Miracle-dz/UniFAR-FTUs huggingface dataset:
Linear transformation to minimize the effects of variability in understory to estimate percent tree canopy cover using RapidEye data

Variability in understory structure is an important problem in estimating tree canopy cover (TCC) with satellite imagery. Differences between understory structure due to the composition and configuration of herbaceous/shrub species often produce different vegetation index values despite these areas having the same TCC. This study offers a linear transformation approach to minimizing the influence of variability in the understory to accurately estimate percent TCC from RapidEye satellite data. TCC was modeled as a function of the Normalized Difference Vegetation Index (NDVI), Normalized Difference Red-Edge Index (NDRE), adjusted (linear transformed) NDVI (NDVIadj), and adjusted NDRE (NDREadj) using simple linear regression. The coefficient of determination of validation () of the models using NDVI, NDRE, NDVIadj, and NDREadj as explanatory variables were, respectively, 0.50 (RMSEvld = 9.64%), 0.38 (RMSEvld = 10.7%), 0.78 (RMSEvld = 6.61%), and 0.73 (RMSEvld = 7.23%). These results showed that the linear tr.
10 Gbps TCP/IP streams from the FPGA for High Energy Physics

The DAQ system of the CMS experiment at CERN collects data from more than 600 custom detector Front-End Drivers (FEDs). During 2013 and 2014 the CMS DAQ system will undergo a major upgrade to address the obsolescence of current hardware and the requirements posed by the upgrade of the LHC accelerator and various detector components. For a loss-less data collection from the FEDs a new FPGA based card implementing the TCP/IP protocol suite over 10Gbps Ethernet has been developed. To limit the TCP hardware implementation complexity the DAQ group developed a simplified and unidirectional but RFC 793 compliant version of the TCP protocol. This allows to use a PC with the standard Linux TCP/IP stack as a receiver. We present the challenges and protocol modifications made to TCP in order to simplify its FPGA implementation. We also describe the interaction between the simplified TCP and Linux TCP/IP stack including the performance measurements.
Mesoscale Analyses of Fungal Networks

We investigate the application of mesoscopic response functions (MRFs) to characterise a large set of networks of fungi and slime moulds grown under a wide variety of different experimental treatments, including inter-species competition and attack by fungivores. We construct "structural networks" by estimating cord conductances (which yield edge weights) from the experimental data, and we construct "functional networks" by calculating edge weights based on how much nutrient traffic is predicted to occur on each edge. Both types of networks have the same topology, and we compute MRFs for both families of networks to illustrate two different ways of constructing taxonomies to group the biological networks into related clusters. Although both network taxonomies generate intuitively sensible groupings of networks across species, treatments, and laboratories, we find that clustering using the functional-network measure appears to give more parsimonious groups. We argue that MRFs provide a useful quantitative measures of network behaviour that can help to summarise an expanding set of increasingly complex experimental biological networks and to present the information in an accessible form.
Humoral Immunity to Hantavirus Infection

