Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Methylation Profiles for Multiple Tumor Suppressor Gene Promoters in Salivary Gland Tumors

Background Methylation profiling of tumor suppressor gene (TSGs) promoters is quickly becoming a powerful diagnostic tool for the early detection, prognosis, and even prediction of clinical response to treatment. Few studies address this in salivary gland tumors (SGTs); hence the promoter methylation profile of various TSGs was quantitatively assessed in primary SGT tissue to determine if tumor-specific alterations could be detected. Methodology DNA isolated from 78 tumor and 17 normal parotid gland specimens was assayed for promoter methylation status of 19 TSGs by fluorescence-based, quantitative methylation-specific PCR (qMSP). The data were utilized in a binary fashion as well as quantitatively (using a methylation quotient) allowing for better profiling and interpretation of results. Principal Findings The average number of methylation events across the studied genes was highest in salivary duct carcinoma (SDC), with a methylation value of 9.6, compared to the normal 4.5 (p<0.0003). There was a variable frequency and individual methylation quotient detected, depending on the TSG and the tumor type. When comparing normal, benign, and malignant SGTs, there was a statistically significant trend for increasing methylation in APC, Mint 1, PGP9.5, RAR-β, and Timp3. Conclusions/Significance Screening promoter methylation profiles in SGTs showed considerable heterogeneity. The methylation status of certain markers was surprisingly high in even normal salivary tissue, confirming the need for such controls. Several TSGs were found to be associated with malignant SGTs, especially SDC. Further study is needed to evaluate the potential use of these associations in the detection, prognosis, and therapeutic outcome of these rare tumors.
State of the Art in Silico Tools for the Study of Signaling Pathways in Cancer

In the last several years, researchers have exhibited an intense interest in the evolutionarily conserved signaling pathways that have crucial roles during embryonic development. Interestingly, the malfunctioning of these signaling pathways leads to several human diseases, including cancer. The chemical and biophysical events that occur during cellular signaling, as well as the number of interactions within a signaling pathway, make these systems complex to study. In silico resources are tools used to aid the understanding of cellular signaling pathways. Systems approaches have provided a deeper knowledge of diverse biochemical processes, including individual metabolic pathways, signaling networks and genome-scale metabolic networks. In the future, these tools will be enormously valuable, if they continue to be developed in parallel with growing biological knowledge. In this study, an overview of the bioinformatics resources that are currently available for the analysis of biological networks is provided.
Unsupervisec cross-validation adaptation algorithms for improved adaptation performance

An unsupervised cross-validation adaptation algorithm and its variation are proposed that introduce the idea of cross-validation in the unsupervised batch-mode adaptation framework to improve the adaptation performance. The first algorithm is constructed on a general adaptation technique such as MLLR and can be used in combination with any adaptation method. The second algorithm is a modified version of the first algorithm and works with lower computational cost by assuming MLLR. These algorithms are extensions of our previously proposed CV training methods and are useful to suppress the negative effect of the conventional unsupervised batch-mode adaptation process that reinforces the errors included in automatic transcriptions. The proposed algorithms were evaluated in domain adaptation, speaker adaptation, and in their combination for large vocabulary spontaneous speech recognition. When the domain and speaker adaptations were combined using a read speech initial model, the relative word error rate reduction by the proposed method was 29% whereas the reduction by the conventional approach was 23%.
Modeling, Analysis and Rapid Manufacturing of Customised Tibia Bone Scaffold

