Miracle-dz/UniFAR-FTUs huggingface dataset:
IMAGING BOTANICAL SUBJECTS WITH OPTICAL COHERENCE TOMOGRAPHY: A FEASIBILITY STUDY

Optical coherence tomography (OCT), an imaging modality that uses reflected near-infrared light to generate micron-scale resolution, cross-sectional images of biological tissue, was applied to imaging of various botanical subjects. Example images are given of sectioned kiwifruit, orange flesh, orange peel, lettuce leaves, and intact cranberries. OCT appears to be well suited for botanical imaging; features at the tissue and cellular level in these subjects were well defined. Cranberries were imaged at different stages of ripeness as judged by flesh color, and repeatable differences were seen in the OCT images of ripe and unripe berries. This preliminary study suggests that OCT can be a valuable tool for non-destructive, morphological imaging of botanical subjects.
Visualization of similarity relationships by onomatopoeia thesaurus map

Onomatopoeia refers to words that represent the sound, appearance, or voice of things, which makes it possible to create expressions that bring a scene to life in a subtle fashion. In this study, we propose an onomatopoeia thesaurus map to enable the construction of a map that visually confirms "similarity relationships between a number of onomatopoetic words" and "similarity relationships between unknown onomatopoetic words and existing onomatopoetic words", which are difficult to grasp from a conventional thesaurus. It is also possible to label objects with onomatopoetic words and visualize the similarity relationships between the objects on a map. In this paper, we introduce an example of labeling onomatopoetic words relating to the textures of sweets (desserts).
The Feasibility of Using OpenCL Instead of OpenMP for Parallel CPU Programming

OpenCL, along with CUDA, is one of the main tools used to program GPGPUs. However, it allows running the same code on multi-core CPUs too, making it a rival for the long-established OpenMP. In this paper we compare OpenCL and OpenMP when developing and running compute-heavy code on a CPU. Both ease of programming and performance aspects are considered. Since, unlike a GPU, no memory copy operation is involved, our comparisons measure the code generation quality, as well as thread management efficiency of OpenCL and OpenMP. We evaluate the performance of these development tools under two conditions: a large number of short-running compute-heavy parallel code executions, when more thread management is performed, and a small number of long-running parallel code executions, when less thread management is required. The results show that OpenCL and OpenMP each win in one of the two conditions. We argue that while using OpenMP requires less setup, OpenCL can be a viable substitute for OpenMP from a performance point of view, especially when a high number of thread invocations is required. We also provide a number of potential pitfalls to watch for when moving from OpenMP to OpenCL.
The Minimum Description Length Principle in Coding and Modeling

We review the principles of minimum description length and stochastic complexity as used in data compression and statistical modeling. Stochastic complexity is formulated as the solution to optimum universal coding problems extending Shannon's basic source coding theorem. The normalized maximized likelihood, mixture, and predictive codings are each shown to achieve the stochastic complexity to within asymptotically vanishing terms. We assess the performance of the minimum description length criterion both from the vantage point of quality of data compression and accuracy of statistical inference. Context tree modeling, density estimation, and model selection in Gaussian linear regression serve as examples.
High field electrical conduction in extremely thin p-xylene polymer films

High field conduction and photoconduction were investigated on the extremely thin polymer films prepared from p-xylene via two different polymerization routes, i.e., plasma polymerization and vapor phase polymerization of p-xylylene bi-radicals, which gave amorphous and semicrystalline polymer films, respectively. The effects of physical and chemical differences were discussed on their electronic conduction.
Binary Classification Using Linear SVM Pyramidal Tree

This paper presents a linear SVM (Support Vector Machine) Pyramidal Tree (SVMPT) for binary classification tasks. SVMPT is a modified version of SVM based Tree Type Neural Networks (SVMTNN), reported earlier in the literature [1]. Both the algorithms use parameter-less SVM proposed by Mangasarian [2] for learning in each node. While SVMTNN insists on 100 percent training accuracy, linear SVMPT uses predetermined threshold value to determine when to stop adding new nodes. Experimental results on standard binary datasets show that the algorithm has good generalization capability, comparable to linear SVMs. We also present experimental results on extensions of linear SVMPT to multi-class datasets and datasets with fuzzy membership for each datapoint.
Supplementary Material II: Additional Experiment Results