Hantaviruses are pathogens that sometimes pass from animals to humans, and they are found in parts of Europe, Asia, and North and South America. When human infection occurs, these viruses can cause kidney or lung failure, and as many as 40% of infected people die. Currently, there are no vaccines or therapeutics for hantavirus-related diseases available. A first step in developing prevention measures is determining what type of immune response is protective. Increasingly it has become clear that the induction of a type of response called a neutralizing antibody response is critical for protection from severe disease. Although virologists first described this family of viruses in the 1950s, there is limited information on what features on the surface of hantaviruses are recognized by the immune system. Here, we review the current state of knowledge of this information, which is critical for the design of effective therapeutics and vaccines. ABSTRACT Hantaviruses are zoonotic pathogens found in parts of Europe, Asia, South America, and North America, which can cause renal and respiratory failure with fatality rates up to 40%. There are currently no FDA-approved vaccines or therapeutics for hantavirus-related diseases; however, it is evident that a robust neutralizing antibody response is critical for protection from severe disease. Although virologists first described this family of viruses in the 1950s, there is limited information on the neutralizing epitopes that exist on the hantavirus antigenic glycoproteins, Gn and Gc, and sites important for the design of effective therapeutics and vaccines. We provide a thorough summary of the hantavirus field from an immunological perspective. In particular, we discuss our current structural knowledge of antigenic proteins Gn and Gc, identification of B cell neutralizing epitopes, previously isolated monoclonal antibodies and their cross-reactivity between different hantavirus strains, and current developments toward vaccines and therapeutics. We conclude with some outstanding questions in the field and emphasize the need for additional studies of the human antibody response to hantavirus infection. IMPORTANCE Hantaviruses are pathogens that sometimes pass from animals to humans, and they are found in parts of Europe, Asia, and North and South America. When human infection occurs, these viruses can cause kidney or lung failure, and as many as 40% of infected people die. Currently, there are no vaccines or therapeutics for hantavirus-related diseases available. A first step in developing prevention measures is determining what type of immune response is protective. Increasingly it has become clear that the induction of a type of response called a neutralizing antibody response is critical for protection from severe disease. Although virologists first described this family of viruses in the 1950s, there is limited information on what features on the surface of hantaviruses are recognized by the immune system. Here, we review the current state of knowledge of this information, which is critical for the design of effective therapeutics and vaccines.
Hybrid Approach for the Semantic Processing of Scientic Papers

We propose a hybrid method for the extraction and characterization of citations in scientic papers using machine learning combined with rule-based approaches. Our protocol consists of the extraction of metadata, bibliography parsing, section titles processing, and nd-grained semantic annotation on the sentece level of texts. This allows us to generate Linked Open Data from a set of research papers in XML.
FIRST FINDING OF EPIBIONT PERITRICH AND SUCTORIAN CILIATES (CILIOPHORA) ON OLIGOCHAETES AND HARPACTICOID COPEPODS FROM THE DEEP-WATER HYPOXIC/ANOXIC CONDITIONS OF THE BLACK SEA

Three species of commensal ciliates ( Cothurnia maritima Ehrenberg, 1838 on oligochaete Tubificoides sp.; Paracineta livadiana (Mereschkowsky, 1881) and Corynophrya lyngbyi (Ehrenberg, 1834) on harpacticoid copepods Amphiascella subdebilis (Willey, 1935), Haloschizopera pontarchis Por, 1959, Cletodes tenuipes Scott, 1896 and Enhydrosoma longifurcatum Sars, 1909) were found in the Black Sea deep-water under hypoxic/anoxic conditions for the first time. Corynophrya lyngbyi is reported for the first time in the Black Sea.
Long-term land management effects on soil properties and microbial populations in a maize-bean rotation at Kabete, Kenya

The effect of continued application of mineral and organic fertilizers on soil agro-properties and soil microbial populations and activity, was studied in a long-term field experiment at Kabete, in the highlands of Kenya. The area is sub-humid with an average bimodal rainfall of 980 mm and two cropping seasons per year. The main treatments were 3 rates of inorganic N and P fertilizers, farmyard manure (FYM) with or without stover retention. Maize and beans were planted during the long and short rain seasons, respectively. Total % N declined by 25% from 0.16% while soil organic carbon decreased from 2 to 1.2%. The soil pH value dropped by 1.3. units from 5.5 but the decrease in bulk density from 1.04 to 1.08 g cm-3 soil in the no-input control treatment was not significant. Use of FYM alone or in combination with chemical fertilizers led to higher numbers of microbes and enhanced microbial respiration than use of chemical fertilizers alone. The topsoil layer had significantly (p = 0.05) higher microbial activity than the sub-soil regardless of management strategy. Bacteria were more numerous {1 × 105 cfu (colonies forming units) g dry wt. soil -1} than fungi (1 × 103 cfu g dry wt. soil -1), which may lead to more soil organic matter (SOM) mineralization and less SOM retention in this cropping system. Integrated use of organic inputs such as farmyard manure and chemical fertilizers is recommended to maintain soil productivity under continuous cultivation. Key words: Land management, fertilizers, farmyard manure, crop residues, soil properties, mineralization, microbial population.
A NEW GENUS AND SPECIES OF TYRANNOSAUROID FROM THE LATE CRETACEOUS (MIDDLE CAMPANIAN) DEMOPOLIS FORMATION OF ALABAMA

