Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple Electrofishing Removals for Eliminating Rainbow Trout in a Small Southern Appalachian Stream

Abstract We evaluated multiple electrofishing removals of rainbow trout Oncorhynchus mykiss as a management tool for the restoration of native brook trout Salvelinus fontinalis in a small southern Appalachian stream. Six, three-pass depletion removal efforts were conducted between Jun 1996 and Oct 1997. Four removals successfully eliminated rainbow trout reproduction. Five removals were required to successfully eliminate rainbow trout from Mannis Branch. During the study, 428 rainbow trout were removed from the treatment area. The initial removal collected 296 (70%) of the total rainbow trout removed and was dominated by adults. Subsequent removals were dominated by age-0 rainbow trout (57–83%). The initial two removals successfully eliminated 96% of the reproductively mature adults as well as 86% of the age-0 fish. In Oct 1996, 105 native southern Appalachian brook trout of various age-classes were reintroduced into Mannis Branch. Surveys conducted in May 1997 indicated adult brook trout successfully spa.
Two-Photon Optical Beam-Induced Current Microscopy of Light-Emitting Diodes

We demonstrate two-photon optical beam-induced current (2P-OBIC) microscopy of light-emitting diodes (LEDs). We utilized a Ti:Sapphire femtosecond laser source operating at 800 nm to derive the 2P-OBIC signal from a 605 nm band-gap LED. The spatial confinement of free carrier generation only at the focus and the quadratic dependence of the 2P-OBIC signal on excitation power are the key principles in two-photon excitation. As a consequence, superior image quality evident in the 2P-OBIC images of LEDs are obtained. These features decrease the linear absorption and wide-angle scattering effects plaguing single-photon optical beam-induced current (1P-OBIC) technique, thereby increasing the resolution of the imaging system in the axial and lateral directions. Thus, the attainment of good axial discrimination in the LED samples is obtained even without a confocal pinhole. In addition, 2P-OBIC images reveal local variations in free carrier densities which are not evident in the single-photon excitation.
RAPID DETECTION AND ENUMERATION OF CONTAMINANTS BY ATP BIOLUMINESCENCE USING THE MILLIFLEX® RAPID MICROBIOLOGY DETECTION AND ENUMERATION SYSTEM

ABSTRACT The Milliflex® Rapid Microbiology Detection and Enumeration System (RMDS) is an automated platform developed for the rapid detection of microbial contaminants in filterable samples. Based on membrane filtration, adenosine triphosphate bioluminescence and image analysis, RMDS gives microorganism enumeration a detection time reduced by a factor of four compared to plate count. After sample filtration and incubation step, a universal lysis solution and bioluminescence reagent are automatically sprayed across the membrane. The membrane is then analyzed in a detection tower where light emission is captured by a charged coupled device camera. Data collected are treated, directly providing a result in colony-forming units. RMDS sensitivity is one cell and is equivalent to traditional microbiology. Rapid detection of bacteria, mixed bacteria and yeast was performed in various industrial samples. RMDS allowed rapid detection of contaminants in different simple and complex matrices such as water, tea, wine and mammalian cells. PRACTICAL APPLICATIONS The Milliflex® Rapid Microbiology Detection and Enumeration System (RMDS) is used to detect and enumerate microorganisms in filterable samples with time to detection in hours. The easy handling of this detection platform enables its use in all kinds of industries from food and beverage industries to biotechnology or pharmaceutical industries where procedures and method validation are stricter. One application is the use of RMDS for purified water testing and rinsing water. Rapid enumeration of contaminants will improve the quality control analysis of industrial products. Rapid release of samples will result in the optimization of manufacturing and product testing, allowing high throughput and simultaneous analysis during the process.
Biofilm synthesis and its relationship with genetic characteristics in clinical methicillin-resistant staphylococci

