted the green light due to the transition from 5D4 to 7Fj (j=3−6) at 489, 543, 585, and 621nm, respectively. (La0.25Gd0.75)0.94Tb0. 06PO4 showed the strongest emission intensity.
Unsupervised Learning of Semantic Relations between Concepts of a Molecular Biology Ontology

In this paper we present an unsupervised model for learning arbitrary relations between concepts of a molecular biology ontology for the purpose of supporting text mining and manual ontology building. Relations between named-entities are learned from the GENIA corpus by means of several standard natural language processing techniques. An in-depth analysis of the output of the system shows that the model is accurate and has good potentials for text mining and ontology building applications.
PII T-Loop Mutations Affecting Signal Transduction to NtrB Also Abolish Yeast Two-Hybrid Interactions

ABSTRACT Mutations A49P and Δ47-53 at the T loop of the Escherichia coli GlnB (PII) protein impair regulatory interactions with the two-component sensor regulator NtrB (P. Jiang, P. Zucker, M. R. Atkinson, E. S. Kamberov, W. Tirasophon, P. Chandran, B. R. Schepke, and A. J. Ninfa, J. Bacteriol. 179: 4342-4353, 1997). We show here that these mutations also impair interactions between PII and NtrB in the yeast two-hybrid system, indicating that defects in NtrB regulation closely reflect binding impairment. The reported results underline the strength of two-hybrid assays for analysis of interactions involving the T loop of PII proteins.
Interprocedural Dataﬂow Analysis, Part III: Newtonian Program Analysis Via Tensor Product CS701

In this lecture, we summarize the interprocedural-dataﬂow-analysis method of Esparza et al., which generalizes Newton’s method from a numerical-analysis algorithm for ﬁnding roots of real-valued functions to a method for ﬁnding ﬁxed-points of systems of equations over semirings. As in its real-valued counterpart, each iteration of the method of Esparza et al. solves a simpler “linearized” problem. We then move on to a recent method of Reps et al., which attempts to provide an improved technique for solving the linearized problems produced during successive rounds of Newton’s method for semirings.
Mathematical modelling of gas separation and storage using advanced materials

Clean, sustainable and cost-efficient fuel alternatives are expected to replace conventional fossil fuel combustion systems as environmental and economic pressures rise. Alternative fuel candidates include synthetic gas, purified natural gas and hydrogen gas. The realization of an alternative fuel-based economy hinges on the efficient separation and storage of gases, for applications such as pollutant capture, synthetic fuel production, fuel purification and fuel storage. Membranes and adsorbents are materials characterized by an internal network of angstrom and nano-sized pores which are designed to separate and store gases, respectively. This thesis is concerned with the development of simple mathematical models to explain and predict gas transport and adsorption properties within advanced materials. Such models will guide the tailoring of porosity to optimize the desired properties. This thesis makes contributions to the following three areas: • Gas separation Firstly, a new model that determines the transport properties of a gas within individual pores is presented. The model considers the interactions of the gas with the surface of the pore to characterize the various transport regimes within pores of different size, shape and composition. This is an entirely new approach to understanding and interpreting the various diffusion regimes known to occur within gas separation membranes. The new model can be used to determine the optimal pore characteristics that maximize the separation of gas mixtures. Secondly, a new empirical relationship between gas diffusion and the membrane free volume is introduced which is found to accurately describe known diffusion behaviour for a range of polymer membranes. This leads to a new method for determining the amount of free volume necessary to achieve a desired gas diffusion rate. • Gas storage Based upon fundamental thermodynamic principles, a new model for gas storage within adsorbents is presented. The model incorporates the interactions between the gas and the internal surface area of the adsorbent, and proves to be an accurate and fast method for predicting storage performance within adsorbents of varying porosities. This novel approach can be used to determine the pore characteristics necessary to store the maximum amount of gas under the required operating conditions. • Physical aging A new physical aging model based on the mechanism of vacancy diffusion is derived that accurately matches existing aging data. Using this model and the existing theory the mechanisms of physical aging are examined, particularly for thin polymer films. Specifically, the new approach provides new insights into the physical aging mechanisms responsible for polymer densification and can be used as a tool to predict the polymer’s performance over time. Finally, the new mathematical models that are presented here provide considerable insight into complex physical processes, and will serve to accelerate the development of alternative energy technologies by providing simple guidelines for material…