Miracle-dz/UniFAR-FTUs huggingface dataset:
Breeding ecology of the Purple Heron Ardea purpurea in Numidia, north-eastern Algeria

During 2002–2007, we assessed the status of the Purple Heron Ardea purpurea in Numidia, Algeria by surveying all the major wetlands in the region. We located six distinct breeding sites; four of these were not previously known. We also investigated nest site selection and determined the species’ reproductive success at Dakhla, a dunary pond during two successive years (2006 and 2007). The egg laying period was comparable to that reported for southern Europe (March-May) and a seasonal change of breeding success was recorded. A growth curve was derived for developing nestlings and the impact of an ectoparasite (mite) infestation upon nestling's growth was considered. We also examined 73 food boluses regurgitated by nestlings and identified 329 prey items. Fish, mainly Gambusia holbrookii and Cyprinus carpio, dominated by mass, whereas insects, mainly aquatic Coleopteran larvae and aeshnids (Odonata), were the most frequent prey (67.1%). Loss of habitat is identified as a major threat to the future of colonial herons in Algeria.
Atmospheric turbulence modeling and aperture analysis for optimizing receiver design and system performance on free space optical communication links

Atmospheric Turbulence Modeling and Aperture Analysis for Optimizing Receiver Design and System Performance on Free Space Optical Communication Links Hasim Meric M.S. in Electrical and Electronics Engineering Supervisor: Prof. Dr. Ayhan Altıntaş and Assist. Prof. Dr. Heba Yüksel September 2012 Strong turbulence measurements that are taken using real time optical wireless experimental setups are valuable when studying the effects of turbulence regimes on a propagating optical beam. In any kind of Free Space Optical (FSO) system, knowing the strength of the turbulence thus the refractive index structure constant (C n), is beneficial for having an optimum bandwidth of communication. Even if the FSO Link is placed very well-high-above the ground just to have weak enough turbulence effects, there can be severe atmospheric conditions that can change the turbulence regime. Having a successful theory that will cover all regimes will give us the chance of directly processing the image in existing or using an additional hardware thus deciding on the optimum bandwidth of the communication line at firsthand.In literature, simulation of beam propagation through turbulent media has always been a tricky subject when it comes to moderate-to-strong turbulent regimes. Creating a well controlled turbulent environment is beneficial as a fast and a practical approach when it comes to testing the optical wireless communication systems in diverse atmospheric conditions.
Development of Core-shell Magnetic Mesoporous SiO2 Microspheres for the Immobilization of Trypsin for Fast Protein Digestion

In the work, we developed glycidoxypropyltrimethoxysilane (GLYMO)-modified Fe3O4@SiO2 core and perpendicularly aligned mesoporous SiO 2 shell (designated Fe3O4@nSiO2@mSiO 2 ) as the novel substrate for the immobilization of large amount of trypsin and applied it for fast protein digestion. Firstly, Fe 3 O 4 @nSiO 2 @mSiO 2 microspheres wer e synthesized. Then, the surface of the microspheres was functionalized with GLYMO for enzyme immobilization.The amount of tr ypsin immobilized on Fe3O4@nSiO2@mSiO2 was about 188 i g/mg, which was much more than that on the previous magnetic materials. Using the trypsin-immobilized magnetic mesoporous SiO 2 microspheres, proteins in samples were fast digested with microwave irradiation. The efficacy of this technique for protein mapping was demonstrated by the mass spectral analysis of the peptide fragmentation of three standard proteins, including cytochrome c (Cyt-c), myglobin (MYG), and bovine serum albumin (BSA). The functionalized magnetic microspheres served not only as substrate for enzyme immobilization, but also as excellent microwave absorbers, thus greatly improved the efficiency of protein digestion. It is also worth noting that by using this novel approach, the protein can be effectively digested within seconds, in contrast to hours required by conventional methods. Moreover, the trypsin-immobilized magnetic mesoporous SiO 2 microspheres exhibit better stability than conventional methods. Furthermore, the feasibility of using this novel strategy for real sample analysis was demonstrated by applying it to the analysis of human pituitary extraction which opens a route for its further application in large-scale proteomic analysis.
Aspen Response to Prescribed Fire under Managed Cattle Grazing and Low Elk Densities in Southwest Montana