Staphylococcus aureus can cause a broad range of infections, including skin infections, pneumonia and bacteraemia. Coagulase-negative staphylococci (CNS), mainly S. epidermidis, have also emerged as important pathogens, especially in immunocompromised patients or those with prosthetic devices, such as intravascular catheters or biomaterials. Of great importance in the initiation of these infections is the ability of staphylococci to adhere to various surfaces, such as host tissues and prosthetic devices and to form biofilm. The staphylococcal adhesins are encoded by a number of genes such as fnbA (S. aureus fibronectin binding protein A), sasG (S. aureus surface protein G), aap (S. epidermidis accumulation associated protein), bhp (Bap homologue protein) and fbe (fibrinogen binding protein epidermidis). In this study, 106 methicillin-resistant S. aureus (MRSA), 145 methicillin-resistant S. epidermidis (MRSE) and 70 non-epidermidis methicillin-resistant CNS (MR-CNS; 58 S. haemolyticus, 10 S. hominis and two S. lugdunensis) were compared in terms of biofilm formation, antimicrobial resistance, clonal distribution and adhesin genes carriage. Isolates were classified into pulsotypes by PFGE and assigned to sequence types by MLST. In total, 121/321 isolates (37.7%) produced biofilm and 219 (68.2%) carried ica operon. The majority was multidrug resistant (94.7%) and carried one or more adhesin genes. MRSE and all other MR-CNS prevailed in biofilm formation (P < 0.001) and antimicrobial resistance (P < 0.05) as compared to MRSA. MRSE also prevailed in ica carriage compared to the other methicillin-resistant staphylococci (P ≤ 0.007) Among MRSE, isolates from bacteraemias prevailed in biofilm formation (P = 0.031), whereas, strains from prosthetic device-associated infections carried more frequently aap (P = 0.003). Even though PFGE showed genetic diversity among MRSE, MLST revealed three major clones (ST2, ST5, ST16). MRSA isolates were less diverse, with five PFGE types and, among them, one major PFGE type (C) consisting of 77/106 strains (72.6%). MLST identified five sequence types: ST5, ST30, ST80, ST225 and ST239. One major PFGE type (h) was identified in S. haemolyticus. A clonal relationship was found concerning fnbA carriage in MRSA, ica carriage in MRSE, and antimicrobial susceptibility in both groups reinforcing the aspect of clonal expansion in hospital settings.
The distribution of sexual reproduction of the geographic parthenogen Eucypris virens (Crustacea: Ostracoda) matches environmental gradients in a temporary lake

Niche segregation may prevent competitive exclusion and promote local coexistence. This typically results in the occupation of different habitats. In the freshwater ostracod Eucypris virens (Jurine, 1820), the distribution of sexual and parthenogenetic populations in the temporary Lake Caracuel, central Spain, was not homogeneous. Parthenogens were found everywhere including the littoral, whereas sexuals were restricted to the centre. We investigated the hypothesis that spatial distribution responded to ecological differences. We studied the ecological significance of this segregation by linking environmental data to male presence, sexual fraction, ploidy, and genetic structure of our model organism in 12 ponds in the lake basin. Hydro-chemical and biological data indicated that the observed segregation is not only spatial but also ecological, with sexual E. virens occurring in ponds with shorter and probably more unpredictable hydroperiod. The correlations between environmental gradients and E. virens po.
Complementary Production of Biofuels by the Green Alga Chlorella vulgaris

There is increasing growing concerns about global warming and rising of oil prices. The aim of the current work was to evaluate the potential of the green alga Chlorella vulgaris as a renewable energy source in term of biofuels. Alga was hetero-trophically grown under both vegetative and induction-conditions. Induction was proceed to enhance cell metabolites mainly oils (for biodiesel) and carbohydrates (for bioethanol-production). BG-II growth medium was used for vegetative growth, while such medium was enriched by ferrous sulfate, sodium acetate and sodium chloride under high light irradiation for induction purposes. De-fatted dried algal cells were subjected to bioethanol production through three different treatments prior yeast fermentation to increase the fermentable sugars content after oils were extracted from algae. This includes direct treatment by Tricoderma sp. , acid hydrolysis and molasses addition. Saccharomyces cerevisiae was used in fermentation action. Results indicated that the oil content of stressed algal cultures was raised to be 14.8% with 26.7% of total carbohydrates versus to 32.14% of crude protein. Fatty acids profile resulted in an increase of saturated fatty acids by about 10.65 %, while unsaturated fatty acids were decreased by 18.57%. Third day of incubation seems to be the optimum for direct fermented or pre acid hydrolyzed-alga in terms of yeast biomass, consumed sugar and alcohol percent By such time 15% of molasses represented the same manner. Also, the maximum alcohol content (38.7%) by acid hydrolyzed; while direct fermentation resulted in 28.7% versus to 36.3% of molasses addition.
Etude des mécanismes d'adhésion des tubes polliniques d'Arabidopsis thaliana par une approche de génétique chimique