Abstract The discovery of a new genus and species of tyrannosauroid from the Demopolis Formation (middle Campanian) of Alabama increases the known diversity of the clade, although it does not elucidate the place of initial dispersal. This subadult tyrannosauroid is the most complete non-avian theropod collected and described from the Cretaceous of eastern North America. In contrast to tyrannosaurids, the new taxon possesses several plesiomorphic characters, including lacrimals that lack a distinct peaked cornual process, and a dorsoventrally shallow horizontal ramus of the maxilla. Autapomorphies include a wide jugal process of the ectopterygoid, a caudal pneumatic foramen of the palatine that pierces the rostral half of the vomeropterygoid process of the bone, an articular surface for the lacrimal on the palatine that is distally positioned on the dorsolateral process, and pedal unguals that have a distinct proximodorsal lip over the articular surface. Cladistic analysis indicates the new taxon is a basal tyrannosauroid and its presence in eastern North America suggests that the recent common ancestor of Tyrannosauridae probably evolved following the transgression of the Western Interior Seaway. Cladistic analysis indicates that Dryptosaurus aquilunguis is also a basal tyrannosauroid but is less derived than the new genus.
Serologic detection of Avian influenza H5 antibodies using a competitive enzyme-linked immunosorbent assay (ELISA)

A competitive enzyme-linked immunosorbent assay (cELISA) for avian influenza (AI) H5 specific antibody detection was previously developed. In this study, additional serum samples from infected and vaccinated birds were tested and the results were compared to other serological tests. Using the samples from experimentally infected chickens, the H5 cELISA was shown to be comparable to other serological assays. Using samples from free-living blue-winged teals and vaccinated birds, a correlation was found between the H5 cELISA and the hemagglutination-inhibition (HI) assay. In conclusion, the H5 cELISA will be a useful tool for the serological diagnosis, surveillance of AI H5 infections, and for measuring of protective antibody levels.
Will Molasses or Conditioning Increase Consumption of Spotted Knapweed by Sheep?

Abstract The spread of the invasive, Eurasian spotted knapweed (Centaurea maculosa Lam.) across the northwestern United States would be reduced if livestock regularly consumed it. We determined if white-face yearling ewes (n = 36) conditioned for 12 days to fresh-cut spotted knapweed, with or without molasses, would increase their use of it during a 5-day field trial and/or a 4-day drylot trial. Ewes were assigned to one of three treatments: ewes not conditioned to spotted knapweed or molasses (NC), ewes conditioned to spotted knapweed (SK), or ewes conditioned to spotted knapweed sprayed with liquid beet molasses (SKM). During conditioning, all groups consumed high amounts of their feed. Nonconditioned ewes (NC) consumed less than ewes conditioned to spotted knapweed (SK, SKM), indicating spotted knapweed did not inhibit initial consumption. In the field, SKM ewes spent more time grazing spotted knapweed and other forbs than SK ewes. In a drylot, time spent eating and intake of spotted knapweed and bromegrass (Bromus inermis Leyss.) varied through time. Conditioning yearling ewes to spotted knapweed, with or without molasses, did not increase consumption of this invasive plant, possibly because sheep inherently graze spotted knapweed only to a certain extent, or we did not use enough spotted knapweed during conditioning.
Consumo, digestibilidade e excreção de uréia e derivados de purinas em vacas de diferentes níveis de produção de leite