Bio Additive Manufacturing (BAM), an interdisciplinary field of Rapid Manufacturing (RM) and Tissue Engineering (TE), aims to manufacture the customised bone scaffold for bone replacement. The hydrodynamic stress induced in cells will depend not only on the culture medium flow rate, but also on the scaffold three- dimensional micro-architecture. This paper presents, the patient’s CT scan data in DICOM format is exported into MIMICS software to convert the 2D images into 3D IGES data. The customised bone scaffolds with pore size of 0.7mm and distance between adjacent edges of pores from 0.6mm to 1mm are created in modeling software (SOLIDWORKS 2011) and porosities of five customised bone scaffolds are determined. The above customised bone scaffolds are analysed in CFD software (ANSYS CFX) for the fluid density 1000 kg/m3 and viscosity 8.2 ×10-4 kgm-1 s-1. The estimated Wall Shear Stress (WSS) at fluid velocities from 0.2mm/s to 1mm/s lies in the range of 7.05 x 10 -4 Pa to 43.4 x 10 -4 Pa. , and these scaffolds are fabricated in Rapid Prototyping (RP) technique.
Estimation of Carbon Abundances in Metal-Poor Stars. I. Application to the Strong G-Band Stars of Beers, Preston, and Shectman

We develop and test a method for the estimation of metallicities ([Fe/H]) and carbon abundance ratios ([C/Fe]) for carbon-enhanced metal-poor (CEMP) stars based on the application of artificial neural networks, regressions, and synthesis models to medium-resolution (1–2 Å) spectra and J - K colors. We calibrate this method by comparison with metallicities and carbon abundance determinations for 118 stars with available high-resolution analyses reported in the recent literature. The neural network and regression approaches make use of a previously defined set of line-strength indices quantifying the strength of the Ca II K line and the CH G band, in conjunction with J - K colors from the Two Micron All Sky Survey Point Source Catalog. The use of near-IR colors, as opposed to broadband B - V colors, is required because of the potentially large affect of strong molecular carbon bands on bluer color indices. We also explore the practicality of obtaining estimates of carbon abundances for metal-poor stars from the spectral information alone, i.e., without the additional information provided by photometry, as many future samples of CEMP stars may lack such data. We find that although photometric information is required for the estimation of [Fe/H], it provides little improvement in our derived estimates of [C/Fe], and hence, estimates of carbon-to-iron ratios based solely on line indices appear sufficiently accurate for most purposes. Although we find that the spectral synthesis approach yields the most accurate estimates of [C/Fe], in particular for the stars with the strongest molecular bands, it is only marginally better than is obtained from the line index approaches. Using these methods we are able to reproduce the previously measured [Fe/H] and [C/Fe] determinations with an accuracy of ≈0.25 dex for stars in the metallicity interval -5.5 ≤ [Fe/H] ≤ -1.0 and with 0.2 ≤ (J - K)0 ≤ 0.8. At higher metallicity, the Ca II K line begins to saturate, especially for the cool stars in our program, and hence, this approach is not useful in some cases. As a first application, we estimate the abundances of [Fe/H] and [C/Fe] for the 56 stars identified as possibly carbon-rich, relative to stars of similar metal abundance, in the sample of "strong G-band" stars discussed by Beers, Preston, and Shectman.
Tranformation of cost-based hypothetical reasoning into two continuous optimization problems and a reasoning method with their collaboration

Cost-based Hypothetical Reasoning is an important framework for knowledge-based systems; however it is a form of non-monotonic reasoning and thus an NP-hard problem. To find a near-optimal solution in polynomial time with respect to problem size, some algorithms have been developed so far using optimization techniques. In this paper, we show two major ways of transforming propositional clauses in the hypothetical reasoning problems into constraints. One transforms the clauses into linear inequalities and is good at getting a low-cost solution, while the other transforms them into non-linear equalities and is good at finding a feasible solution. We them show a method of integrating these two transformations by using augmented Lagrangian method. Here, each variable and constraint is regarded as a processor and the searh is realized by their interaction. Two kinds of processors are derived from the two transformations; the structure of these processors are changed dynamically during the search. The cooperation of these two processors allows to obtain better near-optimal solutions than by our previous SL method. This effect is shown in the experiments using two problems with different problem structures.
Cardiac Autonomic Profile of Soccer, Field Hockey and Basketball Players: A Comparative Study

