Miracle-dz/UniFAR-FTUs huggingface dataset:
Second messenger pathways involved in up-regulation of an L-type calcium channel

Catfish cone horizontal cells contain a voltage-gated L-type calcium channel that is modulated by activation of metabotropic glutamate receptors (mGluRs). Activation of group I mGluRs with the mGluR I agonist, (S)-3,5-dihydroxyphenylglycine [(S) 3,5-DHPG], potentiated peak calcium current amplitude, shifted the membrane potential corresponding to peak current activity, and widened the calcium current's activation range. In this study, we have examined the mechanisms linking activation of the mGluRs with “up-regulation” of calcium current activity. Under whole-cell voltage-clamp conditions favoring expression of the L-type calcium current, we provide evidence that activation of mGluRs initiate the diacylglyceral (DG) second messenger pathway to activate protein kinase C (PKC) and up-regulate calcium channel activity. This evidence was based on results using a number of PKC activators and inhibitors. PKC activators mimicked the effect of (S) 3,5-DHPG on calcium current activity. Up-regulation of the calcium channel by PKC activators or (S) 3,5-DHPG was eliminated if PKC inhibitors were present. These results also demonstrated that activation of group I mGluRs were linked to a pertussis toxin sensitive G-protein. When the GTP analog, guanosine 5-0-(3-thiotriphosphate (GTPγS), was allowed to diffuse into voltage-clamp cells, up-regulation of the calcium channel occurred and mimicked the effect of (S) 3,5-DHPG. However, when pertussis toxin (PTX) was allowed to diffuse into the cell along with GTPγS, GTPγS failed to modulate calcium current activity. IP3 (inositol 1,4,5 triphosphate) is a second product produced by activation of group I mGluRs. Once formed, IP3 can trigger calcium release from IP3-sensitive intracellular stores. To determine if the IP3 second messenger system was involved in up-regulation of calcium channel, (S) 3,5-DHPG was applied to voltage-clamped cone horizontal cells containing different concentrations of the calcium buffer, EGTA. Low concentrations of EGTA failed to buffer calcium released from intracellular stores. In the presence of low EGTA concentrations, (S) 3,5-DHPG's enhancement of the calcium current amplitude was reduced. Inhibition of the calcium current amplitude in low concentrations of EGTA was eliminated in the presence of the intracellular calcium store blocker, heparin. These results suggest that both the DG and IP3 second messenger pathways are involved in modulation of the voltage-gated calcium channel in catfish cone horizontal cells. The DG pathway up-regulates the voltage-gated calcium channel activity whereas calcium released from IP3 intracellular stores inhibits peak current amplitude.
Experimental Heat Transfer : A Journal of Thermal Energy Generation , Transport , Storage , and Conversion

Modeling of Thermal Conductivity of Concrete with Vermiculite Using by Artificial Neural Networks Approaches O. Gencel a b , F. Koksal c , M. Sahin c , M. Y. Durgun a , H. E. Hagg Lobland b & W. Brostow b a Department of Civil Engineering, Faculty of Engineering , Bartin University , Bartin , Turkey b Laboratory of Advanced Polymers and Optimized Materials (LAPOM), Department of Materials Science and Engineering and Center for Advanced Research and Technology (CART) , University of North Texas , Denton , Texas , USA c Department of Civil Engineering, Faculty of Engineering and Architecture , Bozok University , Yozgat , Turkey Accepted author version posted online: 30 Nov 2012.Published online: 17 May 2013.
The Application of Hidden Markov Models (HMMs) in Offline Arabic Handwritten Recognition

: This paper aimed to introduce the fundamental issues of a Hidden Markov Model (HMMs). It attempts to discuss the: mathematical notation of HMMS, the three fundamental problems related to HMMs, and the topologies of HMMS. A further review of research done by HMMS has been discussed to show its application on offline Arabic handwritten.
PATH2iot: A Holistic, Distributed Stream Processing System

