Miracle-dz/UniFAR-FTUs huggingface dataset:
Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift

Herein, the absorption maximum of bacteriorhodopsin (bR) is calculated using our recently developed method in which the whole protein can be treated quantum mechanically at the level of INDO/S-CIS//ONIOM (B3LYP/6-31G(d,p): AMBER). The full quantum mechanical calculation is shown to reproduce the so-called opsin shift of bR with an error of less than 0.04 eV. We also apply the same calculation for 226 different bR mutants, each of which was constructed by replacing any one of the amino acid residues of the wild-type bR with Gly. This substitution makes it possible to elucidate the extent to which each amino acid contributes to the opsin shift and to estimate the inter-residue synergistic effect. It was found that one of the most important contributions to the opsin shift is the electron transfer from Tyr185 to the chromophore upon excitation. We also indicate that some aromatic (Trp86, Trp182) and polar (Ser141, Thr142) residues, located in the vicinity of the retinal polyene chain and the β-ionone ring, respectively, play an important role in compensating for the large blue-shift induced by both the counterion residues (Asp85, Asp212) and an internal water molecule (W402) located near the Schiff base linkage. In particular, the effect of Trp86 is comparable to that of Tyr185. In addition, Ser141 and Thr142 were found to contribute to an increase in the dipole moment of bR in the excited state. Finally, we provide a complete energy diagram for the opsin shift together with the contribution of the chromophore-protein steric interaction.
Extending Course-Grained Reconfigurable Arrays with Multi-Kernel Dataflow

Coarse-Grained Reconfigurable Arrays (CGRAs) are a promising class of architectures for accelerating applications using a large number of parallel execution units for high throughput. While the model allows for tools that can automatically parallelize a single task across many processing elements, all processing elements are required to perform in lock step. This makes applications that involve multiple data streams, multiple tasks, or unpredictable schedules more difficult to program and inefficient in their use of resources. These applications can often be decomposed into a set of communicating kernels, operating independently to achieve the overall computation. Although competing accelerator architectures like Massively Parallel Processor Arrays (MPPAs) can make use of this communicating processes model, it generally requires the designer to decompose the design into as many kernels as there are processors to be used. While this is excellent for executing unrelated tasks simultaneously, the amount of resources easily utilized for a single task is limited. We are developing a new CGRA architecture that enables execution of multiple kernels of computation simultaneously. This greatly extends the domain of applications that can be accelerated with CGRAs. This new architecture poses two problems that we describe in this paper. First, the tools must handle the decomposition, scheduling placement and routing of multiple kernels. Second, the CGRA must include new resources for coordinating and synchronizing the operation of multiple kernels. This paper is a digest of the project’s previously published results [17,18,19,20,21].
Modeling and characterization of forest stands using aerial and terrestrial photogrammetry

The master ‘s thesis focused on forest inventory process based on the photogrammetric point cloud. The study deals with forest stand data collecting using terrestrial and aerial photogrammetry. The raw data – digital images were taken by walking through the forest stand with the imaging device carried on the measuring rod and by the drone with mounted camera. This thesis describes data processing in the Agisoft PhotoScan, where are the raw images processed to the 3D point clouds. 3D point clouds were analysed in the ArcMap SW. From the modelled stems, the cuts at breast height were extracted, from which, the single stem diameter at breast height (DBH) was calculated. Based on ArcMap SW analysis, the tree height was calculated. For the tree height values calculation, the canopy height model (CHM) was created by so-called inversed watershed method. Volume of the individual stems was calculated from the values based on the photogrammetry data. Calculated stand characteristics were compared with ground true data, collected by the conventional methods. The calculation of the stand characteristics was achieved with RMSE 1,5 m error of the tree height, 2,9 cm error of the DBH and 0,14 m3 of the single stem volume. It was concluded that the presented technology can be used for forest inventory. Thanks to the possibility of its operative application, i.e. the possibility of updating the stand data at very short intervals is therefore possible to evaluate the actual thinning interventions in the premature stands, development of the regeneration of the stand, and also the potential threat of the stands by calamitous pests.
- 73-A computer-based course in spectrogram reading

We describe a computer-based course in spectrogram reading built with the CSLU Toolkit. The principal teaching tool is SpeechView, a Toolkit component that displays speech waveform files, spectrograms, and labels. These display types are essential for online spectrogram reading. Other Toolkit modules that are used include: (1) an animated face that allows students to view articulator movements; (2) a speech synthesis system that enables students to compare human and synthesized speech; and (3) a phonetic alignment package that performs automatic labeling of speech. The authors have used these software components to teach three computer-based classes. We have also developed a complete laboratory curriculum, including a speech corpus designed for beginning spectrogram reading. The curriculum and corpus are both summarized in this article. We conclude by describing our work toward an entirely computer-based course in spectrogram reading, including: (1) enhanced spectrogram displays, (2) new labeling tools, and (3) online textual and graphic materials.
Seasonal variation of CDOM and DOC in the Middle Atlantic Bight: Terrestrial inputs and photooxidation

