Miracle-dz/UniFAR-FTUs huggingface dataset:
Successional stage of biological soil crusts: an accurate indicator of ecohydrological condition

Biological soil crusts are a key component of many dryland ecosystems. Following disturbance, biological soil crusts will recover in stages. Recently, a simple classification of these stages has been developed, largely on the basis of external features of the crusts, which reflects their level of development (LOD). The classification system has six LOD classes, from low (1) to high (6). To determine whether the LOD of a crust is related to its ecohydrological function, we used rainfall simulation to evaluate differences in infiltration, runoff, and erosion among crusts in the various LODs, across a range of soil depths and with different wetting pre‐treatments. We found large differences between the lowest and highest LODs, with runoff and erosion being greatest from the lowest LOD. Under dry antecedent conditions, about 50% of the water applied ran off the lowest LOD plots, whereas less than 10% ran off the plots of the two highest LODs. Similarly, sediment loss was 400 g m−2 from the lowest LOD and almost zero from the higher LODs. We scaled up the results from these simulations using the Rangeland Hydrology and Erosion Model. Modelling results indicate that erosion increases dramatically as slope length and gradient increase, especially beyond the threshold values of 10 m for slope length and 10% for slope gradient. Our findings confirm that the LOD classification is a quick, easy, nondestructive, and accurate index of hydrological condition and should be incorporated in field and modelling assessments of ecosystem health. Published in 2012. This article is a U.S. Government work and is in the public domain in the USA.
Cholangiocyte Organoids: The New Frontier in Regenerative Medicine for the Study and Treatment of Cholangiopathies

Cholangiopathies include a group of chronic progressive disorders, affecting the cholangiocytes, the epithelial cells that line the biliary tree, leading to liver parenchymal fibrosis and eventually end-stage liver disease necessitating transplantation. Experimental modeling of these multifactorial cholestatic diseases faces challenges due to the lack of adequate experimental in vitro and in vivo models. A novel approach employs three-dimensional organoid systems that offer several advantages for modeling disease and testing drug response in vitro. Organoids mimic intercellular communication, replicate the architecture of organs, and maintain the cell’s original phenotype. Cholangiocyte organoids provide an in vitro model to study the pathogenesis and pharmacotherapeutic treatment of cholangiopathies and show great promise for regenerative therapies. In particular, patient-derived organoids allow personalized medicine approaches and the study of individual disease characteristics. This review highlights the significance of cholangiocyte organoid models in advancing our understanding of cholangiopathies and driving advancements in regenerative medicine strategies.
An integrated model of visual attention using shape-based features

Apart from helping shed some light on human perceptual mechanisms, modeling visual attention has important applications in computer vision. It has been shown to be useful in priming object detection [16, 29], pruning interest points [26], quantifying visual clutter [23] as well as predicting human eye movements [17]. Prior work has either relied on purely bottom-up approaches [11] or top-down schemes using simple low-level features [16, 19]. In this paper, we outline a top-down visual attention model based on shape-based features. The same shape-based representation is used to represent both the objects and the scenes that contain them. The spatial priors imposed by the scene and the feature priors imposed by the target object are combined in a Bayesian framework to generate a task-dependent saliency map. We show that our approach can predict the location of objects as well as match eye movements (92% overlap with human observers). We also show that the proposed approach performs better than existing bottom-up and top-down computational models.
Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein P

Abstract Gene-specific expansion of the genetic code allows for UGA codons to specify the amino acid selenocysteine (Sec). A striking example of UGA redefinition occurs during translation of the mRNA coding for the selenium transport protein, selenoprotein P (SELENOP), which in vertebrates may contain up to 22 in-frame UGA codons. Sec incorporation at the first and downstream UGA codons occurs with variable efficiencies to control synthesis of full-length and truncated SELENOP isoforms. To address how the Selenop mRNA can direct dynamic codon redefinition in different regions of the same mRNA, we undertook a comprehensive search for phylogenetically conserved RNA structures and examined the function of these structures using cell-based assays, in vitro translation systems, and in vivo ribosome profiling of liver tissue from mice carrying genomic deletions of 3′ UTR selenocysteine-insertion-sequences (SECIS1 and SECIS2). The data support a novel RNA structure near the start codon that impacts translation initiation, structures located adjacent to UGA codons, additional coding sequence regions necessary for efficient production of full-length SELENOP, and distinct roles for SECIS1 and SECIS2 at UGA codons. Our results uncover a remarkable diversity of RNA elements conducting multiple occurrences of UGA redefinition to control the synthesis of full-length and truncated SELENOP isoforms.
Do species of Neacratus with anchor-shaped sclerite of endophallus really belong to Neacratus (Coleoptera: Brentidae: Acratini)?