The PATH2iot open-source platform presents a new approach to stream processing for Internet of Things applications by automatically partitioning and deploying the computation over the available infrastructure (e.g. cloud, field gateways and sensors) in order to meet non-functional requirements including energy, performance and security. The user gives a high-level declarative description of computation in the form of Event Processing Language queries. These are compiled, optimised, and partitioned to meet the non-functional requirements using database system techniques and cost models extended to meet the needs of IoT analytics. The paper describes the PATH2iot system, illustrated by a real-world digital healthcare analytics example, with sensor battery life as the main non-functional requirement to be optimised. It shows that the tool can automatically partition and distribute the computation across a healthcare wearable, a mobile phone and the cloud - increasing the battery life of the smart watch by 416% when compared to other possible allocations. The PATH2iot system can therefore automatically bring the benefits of fog/edge computing to IoT applications.
Isolation and expression of a sterol carrier protein‐2 gene from the yellow fever mosquito, Aedes aegypti

Trafficking of cholesterol in insects is a very important process due to the fact that insects depend on dietary cholesterol to fulfil their physiological needs. We identified a putative mosquito sterol carrier protein‐2 (SCP‐2) cDNA from fourth instar subtracted cDNA library. The AeSCP‐2 protein has high degree homology in the sterol transfer domain to both rat and human SCP‐2. Transcripts of AeSCP‐2 in fourth instars were detected strongly in the midgut, and weakly in the head and hindgut. In the early pupae, AeSCP‐2 transcription was observed in the thorax, head and body wall of abdomen, but not in the gut.
Newton's method and the goldstein step length rule for constrained minimization

A relaxed form of Newton's method is analyzed for the problem, min¿F, with ¿ a convex subset of a real Banach space X, and F:X ¿ R1 twice differentiable in Fréchet's sense. Feasible directions are obtained by minimizing local quadratic approximations Q to F, and step lengths are determined by Goldstein's rule. The results established here yield two significant extensions of an earlier theorem of Goldstein for the special case ¿ = X = a Hilbert space. Connections are made with a recently formulated classification scheme for singular and nonsingular extremals.
Inhibition of nuclear factor kappaB by IkappaB superrepressor gene transfer ameliorates ischemia-reperfusion injury after experimental lung transplantation.

OBJECTIVES Ischemia-reperfusion injury after lung transplantation is associated with significant morbidity and mortality. The activation of the transcription factor nuclear factor kappaB is central to the 2 important pathways that characterize ischemia-reperfusion injury, namely the inflammatory response and apoptosis. The purpose of this study was to determine the effects of nuclear factor kappaB inhibition on experimental lung transplant ischemia-reperfusion injury with gene transfer of the nuclear factor kappaB inhibitor IkappaB in a superrepressor form (IkappaBSR). METHODS An orthotopic left lung transplant model in isogeneic rats was used, with 18 hours of prolonged cold storage of donor lung grafts used to create severe ischemia-reperfusion injury. Donor rats underwent endobronchial gene transfection with saline alone or adenovirus encoding either beta-galactosidase control or IkappaBSR 48 hours before harvest. The function of transplanted lung grafts was assessed on the basis of isolated graft oxygenation, wet/dry lung weight ratio, and myeloperoxidase activity. Nuclear factor kappaB activation was assessed by means of enzyme-linked immunosorbent assay. Apoptotic cell death was assessed by evaluating the levels of histone-associated DNA fragments and caspase-3 activity. RESULTS Treatment of donor lung grafts with IkappaBSR resulted in significantly improved oxygenation compared with that seen in control tissue 24 hours after transplantation. IkappaBSR-treated lungs also demonstrated less pulmonary edema and reduced neutrophil infiltration 24 hours after reperfusion. Nuclear factor kappaB activation and apoptotic cell death induction 2 hours after transplantation was significantly reduced in IkappaBSR-treated lungs compared with in control lungs. CONCLUSIONS Inhibition of nuclear factor kappaB activation by IkappaBSR gene transfer improves transplanted lung graft oxygenation, decreases pulmonary edema and neutrophil sequestration, and reduces apoptotic cell death after experimental lung transplantation.
An essential function for acyl carrier protein in the biosynthesis of membrane-derived oligosaccharides of Escherichia coli.