Background: Heart rate recovery (HRR) and heart rate variability (HRV) provide information about cardiac autonomic control; which indicates the physical fitness level of athletes in different sports. Objectives: The purpose of our study was to compare HRR and HRV profiles in collegiate male soccer, field hockey and basketball athletes, at rest and following activity. Methods: Fifty-five male collegiate athletes (20 soccer, 18 field hockey and 17 basketball players) were recruited on the basis of inclusion criteria and exclusion criteria. HRR was obtained following a bout of sub-maximal exercise on a treadmill. Measures of HRV were assessed at rest and during the last 5 minutes of a 15-min recovery period post-exercise. Results: Soccer players showed the highest and basketball players recorded the lowest resting root mean square of successive differences (RMSSD). The value of RMSSD for basketball group was significantly lower than both soccer (P < 0.001) and field hockey (P = 0.015). At rest, normalized low frequency (LFnu) and low frequency-high frequency ratio were higher for the basketball group (P < 0.05). Basketball players showed significantly faster heart rate recovery than soccer (P= 0.017) and field hockey players (P < 0.001). The post-exercise LFnu value was higher in basketball players when compared with soccer players (P = 0.02) as well as field hockey players (P = 0.001). Conclusions: The results of the present study suggest that basketball players exhibit greater sympathetic outflow, at rest and following activity. The autonomic profiles of soccer and field hockey players were found to be comparable.
Postsynaptic Protein Kinase A Reduces Neuronal Excitability in Response to Increased Synaptic Excitation in the Drosophila CNS

Previous work has identified a role for synaptic activity in the development of excitable properties of motoneurons in the Drosophila embryo. In this study the underlying mechanism that enables two such neurons, termed aCC and RP2, to respond to increased exposure to synaptic excitation is characterized. Synaptic excitation is increased in genetic backgrounds that lack either a cAMP-specific phosphodiesterase (EC:3.1.4, dunce) or acetylcholinesterase (EC:3.1.1.7, ace), the enzyme that terminates the endogenous cholinergic excitation of these motoneurons. Analysis of membrane excitability in aCC/RP2, in either background, shows that these neurons have a significantly reduced capability to fire action potentials (APs) in response to injection of depolarizing current. Analysis of underlying voltage-gated currents show that this effect is associated with a marked reduction in magnitude of the voltage-dependent inward Na+ current (INa). Partially blocking INa in these motoneurons, using low concentrations of TTX, demonstrates that a reduction of INa is, by itself, sufficient to reduce membrane excitability. An analysis of firing implicates an increased AP threshold to underlie the reduction in membrane excitability observed because of heightened exposure to synaptic excitation. Genetic or pharmacological manipulations that either elevate cAMP or increase protein kinase A (PKA) activity in wild-type aCC/RP2 mimic both the reductions in membrane excitability and INa. In comparison, increasing cAMP catabolism or inhibition of PKA activity is sufficient to block the induction of these activity-dependent changes. The induced changes in excitability can be rapid, occurring within 5 min of exposure to a membrane-permeable cAMP analog, indicative that threshold can be regulated in these neurons by a post-translational mechanism that is dependent on phosphorylation.
Geometric deformation-displacement maps

Texture mapping, bump mapping, and displacement maps are central instruments in computer graphics aiming to achieve photo-realistic renderings. In all these techniques, the mapping is typically one-to-one and a single surface location is assigned a single texture color, normal, or displacement. Other specialized techniques have also been developed for the rendering of supplementary surface details such as fur hair, or scales. This work presents an extended view of these procedures and allows one to precisely assign a single surface location with few continuously deformed displacements, each with possibly different texture color or normal, employing trivariate functions in a similar way to freeform deformations. As a consequence, an arbitrary regular geometry could be employed as part of the presented scheme as supplementary surface texture details. This work also augments recent results on texturing and parameterization of surfaces of arbitrary topologies by providing more flexible control over the phase of texture modeling. By completely and continuously parameterizing the space above the surface of the object as a trivariate vector function, we are able, in this work, to not only control the mapping of the texture on the surface but also to control this mapping in the volume surrounding the surface.
Isoforms of the invariant chain regulate transport of MHC class II molecules to antigen processing compartments