4. The weighted-Fβ scores when the proposed post-processing function is applied and optimized for all the compared models (Fig. 4). In our post-processing function, there are three components, 1) smoothing 2) centeredness and 3) contrast enhancement. We try all possible 23 = 8 combinations of these components (including none of the three and all of the three), and report the best score for each model.
Implications of Aerated Stabilization Basin Dredging on Potential Effluent Toxicity to Fish

Benthal solids accumulated in aerated stabilization basins (ASBs) must be dredged to regain treatment capacity. While dredging restores treatment performance, it has been associated occasionally with the failure to meet regulatory effluent toxicity limits at the time of dredging. A first study of its kind was undertaken to investigate the implications of ASB dredging on potential effluent toxicity to fish. The study showed that benthal solid slurry removed from the quiescent zone of an ASB with a hydraulic dredge was toxic to rainbow trout with a 96‐hour median lethal concentration (LC50) of 2.2%. The high ammonia concentration in the sample was the main cause of fish mortality. Hydrogen sulfide and resin and fatty acids also were present in the dredged material at concentrations that could cause fish mortality. These findings have led to best management practices that can be used to mitigate or eliminate fish toxicity issues during dredging operations.
Generalized Hough Transform for Shape Matching

In this paper we propose a novel approach towards shape matching for image retrieval. The system takes advantages of generalized Hough transform, as it works well in detecting arbitrary shapes even in the presence of gaps and in handling rotation, scaling and shift variations, and solves the heavy computational aspect by introducing a preliminary automatic selection of the appropriate contour points to consider in the matching phase. The numerical simulations and comparisons have confirmed the effectiveness and the efficiency of the method proposed.
Mirror Descent Meets Fixed Share (and feels no regret)

Mirror descent with an entropic regularizer is known to achieve shifting regret bounds that are logarithmic in the dimension. This is done using either a carefully designed projection or by a weight sharing technique. Via a novel unified analysis, we show that these two approaches deliver essentially equivalent bounds on a notion of regret generalizing shifting, adaptive, discounted, and other related regrets. Our analysis also captures and extends the generalized weight sharing technique of Bousquet and Warmuth, and can be refined in several ways, including improvements for small losses and adaptive tuning of parameters.
Triple reuptake inhibitors: a patent review (2006 – 2012)

Introduction: The dysfunctions of three very important monoamine neurotransmitters, serotonin (5-HT), norepinephrine (NE) and dopamine (DA), are associated with some of important CNS diseases such as depression; developing the triple reuptake inhibitors (TRIs) that can rebalance 5-HT, NE and DA through the inhibition of the monoamine reuptake transporters will lead to a more effective and safer antidepressant. Areas covered: This article reviews past 7 years' advances in the development of TRIs; a patent review (2006 – 2012), covering the discovery of new chemical entities, and development status of leading TRI clinical candidates. Expert opinion: The development of TRIs has several challenges, including discovering a “single” agent that has the activities against all three monoamine reuptake transporters SERT, NET and DAT. More important is that the agent must have a “right ratio” to be safer and better tolerated for the treatment of depression. The TRIs can potentially be used for the treatment of other CNS diseases, such as pain, Parkinson's and attention deficit hyperactivity disorder (ADHD), depending on ratios of SERT, NET and DAT.
On the number of factors in codings of three interval exchange

We consider exchange of three intervals with permutation (3, 2, 1). The aim of this paper is to count the cardinality of the set 3iet (N) of all words of length N which appear as factors in infinite words coding such transformations. We use the strong relation of 3iet words and words coding exchange of two intervals, i.e., Sturmian words. The known asymptotic formula #2iet(N)/N-3 similar to 1/pi(2) for the number of Sturmian factors allows us to find bounds 1/3 pi(2) +o(1) \textless= #3iet(N)N-4 \textless= 2 pi(2) + o(1)
Treatment of Visceral Leishmaniasis: Model-Based Analyses on the Spread of Antimony-Resistant L. donovani in Bihar, India