Membrane-derived oligosaccharides are branched, substituted beta-glucans localized in the periplasmic space of Escherichia coli and other Gram-negative bacteria. The biosynthesis of membrane-derived oligosaccharides and of analogous periplasmic oligosaccharides found in plant bacteria is of particular interest because it is subject to strict osmotic regulation [Miller, K.J., Kennedy, E.P., and Reinhold, V.N. (1986) Science 231, 48-51]. An enzyme system catalyzing the synthesis of the (beta 1-2)-linked glucan backbone of E. coli membrane-derived oligosaccharides from UDP-glucose requires both a membrane component and a cytosolic protein termed transglucosylation factor. The factor has now been purified to apparent homogeneity and has been found to be identical to acyl carrier protein (ACP), the phosphopantetheine-containing protein of low molecular weight that has long been known to be essential for fatty acid synthesis in E. coli and other organisms. Both are small, heat-stable, highly anionic proteins with identical chromatographic and electrophoretic behavior. ACP of the highest purity has an activity in the transglucosylation system indistinguishable from that of the protein independently purified as transglucosylation factor. Antibody raised against pure ACP completely inhibits transglucosylation activity; this inhibition is overcome by titration of the antibody with either ACP or transglucosylation factor. These findings provide evidence for an essential function of ACP unrelated to the biosynthesis of lipid.
A Hidden Conditional Random Field-Based Approach for Thai Tone Classification

In Thai, tonal information is a crucial component for identifying the lexical meaning of a word. Consequently, Thai tone classification can obviously improve performance of Thai speech recognition system. In this article, we therefore reported our study of Thai tone classification. Based on our investigation, most of Thai tone classification studies relied on statistical machine learning approaches, especially the Artificial Neural Network (ANN)-based approach and the Hidden Markov Model (HMM)-based approach. Although both approaches gave reasonable performances, they had some limitations due to their mathematical models. We therefore introduced a novel approach for Thai tone classification using a Hidden Conditional Random Field (HCRF)- based approach. In our study, we also investigated tone configurations involving tone features, frequency scaling and normalization techniques in order to fine-tune performances of Thai tone classification. Experiments were conducted in both isolated word scenario and continuous speech scenario. Results showed that the HCRF-based approach with the feature F_dF_aF, ERB-rate scaling and a z-score normalization technique yielded the highest performance and outperformed a baseline using the ANN- based approach, which had been reported as the best for the Thai tone classification, in both scenarios. The best performance of HCRF-based approach provided the error rate reduction of 10.58% and 12.02% for isolated word scenario and continuous speech scenario respectively when comparing with the best result of baselines.
A simulation-optimization approach to deploy Internet services in large-scale systems with user-provided resources

Cloud computing systems can benefit from the use of personal and non-dedicated computers, which are currently employed in volunteer computing systems. Being non-dedicated, these resources show random behavior regarding the times they are online (available) and offline. Accordingly, their availability levels are lower than those of traditionally employed dedicated resources. Thus, in order to use non-dedicated resources in cloud computing environments, it is necessary first to solve the problem of how to attain high availability levels for the Internet services deployed over them. Most approaches on how to guarantee high service availability levels with non-dedicated resources are based on the introduction of high degrees of redundancy into the system. However, this praxis leads to an inefficient usage of computational resources and, therefore, to higher operational costs. Accordingly, the focus of this paper is the problem of minimizing the cost of a service deployment over non-dedicated resources while providing a high level of service availability. In order to solve this stochastic optimization problem, the paper proposes a hybrid algorithm that combines a metaheuristic component with a discrete-event simulation component. The metaheuristic component is used to search for an efficient configuration of resources. The simulation component is integrated inside the metaheuristic and used to estimate the service availability of each promising configuration. A numerical experiment section, comparing the performance of several algorithms, contributes to validating the proposed approach as well as to illustrate its potential applications.
A SINGLE-SHOT METHOD FOR DETERMINING DRAINAGE AND IMBIBITION CAPILLARY PRESSURE CURVES