Newly synthesized class II molecules of the major histocompatibility complex must be transported to endosomal compartments where antigens are processed for presentation to class II-restricted T cells. The invariant chain (Ii), which assembles with newly synthesized class II alpha- and beta-chains in the endoplasmic reticulum, carries one or more targeting signals for transport to endosomal compartments where Ii dissociates from alpha beta Ii complexes. Here we show that the transport route of alpha beta Ii complexes is regulated selectively by two forms of Ii (p33 and p35) that are generated by the use of alternative translation initiation sites. Using a novel quantitative surface arrival assay based on labeling with [6-3H]-D-galactose combined with biochemical modification at the cell surface with neuraminidase, we demonstrate that newly synthesized alpha beta Ii molecules containing the Ii-p33 isoform can be detected on the cell surface shortly after passage through the Golgi apparatus/trans-Golgi network. A substantial amount of these alpha beta Ii complexes are targeted to early endosomes either directly from the trans-Golgi network or after internalization from the cell surface before their delivery to antigen processing compartments. The fraction of alpha beta Ii complexes containing the p35 isoform of Ii with a longer cytosolic domain was not detected at the cell surface as determined by iodination of intact cells and the lack of susceptibility to neuraminidase trimming on ice. However, treatment with neuraminidase at 37 degrees C did reveal that some of the alpha beta Ii-p35 complexes traversed early endosomes. These results demonstrate that a fraction of newly synthesized class II molecules arrive at the cell surface as alpha beta Ii complexes before delivery to antigen processing compartments and that class II alpha beta Ii complexes associated with the two isoforms of Ii are sorted to these compartments by different transport routes.
Comments on M-theory on G_2 manifolds and (p,q) webs

Using a reformulation of the method of (p, q) webs, we study the four-dimensional N = 1 quiver theories from M-theory on seven-dimensional manifolds with G2 holonomy. We first construct such manifolds as U(1) quotients of eight-dimensional toric hyper-Kähler manifolds, using N = 4 supersymmetric sigma models. We show that these geometries, in general, are given by real cones on S bundles over complex twodimensional toric varieties, V = Cr+2/C∗. Then we discuss the connection between the physics content of M-theory on such G2 manifolds and the method of (p, q) webs. Motivated by a result of Acharya and Witten [hep-th/0109152], we reformulate the method of (p, q) webs and reconsider the derivation of the gauge theories using toric geometry Mori vectors of V and brane charge constraints. For WP2w1,w2,w3, we find that the gauge group is given by G = U(w1n) × U(w2n) × U(w3n). This is required by the anomaly cancellation condition.
Spectrum of Neuropathophysiology in Spinal Muscular Atrophy Type I

Abstract Neuropathologic findings within the central and peripheral nervous systems in patients with spinal muscular atrophy type I (SMA-I) were examined in relation to genetic, clinical, and electrophysiologic features. Five infants representing the full clinical spectrum of SMA-I were examined clinically for compound motor action potential amplitude and SMN2 gene copy number; morphologic analyses of postmortem central nervous system, neuromuscular junction, and muscle tissue samples were performed and SMN protein was assessed in muscle samples. The 2 clinically most severely affected patients had a single copy of the SMN2 gene; in addition to anterior horn cells, dorsal root ganglia, and thalamus, neuronal degeneration in them was widespread in the cerebral cortex, basal ganglia, pigmented nuclei, brainstem, and cerebellum. Two typical SMA-I patients and a milder case each had 2 copies of the SMN2 gene and more restricted neuropathologic abnormalities. Maturation of acetylcholine receptor subunits was delayed and the neuromuscular junctions were abnormally formed in the SMA-I patients. Thus, the neuropathologic findings in human SMA-I are similar to many findings in animal models; factors other than SMN2 copy number modify disease severity. We present a pathophysiologic model for SMA-I as a protein deficiency disease affecting a neuronal network with variable clinical thresholds. Because new treatment strategies improve survival of infants with SMA-I, a better understanding of these factors will guide future treatments.
Winner-Take-All EM Clustering