Background Pentavalent antimonials have been the mainstay of antileishmanial therapy for decades, but increasing failure rates under antimonial treatment have challenged further use of these drugs in the Indian subcontinent. Experimental evidence has suggested that parasites which are resistant against antimonials have superior survival skills than sensitive ones even in the absence of antimonial treatment. Methods and Findings We use simulation studies based on a mathematical L. donovani transmission model to identify parameters which can explain why treatment failure rates under antimonial treatment increased up to 65% in Bihar between 1980 and 1997. Model analyses suggest that resistance to treatment alone cannot explain the observed treatment failure rates. We explore two hypotheses referring to an increased fitness of antimony-resistant parasites: the additional fitness is (i) disease-related, by causing more clinical cases (higher pathogenicity) or more severe disease (higher virulence), or (ii) is transmission-related, by increasing the transmissibility from sand flies to humans or vice versa. Conclusions Both hypotheses can potentially explain the Bihar observations. However, increased transmissibility as an explanation appears more plausible because it can occur in the background of asymptomatically transmitted infection whereas disease-related factors would most probably be observable. Irrespective of the cause of fitness, parasites with a higher fitness will finally replace sensitive parasites, even if antimonials are replaced by another drug.
Genetic Differences between the Determinants of Lipid Profile Phenotypes in African and European Americans: The Jackson Heart Study

Genome-wide association analysis in populations of European descent has recently found more than a hundred genetic variants affecting risk for common disease. An open question, however, is how relevant the variants discovered in Europeans are to other populations. To address this problem for cardiovascular phenotypes, we studied a cohort of 4,464 African Americans from the Jackson Heart Study (JHS), in whom we genotyped both a panel of 12 recently discovered genetic variants known to predict lipid profile levels in Europeans and a panel of up to 1,447 ancestry informative markers allowing us to determine the African ancestry proportion of each individual at each position in the genome. Focusing on lipid profiles—HDL-cholesterol (HDL-C), LDL-cholesterol (LDL-C), and triglycerides (TG)—we identified the lipoprotein lipase (LPL) locus as harboring variants that account for interethnic variation in HDL-C and TG. In particular, we identified a novel common variant within LPL that is strongly associated with TG (p = 2.7×10−6) and explains nearly 1% of the variability in this phenotype, the most of any variant in African Americans to date. Strikingly, the extensively studied “gain-of-function” S447X mutation at LPL, which has been hypothesized to be the major determinant of the LPL-TG genetic association and is in trials for human gene therapy, has a significantly diminished strength of biological effect when it is found on a background of African rather than European ancestry. These results suggest that there are other, yet undiscovered variants at the locus that are truly causal (and are in linkage disequilibrium with S447X) or that work synergistically with S447X to modulate TG levels. Finally, we find systematically lower effect sizes for the 12 risk variants discovered in European populations on the African local ancestry background in JHS, highlighting the need for caution in the use of genetic variants for risk assessment across different populations.
MECHANISTIC STUDY OF CRACK INITIATION AND PROPAGATION IN CROSSLINKED ULTRA HIGH MOLECULAR WEIGHT POLYETHYLENES (UHMWPE) SUBJECTED TO STATIC AND CYCLIC LOADING

