Miracle-dz/UniFAR-FTUs huggingface dataset:
Process optimization of silicon-on-sapphire vapor-phase epitaxy

Thin (300–600 nm) heteroepitaxial silicon layers were deposited on R-plane sapphire wafers via hydride-chloride CVD technique using SiH<inf>4</inf> and SiCl<inf>4</inf> gas-vapor mixture with PH<inf>3</inf> doping gas diluted by H<inf>2</inf>. Obtained layers were studied with AFM, XRD, SEM, UV scattering and surface PV methods. Influence of SiH<inf>4</inf>:SiCl<inf>4</inf> volume ratio on process and layer parameters was investigated. It was found that the growth rate of Si layer was increased when the volume concentration of SiCl<inf>4</inf> increased (at 900–1000 °C). Therewith the separate increase of SiH<inf>4</inf> and SiCl<inf>4</inf> volume ratio in gas-vapor mixture leads to a change of surface microrelief and Si-sapphire interface parameters. It was determined that the RMS (Rq) roughness of Si surface and microrelief height were decreased when the SiH<inf>4</inf>:SiCl<inf>4</inf> volume ratio in gas-vapor mixture changed from 8:1 to 4:1. XRD and SEM analysis of layers confirmed the improvement of the structure with increasing SiCl<inf>4</inf> volume concentration.
Extrinsic parameter self-calibration and nonlinear filtering for in-vehicle stereo vision systems at urban environments

Present work analyses the continuous self-calibration of extrinsic parameters of a stereo vision system for safe visual odometry applications in vehicles at urban environments. The calibration method determines the extrinsic parameters of a stereo vision system based on knowing the geometry of the ground in front of the cameras. The slight changes of the road profile cause variations in the extrinsic parameters of stereo rig that are necessary to filter and maintain between tolerance values. Then, height, pitch and roll parameters are filtered, to eliminate pose outliers of the stereo rig that appear when a vehicle is maneuvering. The reliable approach at urban environment is firstly composed of the calculation of the road profile slope, the theoretical horizon, and the slope of the straight line in the free map. Secondly, the nonlinear filtering is applied using Unscented Kalman Filter to improve the estimation of height, pitch and roll parameters.
A Combined Methodology to Eliminate Artifacts in Multichannel Electrogastrogram Based on Independent Component Analysis and Ensemble Empirical Mode Decomposition

Cutaneous measurements of electrogastrogram (EGG) signals are heavily contaminated by artifacts due to cardiac activity, breathing, motion artifacts, and electrode drifts whose effective elimination remains an open problem. A common methodology is proposed by combining independent component analysis (ICA) and ensemble empirical mode decomposition (EEMD) to denoise gastric slow-wave signals in multichannel EGG data. Sixteen electrodes are fixed over the upper abdomen to measure the EGG signals under three gastric conditions, namely, preprandial, postprandial immediately, and postprandial 2 h after food for three healthy subjects and a subject with a gastric disorder. Instantaneous frequencies of intrinsic mode functions that are obtained by applying the EEMD technique are analyzed to individually identify and remove each of the artifacts. A critical investigation on the proposed ICA-EEMD method reveals its ability to provide a higher attenuation of artifacts and lower distortion than those obtained by the ICA-EMD method and conventional techniques, like bandpass and adaptive filtering. Characteristic changes in the slow-wave frequencies across the three gastric conditions could be determined from the denoised signals for all the cases. The results therefore encourage the use of the EEMD-based technique for denoising gastric signals to be used in clinical practice.
An interactive English pronunciation dictionary for Korean learners