Summary A small group of nine nominal species belonging to the genus Neacratus Alonso-Zarazaga, Lyal, Sforzi & Bartolozzi, 1999 is studied in detail from a morphological point of view. Lectotypes are designated for Brentus obtusus Lund, 1800 and Nemocephalus fulgidus Kleine, 1928. Three new synonymies are proposed: Nemocephalus brevicostatus Kleine, 1922 n. syn. for Brenthus obtusus Lund, 1800, Nemocephalus longiceps Perroud, 1853 n. syn. for Brenthus famulus Boheman, 1840, and Nemocephalus fulgidus Kleine, 1928 n. syn. for B. famulus Boheman, 1840. A new species, Neacratus pascali n. sp. , is described from French Guiana. New country records are provided for Neacratus obtusus (Bolivia, Ecuador, French Guiana, Grenada, Peru, Trinidad and Tobago, Venezuela), N. puncticeps (Sharp, 1895) (Colombia, Ecuador, Venezuela), N. guatemalensis (Senna, 1893) (Belize, Colombia, El Salvador), N. deplanatus (Sharp, 1895) (Colombia, Costa Rica, French Guiana, Mexico, Panama, Venezuela) and N. famulus (Paraguay). A phylogenetic analysis carried out on this group shows it forms a monophyletic lineage included in a clade containing most of other species of Neacratus, of which it is the type species; it is therefore not justified to create a new generic name. The possible polyphyletism of the genus Neacratus as a whole and the development of an excessively long rostrum in some male Acratini are discussed.
Experimental Characterization and Control of Miniaturized Pneumatic Artificial Muscle

Robotic surgical tools used in minimally invasive surgeries (MIS) require miniaturized and reliable actuators for precise positioning and control of the end-effector. Miniature pneumatic artificial muscles (MPAMs) are a good choice due to their inert nature, high force to weight ratio, and fast actuation. In this paper, we present the development of miniaturized braided pneumatic muscles with an outer diameter of similar to 1.2 mm, a high contraction ratio of about 18%, and capable of providing a pull force in excess of 4 N at a supply pressure of 0.8 MPa. We present the details of the developed experimental setup, experimental data on contraction and force as a function of applied pressure, and characterization of the MPAM. We also present a simple kinematics and experimental data based model of the braided pneumatic muscle and show that the model predicts contraction in length to within 20% of the measured value. Finally, a robust controller for the MPAMs is developed and validated with experiments and it is shown that the MPAMs have a time constant of similar to 10 ms thereby making them suitable for actuating endoscopic and robotic surgical tools.
Peak power reduction in hybrid energy systems with limited load forecasts

Hybrid energy systems, which consist of a load powered by a source and a form of energy storage, find applications in many systems, e.g., the electric grid and electric vehicles. A key problem for hybrid energy systems is the reduction of peak power consumption to ensure cost-efficient operation as peak power draws require additional resources and adversely affect the system reliability and lifetime. Furthermore, in some cases such as electric vehicles, the load dynamics are fast, not perfectly known in advance and the on-board computation power is often limited, making the implementation of traditional optimal control difficult. We aim to develop a control scheme to reduce the peak power drawn from the source for hybrid energy systems with limited computation power and limited load forecasts. We propose a scheme with two control levels and provide a sufficient condition for control of the different energy storage/generation components to meet the instantaneous load while satisfying a peak power threshold. The scheme provides performance comparable to Model Predictive Control, while requiring less computation power and only coarse-grained load predictions. For a case study, we implement the scheme for a battery-supercapacitor-powered electric vehicle with real world drive cycles to demonstrate the low execution time and effective reduction of the battery power (hence temperature), which is crucial to the lifetime of the battery.
Hyper-Ballistic Superdiffusion of Competing Microswimmers

Hyper-ballistic diffusion is shown to arise from a simple model of microswimmers moving through a porous media while competing for resources. By using a mean-field model where swimmers interact through the local concentration, we show that a non-linear Fokker–Planck equation arises. The solution exhibits hyper-ballistic superdiffusive motion, with a diffusion exponent of four. A microscopic simulation strategy is proposed, which shows excellent agreement with theoretical analysis.
Medical school handoff education improves postgraduate trainee performance and confidence*

Abstract Objectives: Determine postgraduate first-year (PGY-1) trainees ability to perform patient care handoffs and associated medical school training. Methods: About 173 incoming PGY-1 trainees completed an OSCE handoff station and a survey eliciting their training and confidence in conducting handoffs. Independent t-tests compared OSCE performance of trainees who reported receiving handoff training to those who had not. Analysis of variance examined differences in performance based on prior handoff instruction and across levels of self-assessed abilities, with significance set at p < 0.05. Results: About 35% of trainees reported receiving instruction and 51% reported receiving feedback about their handoff performance in medical school. Mean handoff performance score was 69.5%. Trainees who received instruction or feedback during medical school had higher total and component handoff performance scores (p < 0.05); they were also more confident in their handoff abilities (p < 0.001). Trainees with higher self-assessed skills and preparedness performed better on the OSCE (p < 0.05). Conclusions: This study provides evidence that incoming trainees are not well prepared to perform handoffs. However, those who received instruction during medical school perform better and are more confident on standardized performance assessments. Given communication failures lead to uncertainty in patient care and increases in medical errors, medical schools should incorporate handoff training as required instruction.
A Novel Evolutionary Swarm Fuzzy Clustering Approach for Hyperspectral Imagery