Abstract The Whitetail Watershed Restoration Project used prescribed fire in 2005 and 2006 to address quaking aspen (Populus tremuloides Michx.) decline, conifer encroachment and altered hydrologic function in a forested watershed in southwest Montana. As part of this effort, we evaluated aspen response to fire in two sub-drainages of the Whitetail Basin three years after treatment. Unburned stands were surveyed to determine whether aspen regeneration was occurring following long term disruption of historical fire return intervals. This information was compared to stem response in nearby burned stands. Regeneration was noted in only one of 40 unburned stands, suggesting aspen stands were declining in this area. Three years after prescribed fire sucker density was significantly higher in the burned stands. This increased the likelihood that stands could regenerate. Based on earlier studies describing suppression of stand regeneration by cattle (Bos taurus) and elk (Cervus elaphus nelsoni) browsing impacts on aspen sucker height and density were measured in a sub-sample of burned stands. Within the first three years post-fire big game and the combination of big game and cattle did not affect sucker density in the burned stands. Although sucker height was significantly less in plots used by ungulates it may not be high enough to prevent regeneration. This assertion was supported by sufficient annual growth rates and the recruitment of individual regeneration stems into burned stands. Results from this study indicate that aspen stands can be successfully regenerated in areas where elk numbers are less than 1 animal/km2 and cattle grazing is closely managed. Monitoring will continue to learn if stand regeneration does occur.
Coffea canephora (Pierre) ex Froehner inoculado con micorriza y bacteria fijadora de nitrógeno en vivero

This study was conducted from November 2012 to May 2013 to evaluate the effect of inoculating C. canephora with Rhizophagus intraradices and / or Azospirillum brasilense in two substrates in nursery on some morphological and physiological yield components and to determine the amount of phosphorus in plant tissue and quantify mycorrhizal colonization. Soil used was mollic Andosol and two prepared substrates: one was soil and river sand and the other was soil plus 30% coffee pulp (1:1 v / v) in five-kg capacity plastic bags. Treatments were the control, Rhizophagus intraradices, Azospirillum brasilense and a combination of the two on each substrate, giving a total of eight treatments in a split plot in randomized block design with five replications. Samples were taken every 28 days to assess morphological and physiological variables and mycorrhizal colonization and phosphorus content during 140 days after transplant (dat). The results show that inoculation of C. canephora in nursery with either of the microorganisms individually favored growth and dry matter accumulation in morphological and physiological yield components relative to the control. A. brasilense promoted greater biomass accumulation during the evaluation and R. intraradices at the end of the study. R. intraradices increased phosphorus content in the tissue of plants, and higher mycorrhizal colonization was found in the first third of the root when inoculated with R. intraradices. ADDITIONAL KEYWORDS: Robusta coffee, Rhizophagus intraradices, Azospirillum brasilense, yield components, phosphorus, mycorrhizal colonization.
Variations in the esterase activity during the germination period of Jatropha curcas seeds

Germination brings out the synthesis or activation of enzymes responsible for the degradation of seeds reserves. Among these enzymes, esterases are involved in the metabolic processes of germination and maturation of plants. They are constitutively expressed in seeds during germination to release the reserve materials for the growing embryo. In the present study, total protein content and esterase activity was monitored in germinating Jatropha curcas seeds. The esterase activity and specific activity observed were 9.07 Âµmoles/min/gm and 0.09258 IU/mg, respectively. Electophoretic analysis for esterase activity showed thirteen bands of esterases, among these 8 esterolytic bands were major and remaining were minor bands. The protein content and esterase activity decreased on 2nd, 4th, 5th and 8th day of seed germination and activity increased on 3rd, 6th, 7th day of germination. Similarly esterase activity increased on 7th day and decreased on 8, 9 and 10th day in the shoot tissue. Â Â
Rest-frame UV spectroscopy of extreme [OIII] emitters at 1.3 < z < 3.7: Toward a high-redshift UV reference sample for JWST

