Miracle-dz/UniFAR-FTUs huggingface dataset:
The evolution of early vertebrate photoreceptors

Meeting the challenge of sampling an ancient aquatic landscape by the early vertebrates was crucial to their survival and would establish a retinal bauplan to be used by all subsequent vertebrate descendents. Image-forming eyes were under tremendous selection pressure and the ability to identify suitable prey and detect potential predators was thought to be one of the major drivers of speciation in the Early Cambrian. Based on the fossil record, we know that hagfishes, lampreys, holocephalans, elasmobranchs and lungfishes occupy critical stages in vertebrate evolution, having remained relatively unchanged over hundreds of millions of years. Now using extant representatives of these ‘living fossils’, we are able to piece together the evolution of vertebrate photoreception. While photoreception in hagfishes appears to be based on light detection and controlling circadian rhythms, rather than image formation, the photoreceptors of lampreys fall into five distinct classes and represent a critical stage in the dichotomy of rods and cones. At least four types of retinal cones sample the visual environment in lampreys mediating photopic (and potentially colour) vision, a sampling strategy retained by lungfishes, some modern teleosts, reptiles and birds. Trichromacy is retained in cartilaginous fishes (at least in batoids and holocephalans), where it is predicted that true scotopic (dim light) vision evolved in the common ancestor of all living gnathostomes. The capacity to discriminate colour and balance the tradeoff between resolution and sensitivity in the early vertebrates was an important driver of eye evolution, where many of the ocular features evolved were retained as vertebrates progressed on to land.
Graphene and Graphene Nanomesh Spintronics

Spintronics, which manipulate spins but not electron charge, are highly valued as energy and thermal dissipationless systems. A variety of materials are challenging the realization of spintronic devices. Among those, graphene, a carbon mono-atomic layer, is very promising for efficient spin manipulation and the creation of a full spectrum of beyond-CMOS spin-based nano-devices. In the present article, the recent advancements in graphene spintronics are reviewed, introducing the observation of spin coherence and the spin Hall effect. Some research has reported the strong spin coherence of graphene. Avoiding undesirable influences from the substrate are crucial. Magnetism and spintronics arising from graphene edges are reviewed based on my previous results. In spite of carbon-based material with only sp2 bonds, the zigzag-type atomic structure of graphene edges theoretically produces spontaneous spin polarization of electrons due to mutual Coulomb interaction of extremely high electron density of states (edge states) localizing at the flat energy band. We fabricate honeycomb-like arrays of low-defect hexagonal nanopores (graphene nanomeshes; GNMs) on graphenes, which produce a large amount of zigzag pore edges, by using a nonlithographic method (nanoporous alumina templates) and critical temperature annealing under high vacuum and hydrogen atmosphere. We observe large-magnitude ferromagnetism, which arises from polarized spins localizing at the hydrogen-terminated zigzag-nanopore edges of the GNMs, even at room temperature. Moreover, spin pumping effects are found for magnetic fields applied in parallel with the few-layer GNM planes. Strong spin coherence and spontaneously polarized edge spins of graphene can be expected to lead to novel spintronics with invisible, flexible, and ultra-light (wearable) features.
Intra-arterial treatment of patients with acute ischemic stroke and internal carotid artery occlusion: a literature review

Introduction Acute ischemic stroke (AIS) due to internal carotid artery (ICA) occlusion has a poor prognosis if treated by intravenous thrombolysis. Intra-arterial (IA) treatment is a promising alternative. However, its effectiveness is still unproven. Methods We collected all publications describing results of IA treatment in acute ICA occlusions. All studies with 10 patients or more providing data on clinical outcome were included. We pooled the results by occlusion site (intracranial, extracranial or tandem occlusions) and treatment method, using recanalization, symptomatic intracranial hemorrhage, mortality and favorable clinical outcome (defined as modified Rankin Scale score 0–2) as outcome measures. Results 32 studies totaling 1107 patients were included. In the population with intracranial ICA occlusion, recanalization (69% vs 38%, p<0.001) and favorable outcome (34% vs 12%, p<0.001) rates were significantly higher for mechanical thrombectomy than for IA thrombolysis. In the population with extracranial ICA occlusion, stenting resulted in a higher recanalization rate (87% vs 48%, p=0.001) and favorable outcome rate (68% vs 15%, p<0.001) and lower mortality (18% vs 41%, p=0.048) than IA thrombolysis. In the tandem occlusion population, a statistically significant lower death rate was found for the group treated with IA thrombolysis only compared with the groups with any mechanical treatment of the intracranial occlusion (0% vs 34%, p=0.002 and 0% vs 33%, p=0.001). Conclusions This review shows that, for patients with AIS due to an extracranial and/or intracranial ICA occlusion, stenting and mechanical thrombectomy are associated with higher recanalization rates and improved functional outcomes compared with IA thrombolysis.
Recent coral reef conditions in Weh Island, Aceh Province, Indonesia