A single-shot method to determine the capillary pressure curve employed a single rotational velocity centrifugation experiment and one-dimensional Centric Scan SPRITE (single-point ramped imaging with T1 enhancement) MRI (magnetic resonance imaging) to determine the fluid saturation distribution, S(r), along the length (r) of the core. A full capillary pressure curve can be directly determined by the relation of S(r) and the capillary pressure distribution, Pc(r). The rotational speed required for the single-shot method can be determined with the Leverett J function value at the irreducible water saturation. Centric scan SPRITE MRI is an ideal method for measuring spatially resolved fluid saturation in rocks. The single-shot method has been applied to measure the primary drainage, as well as imbibition and secondary drainage capillary pressure curves for reservoir rocks. Proper boundary conditions are ensured by maintaining the free water level in contact with the outlet face of the core. Deuterium oxide (D2O) instead of H2O was employed to dissolve salt for preparing synthetic brine to determine fluid saturation with MRI unambiguously. Thus crude oil can be applied for centrifuging at reservoir temperature with the single-shot method. The single-shot method for determining the capillary pressure curve is rapid, cheap, accurate and adaptable. The capillary pressure curve can be obtained straightforwardly with approximately 40 data points. A desktop centrifuge and a desktop permanent magnet based one-dimensional MRI instrument can be employed for the single-shot method. After primary drainage and imbibition measurements, the rock core should be managed to reach a uniform irreducible water saturation distribution and uniform residual oil saturation distribution, respectively. MRI was also employed to check the saturation distribution. Since only a single rotational velocity is employed, there is no pressure effect on rock pore structure due to dramatic rotational speed changes required for traditional methods. The effect of gravity can also be neglected. In addition, the long rock cores preferred for the single-shot method result in a relatively small radial effect and reduced rotational speed; friable and unconsolidated samples may be measured. In addition, application of the single-shot method for a disk-shaped rock sample and the design of non-magnetic centrifuge disk-shaped rock sample holder will also be presented.
Métodos de inteligencia artificial aplicados a química computacional en entornos de computación de alto rendimiento

El principal objetivo de esta tesis es la propuesta de una serie de refinamientos basados en metodos de inteligencia computacional, unidos a metodologia in-silico para el descubrimiento de compuestos bioactivos, gracias a la capacidad de computo proporcionada por la reciente aparicion de las arquitecturas computacionales masivamente paralelas tales como las GPUs (Unidades de Procesamiento Grafico). Los resultados obtenidos en este proyecto podrian por tanto ayudar y formar la base de una nueva y atractiva generacion de aproximaciones para descubrimiento de compuestos bioactivos.
Genome Scan for Quantitative Trait Loci Linked to High-Density Lipoprotein Cholesterol: The NHLBI Family Heart Study

We conducted a genome-wide linkage scan for quantitative trait loci influencing total HDL-cholesterol (HDL-C) concentration in a sample of 1027 whites from 101 families participating in the NHLBI Family Heart Study. To maximize the relative contribution of genetic components of variance to the total variance of HDL-C, the HDL-C phenotype was adjusted for age, age2, body mass index, and Family Heart Study field center, and standardized HDL-C residuals were created separately for men and women. All analyses were completed by the variance components method, as implemented in the program GENEHUNTER using 383 anonymous markers typed at the NHLBI Mammalian Genotyping Service in Marshfield, Wis. Evidence for linkage of residual HDL-C was detected near marker D5S1470 at location 39.9 cM from the p-terminal of chromosome 5 (LOD=3.64). Suggestive linkage was detected near marker D13S1493 at location 27.5 cM on chromosome 13 (LOD=2.36). We conclude that at least 1 genomic region is likely to harbor a gene that influences interindividual variation in HDL cholesterol.
Human papillomavirus and prognoses of patients with cancers of the upper aerodigestive tract

Some studies have shown that human papillomavirus (HPV) infection may play not only an etiologic role in anogenital cancers but also a role in the clinical outcome. The objective of the current study was to determine whether detection of HPV DNA in primary squamous cell carcinomas of the upper aerodigestive tract (UADT) is a prognostic factor in patients with the disease.
Inducible nitric oxide synthase gene expression in vascular cells after transient focal cerebral ischemia.