The objective of this trial was to evaluate the effect of milk production level on intake, digestibility of nutrients, microbial protein synthesis, and nitrogen (N) metabolism in Holstein cows. It was also of particular interest to compare spot urine sampling and total urine collection as methodologies to quantify yield of microbial N using purine derivatives (PD) as indirect microbial markers. Fifteen Holstein cows were grouped by milk yield (5.88 kg/day: LOW treatment; 18.54 kg/day: MEDIUM treatment; and 32.6 kg/day: HIGH treatment) and data analyzed as a completely randomized design. Animals were fed ad libitum corn silage plus one kg of concentrate per each three kg of milk produced. Except for NDF corrected for ash and protein (NDFap), intake of all remaining nutrients was increased by milk yield. Digestibilities of DM and OM and dietary TDN content did not differ among treatments. However, digestibility of CP was higher and that of NDFap was lower on the greatest milk yielding cows (HIGH treatment). Concentrations of milk urea N and serum urea N as well as urinary N excretion were all greatest in the HIGH treatment and were also highly correlated with milk yield. Microbial protein synthesis estimated by PD was lowest on cows in the LOW treatment and did not differ when either spot urine sampling or total urine collection was used. Therefore, spot urine sampling can be used to estimate urinary excretion of nitrogenous compounds and microbial protein synthesis in Holstein cows with different production levels.
Consumer Loans and Credit Cards in an Emerging Market: Econometric Modelling and Policy Implications for Turkey

Since it has important implications in many economic sectors (e.g. construction, car, retail, real estate), analysis of the growth in consumer loans and credit cards (CLCC), which has been witnessed in recent years in Turkey, is particularly important. Our objective is to develop an understanding of the recent growth in CLCC, investigate the causality relationship with other macroeconomic variables and how CLCC responds to the shocks given to other variables and determine the impact of each variable on the variance of CLCC. In this article, we determine the relationships between CLCC and chosen macroeconomic variables and make suggestions about which policy tools should be used to influence, and if necessary to manage, the growth in CLCC. For this purpose, we use monthly data for the period of January 2004-December 2013 of seven macroeconomic variables on money supply, interest rate, income, consumer confidence, inflation, stock market and consumer goods imports. First, we employ the Granger Causality Test to identify the causality relationships between variables. Second, we analyse the variables using a VAR based Impulse-Response and Variance Decomposition Analyses. We found that money supply and interest rates have significant potential as a monetary policy tool and that stock market, consumer confidence, income and import variables had some potential to be used to predict the growth in CLCC.
Data Reduction Using Statistical and Regression Approaches for Ice Velocity Derived by Landsat-8, Sentinel-1 and Sentinel-2

During the last decade, the number of available satellite observations has increased significantly, allowing for far more frequent measurements of the glacier speed. Appropriate methods of post-processing need to be developed to efficiently deal with the large volumes of data generated and relatively large intrinsic errors associated with the measurements. Here, we process and combine together measurements of ice velocity of Russell Gletscher in Greenland from three satellites—Sentinel-1, Sentinel-2, and Landsat-8, creating a multi-year velocity database with high temporal and spatial resolution. We then investigate post-processing methodologies with the aim of generating corrected, ordered, and simplified time series. We tested rolling mean and median, cubic spline regression, and linear non-parametric local regression (LOWESS) smoothing algorithms to reduce data noise, evaluated the results against ground-based GPS in one location, and compared the results between two locations with different characteristics. We found that LOWESS provides the best solution for noisy measurements that are unevenly distributed in time. Using this methodology with these sensors, we can robustly derive time series with temporal resolution of 2–3 weeks and improve the accuracy on the ice velocity to about 10 m/yr, or a factor of three compared to the initial measurements. The presented methodology could be applied to the entire Greenland ice sheet with an aim of reconstructing comprehensive sub-seasonal ice flow dynamics and mass balance.
Crowfootgrass (Dactyloctenium aegyptium) Germination and Response to Herbicides in the Philippines