Abstract. Utama RS, Hadi TA. 2018. Recent coral reef conditions in Weh Island, Aceh Province, Indonesia. Ocean Life 2: 47-53. Over the past several decades the coral reef conditions have been declining globally due to human activities and natural disturbances. In the last decade, several natural phenomena such as a 2010 tsunami and 2016 coral bleaching event have been recorded in Weh Island and resulted in coral cover decline. The aims of this study are to observe current status of coral diversity and reef conditions at Weh Island. The study was carried out during February 2017 at ten study sites. The methods used were Underwater Photo Transect (UPT) analyzed with CPCe 4.1. software. Live coral coverage ranging from 10% to 57,33% with average live coral cover at Weh island at 28.48% ± 5.334 (moderate condition). 82 species, 31 genera, 13 families of coral were recorded in this study with four species found at all sites. No take and no anchor zones from Panglima Laot regulation at the Iboih areas provide a positive impact for maintaining coral health.
Distance-enhancing codes for digital recording

We review recent progress in the design of high-rate, distance-enhancing codes that achieve the matched-filter-bound (MFB) on the E/sup 2/PR4 channel, h(D)=(1-D)(1+D)/sup 3/, including a rate 8/9 block code satisfying a time-varying maximum-transition-run (TMTR) constraint. We then prove that these TMTR codes also achieve the MFB on the E/sup 3/PR4 channel, h(D)=(1-D)(1+D)/sup 4/. Finally, we describe a TMTR constraint that achieves the MFB on the PR2 channel, h(D)=(1+D)/sup 2/, and the EPR2 channel, h(D)=(1+D)/sup 3/, both of which are of interest as channel models in optical recording, and we present a new, rate 3/4 block code that satisfies this constraint. Computer simulation results confirm that the codes provide substantial performance improvement in additive, white, Gaussian noise (AWGN).
Testing Properties of Sparse Images

We initiate the study of testing properties of images that correspond to sparse 0/1-valued matrices of size n × n. Our study is related to but different from the study initiated by Raskhodnikova (Proceedings of RANDOM, 2003), where the images correspond to dense 0/1-valued matrices. Specifically, while distance between images in the model studied by Raskhodnikova is the fraction of entries on which the images differ taken with respect to all n^2 entries, the distance measure in our model is defined by the fraction of such entries taken with respect to the actual number of 1’s in the matrix. We study several natural properties: connectivity, convexity, monotonicity, and being a line. In all cases we give testing algorithms with sub linear complexity, and in some of the cases we also provide corresponding lower bounds.
Scalable Graph Hashing with Feature Transformation

Hashing has been widely used for approximate nearest neighbor (ANN) search in big data applications because of its low storage cost and fast retrieval speed. The goal of hashing is to map the data points from the original space into a binary-code space where the similarity (neighborhood structure) in the original space is preserved. By directly exploiting the similarity to guide the hashing code learning procedure, graph hashing has attracted much attention. However, most existing graph hashing methods cannot achieve satisfactory performance in real applications due to the high complexity for graph modeling. In this paper, we propose a novel method, called scalable graph hashing with feature transformation (SGH), for large-scale graph hashing. Through feature transformation, we can effectively approximate the whole graph without explicitly computing the similarity graph matrix, based on which a sequential learning method is proposed to learn the hash functions in a bitwise manner. Experiments on two datasets with one million data points show that our SGH method can outperform the state-of-the-art methods in terms of both accuracy and scalability.
Evaluation of Antibacterial and Antitumor Activities of Some Turkish Endemic Plants