Au cours de la reproduction sexuee des plantes, la germination du pollen et la croissance des tubes polliniques sont soumises a un controle spatio-temporel dans les tissus femelles afin d'acheminer les gametes mâles jusqu'aux ovules. Le tube pollinique est une cellule a croissance rapide entouree d'une matrice extracellulaire riche en polysaccharides. La croissance polarisee des tubes polliniques et leurs capacites a percevoir des signaux externes permettent de les guider a travers le tissu de transmission de l'organe femelle. Parmi ces signaux, un mecanisme de guidage par adhesion a ete postule chez le lys. Peu de travaux concernent les tubes polliniques de la plante modele Arabidopsis thaliana. Dans le but d'identifier les interactions impliquees dans l'adhesion des tubes polliniques, nous avons entrepris 1- de caracteriser les composes parietaux des tubes et des cellules du tissu de transmission qui sont la premiere interface de contact entre ces cellules ; 2 - d'utiliser une approche de genetique chimique pour identifier des molecules impliquees dans l'adhesion cellulaire. Nos resultats indiquent que la paroi des tubes polliniques d'Arabidopsis se compose d'une double paroi riche en callose, pour la paroi interne et en pectines et xyloglucanes pour la paroi externe. Nous avons alors caracterise la structure des xyloglucanes et mis en evidence que ce polymere est fortement fucosyle et O-acetyle. Cette caracteristique structurale semble etre conservee parmi les especes. L'abondance de l'arabinose provenant des chaines laterales du rhamnogalacturonane de type 1 a ete egalement mise en evidence. Pour etudier l'adhesion, nous avons reconstitue une matrice a partir de polysaccharides parietaux extraits de fleurs mais aussi d'organes vegetatifs de la plante. Les tubes polliniques adherent sur des pectines extraites a l'imidazole de fleurs et de feuilles d'Arabidopsis. Cette matrice nous a permis de constituer un test d'adhesion assez efficace et significatif pour le soumettre a une analyse de genetique chimique. Cette methode consiste a etudier des processus biologiques en les perturbant via le criblage de petites molecules chimiques. Parmi les 258 molecules en notre possession, cinq ont montre des resultats prometteurs en reduisant significativement l'adhesion des tubes polliniques. De plus, avec certaines molecules, un effet dose-reponse a pu etre mis en evidence.
Antioxidative Activity of Peptides Prepared from Okara Protein

Protease hydrolyses of an Okara protein yielded antioxidative activity against the peroxidation of linoleic acid in an aqueous system at pH 7.0. Four antioxidative peptides were isolated from the hydrolysate prepared with Protease N by size exclusion chromatography and reversed-phase HPLC. The peptides were composed of two and three amino acid residues, including aromatic amino acid at the C terminal end. Their amino acid sequences were determined to be Ala-Tyr, Gly-Tyr-Tyr, Ala-Asp-Phe, and Ser-Asp-Phe, respectively. The antioxidative activity of Gly-Tyr-Tyr is nearly equal to that of carnosine.
Strong seasonal disequilibrium measured between the oxygen isotope signals of leaf and soil CO2 exchange

