Miracle-dz/UniFAR-FTUs huggingface dataset:
Lithography-Free Plasmonic Color Printing with Femtosecond Laser on Semicontinuous Silver Films

Plasmonic color printing with semicontinuous metal films is a lithography-free, non-fading, and environment-friendly method of generation of bright colors. Such films are comprised of metal nanoparticles, which resonate at different wavelengths upon light illumination depending on the size and shape of the nanoparticles. To achieve an experimentally demonstrated structure that was optimized in terms of broader color range and increased stability, variable Ag semicontinuous metal films were deposited on a metallic mirror with a sub-wavelength-thick dielectric spacer. Femtosecond laser post-processing was then introduced to extend the color gamut through spectrally induced changes from blue to green, red, and yellow. Long-term stability and durability of the structures were addressed to enable non-fading colors with an optimized overcoating dielectric layer. The thickness of the proposed designs is on the order of 100 nanometers, and it can be deposited on any substrate. These structures generate a broad range of long-lasting colors in reflection that can be applied to real-life artistic or technological applications with a spatial resolution on the order of 0.3 mm or less.
Anonymization of labeled TOF-MRA images for brain vessel segmentation using generative adversarial networks

Anonymization and data sharing are crucial for privacy protection and acquisition of large datasets for medical image analysis. This is a big challenge, especially for neuroimaging. Here, the brain's unique structure allows for re-identification and thus requires non-conventional anonymization. Generative adversarial networks (GANs) have the potential to provide anonymous images while preserving predictive properties. Analyzing brain vessel segmentation as a use case, we trained 3 GANs on time-of-flight (TOF) magnetic resonance angiography (MRA) patches for image-label generation: 1) Deep convolutional GAN, 2) Wasserstein-GAN with gradient penalty (WGAN-GP) and 3) WGAN-GP with spectral normalization (WGAN-GP-SN). The generated image-labels from each GAN were used to train a U-net for segmentation and tested on real data. Moreover, we applied our synthetic patches using transfer learning on a second dataset. For an increasing number of up to 15 patients we evaluated the model performance on real data with and without pre-training. The performance for all models was assessed by the Dice Similarity Coefficient (DSC) and the 95th percentile of the Hausdorff Distance (95HD). Comparing the 3 GANs, the U-net trained on synthetic data generated by the WGAN-GP-SN showed the highest performance to predict vessels (DSC/95HD 0.82/28.97) benchmarked by the U-net trained on real data (0.89/26.61). The transfer learning approach showed superior performance for the same GAN compared to no pre-training, especially for one patient only (0.91/25.68 vs. 0.85/27.36). In this work, synthetic image-label pairs retained generalizable information and showed good performance for vessel segmentation. Besides, we showed that synthetic patches can be used in a transfer learning approach with independent data. This paves the way to overcome the challenges of scarce data and anonymization in medical imaging.
Efficient isolation and quantification of circulating tumor cells in non-small cell lung cancer patients using peptide-functionalized magnetic nanoparticles

Background Circulating tumor cells (CTCs) carry a wealth of information on primary and metastatic tumors critical for enhancing the understanding of the occurrence, progression and metastasis of non-small cell lung cancer (NSCLC). However, the low sensitivity of traditional tumor detection methods limits the application of CTCs in the treatment and disease surveillance of NSCLC. Therefore, CTCs isolation and detection with high sensitivity is highly desired especially for NSCLC patients, which is significant because of high occurrence and mortality. While it is very challenging because of the lower expression of CTC positive biomarkers such as epithelial cell adhesion molecules and cytokeratins (EpCAM and CKs), herein we report a method based on peptide-functionalized magnetic nanoparticles with high CTC capture efficiency, which demonstrates superiority in NSCLC clinical applications. Methods For analysis and comparison of the peptide-functionalized magnetic nanoparticles (TumorFisher, Nanopep Corp.) and the antibody-modified magnetic beads (CellSearch, Janssen Diagnostics, LLC), two NSCLC cell lines, A549 and NCI-H1975 were chosen to measure the binding affinity and capture efficiency. In order to compare the effect of the clinical application of these two detection systems, 7 early stage patients with NSCLC were enrolled in this study. To further explore the clinical utility of CTC counting in different stages, 81 NSCLC patients in stage I–IV were enrolled for CTC enumeration and statistical analysis. Results The binding affinities of the recognition peptide to A549 and NCI-H1975 are 76.7%±11.0% and 70.1%±4.8%, respectively, which is similar with the positive control group (anti-EpCAM antibodies). CTCs were captured in 5/7 (71.4%) of early stage NSCLC patients with NSCLC in TumorFisher system, which is higher than CellSearch, and the false negative of TumorFisher is much lower than CellSearch. In a larger clinical cohort, the CTC numbers of NSCLC patients varied in different stages and the overall detection rate of TumorFisher was 59/81 (72.8%), with the similar proportion in stage I (21/29, 72.4%), II (17/22, 77.3%) and III (16/21, 76.2%). Conclusions Highly efficient CTC isolation technique based on peptide-magnetic nanoparticles was firstly applied in NSCLC patients. Compared with the antibody-based the technique, the higher CTC detection rates (71.4%) in NSCLC patient blood samples were demonstrated for the patients in different stages, I–IV, especially in early stages. This indicates the feasibility of the clinical utility of this new technique in early stage screening, prognosis and therapy evaluation of NSCLC.
A Comparison of the Bioavailability of DL -Methionine and Methionine Hydroxy Analogue Acid for the Commercial Laying Hen

