Miracle-dz/UniFAR-FTUs huggingface dataset:
Focused Ultrasound Thermal Therapy Monitoring using Ultrasound, Infrared Thermal, and Photoacoustic Imaging Techniques.

Focused ultrasound (FUS) is a promising thermal treatment modality which deposits heat noninvasively in a confined tissue volume to treat localized diseased tissue or malignancy through hyperthermia or high temperature ablation. FUS compatible guiding and monitoring systems to provide real-time information on tissue temperature and/or status (e.g., native or necrotized) are important to ensure safe and effective treatment outcome; however, current development of such systems are restricted to ultrasound and magnetic resonance imaging (MRI). The work described in this dissertation represents efforts not only to explore new tools to evaluate current monitoring techniques but also to develop new FUS monitoring modalities. In the first study, a new evaluation platform for ultrasound thermometry using infrared (IR) thermography was developed and demonstrated using phantoms subjected to FUS heating, providing a fast calibration and validation tool with spatiotemporal temperature information unavailable with traditional thermocouple measurements. In the second study, IR thermography was investigated as a new tool for high temperature FUS ablation monitoring. The spatiotemporal temperature characteristics in correspondence to lesion formation and bubble activities were identified using simultaneous IR and bright-field imaging. Tissue-specific thermal damage threshold, which is critical for accurate estimation of tissue status based on temperature time history, was also obtained using the same system. In the final study, we developed a novel dual-wavelength photoacoustic (PA) sensing technique for monitoring tissue status during thermal treatments, which is capable of separating the two effects from temperature rise and changes in optical properties due to tissue alteration. Experimental validations of the theoretical derivation were carried out on ex-vivo cardiac tissue using water-bath heating on lesions generated by FUS. Future directions of research include in-vivo technique demonstration where effects such as blood perfusion on FUS heating need to be considered. When FUS operates in the non-ablative regime without causing irreversible changes in tissue, treatment monitoring techniques investigated in this study also have the potential to be translated into diagnostic tools.
Formation of the parasporal inclusion of Bacillus thuringiensis.

Under given experimental conditions, a reproducible sequence of biochemical events can be measured during sporulation in Bacillus thuringiensis. Electron microscope studies reveal that, during its formation, the crystalline inclusion of Bacillus thuringiensis is closely associated with the exosporium. This association persists through several serial sections and can also be demonstrated in a mutant strain which is biochemically blocked soon after crystal formation. Two asporogenic crystalliferous strains produce a toxin active on larvae of Plutella maculipennis whereas two sporogenic, acrystalliferous strains are not toxic. Data from immunological assays and from pulse-chase and label-chase experiments with [14C]leucine indicate that the crystal protein is synthesized at the time of appearance of crystal antigens. It is suggested that the crystal is synthesized and assembled on the exosporium.
Einstein’s Photon Concept Quantified by the Bohr Model of the Photon

The photon is modeled as a monochromatic solution of Maxwell’s equations confined as a soliton wave by the principle of causality of special relativity. The soliton travels rectilinearly at the speed of light. The solution can represent any of the known polarization (spin) states of the photon. For circularly polarized states the soliton’s envelope is a circular ellipsoid whose length is the observed wavelength (λ), and whose diameter is λ/π; this envelope contains the electromagnetic energy of the wave (hv = hc/λ). The predicted size and shape is confirmed by experimental measurements: of the sub‐picosecond time delay of the photo‐electric effect, of the attenuation of undiffracted transmission through slits narrower than the soliton’s diameter of λ/π, and by the threshold intensity required for the onset of multiphoton absorption in focussed laser beams. Inside the envelope the wave’s amplitude increases linearly with the radial distance from the axis of propagation, being zero on the axis. Outside the .
pTest: An adaptive testing tool for concurrent software on embedded multicore processors

More and more processor manufacturers have launched embedded multicore processors for consumer electronics products because such processors provide high performance and low power consumption to meet the requirements of mobile computing and multimedia applications. To effectively utilize computing power of multicore processors, software designers interest in using concurrent processing for such architecture. The master-slave model is one of the popular programming models for concurrent processing. Even if it is a simple model, the potential concurrency faults and unreliable slave systems still lead to anomalies of entire system. In this paper, we present an adaptive testing tool called pTest to stress test a slave system and to detect the synchronization anomalies of concurrent software in the master-slave systems on embedded multicore processors. We use a probabilistic finite-state automaton(PFA) to model the test patterns for stress testing and shows how a PFA can be applied to pTest in practice.
Reconstitution of TCP80/NF90 translation inhibition activity in insect cells.