In land cover assessment, classes often gradually change from one to another. Therefore, it is difficult to allocate sharp boundaries between different classes of interest. To overcome this issue and model such conditions, fuzzy techniques that resemble human reasoning have been proposed as alternatives. Fuzzy C-means is the most common fuzzy clustering technique, but its concept is based on a local search mechanism and its convergence rate is rather slow, especially considering high-dimensional problems (e.g., in processing of hyperspectral images). Here, in order to address those shortcomings of hard approaches, a new approach is proposed, i.e., fuzzy C-means which is optimized by fractional order Darwinian particle swarm optimization. In addition, to speed up the clustering process, the histogram of image intensities is used during the clustering process instead of the raw image data. Furthermore, the proposed clustering approach is combined with support vector machine classification to accurately classify hyperspectral images. The new classification framework is applied on two well-known hyperspectral data sets; Indian Pines and Salinas. Experimental results confirm that the proposed swarm-based clustering approach can group hyperspectral images accurately in a time-efficient manner compared to other existing clustering techniques.
Vision-based Pirouettes using the Radial Obstacle Profile

Mapping algorithms commonly use “radial sweeps” of the surrounding environment as input. Producing a sweep is a challenging task for a robot using only vision. With no odometers to measure turn angles, a vision-based robot must have another method to verify rotations. In this paper we propose using the Radial Obstacle Profile (ROP) which gives the radial distance to the nearest obstacle in any direction in the robot’s field of view. By matching the ROPs before and after a turn, the robot should be able to verify that the expected angle of rotation matches the actual angle. Combining successive ROPs then produces a radial sweep. Keywords—computer and robot vision;wheeled mobile robots; mapping; radial obstacle profile
FPGA fingerprinting techniques for protecting intellectual property

As CAD tools and semiconductor technology improvements increase market opportunities for reusable hardware components, it becomes more important to produce techniques for protecting intellectual property rights. This work presents a method of fingerprinting an FPGA design component, so that products in the field can be used to identify both the component designer as well as the customer of record. These techniques are efficient, have extremely low impact on design quality, and are resistant to tampering.
The missing log in large deviations for triangle counts

This paper solves the problem of sharp large deviation estimates for the upper tail of the number of triangles in an Erdős‐Rényi random graph, by establishing a logarithmic factor in the exponent that was missing till now. It is possible that the method of proof may extend to general subgraph counts. © 2011 Wiley Periodicals, Inc. Random Struct. Alg. , 40, 437–451, 2012
Brain Network Analysis: Separating Cost from Topology Using Cost-Integration

A statistically principled way of conducting brain network analysis is still lacking. Comparison of different populations of brain networks is hard because topology is inherently dependent on wiring cost, where cost is defined as the number of edges in an unweighted graph. In this paper, we evaluate the benefits and limitations associated with using cost-integrated topological metrics. Our focus is on comparing populations of weighted undirected graphs that differ in mean association weight, using global efficiency. Our key result shows that integrating over cost is equivalent to controlling for any monotonic transformation of the weight set of a weighted graph. That is, when integrating over cost, we eliminate the differences in topology that may be due to a monotonic transformation of the weight set. Our result holds for any unweighted topological measure, and for any choice of distribution over cost levels. Cost-integration is therefore helpful in disentangling differences in cost from differences in topology. By contrast, we show that the use of the weighted version of a topological metric is generally not a valid approach to this problem. Indeed, we prove that, under weak conditions, the use of the weighted version of global efficiency is equivalent to simply comparing weighted costs. Thus, we recommend the reporting of (i) differences in weighted costs and (ii) differences in cost-integrated topological measures with respect to different distributions over the cost domain. We demonstrate the application of these techniques in a re-analysis of an fMRI working memory task. We also provide a Monte Carlo method for approximating cost-integrated topological measures. Finally, we discuss the limitations of integrating topology over cost, which may pose problems when some weights are zero, when multiplicities exist in the ranks of the weights, and when one expects subtle cost-dependent topological differences, which could be masked by cost-integration.
Molecular cloning of cDNA for proteasomes (multicatalytic proteinase complexes) from rat liver: primary structure of the largest component (C2).