Abstract Two 8-wk experiments, using Hy-Line W36® hens, compared two sources of methionine (Met) activity. The basal corn-soybean meal diet was deficient in methionine. 0.028, 0.055, 0.083 and 0.138% supplemental DL-Methionine (DLM) or methionine hydroxyl analogue acid (MHAA) were supplemented to the basal diet on an equimolar basis as DLM or MHAA in Experiment 1. The 0.138% level was replaced with 0.165% in Experiment 2. In Experiment 2 supplemental lysine (Lys), arginine (Arg), tryptophan (Trp), ahreonine (Thr), valine (Val), and isoleucine (Ile) were added to the basal diet. Regression equations were calculated and we fitted using linear analysis for egg content regressed on Met intake. The data from these experiments indicate that DLM and MHAA are equal on a molar basis.
Morphological and molecular systematics of the ‘Cliona viridis complex’ from south-eastern Brazil

Bioeroding sponges of the Cliona viridis species complex play a large role in carbonate cycling and reef health. In the present study we provide the first record and a description of a Mediterranean lineage of C. viridis (Schmidt, 1862) in the south-western Atlantic. Specimens were collected in Maricás Archipelago, Rio de Janeiro State in September 2010 by scuba diving at 10–12 m depth and deposited in the Porifera collection of Museu Nacional, Universidade Federal do Rio de Janeiro. Morphologically, the specimens presently examined are very similar to those described in the beta and gamma growth form from the Mediterranean. The Brazilian and Mediterranean specimens share large and irregular papillae over 2 cm in diameter, megasclere tylostyles up to 500 µm long and microsclere spirasters with up to five twists and 34 µm long. A Maximum Likelihood analysis of 28S rDNA of C. viridis, C. aprica, C. jullieni, C. schmidti and C. varians was performed for a genetic identification of the Brazilian specimens. The Brazilian material is phylogenetically closer to the Mediterranean C. viridis than to the Caribbean and Indian Ocean members of this species complex included in the present analysis. Our results suggest that C. viridis is a cryptogenic species with a distribution extending from the Mediterranean to the eastern Atlantic and in the SE Brazilian coast or further.
Deep Metric Learning Meets Deep Clustering: An Novel Unsupervised Approach for Feature Embedding

Unsupervised Deep Distance Metric Learning (UDML) aims to learn sample similarities in the embedding space from an unlabeled dataset. Traditional UDML methods usually use the triplet loss or pairwise loss which requires the mining of positive and negative samples w.r. t. anchor data points. This is, however, challenging in an unsupervised setting as the label information is not available. In this paper, we propose a new UDML method that overcomes that challenge. In particular, we propose to use a deep clustering loss to learn centroids, i.e., pseudo labels, that represent semantic classes. During learning, these centroids are also used to reconstruct the input samples. It hence ensures the representativeness of centroids - each centroid represents visually similar samples. Therefore, the centroids give information about positive (visually similar) and negative (visually dissimilar) samples. Based on pseudo labels, we propose a novel unsupervised metric loss which enforces the positive concentration and negative separation of samples in the embedding space. Experimental results on benchmarking datasets show that the proposed approach outperforms other UDML methods.
Design and Fabrication of Novel Digital Transcranial Electrical Stimulator for Medical and Psychiatry Applications