Acid beta-glucosidase (GCase) is the enzyme deficient in Gaucher disease, an inherited metabolic prototype for enzyme and gene therapy. An 80-kDa mammalian cytoplasmic protein (TCP80/NF90) was discovered to interact with the GCase mRNA coding region and inhibit its translation in vitro and ex vivo. Human TCP80/NF90 is identical to NF90, an IL-2 enhancer protein, and MPP4, an M-phase phosphoprotein. The interaction of recombinant TCP80/NF90 with GCase mRNA was evaluated using the baculovirus/Sf9 insect cell system since these cells lack this protein. Purified recombinant and isolated mammalian cytoplasmic TCP80/NF90 had identical functions including binding of coding regions of selected RNAs and inhibition of their in vitro translation. Individual baculoviruses containing the human TCP80/NF90 cDNA (vSf9/TCP80) and GCase cDNA (vSf9/GCase) were used to co-infect Sf9 cells. The presence of preformed TCP80/NF90 significantly (>87%) inhibited wild-type GCase mRNA translation in these cells, but baculovirus containing a mutant GCase did not. Sf9 cells co-infected with vSf9/TCP80 showed a major reduction of GCase RNA polysome association. These results show that the multifunctional protein, TCP80/NF90, can function in vivo as a translation inhibitory protein and include alterations of mRNA binding to polysomes as a component of its mechanism of action.
Simulation of the attachment system with various tip shapes contacting rough surface

In this paper, we investigate the effects of various contact shapes on the adhesion performance for the attachment system contacting rough surfaces. Four different tip shapes of sphere, flat punch, torus and tape are considered. We demonstrate the effect of the tip size and the elastic modulus on the adhesion force through the adhesion analysis for single tips with four different shapes. In order to investigate an effect of tip shape on adhesion performance for the attachment system contacting rough surface with different σ values, single level attachment system was simulated. The attachment system is modeled from the geometrical size of spatulae of Tokay gecko. The effect of tip shape on the adhesion enhancement and how far its effect can be reached for the surface roughness are investigated. It is shown that the effect of tip shape on the adhesion enhancement is limited to the surface roughness with smaller than several micrometers and further adhesion enhancement can not be expected at rougher surfaces.
Role of the Pro23Leu mutation in a family affected by retinitis pigmentosa in the Basque Country

Retinitis pigmentosa (RP) is a degenerative disorder localized in the outer part of the retina that leads mainly to night blindness and loss of peripheral visual field. We screened RP patients for mutations in the rhodopsin gene (1) using polymerase chain reaction (PCR), denaturing gradient gel electrophoresis, restriction analysis and sequencing. One of these patients (II 1) (66 years old) was initially classified as a sporadic case (SCRP) (Fig. 1). He suffered from bad night vision since he was between 5 and 8 years old with slow progression. His brother (II 2) was not ophthalmologically examined, but did not have any RP symptoms, only some optic defects. None of III 1, III 2 and III 3 (in their 20’s or 30’s) showed any RP symptoms, but they all had optic defects; one had also ambliopy. III 2 and III 3 were examined electrophysiologically. Whereas III 3 had a normal electroretinogram, the answer to flashes of blue light in III 2, presented a b-wave amplitude in a subnormal range with values of 14.4 for his right eye and 12.8 for his left eye. The values in III 3 were 105 and 103, respectively. In the cone response to big stimuli under scotopic conditions, the b-wave amplitude was 85 and 70 in III 2 compared to 121 and 135 in III 3. We found a heterozygous C-T transition in the second nucleotide of codon 23 causing a Proline23Leucine (Pro23Leu) mutation in II 1, III 1, III 2 and III 3. Dryja et al. (2) reported this mutation as responsible for one case of autosomal dominant RP (ADRP) but unfortunately without clinical description. In our case, only II 1 had clear signs of RP. Interestingly, b-wave amplitude is the first sign of a rod dysfunction and is used as an indication of early diagnosis even without retinal degeneration or abnormal fundus. We cannot determine at this point to what extent this could mean a rod dysfunction in III 2. A continuous follow-up will be necessary for the next few years to answer this. We could be facing a dominant form of RP with incomplete penetrance and variable expression instead of the SCRP. The lack of symptoms in individuals carrying this Pro23Leu mutation makes us speculate with the presence of some other internal and/or external factors (3) which could also influence in the onset. This patient did not visit an ophthalmologist until he was 36 years old and he was diagnosed with RP at 55 years of age. This seems to represent a late onset and none of his offspring have reached that age yet. In addition, they take precautions such as wearing sunglasses or protecting themselves against the sunlight etc. Cases of ADRP with incomplete penetrance and marked variation in their expressivity have already been reported (4, 5). In conclusion, we think the mutation Pro23Leu found here is related to RP, although a clinical follow-up will be necessary to confirm the role of this mutation in this case.
Efficient Multi-Modal Least-Squares Alignment of Medical Images Using Quasi-Orientation Maps