The oxygen isotope composition (δ18O) of atmospheric CO2 is among a very limited number of tools available to constrain estimates of the biospheric gross CO2 fluxes, photosynthesis and respiration at large scales. However, the accuracy of the partitioning strongly depends on the extent of isotopic disequilibrium between the signals carried by these two gross fluxes. Chamber‐based field measurements of total CO2 and CO18O fluxes from foliage and soil can help evaluate and refine our models of isotopic fractionation by plants and soils and validate the extent and pattern of isotopic disequilibrium within terrestrial ecosystems. Owing to sampling limitations in the past, such measurements have been very rare and covered only a few days. In this study, we coupled automated branch and soil chambers with tuneable diode laser absorption spectroscopy techniques to continuously capture the δ18O signals of foliage and soil CO2 exchange in a Pinus pinaster Aït forest in France. Over the growing season, we observed a seasonally persistent isotopic disequilibrium between the δ18O signatures of net CO2 fluxes from leaves and soils, except during rain events when the isotopic imbalance became temporarily weaker. Variations in the δ18O of CO2 exchanged between leaves, soil and the atmosphere were well explained by theory describing changes in the oxygen isotope composition of ecosystem water pools in response to changes in leaf transpiration and soil evaporation.
Molecular characterization of phototrophic microorganisms in the forefield of a receding glacier in the Swiss Alps

Recently deglaciated areas are ideal environments to study soil formation and primary microbial succession where phototrophic microorganisms may play a role as primary producers. The aim of our study was to investigate the cyanobacterial and green algal community composition in three different successional stages of the Damma glacier forefield in the Swiss Alps using 16S rDNA and ITS rDNA clone libraries. Cyanobacterial target sequences varied along the glacier forefield, with the highest cyanobacterial 16S rRNA gene copies found in sparsely vegetated soils. Sequence analysis revealed that the phototrophic communities were distinct in each of the three soil environments. The majority of the cyanobacterial sequences retrieved from barren soils were related to the Oscillatoriales. The diversity in sparsely vegetated soils was low, and sequences closely related to Nostoc sp. dominated. The majority of the algal phylotypes are related to members of the Trebouxiophyceae known to live as symbiotic partners in lichens. We conclude that the community composition appears to shift markedly along the chronosequence, indicating that each soil environment selects for its phototrophic community. When cyanobacteria occur together with eukaryotic microalgae, they form a rich source of organic matter and may be important contributors of carbon in nutrient-deficient deglaciated soils.
A Considerably Improved Method for Preparing Plastic Epidermal Imprints

The use of Duco cement for making epidermal imprints for microscopic examination is described. The procedure is similar to that employed for several other synthetic and natural liquids and involves the application and spreading of the liquid plastic which upon drying gives a thin transparent film. This is then peeled off and examined under the microscope. The imprint gives excellent replication of different kinds of surfaces, and the imprint shape is maintained permanently. From a detailed comparison made between Duco cement and other products in common use, the former seems to be a considerable improvement over other similar products. Photomicrographs are presented of some surface imprints obtained using it.
Feeding on roots in the humus layer by adult pine weevil, Hylobius abietis

1 The consumption by adult pine weevil, Hylobius abietis, of the bark of roots present in the humus layer was assessed in a field study conducted in southern Sweden during two years (1998 and 2002). The study sites were divided into two areas: (i) a shelterwood where 80–100 mature Scots pine trees per hectare remained after cutting and (ii) a clearcut where no trees were left.
avb3 integrin expression increases elasticity in human melanoma cells

Living cells interact with the extracellular matrix (ECM) transducing biochemical signals into mechanical cues and vice versa. Thanks to this mechano-transduction process, cells modify their internal organization and upregulate their physiological functions differently. In this complex mechanism integrins play a fundamental role, connecting the extracellular matrix with the cytoskeleton. Cytoskeletal rearrangements, such as the increase of the overall contractility, impact cell mechanical properties, the entire cell stiffness, and cell deformability. How cell mechanics is influenced via different integrins and their interaction with ECM in health and disease is still unclear. Here, we investigated the influence of avb3 integrin expression on the mechanics of human melanoma M21 cells using atomic force microscopy and micro-constriction. Evidence is provided that (i) avb3 integrin expression in human melanoma cells increases cell stiffness in both adherent and non-adherent conditions; (ii) replacing avb3 with aIIbb3 integrin in melanoma cells, cell stiffness is increased under adherent, while decreased under nonadherent conditions; (iii) avb3 integrin cell stiffening is also maintained when cells adhere to fibronectin, but this phenomenon does not strongly depend on the fibronectin concentration. In all, this study sheds light on the role of avb3 in regulating cellular mechanics. © 2020 Elsevier Inc. All rights reserved.
Risk assessment via layered mobile contact tracing for epidemiological intervention