Extensive surveys of the fluorescence and absorption of chromophore‐containing dissolved organic matter (CDOM), dissolved organic C (DOC) concentration, chlorophyll fluorescence, and salinity were performed during August and November 1993 and March and April 1994 along a cruise line extending from the mouth of Delaware Bay southeast to the Sargasso Sea. With shallow stratification in August, photobleaching dramatically altered the optical properties of the surface waters, with ∼70% of the CDOM absorption and fluorescence lost through photooxidation in the waters at the outer shelf. S, the slope of the log‐linearized absorption spectrum of CDOM, increased offshore and seemed to increase with photodegradation. The increase in S combined with the seasonal variation in the relationship between Chl and CDOM underscores the difficulty in developing algorithms to predict Chl concentrations in turbid coastal waters with ocean color data. Despite the photooxidation of CDOM, the seasonal variation in the CDOM fluorescence‐absorption relationship and fluorescence quantum yields was <15%. When using appropriate methods, the airborne lidar approach for remote determination of CDOM absorption coefficients seems to be a very robust technique. The photooxidation of CDOM in August also affected the relationship between CDOM and DOC concentration in the surface waters, although for the rest of the year the relationship was reasonably linear. The results of a simple model suggest ∼10% of the DOC in the mixed layer was directly converted photochemically to dissolved inorganic C (DIC).
FBMIS: A Fuzzy-Based Multi-interface System for Cellular and Ad Hoc Networks

Several solutions have been proposed for improving the Quality of Service (QoS) in wireless cellular networks, such as Call Admission Control (CAC) and handover strategies. However, none of them considers the usage of different interfaces for different conditions. In this work, apart from using only Base Stations (BSs) as an important device of cellular networks, we propose a multi-interface approach in order to avoid BS overloads and improve the QoS of wireless communications. We propose a system, where each node is equipped with two interfaces: the traditional cellular network interface and Mobile Ad hoc Networks (MANET) interface. The main difficulty for this system is how to choose the right interface in order to guarantee a minimal usage of network resources and at the same time keeping the communication performance in a satisfactory level. For this purpose, in this paper we propose a Fuzzy-Based Multi-Interface System (FBMIS), where each node is able to switch from cellular to Ad hoc and vice versa. We consider three input parameters and one output parameter. From the simulation results, our system shows a good performance.
Functions of the Frontal Lobes: Relation to Executive Functions

Abstract Proceeding from the assumptions that specific frontal regions control discrete functions and that very basic cognitive processes can be systematically manipulated to reveal those functions, recent reports have demonstrated consistent anatomical/functional relationships: dorsomedial for energization, left dorsolateral for task setting, and right dorsolateral for monitoring. There is no central executive. There are, instead, numerous domain general processes discretely distributed across several frontal regions that act in concert to accomplish control. Beyond these functions, there are two additional “frontal” anatomical/functional relationships: ventral–medial/orbital for emotional and behavioral regulation, and frontopolar for integrative—even meta-cognitive—functions. (JINS, 2011, 17, 759–765)
Evaluating Stability and Comparing Output of Feature Selectors that Optimize Feature Subset Cardinality

Stability (robustness) of feature selection methods is a topic of recent interest, yet often neglected importance, with direct impact on the reliability of machine learning systems. We investigate the problem of evaluating the stability of feature selection processes yielding subsets of varying size. We introduce several novel feature selection stability measures and adjust some existing measures in a unifying framework that offers broad insight into the stability problem. We study in detail the properties of considered measures and demonstrate on various examples what information about the feature selection process can be gained. We also introduce an alternative approach to feature selection evaluation in the form of measures that enable comparing the similarity of two feature selection processes. These measures enable comparing, e.g., the output of two feature selection methods or two runs of one method with different parameters. The information obtained using the considered stability and similarity measures is shown to be usable for assessing feature selection methods (or criteria) as such.
Efﬁcient Segmental Conditional Random Fields for Phone Recognition

Recently the initial attempt has been made to use segment-based direct models on their own for phone classiﬁcation and recognition without the aid of an HMM lattice. This paper follows this line of research to further investigate these one-pass segmental direct models on phone recognition using posteriors as input. We make the ﬁrst direct comparison between a frame-based system and a segmental system using the same base features, and explore the utilization of transition features in a direct segmental model for the ﬁrst time. The results show that transition features can be very beneﬁcial, particularly the ones surrounding the segment boundaries. In order to efﬁciently incorporate such features, we propose the Boundary-Factored SCRF, which reduces the time complexity of a Segmental Conditional Random Field (SCRF) to that of a frame-level CRF.
A novel wavelet-based generalized sidelobe canceller