Purpose: To investigate the antibacterial and antitumor activities of the aerial parts of 8 different Turkish endemic plants (Phlomis russeliana, Phlomis armeniaca, Astragalus brachypterus, Astrantia maxima, Ptilostemon afer, Senecio castagneanus, Echium orientale and Arum euxinum). Methods: Two different bioassays were performed to evaluate the antibacterial and antitumor activities of the endemic plants. For each plant, 3 types of extracts (aqueous, methanol and ethanol) were prepared, giving a total of 24 extracts tested. The disc diffusion assay was used to screen for antibacterial activity against 10 bacteria including Streptococcus pyogenes, Staphylococcus aureus, Staphylococcus epidermidis, Escheria coli, Pseudomonas aeruginosa, Salmonella typhimurium, Serratia marcescens, Proteus vulgaris, Enterobacter cloacea, and Klebsiella pneumoniae. Five different antibiotics (ampicillin, carbenicillin, chloramphenicol, erythromycin and tetracycline) were used as positive controls. Antitumor activity was evaluated using potato disc diffusion bioassay with camptothecin as positive control. Results: The highest antibacterial activity was observed for all extracts of A. brachypterus against S. pyogenes (15.0 - 16.3 mm inhibition zone). The aqueous extract of S. castagneanus showed the strongest antibacterial activity against S. pyogenes (14.3 mm). Furthermore, alcohol extracts (ethanol and methanol) of P. russeliana exhibited moderate activity against S. epidermidis (9 and 8.5 mm, respectively) and S. pyogenes (9.5 mm). High antitumor activity was observed for all extracts of A. brachypterus (91.7 - 100 % tumor inhibition). In addition, ethanol extract of P. russeliana (75 % inhibition) exhibited strong antitumor activity. Conclusion: The present study reveals the strong antibacterial and antitumor activities of A. brachypterus. However, the active components of the plant extracts needs to be identified in future studies.
Evidence of a role for TRPC channels in VEGF-mediated increased vascular permeability in vivo.

Vascular endothelial growth factor (VEGF) increases vascular permeability by stimulating endothelial Ca(2+) influx. Here we provide evidence that links VEGF-mediated increased permeability and endothelial intracellular Ca(2+) concentration ([Ca(2+)](i)) with diacylglycerol (DAG)-mediated activation of the transient receptor potential channels (TRPCs). We used the Landis-Michel technique to measure changes in hydraulic conductivity (L(p)) and fluorescence photometry to quantify changes in endothelial [Ca(2+)](i) in individually perfused Rana mesenteric microvessels in vivo and transfected nonendothelial cells in vitro. The membrane-permeant DAG analog 1-oleoyl-2-acetyl-sn-glycerol (OAG, 100 microM), which is known to increase Ca(2+) influx through TRPCs, transiently increased L(p) 3.8 +/- 1.2-fold (from 1.6 +/- 0.8 to 9.8 +/- 2.7 x 10(-7) cm.s(-1). cmH(2)O(-1); P < 0.0001; n = 18). Protein kinase C inhibition by bisindolylmaleimide (1 microM) did not affect the OAG-induced increases in L(p). OAG also significantly increased microvascular endothelial [Ca(2+)](i) in vivo (n = 13; P < 0.0001), which again was not sensitive to protein kinase C inhibition. VEGF induced a transient increase in endothelial [Ca(2+)](i) in human embryonic kidney cells (HEK-293) that were cotransfected with VEGF receptor 2 and TRPC-6 but not with control, VEGF receptor 2, or TRPC-6 expression vector alone (P < 0.01; n = 9). Flufenamic acid, which has been shown to enhance activity of TRPC-6 but inhibit TRPC-3 and -7, enhanced the VEGF-mediated increase in L(p) in approximately half of the vessels tested but inhibited the response in the other half of the vessels. These data provide evidence consistent with the hypothesis that VEGF increases vascular permeability via DAG-mediated Ca(2+) entry through TRPCs. Although the exact identities of the TRPCs remain to be confirmed, TRPC-6 appears to be a likely candidate in approximately half of the vessels.
Low Coronary Microcirculatory Resistance Associated With Profound Hypotension During Intravenous Adenosine Infusion: Implications for the Functional Assessment of Coronary Stenoses