There is strong interest globally amidst the current COVID-19 pandemic in tracing contacts of infectious patients using mobile technologies, both as a warning system to individuals and as a targeted intervention strategy for governments. Several governments, including India, have introduced mobile apps for this purpose, which give a warning when the individual's phone establishes bluetooth contact with the phone of an infected person. We present a methodology to probabilistically evaluate risk of infection given the network of contacts that individuals are likely to encounter in real life. Instead of binary "infected" or "uninfected" statuses, an infection risk probability is maintained which can be efficiently calculated based on probabilities of recent contacts, and updated when a recent contact is diagnosed with a disease. We demonstrate on realistic networks that this method sharply outperforms a naive immediate-contact method even in an ideal circumstance that all infected persons are known to the naive method. We demonstrate robustness to missing contact information (such as when phones fail to make bluetooth contact or the app is not installed). We show, within our model, a strong flattening of the infectious peak when even a small fraction of cases are identified, tested and isolated. In the real world, where most known-infected persons are isolated or quarantined and where many individuals may not carry their mobiles in public, we believe the improvement offered by our method warrants consideration. Importantly, in view of widespread concerns on privacy and contact-tracing, our method relies mainly on direct contact data that can be stored locally on users' phones, and uses limited communication via intermediary servers only upon testing, mitigating privacy concerns.
ASSIMILATION OF GOES-R ATMOSPHERIC MOTION VECTORS (AMVS) IN THE NCEP GLOBAL FORECAST SYSTEM

In preparation for GOES-R launch, proxy AMV data created using imagery from Meteosat-9 & 10 Spinning Enhanced Visible Infra-Red Imager (SEVIRI) and the new nested tracking algorithm have been assimilated in the National Centers for Environmental Prediction (NCEP) Global Forecast System (GFS). Results show neutral to slightly positive impact on the forecast skill from the inclusion of this new wind data. Modifications to the Gridpoint Statistical Interpolation (GSI) software will be presented. Changes enacted to promote a positive GOES-R AMV data impact on the GFS were made to the quality control procedures, the observation error setting and to include a log normal vector departure check.
Zoeal Development of Telmessus acutidens(Crustacea: Decapoda: Brachyura: Atelecyclidae) Reared in the Laboratory

An ovigerous hair crab, Telmessus acutidens, was collected in South Korean waters and its larvae were reared in the laboratory. The larval development consists of four zoeal (including an extra zoeal stage) and one megalopal stages. Four zoeal stages are described and illustrated in detail. The zoeas of the present material show some differences from Kurata (1963)'s plankton-collected zoea of T. acutidens in the characteristics of the carapace spines, an endopod and an exopod of the antenna, and the posterolateral process of the abdominal somite. Kurata's zoea agreed well with that of T. cheiragonus. So, it is suggested that Kurata's zoea may be the second zoea of T. cheiragonus.
Dissection of the Species-Area Relationship Among Wood-Boring Insects and Their Host Plants

The species-area relationship between wood-boring insects and the geographic range of their host plants is derived from the tendency for wide-ranging plants to be a part of more wood-boring insect communities than plants with smaller geographic ranges. In contrast to the expectation of the area-per se hypothesis, plants in a given forest that have large geographic ranges do not show richer wood-boring insect faunas than co-occurring plants with small ranges. The passive-sampling hypothesis can also be excluded because sampling differences do not account for the pattern. Only the habitat-heterogeneity explanation for the species-area relationship is consistent with the data and analyses presented.