In this article, we design a novel Transcranial Electrical Stimulator for medical applications, which is very cheap and can produce the desired signals very accurately. Our fabricated stimulator generates all current signals related to Transcranial Electrical Stimulation (TES) methods, i.e. Transcranial Direct Current Stimulation (tDCS), Transcranial Pulsed Current Stimulation (tPCS), Cranial Electrotherapy Stimulation (CES), and Microcurrent Electrical Therapy (MET). The proposed device has been constructed of an advanced digital controller which makes it tunable. One of the major advantages of the device is its ability to generate Burst pulses.
In-vitro mass propagation of the near-extinct Mammillaria san-angelensis Sanchez-Mejorada

SummaryThe genus Mammillaria includes many valuable species some of which are near to extinction. The beautiful white-spined M. san-angelensis has been reported to be extinct. Using the related species M. haageana in preliminary trials, the in-vitro mass propagation from young seedlings of the near-extinct M. san-angelensis has been achieved. Morphogenetic responses in M. haageana and M. san-angelensis were similar. The results were influenced mainly by two factors: the presence of the cytokinin 6-benzyladenine (BA) and the origin of the explant. Callus formation rarely occurred; however, shoots and multiple shoots were obtained when tip (apical) explants were exposed to different concentrations of BA and naphthalene acetic acid (NAA). Only multiple shoots were apparent when lateral explants were exposed to similar experimental conditions. Mass regeneration was most successful when lateral explants were subjected to three treatments: BA alone at 0.1 mg l−1; BA 0.1 mg l−1 combined with NAA at 0.01 and BA 1.
Solving the k-sparse Eigenvalue Problem with Reinforcement Learning

We examine the possibility of using a reinforcement learning (RL) algorithm to solve large-scale eigenvalue problems in which the desired the eigenvector can be approximated by a sparse vector with at most $k$ nonzero elements, where $k$ is relatively small compare to the dimension of the matrix to be partially diagonalized. This type of problem arises in applications in which the desired eigenvector exhibits localization properties and in large-scale eigenvalue computations in which the amount of computational resource is limited. When the positions of these nonzero elements can be determined, we can obtain the $k$-sparse approximation to the original problem by computing eigenvalues of a $k\times k$ submatrix extracted from $k$ rows and columns of the original matrix. We review a previously developed greedy algorithm for incrementally probing the positions of the nonzero elements in a $k$-sparse approximate eigenvector and show that the greedy algorithm can be improved by using an RL method to refine the selection of $k$ rows and columns of the original matrix. We describe how to represent states, actions, rewards and policies in an RL algorithm designed to solve the $k$-sparse eigenvalue problem and demonstrate the effectiveness of the RL algorithm on two examples originating from quantum many-body physics.
Phytochemical and Antioxidant Evaluation of Moullava spicata (Dalzell) Nicolson Leaf Extract

Background: Moullava spicata (Dalzell) Nicolson is an endemic medicinal plant and its leaves are used to treat many diseases. Aims: The aim of the study was to evaluate the phytochemical, antifungal and antioxidant status of Moullava spicata leaf extract. Methods and Materials: The total phenolic content of leaf was measured by FolinCiolteau’s assay. Antioxidant activity of the plant was detected by using in-vitro 2,2diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonicacid) (ABTS), Phosphomolybdenum reduction and Ferric reducing antioxidant power (FRAP) assay. Antifungal activity was detected by Agar cup diffusion method. Result: The phytochemical analysis showed that extracts of M. spicata contained pharmacologically important phytochemicals. Acetone extract showed higher total antioxidants activity and reducing power. However DPPH and ABTS scavenging activity were higher in methanol and acetone extracts respectively. Conclusion: Present study showed pharmacologically significant phytochemical and high antioxidant status on leaf. Research Article Annual Research & Review in Biology, 4(1): 188-197, 2014 189
Construction and Maintenance of the Incubation Mounds of the Australian Brush-turkey Alectura lathami