Background—Intravenous adenosine infusion produces coronary and systemic vasodilatation, generally leading to systemic hypotension. However, adenosine-induced hypotension during stable hyperemia is heterogeneous, and its relevance to coronary stenoses assessment with fractional flow reserve (FFR) remains largely unknown. Methods and Results—FFR, coronary flow reserve, and index of microcirculatory resistance were measured in 93 stenosed arteries (79 patients). Clinical and intracoronary measurements were analyzed among tertiles of the percentage degree of adenosine-induced hypotension, defined as follows: %&Dgr;Pa=–[100–(hyperemic aortic pressure×100/baseline aortic pressure)]. Overall, %&Dgr;Pa was –13.6±12.0%. Body mass index was associated with %&Dgr;Pa (r=0.258; P=0.025) and obesity, an independent predictor of profound adenosine-induced hypotension (tertile 3 of %&Dgr;Pa; odds ratio, 3.95 [95% confidence interval, 1.48–10.54]; P=0.006). %&Dgr;Pa was associated with index of microcirculatory resistance (&rgr;=0.311; P=0.002), coronary flow reserve (r=–0.246; P=0.017), and marginally with FFR (r=0.203; P=0.051). However, index of microcirculatory resistance (&bgr;=0.003; P<0.001) and not %&Dgr;Pa (&bgr;=–0.001; P=0.564) was a predictor of FFR. Compared with tertiles 1 and 2 of %&Dgr;Pa (n=62 [66.6%]), stenoses assessed during profound adenosine-induced hypotension (n=31 [33.3%]) had lower index of microcirculatory resistance (12.4 [8.6–22.7] versus 20 [15.8–35.5]; P=0.001) and FFR values (0.77±0.13 versus 0.83±0.12; P=0.021), as well as a nonsignificant increase in coronary flow reserve (2.5±1.1 versus 2.2±0.87; P=0.170). Conclusions—The modification of systemic blood pressure during intravenous adenosine infusion is related to hyperemic microcirculatory resistance in the heart. Profound adenosine-induced hypotension is associated with obesity, lower coronary microcirculatory resistance, and lower FFR values.
Faulting and volcanism in the axial valley of the slow‐spreading center of the Mariana back arc basin from Wadatsumi side‐scan sonar images

We analyzed in detail the geology of the median valley floor of the Mariana Basin slow‐spreading ridge using sea surface geophysical data and a high‐resolution deep‐tow side‐scan sonar survey over one spreading segment. Analysis of surface magnetic data indicates highly asymmetric accretion, with the half‐spreading rate on the western side of the basin being two to three times larger than on the eastern side. Surface magnetic and reflectivity data together suggest that asymmetric spreading is accomplished through eastward ridge jumps of ∼10 km of amplitude. Deep‐tow backscatter data indicate along‐axis variations of the volcanic processes with the emplacement of smooth and hummocky flows at the segment center and end, respectively. This variation likely relates to changes in the effusion rate due to the deepening or even disappearance of the magma chamber toward the segment end. Concerning tectonic processes, we find a power law distribution of the fractures, with an exponent of 1.74. This suggests that within the inner valley floor, fracture growth prevails over fracture nucleation and coalescence and that fractures accommodate less than 8% of the strain. According to our calculation based on a ratio of 0.02 to 0.03 between the vertical displacement and the length of faults, the amount of tectonic strain accommodated in the inner valley floor would consistently be ∼1.1–3.4%. Data also show two distinct sets of fractures. One trend is parallel to the rift direction at the segment center (∼N160°E) and perpendicular to the plate separation direction. Another set trends ∼17° oblique to this direction (∼N175°E) and is located over the eastern part of the valley, in the vicinity of a major bounding fault also trending ∼N175°E, that is, obliquely to the direction of plate motion. We modeled the stress field near a major fault that is oblique to the regional stress field associated with plate separation using a three‐dimensional boundary element approach. We found that the orientation of the predicted fissuring near the oblique fault is locally rotated by ∼15° due to a flexure of the bending plate close to this fault.
Comparison of two different classifiers for mental tasks-based Brain-Computer Interface: MLP Neural Networks vs. Fuzzy Logic

This study is devoted to the classification of fourclass mental tasks data for a Brain-Computer Interface protocol. In such view we adopted Multi Layer Perceptron Neural Network (MLP) and Fuzzy C-means analysis for classifying: left and right hand movement imagination, mental subtraction operation and mental recitation of a nursery rhyme. Five subjects participated to the experiment in two sessions recorded in distinct days. Different parameters were considered for the evaluation of the performances of the two classifiers: accuracy, that is, percentage of correct classifications, training time and size of the training dataset. The results show that even if the accuracies of the two classifiers are quite similar, the MLP classifier needs a smaller training set to reach them with respect to the Fuzzy one. This leads to the preference of MLP for the classification of mental tasks in Brain Computer Interface protocols.
Comparing Features for Acoustic Anger Classification in German and English IVR Portals