Deep spectroscopy of galaxies in the reionization era has revealed intense C III] and C IV line emission (EW >15 − 20 Å). In order to interpret the nebular emission emerging at z > 6, we have begun targeting rest-frame UV emission lines in galaxies with large specific star formation rates (sSFRs) at 1.3 < z < 3.7. We find that C III] reaches the EWs seen at z > 6 only in large sSFR galaxies with [O III]+Hβ EW >1500 Å. In contrast to previous studies, we find that many galaxies with intense [O III] have weak C III] emission (EW =5 − 8 Å), suggesting that the radiation field associated with young stellar populations is not sufficient to power strong C III]. Photoionization models demonstrate that the spread in C III] among systems with large sSFRs ([O III]+Hβ EW >1500 Å) is driven by variations in metallicity, a result of the extreme sensitivity of C III] to electron temperature. We find that the strong C III] emission seen at z > 6 (EW >15 Å) requires metal poor gas (≃ 0.1 Z⊙) whereas the weaker C III] emission in our sample tends to be found at moderate metallicities (≃ 0.3 Z⊙). The luminosity distribution of the C III] emitters in our z ≃ 1 − 3 sample presents a consistent picture, with stronger emission generally linked to low luminosity systems (MUV > −19.5) where low metallicities are more likely. We quantify the fraction of strong C III] and C IV emitters at z ≃ 1 − 3, providing a baseline for comparison against z > 6 samples. We suggest that the first UV line detections at z > 6 can be explained if a significant fraction of the early galaxy population is found at large sSFR (>200 Gyr−1) and low metallicity (<0.1 Z⊙).
Trichloroethylene: Using New Information To Improve the Cancer Characterization

The views expressed in this paper are those of the authors and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency. Assessments of TCE's potential to cause cancer in humans have had to address issues concerning the strength of the human evidence and the relevance of the animal tumors to humans. The epidemiological database now includes analyses of multiple studies and molecular information. A recent analysis strongly suggests that TCE may induce cancer in humans at multiple sites, including kidney, liver, and lympho-hematopoietic cancer. Molecular analyses have found mutations of the von Hippel-Lindau tumor suppressor gene in renal tumors of TCE-exposed individuals. The animal bioassays have been followed up with mechanistic studies that provide insight into TCE's possible modes of action at each tumor site. This information suggests that TCE may act through mechanisms that can be relevant to human cancers. The mechanistic information can also be used to identify risk factors that may make some people more susceptible to TCE's adverse effects, allowing a fuller characterization of TCE's cancer potential in different groups of people.
Dynamic proofs of retrievability with low server storage

Proofs of Retrievability (PoRs) are protocols which allow a client to store data remotely and to efficiently ensure, via audits, that the entirety of that data is still intact. A dynamic PoR system also supports efficient retrieval and update of any small portion of the data. We propose new, simple protocols for dynamic PoR that are designed for practical efficiency, trading decreased persistent storage for increased server computation, and show in fact that this tradeoff is inherent via a lower bound proof of time-space for any PoR scheme. Notably, ours is the first dynamic PoR which does not require any special encoding of the data stored on the server, meaning it can be trivially composed with any database service or with existing techniques for encryption or redundancy. Our implementation and deployment on Google Cloud Platform demonstrates our solution is scalable: for example, auditing a 1TB file takes 16 minutes at a monetary cost of just $0.23 USD. We also present several further enhancements, reducing the amount of client storage, or the communication bandwidth, or allowing public verifiability, wherein any untrusted third party may conduct an audit.
Machine-learned Regularization and Polygonization of Building Segmentation Masks

We propose a machine learning based approach for automatic regularization and polygonization of building segmentation masks. Taking an image as input, we first predict building segmentation maps exploiting generic fully convolutional network (FCN). A generative adversarial network (GAN) is then involved to perform a regularization of building boundaries to make them more realistic, i.e., having more rectilinear outlines which construct right angles if required. This is achieved through the interplay between the discriminator which gives a probability of input image being true and generator that learns from discriminator's response to create more realistic images. Finally, we train the backbone convolutional neural network (CNN) which is adapted to predict sparse outcomes corresponding to building corners out of regularized building segmentation results. Experiments on three building segmentation datasets demonstrate that the proposed method is not only capable of obtaining accurate results, but also of producing visually pleasing building outlines parameterized as polygons.
Bi-Lipschitz geometry of quasiconformal trees