Most male Australian Brush-turkeys at Mt. Tamborine in south-eastem Queensiand began to construct incubation mounds in winter (May-June) following falls of rain that thoroughly dampened the leaf-litter. Mounds were tended for up to nine months before being abandoned around January-February. Two distinct phases of activity were identified: the Construction Phase, characterised by accumulation of mound-materials by the males, and the Maintenance Phase when the amount of mound-work was greatly reduced. The mean temperatures of mounds was 33.3°C. Thermal stability was achieved without the direct manipulations of mounds by males. There was little indication of pair bonding between males and females, suggesting a non-monogamous mating system.
Applications of Stable Isotope Technology in Physiological Ecology

Analyses of the natural abundances of stable isotopes of carbon, hydrogen, oxygen, nitrogen and sulphur have widespread applications for the natural sciences. In the short term, the relative depletion of '3C in plants has been used to model photosynthetic limitation and carboxylation pathway, and leads to the long-term analysis of canopy water-use efficiency, trophic levels in ecosystems and evaluation of changes in global CO2 supply. Alternatively, the abundance of D (2H) and 180 in waters, sediments and plants has been used to model climate change over millennia, although the initial fractionation processes in plants still require elucidation. While '5N and 34S are apparently not subject to such large fractionation during assimilation by primary producers, they can be used to deduce origins and sources of N and S fertilization in ecosystems. With a wealth of recent review material dealing with the specific applications of these isotopes (Kaplan, 1975; DeNiro, 1987; Peterson & Fry, 1987; Raven, 1987; Ehleringer & Osmond, 1989; Rundel, Ehleringer & Nagy, 1989), a brief review such as this must attempt to summarize and integrate recent developments. Given the exponential interest in stable isotope analyses, the aim of the following article should be: first, to highlight methodological and theoretical constraints for any new study; second, to evaluate the current applications in physiological ecology; and finally to suggest some potential developments. It is hoped that anyone planning an excursion into this field will find this approach useful, although apologies must be made for the subjectivity and brevity with which these applications have been selected and summarized and for the preponderance of the applications involving carbon. Where appropriate, reference will be made to more comprehensive studies which will enable the detailed background of each isotope to be investigated, although applications involving the addition of stable isotopes for 'labelling' are not considered.
Regulation of Heat-Induced Apoptosis by Loss of miR-23a-Dependent Control of Noxa in Human Cells and its Suppression by HSP70

REGULATION OF HEAT-INDUCED APOPTOSIS BY LOSS OF MIR-23ADEPENDENT CONTROL OF NOXA IN HUMAN CELLS AND ITS SUPPRESSION BY HSP70 Rabih Roufayel Advisor: University of Guelph, 2015 Dr. Richard D. Mosser Protein damaging stress such as hyperthermia can activate a process of cellular destruction known as apoptosis. Exposure to hyperthermia can also induce the synthesis of heat shock proteins including HSP70, which can protect cells from stress-induced apoptosis. Apoptosis is controlled by proand anti-apoptotic members of the Bcl-2 family. The pro-apoptotic BH3-only protein NOXA activates this death pathway by inhibiting the anti-apoptotic Bcl-2 family protein MCL-1. In this thesis we sought to investigate (i) whether Noxa mRNA levels are regulated post-transcriptionally by miRNA-mediated suppression, (ii) if expression of this miRNA is altered in heat stressed cells and (iii) if the effect of hyperthermia on expression of this miRNA is affected by HSP70 levels. We found that the miRNA miR-23a binds the Noxa mRNA 3’ UTR and suppresses translation. miR-23a has a short half-life, which is reduced in heat shocked cells leading to Noxa mRNA stabilization and increased NOXA protein expression. Cells overexpressing HSP70 contain elevated levels of miR-23a due to a reduced turnover rate. miR-23a levels remain elevated in HSP70 expressing cells exposed to hyperthermia and consequently NOXA protein levels are not increased and apoptosis is suppressed. This thesis also provides evidence that CDK5, an atypical cyclin-dependent kinase, regulates the expression of miR-23a. Hyperthermic treatment led to a loss of CDK5 tyrosine-15 phosphorylation, which was prevented by HSP70 overexpression. Treatment with the CDK5 inhibitor roscovitine caused an increase in NOXA protein levels and sensitized cells to heat-induced apoptosis. The accumulation of NOXA was not due to an effect of CDK5 on the stability of NOXA since its half-life was not affected in roscovitine-treated cells or in cells expressing a dominant-negative CDK5. Instead, CDK5 inhibition resulted in a decrease in miR-23a levels causing Noxa mRNA levels to accumulate. Cells overexpressing miR-23a were found to be resistant to roscovitine induced cell death. All together, these results indicate that HSP70 inhibits stress-induced apoptosis by maintaining miR-23a levels and thereby preventing NOXA accumulation. We suggest that HSP70 could be beneficial to tumor cells by helping to maintain the expression of oncogenic miRNAs under conditions of cellular stress.
Mixed-function Oxidase and Glutathione S-Transferase Activity in a Susceptible and a Fenitrothion-resistant Strain of Oryzaephilus surinamensis (Coleoptera: Cucujidae)