This paper presents a novel narrowband adaptive beamformer with the generalized sidelobe canceller (GSC) as the underlying structure. The new beamformer employs the regular M-band wavelet filters in the design of the blocking matrix of the GSC, which, as justified analytically, can indeed block the desired signals as required, provided the wavelet filters have sufficiently high regularity. Additionally, the eigenvalue spreads of the covariance matrices of the blocking matrix outputs, as demonstrated in various scenarios, decrease, thus accelerating the convergence speed of the succeeding least mean squares (LMS) algorithm. Also, the new beamformer belongs to a specific type of partially adaptive beamformers, wherein only a portion of weights is utilized in the adaptive processing. Consequently, the computational complexity is substantially reduced as compared with previous approaches. The issues of choosing the parameters involved for superior performance are addressed as well. Simulation results are furnished to justify this new approach.
Emergent Stenting to Treat Patients With Carotid Artery Dissection: Clinically and Radiologically Directed Therapeutic Decision Making

Background and Purpose— Carotid artery dissection (CAD) is a common cause of stroke in young patients. Clots formed at the low-flow zone in the false arterial lumen may give rise to distal emboli, and the mural hematoma may eventually occlude the artery. Anticoagulation is currently the accepted treatment, but it is unknown which patients will improve spontaneously, which will respond to anticoagulation, and which will have an exacerbation of ischemic symptoms despite therapy. Endovascular treatment of CAD may be an attractive alternative to anticoagulation, and methods of identifying patients who stand to benefit from such therapy need to be established. Methods— We present here 3 cases of spontaneous symptomatic CAD in which endovascular stenting procedures were performed on the basis of a paradigm aimed at identifying potentially salvageable but at-risk brain tissue by combining clinical with MRI (diffusion and perfusion) and angiographic data. Results— Diffusion-perfusion MRI mismatches and/or evidence of cerebral ischemia on angiographic parenchymography were identified in all patients. They did not respond to anticoagulation, were therefore treated with endovascular stents, and had excellent outcomes. Conclusions— Endovascular stent placement may be an immediate, effective, and safe method of restoring vessel lumen integrity. It may be considered for selected patients who are clinically symptomatic despite anticoagulant treatment and in whom neuroimaging methods suggest that the neurological signs originate from a viable, hypoperfused, ischemic penumbra.
Stereological study on the effect of vitamin C in preventing the adverse effects of bisphenol A on rat ovary

Background: Bisphenol A (BPA), an environmental pollutant, can generate free radicals which damages the reproductive system. Vitamin C is an antioxidant which may prevent the adverse effects of free radicals. Objective: The aim was to investigate the effect of vitamin C on the ovary tissue in rats treated with BPA. Materials and Methods: In this experimental study, 24 female Wistar rats (200±20 gr) were randomly divided into 4 groups (n=6): control, BPA (60 µg/Kg/day), vitamin C (150 mg/Kg/day) and BPA + vitamin C and orally treated for 20 days. The left ovaries were taken out, fixed for tissue processing and studied using stereological methods. Data were analyzed with SPSS using one-way ANOVA, and the means were considered significantly different at (p<0.05). Results: The total volume of ovary and cortex (p<0.01), medulla (p<0.05), the volume of corpus luteum (p<0.001) and the mean number of antral follicles (p<0.001) significantly reduced in BPA group compared with control, while the number of atretic follicles increased (p<0.05). The volume of oocyte (p<0.01) and its nucleus (p<0.001) in the antral follicles and the thickness of zona pellucida (ZP) in the secondary (p<0.05) and antral (p<0.001) follicles significantly decreased in BPA group compared with controls. The above parameters in the BPA + vitamin C group were compensated to control level. Conclusion: Vitamin C can be used as a potential antioxidant in the case of BPA toxication
Designing interactive user interface supporting entity search over DBpedia

The Linked Open Data provides useful information on huge number of related entities gathered from numerous distributed data sources residing in the cloud. Searching for the required information in this big data is one of the key challenges, in the domain of Information Retrieval, where various studies have been conducted for multiple purposes. These studies highlighted three main challenges: querying ambiguity, information incompleteness, and visualization techniques. In this paper, we introduce a visualization approach which provides a more informative view and additional understanding of semantic data over DBpedia. We show that our proposed solution, considered as efficient for users, overcomes the other existing ones by hiding complexity, and by offering users the information of interest.
An Efficient Primal-Dual Method for L1TV Image Restoration