Many total joint replacement (TJR) designs incorporate a hard bearing material articulating against a soft bearing (polymeric) material. The bearing polymer, typically made of ultra high molecular weight polyethylene (UHMWPE) has been successfully used for the last four decades. However, these bearing materials can fail as a result of in vivo mechanical loads. Reports suggest that the fracture resistance of UHMWPE could be improved which can help the longevity of the components in vivo. Fatigue crack propagation behavior of two crosslinked UHMWPE formulations was investigated to estimate the mechanical governing factor for stable crack propagation. Frequency, waveform and R-ratio were varied between test conditions to determine the governing factor for fatigue crack propagation. It was found that the crack propagation velocity in crosslinked UHMWPE is driven by peak stress intensity (Kmax) in a loading cycle. The findings suggest that stable crack propagation can occur in a static mode rather than in a cyclic mode. Crack initiation from a notch under fatigue conditions is also investigated for remelted 100 kGy material and compared to crack initiation under constant loading conditions. Crack initiation times for fatigue loading conditions were found to be substantially lower compared to static loading conditions. The results suggest that the crosslinked UHMWPE material is resistant under static loading conditions compared to fatigue loading conditions.Fracture resistance of two crosslinked UHMWPE formulations was also investigated. Fracture research utilizing the traditional LEFM and EPFM approaches has not yielded a definite failure criterion for UHMWPE. Therefore, an advanced viscous fracture model has been applied to various notched compact tension specimen geometries to estimate the fracture resistance. Results suggest that the viscous fracture model can be applied to the crosslinked UHMWPE materials and a single value of critical energy (Jc) governs crack initiation and propagation in these materials. This is the first report of a mechanistic approach to crack initiation and propagation in UHMWPE for a range of clinically relevant stress-concentration geometries. A combination of structural analysis of components and material parameter quantification is a path to effective failure prediction in total joint replacement bearings.
Classification of finger pairs from one hand based on spectral features in human EEG

Individual finger movements are well-articulated movements of fine body parts, the successful decoding of which can provide extra degrees of freedom to drive brain computer interface (BCI) applications. Past studies present some unique features revealed from spectral principal component analysis (PCA) on electrophysiological data recorded in both the surface of the brain (electrocorticography, ECoG) and the scalp (electroencephalography, EEG). These features contain discriminable information about fine individual finger movements from one hand. However, the efficacy of these spectral features has not been well investigated under the application of various classifiers. In the present study, we set out to investigate the topic using noninvasive human EEG. Several classifiers were chosen to explore their capability in capturing the spectral PC features to decode individual finger movements pairwisely from one hand using noninvasive EEG, aiming to investigate the efficacy of these spectral features in a decoding task.
A robust method for extracting the mechanical properties of thin films with rough surfaces by nanoindentation

Surface roughness and finite sample thickness are major sources of error in the nanoindentation measurements of thin films as the former makes it difficult to determine the effective contact point between the indenter and sample while the latter limits the usable depth range to be no more than ∼10% of the film thickness. Combining a closed-form model of a film/substrate system with the ability of nanoindentation to monitor the contact depth, the present method defines the two-dimensional shape profile of the indenter contacting the composite system with one unknown constant associated with the model and another unknown constant associated with the effective contact point. On the basis that the obtained shape profile of the rigid indenter is identical to the pre-determined indenter shape profile function, the method extrapolates the two constants simultaneously so as to determine the effective contact point. The method was demonstrated for amorphous diamond-like carbon (DLC) coatings.
A unified strategy for search and result representation for an online bibliographical catalogue

Purpose – One of the biggest concerns of modern information retrieval systems is reducing the user effort required for manual traversal and filtering of long matching document lists. Thus, the first goal of this research is to propose an improved scheme for representation of search results. Further, it aims to explore the impact of various user information needs on the searching process with the aim of finding a unified searching approach well suited for different query types and retrieval tasks.Design/methodology/approach – The BoW online bibliographical catalogue is based on a hierarchical concept index to which entries are linked. The key idea is that searching in the hierarchical catalogue should take advantage of the catalogue structure and return matching topics from the hierarchy, rather than just a long list of entries. Likewise, when new entries are inserted, a search for relevant topics to which they should be linked is required. Therefore, a similar hierarchical scheme for query‐topic matching .
Caspase Cleavage of Gene Products Associated with Triplet Expansion Disorders Generates Truncated Fragments Containing the Polyglutamine Tract*