Abstract Crowfootgrass, a C4 species, is one of the principal weeds of dry-seeded rice in Asia. Weed management decisions for this species can be derived from knowledge of its seed germination biology. Experiments were conducted in the laboratory and screenhouse to determine the effects of light, alternating day/night temperatures, water stress, seed burial depth, and rice residue on seed germination and seedling emergence of crowfootgrass and to evaluate the response of this weed to commonly available selective POST herbicides in the Philippines. Light stimulated seed germination, but it was not an absolute requirement for germination. Germination in the light/dark regime was greater at alternating day/night temperatures of 25/15 C (92%) than at 30/20 (70%) or 35/25 C (44%). The osmotic potential required for 50% inhibition of maximum germination was −0.23 MPa, although some seeds germinated at −0.6 MPa. Seedling emergence was greatest for the seeds placed on the soil surface (64%), and emergence declined with increased burial depth in soil. No seedlings emerged from a burial depth of 6 cm or greater. Seedling emergence of crowfootgrass was reduced by the addition of rice residue to the soil surface at rates equivalent to 4 to 6 Mg ha−1. Fenoxaprop-p-ethyl + ethoxysulfuron at 45 g ai ha−1 provided excellent control of crowfootgrass when applied at the four- (99%) and six-leaf (86%) stage. The information gained from this study could contribute to developing components of integrated weed management strategies for crowfootgrass. Soil inversion by tillage to bury weed seeds below their maximum depth of emergence, use of crop residue as mulch, and early application of an effective POST herbicide could serve as important tools for managing crowfootgrass. Nomenclature: Bispyribac-sodium; fenoxaprop-p-ethyl + ethoxysulfuron; penoxsulam + cyhalofop; crowfootgrass, Dactyloctenium aegyptium (L.) Willd. DTTAE; rice, Oryza sativa L.
Influence of Feeding on the Metabolic Rate of the Lizard, Eulamprus tympanum

Abstract We measured the increase in metabolic rate following feeding, or the specific dynamic action (SDA) of feeding, in the lizard Eulamprus tympanum that feeds opportunistically and frequently. The SDA of most reptiles studied to date is pronounced in relation to other vertebrates, but most species for which data are available consume large meals infrequently. We chose to measure SDA in E. tympanum because it is typical of most lizards in that it feeds frequently. The SDA pattern of E. tympanum is typical of other animals, where metabolic rate increases to a peak following feeding then gradually decreases to prefeeding values. Metabolic rate in E. tympanum increases by up to 2.4 times the prefeeding values and remains elevated for up to 48 h. The SDA effect is much less in a lizard that feeds opportunistically and frequently than in sit-and-wait foraging reptiles. The duration of the SDA is greater in E. tympanum than in many other vertebrates and may be related to an ectothermic lifestyle, meal size, or diet composition. On the basis of diet and feeding strategy, E. tympanum is probably typical of lizards that feed frequently, but there are too few data to make detailed comparisons.
The population abundance, distribution pattern and culture studies of isolated microalgal strains from selective sampling sites along the south east coast of India

The present study was conducted to understand the microalgal dynamics and surveillance in the selective sites along the south east coast of India. Algal isolation was carried out in 61 sampling stations characterized by different ecological features. In total 10 microalgal species were isolated under laboratory condition from the collected samples. The composition of microalgal distribution and their surveillance were related to the environmental factors are discussed in the present paper. From the results it was observed that Isochrysis galbana [MA1] has the maximum surveillance at 37 spots [60.7%]. It was also observed that 25.7% of the collection spots may share same microalgal dynamics and surveillance. In order to understand the better background information about the importance of culture condition in the optimal growth of microalgal strains, experimental setup were designed using modified Walne’s and Guillard f/2 medium. Studies were also carried out to understand the relation between the growth conditions and environmental factors including salinity, temperature, pH and dissolved oxygen. The growth study was further designed by providing the culture setup with 2 different light : dark illustration of 24:0 with 1000 lux setup and 16:8 with 1000 lux. The results show 70% of the isolated samples grown in Walne’s medium and 60% of samples grown on guillard’s f/2 medium prefer to grow optimally under 16:8 light: dark illustration. It was also observed that Walne’s medium encourages better growth for the collected microalgal samples when compared with the Guillard’s medium.