Subcellular preparations of larval and adult Oryzaephilus surinamensts (L.) were used to study involvement of mixed-function oxidases and glutathione S-transferases in the resistance mechanism of a strain highly resistant to fenitrothion. Cytochrome P450 levels per milligram microsomal protein were 3- and 10-fold greater in resistant larvae and adults, respectively, compared with susceptible insects; corresponding increases for aldrin epoxidase activities were 14- and 50-fold. Increases in glutathione S-transferase activities in the resistant strain were minor compared with those of the susceptible strain. Enhanced levels of mixed-function oxidases may indicate a possible biochemical mechanism for fenitrothion resistance in this strain.
Control Issues of KKLT

We analyze to which extent the KKLT proposal for the construction of de Sitter vacua in string theory is quantitatively controlled. Our focus is on the quality of the 10d supergravity approximation. As our main finding, we uncover and quantify an issue which one may want to call the “singular‐bulk problem”. In particular, we show that, requiring the curvature to be small in the conifold region, one is generically forced into a regime where the warp factor becomes negative in a significant part of the Calabi‐Yau orientifold. This implies true singularities, independent of the familiar, string‐theoretically controlled singularities of this type in the vicinity of O‐planes. We also discuss possible escape routes as well as other control issues, related to the need for a large tadpole and hence for a complicated topology.
Physical Grounds for Causal Perspectivalism

We ground the asymmetry of causal relations in the internal physical states of a special kind of open and irreversible physical system, a causal agent. A causal agent is an autonomous physical system, maintained in a steady state, far from thermal equilibrium, with special subsystems: sensors, actuators, and learning machines. Using feedback, the learning machine, driven purely by thermodynamic constraints, changes its internal states to learn probabilistic functional relations inherent in correlations between sensor and actuator records. We argue that these functional relations just are causal relations learned by the agent, and so such causal relations are simply relations between the internal physical states of a causal agent. We show that learning is driven by a thermodynamic principle: the error rate is minimised when the dissipated power is minimised. While the internal states of a causal agent are necessarily stochastic, the learned causal relations are shared by all machines with the same hardware embedded in the same environment. We argue that this dependence of causal relations on such ‘hardware’ is a novel demonstration of causal perspectivalism.
Exploring the potential activity spectrum of two 5-nitroindazolinone prototypes on different Trypanosoma cruzi strains

In the present study, the potential activity of two 5-nitroindazole derivatives previously proposed as suitable antichagasic prototypes was further evaluated on diverse Trypanosoma cruzistrains belonging to two discrete typing units (DTUs) frequently associated with human infection (i.e. DTUs TcII and TcVI). The trypanocidal profile that both 2-benzyl-1-propyl (22) and 2-benzyl-1-butyl (24) derivatives achieved on Tulahuen amastigotes (IC50 = 3·56 ± 0·99 and 6·31 ± 1·04 µM, respectively) correlates with that of formerly obtained on CL Brener, corroborating an outstanding activity on DTU TcVI parasites. Moreover, a sequential screening on extracellular and intracellular stages of T. cruzi Y (DTU TcII) demonstrated also the effectiveness of 22 and 24 over this strain on a similar range of activity (IC50 epimastigotes = 3·55 ± 0·47 and 7·92 ± 1·63 µM, IC50 amastigotes = 2·80 ± 0·46 and 9·02 ± 5·26 µM, respectively). These results, supported by a lack of toxicity registered over either L929 fibroblasts or primary cultures of cardiomyocytes, confirm that 5-nitroindazolinones 22 and 24 display great selectivity on both drug-sensitive (CL and Tulahuen) and drug-moderately resistant (Y) T. cruzi strains, and therefore, represent an important outcome in the research of Chagas disease chemotherapy.