A quasiconformal tree is a doubling metric tree in which the diameter of each arc is bounded above by a fixed multiple of the distance between its endpoints. We study the geometry of these trees in two directions. First, we construct a catalog of metric trees in a purely combinatorial way, and show that every quasiconformal tree is bi-Lipschitz equivalent to one of the trees in our catalog. This is inspired by results of Herron-Meyer and Rohde for quasi-arcs. Second, we show that a quasiconformal tree bi-Lipschitz embeds in a Euclidean space if and only if its set of leaves admits such an embedding. In particular, all quasi-arcs bi-Lipschitz embed into some Euclidean space.
Unsupervised Discovery of 3D Physical Objects from Video

We study the problem of unsupervised physical object discovery. Unlike existing frameworks that aim to learn to decompose scenes into 2D segments purely based on each object's appearance, we explore how physics, especially object interactions, facilitates learning to disentangle and segment instances from raw videos, and to infer the 3D geometry and position of each object, all without supervision. Drawing inspiration from developmental psychology, our Physical Object Discovery Network (POD-Net) uses both multi-scale pixel cues and physical motion cues to accurately segment observable and partially occluded objects of varying sizes, and infer properties of those objects. Our model reliably segments objects on both synthetic and real scenes. The discovered object properties can also be used to reason about physical events.
Phylogenetic systematics and historical biogeography of the Neotropical electric fish Gymnotus (Teleostei: Gymnotidae)

Abstract Phylogenetic interrelationships of the Neotropical electric fish genus Gymnotus are documented from comparative study of phenotypic data. A data matrix was compiled of 113 phenotypic characters for 40 taxa, including 31 recognized Gymnotus species, six allopatric populations of G. carapo, two allopatric populations of G. coropinae, and three gymno‐tiform outgroups. MP analysis yielded 15 trees of equal length, the strict consensus of which is presented as a working hypothesis of Gymnotus interrelationships. Diagnoses are presented for 26 clades, including three species groups; the G. cylindricus group with two species restricted to Middle America, the G. pantherinus group with 12 species in South America, and the G. carapo group with 16 species in South America. The basal division of Gymnotus is between clades endemic to Middle and South America. Both the G. pantherinus and G. carapo groups include trans‐Andean sister‐taxon pairs, suggesting a minimum date for the origins of these groups in the late Middle Miocene (c. 12 Ma.). The geographically widespread species G. carapo is paraphyletic. Analysis of character state evolution shows characters of external morphology are more phylogenetically plastic and provide more phylogenetic information in recent branches than do characters of internal morphology, which themselves provide the more information in deeper branches. Nine regional species assemblages of Gymnotus are recognized, none of which is monophyletic. There are at least two independent origins of Gymnotus species in sediment rich, high conductivity, perennially hypoxic whitewater floodplains (varzea´) derived from an ancestral condition of being restricted to low conductivity non‐floodplain (terra firme) black and clearwater rivers and streams. These phylogenetic, biogeographic and ecological patterns suggest a lengthy and complex history involving numerous instances of speciation, extinction, migration and coexistence in sympatry. Evolution in Gymnotus has been a continent‐wide phenomenon; i.e. Amazonian species richness is not a consequence of strictly Amazonian processes. These patterns are similar to those of other highly diverse groups of Neotropical fishes and do not resemble those of monophyletic, rapidly generated species flocks.
Generation of a Chattonella antiqua bloom by imposing a shallow nutricline in a mesocosm