Image restoration based on an `-data-fitting term and edge preserving total variation regularization is considered. The associated non-smooth energy minimization problem is handled by utilizing Fenchel-duality and dual regularization techniques. The latter guarantee uniqueness of the dual solution and an efficient way for reconstructing a primal solution, i.e. the restored image, from a dual solution. For solving the resulting primal-dual system, a semismooth Newton solver is proposed and its convergence is studied. The paper ends by a report on restoration results obtained by the new algorithm for saltand-pepper or random-valued impulse noise including blurring. A comparison with other methods is provided as well.
Adaptive sampling of intersectable models exploiting image and object-space coherence

We present a sampling strategy and rendering framework for intersectable models, whose surface is implicitly defined by a black box intersection test that provides the location and normal of the closest intersection of a ray with the surface. To speed up image generation despite potentially slow intersection tests, our method exploits spatial coherence by adjusting the sampling resolution in image space to the surface variation in object space. The result is a set of small, view-dependent bilinear surface approximations, which are rendered as quads using conventional graphics hardware. The advantage of this temporary rendering representation is two-fold: First, rendering is performed on the GPU, leaving CPU time for ray intersection computation. As the number of primitives is typically small, complex per vertex or per fragment programs can be used to achieve a variety of rendering effects. Second, bilinear surface approximations are derived from the geometry and can be reused in other views. Here, graphics hardware is exploited to determine the subset of image space in need of re-sampling. We demonstrate our system by ray casting an implicit surface defined from point samples, for which current ray-surface intersection computations are usually too slow to generate images at interactive rates.
Implementation of Artificial Neural Networks for Prediction of Chloride Penetration in Concrete

Ahmed Mohamed, O. , Ati, M. , & Al Hawat, W. (2018). Implementation of Artificial Neural Networks for Prediction of Chloride Penetration in Concrete. International Journal of Engineering & Technology, 7(2.28), 47-52. doi:http://dx.doi. org/10.14419/ijet.v7i2.28.12880
An evaluation of TCP-based rate-control algorithms for adaptive internet streaming of H.264/SVC

Recent work in TCP video streaming indicates that multimedia streaming via TCP provides satisfactory performance when the achievable TCP throughput is approximately twice the media bit rate. However, these conditions may not be achievable on the Internet, e.g., when the delivery path offers insufficient bandwidth or becomes congested due to competing traffic. Therefore, adaptive streaming for videos over TCP is required and a number of rate-control algorithms for video streaming have been proposed and evaluated in the literature. \\ In this paper, we evaluate and compare three existing rate-control algorithms for TCP streaming in terms of the (PSNR) quality of the delivered video and in terms of the timeliness of delivery. The contribution of the paper is that, to the best of our knowledge, this is the first evaluation of TCP-based streaming in an Internet-like setting making use of the scalability features of the H.264/SVC video codec. Two simple bandwidth estimation algorithms and a priority-/deadline-driven approach are described to adapt the bit rates of, and transmit, the H.264/SVC video in a rate-distortion optimal manner. The results indicate that the three algorithms perform robustly in terms of video quality and timely delivery, both on under-provisioned links and in case of competing TCP flows. The priority-/deadline-driven technique is even more stable in terms of packet delays and jitter; thus, client buffers can be dimensioned more easily.
Ordering Sentences According to Topicality

This paper addresses the problem of finding or producing the best ordering of the sentences in a text. I focus on using semantic properties of the words, as well as the high-level structure of each of the texts, to produce or choose the best ordering. In choosing an original sentence ordering from a group of sentential permutations of the same text, information about the topic of the text is helpful when added to information about coherence. A term distribution method of determining the semantic properties of words is successfully used to locate the most topical sentence in each text.
Relationships between Verbal and Visuospatial Working Memories and Source Monitoring among Young Children

The results of previous studies examining the relationship between source monitoring and working memory in young children are not consistent. One of the reasons for this inconsistency is concerning the modalities of information with which working memory tasks deal. The present study investigated how young children’s verbal and visuospatial working memory capacity would be related to respective source-monitoring tasks with visually or verbally presented stimuli. Children aged four (n = 21) and five years (n = 21) participated in this study. They completed two verbal working memory tasks, namely, the backward digit span and listening span tests; and two visuospatial working memory tasks, namely, a comparative line test and a rotated figure test. In the source-monitoring task, first, an adult man and an adult woman read two different picture books to groups of children. Subsequently, they read short sentences aloud and showed pictures to the children. Each child then performed recognition tests for the sentences and the pictures, and required to decide on the appropriate source. Hierarchical multiple regression analyses revealed the following results: The verbal working memory task (i.e., the backward digit span) was a significant factor explaining performance on the verbal source-monitoring task, whereas the visuospatial working memory task (i.e., a rotated figure test) explained the performance on the visual source-monitoring task.