The neurodegenerative diseases Huntington disease, dentatorubropallidoluysian atrophy, spinocerebellar atrophy type 3, and spinal bulbar muscular atrophy are caused by expansion of a polyglutamine tract within their respective gene products. There is increasing evidence that generation of truncated proteins containing an expanded polyglutamine tract may be a key step in the pathogenesis of these disorders. We now report that, similar to huntingtin, atrophin-1, ataxin-3, and the androgen receptor are cleaved in apoptotic extracts. Furthermore, each of these proteins is cleaved by one or more purified caspases, cysteine proteases involved in apoptotic death. The CAG length does not modulate susceptibility to cleavage of any of the full-length proteins. Our results suggest that by generation of truncated polyglutamine-containing proteins, caspase cleavage may represent a common step in the pathogenesis of each of these neurodegenerative diseases.
A local search method for graph clustering heuristics based on partitional Distribution learning

The community structure of complex networks reveals hidden relationships in the organization of their constituent nodes. Indeed, many practical problems stemming from different fields of knowledge such as Biology, Sociology, Chemistry and Computer Science can be modeled as a graph. Therefore, graph analysis and community detection have become a key component for understanding the inherent relational characteristics underlying different systems and processes. In this regard, distinct unsupervised quality metrics such as conductance, coverage and modularity, have upsurged in order to evaluate the clustering arrangements based on structural and topological characteristics of the cluster space. In this regard graph clustering can be formulated as an optimization problem based on the maximization of one of such metrics, for which a number of nature-inspired heuristic solvers has been proposed in the literature. This paper elaborates on a novel local search method that allows boosting the convergence of such heuristics by estimating and sampling the cluster arrangement distribution from the set of intermediate produced solutions of the algorithm at hand. Simulation results reveal a generalized better performance compared towards other community detection algorithms in synthetic and real datasets.
Heterogeneous ribonucleoprotein C displays a repressor activity mediated by T-cell intracellular antigen-1-related/like protein to modulate Fas exon 6 splicing through a mechanism involving Hu antigen R

T-cell intracellular antigen (TIA)-proteins are known regulators of alternative pre-mRNA splicing. In this study, pull-down experiments and mass spectrometry indicate that TIAR/TIAL1 and hnRNP C1/C2 are associated in HeLa nuclear extracts. Co-immunoprecipitation and GST-pull-down assays confirmed this interaction. Interestingly, binding requires the glutamine-rich (Q-rich) C-terminal domain of TIAR and the leucine-rich plus acidic residues-rich C-terminal domains of hnRNP C1/C2. This interaction also occurs in an RNA-dependent manner. Recombinant GFP-TIAR and RFP-hnRNP C1 proteins display partial nuclear co-localization when overexpressed in HeLa cells, and this requires the Q-rich domain of TIAR. hnRNP C1 overexpression in the presence of rate-limiting amounts of TIAR in HeLa and HEK293 cells affects alternative splicing of Fas and FGFR2 minigenes, promoting Fas exon 6 and FGFR2 exon K-SAM skipping, respectively. The repressor activity of hnRNP C1 on Fas exon 6 splicing is mediated by Hu antigen R (HuR). Experiments involving tethering approaches showed that the repressor capacity of hnRNP C1 is associated with an exonic splicing silencer in Fas exon 6. This effect was reversed by splice-site strengthening and is linked to its basic leucine zipper-like motif. These results suggest that hnRNP C1/C2 acts as a bridge between HuR and TIAR to modulate alternative Fas splicing.
Active Learning for Cost-Sensitive Classification

We design an active learning algorithm for cost-sensitive multiclass classification: problems where different errors have different costs. Our algorithm, COAL, makes predictions by regressing to each label's cost and predicting the smallest. On a new example, it uses a set of regressors that perform well on past data to estimate possible costs for each label. It queries only the labels that could be the best, ignoring the sure losers. We prove COAL can be efficiently implemented for any regression family that admits squared loss optimization; it also enjoys strong guarantees with respect to predictive performance and labeling effort. We empirically compare COAL to passive learning and several active learning baselines, showing significant improvements in labeling effort and test cost on real-world datasets.