We present research towards developing a pronunciation dictionary that features sensitivity to learners’ native phonology, specifically designed for Korean learners of English-as-a-Foreign-Language (EFL). We envision a future system that can record and process learners’ imitationof thedictionary pronunciation and instantly provide segmental and prosodic feedback on accent. Towards this goal, we have designed and collected a speech corpus to address the phonological and prosodic issues of Korean EFL learners. We leverage the SUMMIT speech recognizer’s ability to model phonological rules to automatically identify non-native phonological phenomena. These phonological rules were carefully constructed to account for the influence of learners’ native language (Korean) on the target language (English). Feedback messages are provided to the learner to point out the non-native phonological variations detected by the speech recognizer in order to help them improve segmental pronunciation. Instructions are also given to the user on the prosodic aspects of the pronunciation, which are based on detected duration and cues. We evaluated the effectiveness of the feedback mechanism by rating 222 English utterances from six native Korean subjects, before and after receiving native-language dependent feedback messages. Human raters judged 61% of the utterances as improved after feedback.
Classical double inverted pendulum — A complex overview of a system

The purpose of this article is to perform an in-depth analysis of the classical double inverted pendulum system using the Inverted Pendula Modeling and Control (IPMaC), a Simulink block library designed by the authors of the paper. The custom function blocks included in the IPMaC offer comprehensive program support for the modeling, simulation and control of classical and rotary inverted pendula systems. The library also incorporates software tools which provide a user-friendly graphical interface (GUI) to modeling and linearization procedures. With the aid of appropriate function blocks, GUI tools and demonstration schemes from the IPMaC, the classical double inverted pendulum system is analyzed, modeled and successfully stabilized in the unstable inverted position.
Intra-operative prostate motion tracking using surface markers for robot-assisted laparoscopic radical prostatectomy

Radical prostatectomy surgery (RP) is the gold standard for treatment of localized prostate cancer (PCa). Recently, emergence of minimally invasive techniques such as Laparoscopic Radical Prostatectomy (LRP) and Robot-Assisted Laparoscopic Radical Prostatectomy (RARP) has improved the outcomes for prostatectomy. However, it remains difficult for the surgeons to make informed decisions regarding resection margins and nerve sparing since the location of the tumor within the organ is not usually visible in a laparoscopic view. While MRI enables visualization of the salient structures and cancer foci, its efficacy in LRP is reduced unless it is fused into a stereoscopic view such that homologous structures overlap. Registration of the MRI image and peri-operative ultrasound image using a tracked probe can potentially be exploited to bring the pre-operative information into alignment with the patient coordinate system during the procedure. While doing so, prostate motion needs to be compensated in real-time to synchronize the stereoscopic view with the pre-operative MRI during the prostatectomy procedure. In this study, a point-based stereoscopic tracking technique is investigated to compensate for rigid prostate motion so that the same motion can be applied to the pre-operative images. This method benefits from stereoscopic tracking of the surface markers implanted over the surface of the prostate phantom. The average target registration error using this approach was 3.25±1.43mm.
Frame Counter: Achieving Accurate and Real-Time Link Estimation in Low Power Wireless Sensor Networks

Link estimation is a fundamental component of forwarding protocols in wireless sensor networks. In low power forwarding, however, the asynchronous nature of widely adopted duty-cycled radio control brings new challenges to achieve accurate and real- time estimation. First, the repeatedly transmitted frames (called wake-up frame) increase the complexity of accurate statistic, especially with bursty channel contention and coexistent interference. Second, frequent update of every link status exhausts the limited energy supply due to long duration of beacon broadcast. In this paper, we propose meter (Distributed Frame Counter), which takes the opportunities of link overhearing to update link status in real time. Furthermore, meter does not only depend on counting the successfully decoded wake-up frames, but also counts the corrupted ones by exploiting the feasibility of ZigBee identification based on short-term sequence of the received signal strength. We implement meter in TinyOS and further evaluate the performance through extensive experiments on indoor and outdoor testbeds. The results demonstrate that meter can significantly improve the performance of the state-of-the-art link estimation schemes.
Nonlinear ray tracing for vessel enhanced visualization

3D visualization of angiography data is an important preprocessing step in diagnosis of vascular disease. This paper describes an efficient volume rendering method to emphasize feature-rich region (or focus) in the 3D angiography data. The method takes the input 3D angiography data and computes the focus with user specification or certain feature extraction algorithms. Then, a distance map is constructed based on the description of the focused region(s). While rendering the 3D angiography data, the nonlinear ray tracing method is used and the gradient of the distance volume is applied to guide ray marching. In the result image, the focused region(s) appears larger than in the normal ray-casting image, while the context (other regions of the volume) can be still preserved in the image (maybe displayed in a shrink size). This method avoids deforming the original volume to magnify focus regions, which is expensive to compute, thus improves the performance.
An integrated approach identifies new oncotargets in melanoma