A printed circuit board with a microstrip radio frequency delay line deposited thereon. In addition, a plurality of delay line segments are deposited on the board in close proximity to one end of the delay line. To achieve an overall desired delay length, one of the delay line segments is selected and serially inserted in circuit with the delay line by populating a surface mount circuit element between terminals at the ends of the delay line and the selected delay line segment.
Spatial Resolution of Single-Cell Exocytosis by Microwell-Based Individually Addressable Thin Film Ultramicroelectrode Arrays

We report the fabrication and characterization of microwell-based individually addressable microelectrode arrays (MEAs) and their application to spatially and temporally resolved detection of neurotransmitter release across a single pheochromocytoma (PC12) cell. The microwell-based MEAs consist of 16 4-μm-width square ultramicroelectrodes, 25 3-μm-width square ultramicroelectrodes, or 36 2-μm-width square ultramicroelectrodes, all inside a 40 × 40 μm square SU-8 microwell. MEAs were fabricated on glass substrates by photolithography, thin film deposition, and reactive ion etching. The ultramicroelectrodes in each MEA are tightly defined in a 30 × 30 μm square area, which is further encased inside the SU-8 microwell. With this method, we demonstrate that these microelectrodes are stable, reproducible, and demonstrate good electrochemical properties using cyclic voltammetry. Effective targeting and culture of a single cell is achieved by combining cell-sized microwell trapping and cell-picking micropipet techniques. The surface of the microelectrodes in the MEA was coated with collagen IV to promote cell adhesion and further single-cell culture, as good adhesion between the cell membrane and the electrode surface is critical for the quality of the measurements. Imaging the spatial distribution of exocytosis at the surface of a single PC12 cell has also been demonstrated with this system. Exocytotic signals have been successfully recorded from eight independent 2-μm-wide ultramicroelectrodes from a single PC12 cell showing that the subcellular heterogeneity in single-cell exocytosis can be precisely analyzed with these microwell-based MEAs.
Timed Automata Semantics for Visual e-Contracts

C-O Diagrams have been introduced as a means to have a more visual representation of electroniccontracts, where it is possible to represent the obligations, permissions and prohibitions of the dif-ferent signatories, as well as what are the penalties in case of not fulﬁllment of their obligations andprohibitions. In such diagrams we are also able to represent absolute and relative timing constraints.In this paper we present a formal semantics for C-O Diagrams based on timed automata extendedwith an ordering of states and edges in order to represent different deontic modalities.
Towards distributed objects for real-time systems

This paper illustrates that several of the new features specified in the revised Ada standard facilitate programming real-time distributed/parallel applications. In particular, the Ada Distributed Systems Annex supports both statically bound and the more object-oriented dynamically bound remote procedure calls. These features are used to implement a paradigm for composing asynchronous remote procedure calls when both input and output parameters are required. The paradigm is based upon the notion of a distributed object through which the output parameters may be returned without blocking the execution of the caller. Such paradigms, when combined with the enhanced features for concurrency and data synchronization, suggest that Ada will contribute towards understanding some of the issues relevant to developing efficient implementations of distributed objects to support the next generation of real time systems. <<ETX>>
A longitudinal study of upper secondary school students’ values and beliefs regarding policy responses to climate change

Abstract This article explores changes of environmental values and beliefs among secondary school business and economics students regarding government and market solutions to climate change. The quantitative study is longitudinal and a survey was administrated to students at two occasions including 212 participants in the first measurement. Results show a small significant increase in importance for altruistic, biospheric and egoistic value orientations at average. At an individual level, there are substantial movements over time. Nearly two-thirds of the students changed the strength of their value orientations over time. Taxes and legislation were regarded as the most effective solutions to climate change, however there was a decrease in seeing market prices as important mechanisms for change. Analysis suggested no direct relationship between change in environmental value orientation and change in norms. However indirect associations were mediated by changing beliefs in the efficacy of education and information and the efficacy of tax policies. For example, students who became more egoistic and more convinced about the efficacy of tax were less likely than others to be willing to take personal actions.