In image registration, similarity metrics are used to determine the optimal alignment between two images. A common metric used for judging image similarity is the weighted sum of squared differences (SSD) cost function. Recently, it was demonstrated that the evaluation of the SSD cost function can be performed efficiently using the Fast Fourier Transform (FFT) to determine the optimal translation between two images based on pixel intensities. This paper extends this efficient approach by introducing the concept of quasiorientation maps as features into the alignment framework. This feature-based method is invariant to intensity mappings, making it suitable for aligning medical images acquired with different modalities. Experimental results demonstrate overall multi-modal image alignment performance to be superior to that of
LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature

As a novel class of noncoding RNAs, long noncoding RNAs (lncRNAs) have been verified to be associated with various diseases. As large scale transcripts are generated every year, it is significant to accurately and quickly identify lncRNAs from thousands of assembled transcripts. To accurately discover new lncRNAs, we develop a classification tool of random forest (RF) named LncRNApred based on a new hybrid feature. This hybrid feature set includes three new proposed features, which are MaxORF, RMaxORF and SNR. LncRNApred is effective for classifying lncRNAs and protein coding transcripts accurately and quickly. Moreover,our RF model only requests the training using data on human coding and non-coding transcripts. Other species can also be predicted by using LncRNApred. The result shows that our method is more effective compared with the Coding Potential Calculate (CPC). The web server of LncRNApred is available for free at http://mm20132014.wicp. net:57203/LncRNApred/home.jsp.
Long‐term maintenance of hepatocyte functional activity in co‐culture: Requirements for sinusoidal endothelial cells and dexamethasone

Sinusoidal cells isolated from adult rat liver have been established in primary culture and in cell line. The presence of factor VIII R:Ag and peroxidatic/phagocytosis activities were the criteria used to distinguish in freshly isolated cells the endothelial cells from the Kupffer cells and suggested the endothelial origin of the cell line. Using a co‐culture system, the effect of sinusoidal liver cells on hèpatocyte functional activity was characterized. A plateau in which the state of differentiation was stabilized could be generated for co‐cultured hepatocytes isolated from adult rat and a disappearance of the initial expression of α1‐fetoprotein (AFP) and the increase and/or maintenance of albumin secretion were measured with co‐cultured hepatocytes isolated from suckling rat. The presence of dexamethasone was required for such beneficial effect. The hepatocyte‐stabilizing activity was also produced by a pulmonary endothelial cell line.
Src Family Tyrosine Kinase Regulates Intracellular pH in Cardiomyocytes

The Anion Cl−/HCO3 − Exchangers AE1, AE2, and AE3 are membrane pH regulatory ion transporters ubiquitously expressed in vertebrate tissues. Besides relieving intracellular alkaline and CO2 loads, the AEs have an important function during development and cell death and play a central role in such cellular properties as cell shape, metabolism, and contractility. The activity of AE(s) are regulated by neurohormones. However, little is known as to the intracellular signal transduction pathways that underlie this modulation. We show here that, in cardiomyocytes that express both AE1 and AE3, the purinergic agonist, ATP, triggers activation of anion exchange. The AE activation is observed in cells in which AE3 expression was blocked but not in cells microinjected with neutralizing anti-AE1 antibodies. ATP induces tyrosine phosphorylation of AE1, activation of the tyrosine kinase Fyn, and association of both Fyn and FAK with AE1. Inhibition of Src family kinases in vivo by genistein, herbimycin A, or ST638 prevents purinergic activation of AE1. Microinjection of either anti-Cst.1 antibody or recombinant CSK, both of which prevent activation of Src family kinase, significantly decreases ATP-induced activation of AE. Microinjection of an anti-FAK antibody as well as expression in cardiomyocytes of Phe397 FAK dominant negative mutant, also prevents purinergic activation of AE. Therefore, tyrosine kinases play a key role in acute regulation of intracellular pH and thus in cell function including excitation–contraction coupling of the myocardium.
An O ( 1 ) Time Complexity Software Barrier