Melanoma is an aggressive skin cancer; an early detection of the primary tumor may improve its prognosis. Despite many genes have been shown to be involved in melanoma, the full framework of melanoma transformation has not been completely explored. The characterization of pathways involved in tumor restraint in in vitro models may help to identify oncotarget genes. We therefore aimed to probe novel oncotargets through an integrated approach involving proteomic, gene expression and bioinformatic analysis We investigated molecular modulations in melanoma cells treated with ascorbic acid, which is known to inhibit cancer growth at high concentrations. For this purpose a proteomic approach was applied. A deeper insight into ascorbic acid anticancer activity was achieved; the discovery of deregulated processes suggested further biomarkers. In addition, we evaluated the expression of identified genes as well as the migration ability in several melanoma cell lines. Data obtained by a multidisciplinary approach demonstrated the involvement of Enolase 1 (ENO1), Parkinsonism-associated deglycase (PARK7), Prostaglansin E synthase 3 (PTGES3), Nucleophosmin (NPM1), Stathmin 1 (STMN1) genes in cell transformation and identified Single stranded DNA binding protein 1 (SSBP1) as a possible onco-suppressor in melanoma cancer.
Glioblastoma multiforme: State of the art and future therapeutics

Background: Glioblastoma multiforme (GBM) is the most common and lethal primary malignancy of the central nervous system (CNS). Despite the proven benefit of surgical resection and aggressive treatment with chemo- and radiotherapy, the prognosis remains very poor. Recent advances of our understanding of the biology and pathophysiology of GBM have allowed the development of a wide array of novel therapeutic approaches, which have been developed. These novel approaches include molecularly targeted therapies, immunotherapies, and gene therapy. Methods: We offer a brief review of the current standard of care, and a survey of novel therapeutic approaches for treatment of GBM. Results: Despite promising results in preclinical trials, many of these therapies have demonstrated limited therapeutic efficacy in human clinical trials. Thus, although survival of patients with GBM continues to slowly improve, treatment of GBM remains extremely challenging. Conclusion: Continued research and development of targeted therapies, based on a detailed understanding of molecular pathogenesis can reasonably be expected to yield improved outcomes for patients with GBM.
Existential neuroscience: a proximate explanation of religion as flexible meaning and palliative

The cognitive science of religion has made great strides in the past decade (e.g., Boyer, 2008), with more and better research from many disciplines asking basic questions about why religions exist, persist, thrive, and heal. The journal that is publishing these very words, Religion, Brain & Behavior, is testament to the accelerating nature of this interdisciplinary movement, as is the breadth and quality of the commentaries that our target article generated. We are grateful that these commentaries have forced us not only to think deeply about the ideas contained therein, but also to elaborate upon our own model. Rather than addressing each reply in turn, we built our response around the major themes that emerged. Overall, there was consensus satisfaction with our basic neuroscience findings linking religious belief with brain-based error-related distress. There was less satisfaction, however, with the way we broadly interpreted these data. Paying heed to the most frequent questions and ideas put forth by the commentators, we organized our response as follows: we (1) discuss our use of the term ‘‘meaning,’’ (2) contrast the kind of proximate explanations provided by the motivated meaning model with ultimate explanations provided by evolutionary models, (3) provide evidence for why flexible meaning systems like religion may be better palliatives than scrutable meaning systems like science, and (4) suggest that an affective interpretation of anterior cingulate cortex (ACC) activity accounts for more data than a purely cognitive explanation, but also note that both explanations might be functionally isomorphic. We end by mapping out the kinds of future studies that we are now planning and that were inspired by the valuable commentaries.
Generation of Immortalized Equine Chondrocytes With Inducible Sox9 Expression Allows Control of Hypertrophic Differentiation