Acoustic anger detection in voice portals can help to enhance human computer interaction. In this paper we report about the performance of selected acoustic features for anger classification. We evaluate the performance of the features on both a German and an American English dialogue voice portal database which contain “real” speech, i.e. non-acted, continuous speech of narrow-band quality. Deploying a large-scale feature extraction we determine the optimal set of features for each language. To obtain the ranking we use an Information-Gain Ratio filter. Analyzing the most promising features we notice a predominance of MFCC and loudness features. However, for the English database also pitch features proved importance. We further calculate classification scores for our setups using discriminative training and Support-Vector Machine classification. The developed systems show that Emotion Recognition in both English and German language can be processed very similarily.
Synchronization of Dendritic Cell Activation and Antigen Exposure Is Required for the Induction of Th1/Th17 Responses

The dendritic cell (DC) targeting/activation patterns required to elicit Th1/Th17 responses remain undefined. One postulated requirement was that of a physical linkage between Ags and immunomodulators. Accordingly, the separate same-site administration of Ag85B–ESAT-6 (hybrid-1 protein; H1), a mycobacterial fusion Ag, and the CAF01 liposome-based adjuvant induced similar Ab and weak Th2 responses as those of coformulated H1/CAF01 but failed to elicit Th1/Th17 responses. Yet, this separate same-site injection generated the same type and number of activated Ag+/adjuvant+ DCs in the draining lymph nodes (LN) as that of protective H1/CAF01 immunization. Thus, targeting/activating the same DC population by Ag and adjuvant is not sufficient to elicit Th1/Th17 responses. To identify the determinants of Th1/Th17 adjuvanticity, in vivo tracking experiments using fluorescently labeled Ag and adjuvant identified that a separate same-site administration elicits an additional early Ag+/adjuvant− DC population with a nonactivated phenotype, resulting from the earlier targeting of LN DCs by H1 than by CAF01 molecules. This asynchronous targeting pattern was mimicked by the injection of free H1 prior to or with, but not after, H1/CAF01 or H1/CpG/ aluminum hydroxide immunization. The injection of soluble OVA similarly prevented the induction of Th1 responses by OVA/CAF01. Using adoptively transferred OT-2 cells, we show that the Ag targeting of LN DCs prior to their activation generates nonactivated Ag-pulsed DCs that recruit Ag-specific T cells, trigger their initial proliferation, but interfere with Th1 induction in a dose-dependent manner. Thus, the synchronization of DC targeting and activation is a critical determinant for Th1/Th17 adjuvanticity.
Generic Atmospheric Correction Model for Interferometric Synthetic Aperture Radar Observations

For mapping Earth surface movements at larger scale and smaller amplitudes, many new synthetic aperture radar instruments (Sentinel‐1A/B, Gaofen‐3, ALOS‐2) have been developed and launched from 2014–2017, and this trend is set to continue with Sentinel‐1C/D, Gaofen‐3B/C, RADARSAT Constellation planned for launch during 2018–2025. This poses more challenges for correcting interferograms for atmospheric effects since the spatial‐temporal variations of tropospheric delay may dominate over large scales and completely mask the actual displacements due to tectonic or volcanic deformation. To overcome this, we have developed a generic interferometric synthetic aperture radar atmospheric correction model whose notable features comprise (i) global coverage, (ii) all‐weather, all‐time useability, (iii) correction maps available in near real time, and (iv) indicators to assess the correction performance and feasibility. The model integrates operational high‐resolution European Centre for Medium‐Range Weather Forecasts (ECMWF) data (0.125° grid, 137 vertical levels, and 6‐hr interval) and continuous GPS tropospheric delay estimates (every 5 min) using an iterative tropospheric decomposition model. The model's performance was tested using eight globally distributed Sentinel‐1 interferograms, encompassing both flat and mountainous topographies, midlatitude and near polar regions, and monsoon and oceanic climate systems, achieving a phase standard deviation and displacement root‐mean‐square (RMS) of ~1 cm against GPS over wide regions (250 by 250 km). Indicators describing the model's performance including (i) GPS network and ECMWF cross RMS, (ii) phase versus estimated atmospheric delay correlations, (iii) ECMWF time differences, and (iv) topography variations were developed to provide quality control for subsequent automatic processing and provide insights of the confidence level with which the generated atmospheric correction maps may be applied.