Proteasomes (multicatalytic proteinase complexes) from rat liver are composed of at least 13 nonidentical components [Tanaka, K. , Yoshimura, T. , Ichihara, A. , Ikai, A. , Nishigai, M. , Morimoto, M. , Sato, M. , Tanaka, N. , Katsube, Y. , Kameyama, K. , & Takagi, T. (1988) J. Mol. Biol. 203, 985-996]. The nucleotide sequence of one major component (C2) of the proteasomes has been determined from a recombinant cDNA clone isolated by screening a rat liver cDNA library with a mixture of synthetic deoxyribonucleotides as a probe. The sequence was composed of 1174 nucleotides including a coding region for the entire protein and noncoding regions of both the 5'- and 3'-sides. The polypeptide deduced from the open reading frame consisted of 263 amino acid residues, and its molecular weight was calculated to be 29,516. The partial amino acid sequences of several fragments (approximately 45% of the total residues), which were obtained by cleavage of C2 with lysyl endopeptidase and cyanogen bromide, were determined by automated Edman degradation and found to be in complete accordance with those deduced from the cDNA sequence. The amino acid composition of C2, determined by chemical analysis, was also consistent with that deduced from the cDNA sequence, indicating that the cloned cDNA actually encoded component C2. Computer analysis revealed little structural similarity of C2 to other proteins reported so far. Northern blot hybridization analyses showed that the mRNA encoding this novel protein C2 was expressed in all the rat tissues examined and in a variety of eukaryotic organisms such as amphibia, birds, and mammals with slight species-specific differences in size. (ABSTRACT TRUNCATED AT 250 WORDS)
Multi-depth cross-calibration of remote eye gaze trackers and stereoscopic scene systems

We present a robust and accurate technique for the cross-calibration of 3D remote gaze trackers with stereoscopic scene vision systems between which no common imaging area exists. We empirically demonstrate that a multi-depth calibration approach yields remarkably superior results for obtaining 3D Point-of-Gaze (PoG) when compared with traditional methods using monocular scene cameras and co-planar eye gaze calibration points.
Language Model Based on Word Clustering

Category-based statistic language model is an important method to solve the problem of sparse data. But there are two bottlenecks about this model: (1) the problem of word clustering, it is hard to find a suitable clustering method that has good performance and not large amount of computation. (2) class-based method always loses some prediction ability to adapt the text of different domain. The authors try to solve above problems in this paper. This paper presents a definition of word similarity by utilizing mutual information. Based on word similarity, this paper gives the definition of word set similarity. Experiments show that word clustering algorithm based on similarity is better than conventional greedy clustering method in speed and performance. At the same time, this paper presents a new method to create the vari-gram model.
Seismic Impact of the Mw 9.0 Tohoku Earthquake in Eastern China

Abstract The 2011 Tohoku earthquake ( M w 9.0) in Japan caused significant coseismic displacement in much of eastern China, where seismic activity has been intense and damaging earthquakes numerous. Did the Tohoku earthquake change the stress field and seismic activity in eastern China? Here, we used a viscoelastic deformation model of layered spherical earth to calculate the coseismic and postseismic displacements and compared the results with Global Positioning System data for eastern China. Using the best‐fitting model, we then calculated the coseismic and postseismic Coulomb stress changes on major active faults in eastern China. Our results show that the Coulomb stress changes caused by the Tohoku earthquake on these faults are less than 0.002 MPa, so were unlikely to significantly alter the stress field or trigger earthquakes in eastern China. Online Material: Tables of coseismic displacement at 67 stations and time‐dependent displacements before and after the M 9.0 Tohoku earthquake.
Evaluation of Role of Myofibroblasts in Oral Cancer: A Systematic Review

Aim To conduct a systematic review on the role of myofibroblasts in progression of oral cancer. The myofibroblast is essential for the integrity of the mammalian body by virtue of its role in wound healing, but it also plays a negative role due to their role in promoting tumor development. Settings and design Systematic review. Materials and methods Bibliographic searches were conducted in several electronic databases using all publications in PubMed, PubMed central, EMBASE, CancerLit, Google scholar, and Cochrane CCTR between 1990 and June 2015. Results The search of all publications from various electronic databases revealed 1,371 citations. The total number of studies considered for systematic review was 43. The total number of patients included in the studies was 990. Conclusion Myofibroblasts are a significant component in stroma of oral cancer cases, though not identified in all cases. This systematic review shows that clinical, pathological, and immunohistochemistry tests have correlated the presence of high myofibroblast count in oral cancer cell stroma. Key Messages Myofibroblasts play a significant role in oral cancer invasion and progression. Various studies have demonstrated their association with oral cancer. This review tends to highlight their role in the pathogenesis of oral cancer over the decade. How to cite this article Sekhon HK, Sircar K, Kaur G, Marwah M. Evaluation of Role of Myofibroblasts in Oral Cancer: A Systematic Review. Int J Clin Pediatr Dent 2016;9(3):233-239.