A mesocosm was installed in the Seto Inland Sea where outbreaks of Chattonella antiqua (red tide) have frequently been observed. An artificial, shallow (6-m depth) nutrient stratification analogous to that observed with C. antiqua in nature was imposed. The initial bottom temperature of 20-22°C was optimum for C. antiqua excystmcnt as seeding, and the surface temperature of 25-27°C was optimum for growth. Excess nitrogen and phosphate compared with silicate changed the phytoplankton community from a mixture of diatoms and dinoflagellates to one of dinoflagellate dominance. Absence of copper toxicity was essential for growth of C. antiqua. Cessation of vertical circulation promoted accumulation of dinoflagellates at the water surface, and selective grazing toward small-size dinoflagellates by zooplankton controlled the population of dinoflagellates. C. antiqua could reach a depth of 7.5 m during diel vertical migration, and its migration speed was -0.8 m h-l; upward and downward speeds were the same. Outbreaks of C. antiqua were favored by artificial eutrophication and subsequent maintenance of a stable, shallow nutricline at a depth (6 m) such that C. antiqua could take up nutrients in the nutrient-rich lower layer at night. Chattonella antiqua (Hada) Ono (Raphidophyceae, spindle shape, 50-l 30 pm long) is the flagellate that causes most red tides in summer in the Seto Inland Sea of Japan; this flagellate caused severe damage to aquacultured yellowtail during the 1970s and 1980s. In the Seto Inland Sea, heavy rains from mid-June to mid-July supply large amounts of freshwater and nutrients; the nutrients are distributed throughout the water column by -20 July. Concentrations of POd3- and N are -0.1 and 3 PM at the surface and -0.5 and 5 PM at the bottom (20 m). A 2-3-week period of hot sunny weather follows, and inhibition of vertical mixing leads to stable salinity and temperature stratification. Phosphate and N in the surface waters are rapidly utilized (mainly by diatoms) at the beginning of August and could be limiting for C. antiqua, although -0.5 PM P043- and 5 PM N remain available below the nutricline. In 5 yr of observation, the presence of a shallow P-Cline (5-7 m) was most characteristic in 1987, the year of the C. antiqua outbreak, compared to other years (1984, 1985, 1986, 198 8) in which P-clines were usually found at 12
COVID-19 Symptoms Detection Based on NasNetMobile with Explainable AI Using Various Imaging Modalities

The outbreak of COVID-19 has caused more than 200,000 deaths so far in the USA alone, which instigates the necessity of initial screening to control the spread of the onset of COVID-19. However, screening for the disease becomes laborious with the available testing kits as the number of patients increases rapidly. Therefore, to reduce the dependency on the limited test kits, many studies suggested a computed tomography (CT) scan or chest radiograph (X-ray) based screening system as an alternative approach. Thereby, to reinforce these approaches, models using both CT scan and chest X-ray images need to develop to conduct a large number of tests simultaneously to detect patients with COVID-19 symptoms. In this work, patients with COVID-19 symptoms have been detected using eight distinct deep learning techniques, which are VGG16, InceptionResNetV2, ResNet50, DenseNet201, VGG19, MobilenetV2, NasNetMobile, and ResNet15V2, using two datasets: one dataset includes 400 CT scan and another 400 chest X-ray images. Results show that NasNetMobile outperformed all other models by achieving an accuracy of 82.94% in CT scan and 93.94% in chest X-ray datasets. Besides, Local Interpretable Model-agnostic Explanations (LIME) is used. Results demonstrate that the proposed models can identify the infectious regions and top features; ultimately, it provides a potential opportunity to distinguish between COVID-19 patients with others.
Optical readout studies of the Thick-COBRA gaseous detector

The performance of a Thick-COBRA (THCOBRA) gaseous detector is studied using an optical readout technique. The operation principle of this device is described, highlighting its operation in a gas mixture of Ar/CF4 (80/20 %) for visible scintillation light emission. The contributions to the total gain from the holes and the anode strips as a function of the applied bias voltage were visualized. The preservation of spatial information from the initial ionizations was demonstrated by analyzing the light emission from 5.9 keV X-rays of an 55Fe source. The observed non-uniformity of the scintillation light from the holes supports the claim of a space localization accuracy better than the pitch of the holes. The acquired images were used to identify weak points and sources of instabilities in view of the development of new optimized structures.