BACKGROUND AND PURPOSE We investigated whether inducible nitric oxide synthase (iNOS) is expressed after transient cerebral ischemia and, if so, we sought to define the temporal profile and cellular localization of the expression and the role of iNOS in the mechanism of ischemic brain injury. METHODS The middle cerebral artery in rats was occluded for 2 hours by an intraluminal filament. The occurrence of transient ischemia and reperfusion was confirmed by laser-Doppler flowmetry (n = 5). iNOS message in the ischemic neocortex was determined by reverse-transcription polymerase chain reaction. iNOS enzymatic activity was assessed by citrulline assay. The cellular localization of iNOS expression was determined by immunohistochemistry. RESULTS iNOS mRNA was maximally expressed in postischemic brain at 12 hours and was not present at 4 days (n = 3 per time point). iNOS mRNA was not observed in the contralateral cerebral cortex. iNOS enzymatic activity developed in the postischemic brain between 12 and 24 hours (P < .05) and subsided at 4 days (n = 4 to 8 per time point). iNOS immunoreactivity in the ischemic region was restricted to the wall of capillaries and of larger blood vessels at 12 to 24 hours. In regions of early necrosis, inflammatory cells were iNOS positive. Treatment with the iNOS inhibitor aminoguanidine (n = 5; 100 mg/kg IP, BID for 4 days), starting 6 hours after ischemia, reduced infarct size in neocortex by 36 +/- 7% in comparison with vehicle-treated controls (n = 5) (P < .05). CONCLUSIONS Transient focal ischemia leads to iNOS expression in postischemic brain. However, the spatial and temporal patterns of expression differ from those occurring in permanent ischemia: iNOS is induced earlier and predominantly in vascular cells rather than in neutrophils. Thus, the temporal profile and localization of postischemic iNOS expression depend on the nature of the ischemic insult. The finding that aminoguanidine reduces infarct size adds further support to the hypothesis that postischemic iNOS expression contributes to ischemic brain damage.
INTERFACIAL STRESS TRANSFER IN CARBON NANOTUBE SYSTEMS

ABSTRACT: Stress transfer is of paramount importance in composite materials, since load must be transferred from the matrix to the reinforcement element as efficiently as possible in order to fully realize the potential of the latter. In addition, the benefits obtained from a given reinforcement are conventionally measured in terms of its volume fraction, so efficient usage of the occupied volume places another requirement on a successful reinforcement. Understanding load transfer is key in Multiwalled carbon nanotubes, for which it is known that the intershell interactions are orders of magnitude weaker than those along the principal axis. Traditionally stress transfer in composites has been analyzed through shear lag load models, which prescribe an interfacial shear stress as a function of the local deformation. The present work assumes the validity of continuum mechanics at the scales of interest and introduces a different concept called shear transfer efficiency that quantifies the ability of a given interface to withstand the shear stress necessary to transfer load. The two approaches are demonstrated to be equal for a two-shell structure and for larger structures the much simpler shear transfer model is able to reproduce numerical solutions of the shear lag model, with reasonable accuracy. The length dependence of the effective elastic properties typical of shear lag models is not present in the corresponding shear transfer model. The models developed based on the shear transfer efficiency are capable of capturing the experimentally observed decrease in stiffness as the size of the carbon nanotube structure is increased, under a variety of deformation modes. Interestingly, experiments performed independently by two research groups are brought into agreement without adjustment of parameters.
Conventional vs endobronchial ultrasound-guided transbronchial needle aspiration: a randomized trial.

STUDY OBJECTIVE Our group performed a randomized trial to assess whether the addition of endobronchial ultrasound (EBUS) guidance will lead to better results than standard transbronchial needle aspiration (TBNS). EBUS guidance seems to be beneficial in increasing the yield of TBNA but has not been proven to be superior to conventional procedures in a randomized trial. METHODS Consecutive patients who were referred for TBNA were randomized to an EBUS-guided and a conventional TBNA arm. Patients with subcarinal lymph nodes were randomized and analyzed separately (group A) from all other stations (group B). A positive result was defined as either lymphocytes or a specific abnormality on cytology. RESULTS Two hundred patients were examined (100 patients each in groups A and B). Half of the patients underwent EBUS-guided TBNA rather than conventional TBNA. In group A, the yield of conventional TBNA was 74% compared to 86% in the EBUS group (difference not significant). In group B, the overall yields were 58% and 84%, respectively. This difference was statistically highly significant (p < 0.001). The average number of passes was four. CONCLUSION EBUS guidance significantly increases the yield of TBNA in all stations except in the subcarinal region. It should be considered to be a routine adjunct to TBNA. On-site cytology may be unnecessary, and the number of necessary needle passes required is low.