Immortalization of chondrocytes enables long term in vitro culture; however, the chondrogenic capacity of transformed cells varies, thus highlighting the need to develop a proliferative and tuneable chondrocyte cell line where hypertrophic differentiation can be controlled. In this study the SV40 large T antigen and human telomerase reverse transcriptase were employed to immortalize pooled equine chondrocytes through lentiviral vector mediated transduction either singly or on combination. Transformed chondrocytes proliferated stably over multiple passages, but resulted in significantly lower expression of chondrocyte specific collagen II mRNA (P < 0.0001) and up regulation of the hypertrophic marker collagen X (P < 0.0001) in three dimensional cultures. A Col2a1 promoter driven GFP reporter was constructed for real time monitoring of chondrogenic differentiation and a significant increase in promoter activation was observed in cultures treated with the growth factor TGFβ‐3 (P < 0.05). To recapitulate the native articular chondrocyte phenotype we further transduced large T antigen immortalized chondrocytes with lentiviral vectors allowing either constitutive or doxycycline inducible expression of Sox9. In 3D cultures, the Sox9 over‐expressing chondrocytes secreted significantly higher levels of extracellular matrix polysaccharide glycosaminoglycan (P < 0.05), while up‐regulating collagen II and Aggrecan mRNA (P < 0.05) in both expression systems with a similar patterns observed with imunohistochemical staining. High levels of collagen X mRNA and protein were maintained with constitutive sox9 reflecting hypetrophic differentiation but significantly lower expression could be achieved with inducible Sox9. In conclusion, immortalization of equine chondrocytes results in stable proliferation but a reduction of chondrogenic potential whilst modulation of sox9 expression enabled control of hypertrophic characteristics. J. Cell. Biochem. 118: 1201–1215, 2017. © 2016 Wiley Periodicals, Inc.
Involvement of the Toll-Like Receptor/Nitric Oxide Signaling Pathway in the Pathogenesis of Cervical Cancer Caused by High-Risk Human Papillomavirus Infection

Human papillomavirus (HPV) can activate Toll-like receptor (TLR)/nitric oxide (NO) signaling pathways; however, whether the TLR/NO pathway is involved in cervical cancer caused by high-risk HPV (HR-HPV) remains unclear. In this study, 43 HR-HPV-positive patients with cervical cancer (CC group), 39 HR-HPV-positive patients with a healthy cervix (HR-HPV group), and 33 HR-HPV-negative controls were recruited. NO concentration in cervical canal and expression of inducible NO synthase (iNOS) in cervical tissues were detected. Expressions of key TLR/NO pathway genes (TLR3/4/7/8, NF-κB p65, and iNOS) in cervical epithelial cells were detected by quantitative reverse transcription PCR. Expressions of TLR4, NF-κB p65, and iNOS in CaSki, HeLa, and C33a cells were determined by Western blot. NO concentration in cervical canal of CC group was significantly higher than in other groups (P < 0.05). Positive rates of iNOS in cervical tissues were 72.1%, 28.2%, and 3.1% in the CC group, HR-HPV group, and controls, respectively (P < 0.05). Levels of TLR3, TLR4, TLR7, TLR8, NF-κB p65, and iNOS in cervical epithelial cells were higher in CC group than in other groups (P < 0.05). Both mRNA and protein levels of TLR4, NF-κB p65, and iNOS were higher in HPV-positive HeLa and CaSki cells than in HPV-negative C33a cells (P < 0.05). Together, these results suggest that TLR/NO signaling pathway may be involved in pathogenesis of cervical cancer caused by HR-HPV.
Effect of Microstructure on the Thermal Properties of Sintered Iron-copper Composites