As network latency rapidly approaches thousands of processor cycles and multiprocessors systems become larger and larger, the primary factor in determining a barrier algorithm’s performance is the number of serialized network latencies it requires. All existing barrier algorithms require at least ✂☎✄✝✆✟✞✡✠☞☛✍✌ round trip message latencies to perform a single barrier operation on an ☛ -node shared memory multiprocessor. In addition, existing barrier algorithms are not well tuned in terms of how they interact with modern shared memory systems, which leads to an excessive number of message exchanges to signal barrier completion. The contributions of this paper are threefold. First, we identify and quantitatively analyze the performance deficiencies of conventional barrier implementations when they are executed on real (non-idealized) hardware. Second, we propose a queue-based barrier algorithm that has effectively ✂✎✄✑✏✒✌ time complexity as measured in round trip message latencies. Third, by exploiting a hardware write-update (PUT) mechanism for signaling, we demonstrate how carefully matching the barrier implementation to the way that modern shared memory systems operate can improve performance dramatically. The resulting optimized algorithm only costs one round trip message latency to perform a barrier operation across ☛ processors. Using a cycle-accurate execution-driven simulator of a future-generation SGI multiprocessor, we show that the proposed queue-based barrier outperforms conventional barrier implementations based on load-linked/storeconditional instructions by a factor of 5.43 (on 4 processors) to 93.96 (on 256 processors).
Specifying label layout style by example

Creating high-quality label layouts in a particular visual style is a time-consuming process. Although automated labeling algorithms can aid the layout process, expert design knowledge is required to tune these algorithms so that they produce layouts which meet the designer's expectations. We propose a system which can learn a labellayout style from a single example layout and then apply this style to new labeling problems. Because designers find it much easier to create example layouts than tune algorithmic parameters, our system provides a more natural workflow for graphic designers. We demonstrate that our system is capable of learning a variety of label layout styles from examples.
Extracting Social Networks to Understand Interaction

Web forums are a huge data source. They allow people to interact with unknown individuals. Studying forums shows that the interaction is not obvious only through the structure but also through the content of the post. Taking into account this observation, we extract a social network with different kinds of relationships i.e. the structural relation, the name and the text quotations relation. We present here the promising results we obtain, and the difficulties we face while extracting the quotations in this kind of textual content. These results are obtained from real data (from two information websites) which make the validation difficult. So, we create a validation protocol composed of two steps and based on human raters. Finally, we will see the objective of this work which is understanding interactions in order to extract the social roles of individuals.
Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana

With respect to upstream regions of microRNA (miRNA) target sites located in protein coding sequences, experimental studies have suggested rare codons, rather than frequent codons, are important for miRNA function, because they slow down the local translational process. But, whether there is a trend of reduced translation efficiency near miRNA targets is still unknown. Using Arabidopsis thaliana, we perform genome-wide analysis of synonymous codon usage in upstream regions of miRNA target sites. At the whole genome level, we find no significant selection signals for decreased translational efficiency. However, the same genome analyses do show substantial variations of translation efficiency reduction among miRNA targets. We find that miRNA conservation level, gene codon usage bias, and the mechanism of miRNA action can account for the differences in translation efficiency. But gene's GC content, gene expression level, and miRNA target's conservation level have no effect on local translation efficiency of miRNA targets. Although local translation efficiency in the upstream region of miRNA targets is related to miRNA function in A. thaliana, the selection signal of rare codon usage in that region is weak. We propose some other biological factors are more important than local translation efficiency in miRNA action when miRNA targets are located in protein coding sequences.
Optical Components and Systems

This article gives an overview of geometrical optics and includes the most important formulas as well as a few optical systems of general interest. It describes the main optical components such as lenses, mirrors, plane plates, prisms, fibers, and thin films and their influence on light beams as light propagation and polarization. The principles of reflection and refraction are discussed as well as the optical imaging based on first-order optics. The basic formulas are given. The discussion on plano-optics considers the spectral properties of filters and prisms, the change of image orientation by a single prism and prism systems, beam splitting, and polarization effects due to birefringence of crystal components. Total internal reflection can guide light in optical fibers. Different fiber types are described. Besides single components as best-form lenses and doublets, only multielement optical systems can meet the requirements of different imaging applications. Therefore, a selection of well-known optical systems considering their main properties is described. This includes camera lenses, microscopes, and more sophisticated optical systems as well as a short side-glance on the requirements of interferometers that cannot be described by the geometrical optics approach. Furthermore, a section on optical bench systems summarizes the necessary support of optics by mechanical components. This includes bench profiles and structural systems using the micro bench. Keywords: geometrical optics; technical optics; optical components; optical systems; optical bench system; lenses; mirrors; prisms; polarizers; optical fibers
AGC Parameter Determination for an Oil Facility Electric System

It is necessary to accurately estimate parameters to have a better prediction on the response of a generator under different operating conditions. Since automatic generation control (AGC) is closely related to the real power and frequency of the unit, the dynamic parameters that are required by a standard AGC function are determined for the electric system of an oil facility. Speed droop characteristics, governor deadbands, and generation ramp rates are evaluated using field tests on thermal units. Frequency bias for the area control error calculation is also presented. Test procedures for each parameter calculation are described in detail for thermal units of 1, 3, and 3.75 MW installed at Ecuadorian oil well facilities. Test results for these units demonstrate the practicability of the proposed test procedures.