Copper is a well know material for use as heat sink or heat exchanger. However, copper has a considerable low tensile strength and temperature limit. A material that has a good thermal conductivity, low cost, but also resistance is the desired. Effects of copper on the sintering and thermal properties of iron-copper composites produced by powder metallurgy and Fe on copper-iron composites have been investigated. Copper and iron were varied from 20 to 80 vol.% in the samples, alternating the continuous phase. Sintering studies were performed by in-situ dilatometry aiming to define the proper conditions for sintering, without swelling normally associated with copper. Results indicate that the type of sintering, final microstructure, specially the phases relation and distribution and not only the amount of copper, have a great effect into the thermal properties. By controlling the sintering parameters, it is possible to obtain dimensionally stable samples with higher thermal conductivity and lower copper amount.
Shielding Engineered Islets With Mesenchymal Stem Cells Enhance Survival Under Hypoxia

In the present study we focused on the improvisation of islet survival in hypoxia.The Islet like cell aggregates (ICAs) derived from wharton's jelly mesenchymal stem cells (WJ MSC) were cultured with and without WJ MSC for 48 h in hypoxia and normoxia and tested for their direct trophic effect on β cell survival. The WJ MSCs themselves secreted insulin upon glucose challenge and expressed the pancreatic markers at both transcription and translational level (C‐peptide, Insulin, Glucagon, and Glut 2). Direct contact of MSCs with ICAs facilitated highest viability under hypoxia as evidenced by fluorescein diacetate/propidium iodide and 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay. The cytokine analysis of the co‐cultured ICAs revealed amplification of anti‐inflammatory cytokine like TGFβ and TNFα accompanied by depletion of pro‐inflammatory cytokines. The increment in VEGF and PDGFa was also seen showing their ability to vascularize upon transplantation. This was further accompanied by reduction in total reactive oxygen species, nitric oxide, and super oxide ions and down regulation of Caspase3, Caspase8, p53, and up regulation of Bcl2 confirming prevention of apoptosis in ICAs. The western blot analysis confirmed the cytoprotective effect of WJ MSC on ICAs as they enhanced the anti‐apoptotic marker BCL2 and reduced the expression of apoptotic markers, Annexin 5 and Caspase 3. There was a significant reduction in the expression of p38 protein in the presence of MSCs making the ICAs responsive to glucose. Taken together our data demonstrate for the first time that the WJ MSC expressed pancreatic markers and their supplementation protected engineered islets against hypoxia and oxidative stress. J. Cell. Biochem. 118: 2672–2683, 2017. © 2017 Wiley Periodicals, Inc.
Plant Homeo Domain Finger Protein 8 Regulates Mesodermal and Cardiac Differentiation of Embryonic Stem Cells Through Mediating the Histone Demethylation of pmaip1

Histone demethylases have emerged as key regulators of biological processes. The H3K9me2 demethylase plant homeo domain finger protein 8(PHF8), for example, is involved in neuronal differentiation, but its potential function in the differentiation of embryonic stem cells (ESCs) to cardiomyocytes is poorly understood. Here, we explored the role of PHF8 during mesodermal and cardiac lineage commitment of mouse ESCs (mESCs). Using a phf8 knockout (ph8‐/Y) model, we found that deletion of phf8 in ESCs did not affect self‐renewal, proliferation or early ectodermal/endodermal differentiation, but it did promote the mesodermal lineage commitment with the enhanced cardiomyocyte differentiation. The effects were accompanied by a reduction in apoptosis through a caspase 3‐independent pathway during early ESC differentiation, without significant differences between differentiating wide‐type (ph8+/Y) and ph8‐/Y ESCs in cell cycle progression or proliferation. Functionally, PHF8 promoted the loss of a repressive mark H3K9me2 from the transcription start site of a proapoptotic gene pmaip1 and activated its transcription. Furthermore, knockdown of pmaip1 mimicked the phenotype of ph8‐/Y by showing the decreased apoptosis during early differentiation of ESCs and promoted mesodermal and cardiac commitment, while overexpression of pmaip1 or phf8 rescued the phenotype of ph8‐/Y ESCs by increasing the apoptosis and weakening the mesodermal and cardiac differentiation. These results reveal that the histone demethylase PHF8 regulates mesodermal lineage and cell fate decisions in differentiating mESCs through epigenetic control of the gene critical to programmed cell death pathways. Stem Cells 2016;34:1527–1540