Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Association Mapping for Kernel and Malting Quality Traits Using Historical European Barley Records

Malting quality is an important trait in breeding barley (Hordeum vulgare L.). It requires elaborate, expensive phenotyping, which involves micro-malting experiments. Although there is abundant historical information available for different cultivars in different years and trials, that historical information is not often used in genetic analyses. This study aimed to exploit historical records to assist in identifying genomic regions that affect malting and kernel quality traits in barley. This genome-wide association study utilized information on grain yield and 18 quality traits accumulated over 25 years on 174 European spring and winter barley cultivars combined with diversity array technology markers. Marker-trait associations were tested with a mixed linear model. This model took into account the genetic relatedness between cultivars based on principal components scores obtained from marker information. We detected 140 marker-trait associations. Some of these associations confirmed previously known quantitative trait loci for malting quality (on chromosomes 1H, 2H, and 5H). Other associations were reported for the first time in this study. The genetic correlations between traits are discussed in relation to the chromosomal regions associated with the different traits. This approach is expected to be particularly useful when designing strategies for multiple trait improvements.
PAPER Environmental and socio-economic factors shaping the geography of floristic collections in China

Aim Effortincollectingbiodiversityinformationoftenvariesstronglyinspaceand may be driven by environmental,cultural and socio-economic factors.Understanding the constraints on collecting effort is crucial for identifying potential bias in distributional databases and for making future surveys more efficient. Here we test six competing hypotheses on drivers of geographical variation in collecting effort andidentifythemainfactorsshapingthegeographyof floristiccollectionsinChina. Location China. Methods We used the most comprehensive database of Chinese vascular plant distributions including 4,338,516 county-level occurrences derived from herbarium specimens and literature sources. Explanatory variables were assembled representing six different hypotheses: accessibility, human population density, the ‘botanist effect’, mountains, water availability and conservation priority. Ordinary least-squares models with eigenvector-based spatial filters were applied to investigate their effects on spatial patterns of two different facets of collecting effort, i.e. collection density and inventory incompleteness.
Comparison of Two Methods of Calculating Breeding Efficiency of Crossbred Cattle and Murrah Buffaloes

A total of 1474 and 1935 production and reproduction records of crossbred cattle and Murrah buffaloes from the year 1992 to 2012 were utilized in the present study to investigate breeding efficiency (BE) at Gadvasu Dairy farm. Breeding efficiency was calculated using Wilcox (1957) and Tomar (1965) methods and then Least squares of Harvey (1990) model was used to study the effects of various non-genetic factors (period, season) on breeding efficiency. Average breeding efficiency of Crossbred Cattle was 82.31 ± 0.97% ranging from 75% to 85% by Wilcox method and 98.14 ± 1.09% ranging from 95% to 99% by Tomar method. Breeding efficiency of Buffaloes was 78.03 ± 1.01% ranging from 69% to 84% by Wilcox method (1957) and 78.39 ± 0.39% ranging from 74% to 80% by Tomar method under the present management and production conditions. The little differences in two methods may be attributed to different methods of calculation as well as large variation in the no. of calvings, calving interval and age at first calving across 20 years. Hence it may further be concluded that the two methods were equally useful in the calculation of reproductive efficiency in dairy animals.
Solid lipid nanoparticles carrying Eugenia caryophyllata essential oil: the novel nanoparticulate systems with broad‐spectrum antimicrobial activity

In this study, solid lipid nanoparticles containing Eugenia caryophyllata essential oil (SLN‐EO) were prepared by high‐shear homogenization and ultrasound methods, and used to eradicate pathogens. SLN formulations were evaluated for their size, zeta potential and encapsulation efficacy (EE). The morphological and thermal properties of the formulations were analysed by transmission electron microscopy (TEM) and differential scanning calorimetry methods. The lead formulations were chosen and tested with minimum inhibitory concentration (MIC), MBC and time‐kill methods to investigate the antimicrobial activity against Salmonella typhi, Pseudomonas aeruginosa, Staphylococcus aureus and Candida albicans. The particle size of three final formulations were 397 ± 10·1, 786·9 ± 11 and 506·4 ± 22 nm respectively. The zeta potential of all formulations was negative values. The size of the formulations was slightly increased during 3 months storage at 25°C. The TEM imaging showed that formulation had spherical shape. The EE of EO was estimated approximately 70%. MIC and MCC values of SLN‐EO were lower than those of the oil alone. The time‐kill studies showed that SLN‐EO was either equivalent to or better than EO (P‐value <0·05). The results of this study highlighted the effectiveness of SLN formulations against human pathogens.
Deep Q networks for visual fighting game AI

Recently, the introduction of vision-based deep Q learning demonstrated successful results in Atari, and Visual Doom AI platform. Unlike the previous study, the fighting game assumes two players with a relatively large number of actions. In this study, we propose to use deep Q Networks (DQN) for the visual fighting game AI competitions. The number of actions was reduced to 11 and the sensitivity of several control parameters was tested using the visual fighting platform. The experimental results show the potential of the DQN approach for the two- player real-time fighting game.
Quantitative positron emission tomography reveals regional differences in aerobic glycolysis within the human brain

Glucose and oxygen metabolism are tightly coupled in the human brain, with the preponderance of the brain’s glucose supply used to generate ATP via oxidative phosphorylation. A fraction of glucose is consumed outside of oxidative phosphorylation despite the presence of sufficient oxygen to do so. We refer to this process as aerobic glycolysis. A recent positron emission tomography study reported that aerobic glycolysis is uniform within gray matter. Here, we analyze the same data and demonstrate robust regional differences in aerobic glycolysis within gray matter, a finding consistent with previously published data.
SeamSeg: Video Object Segmentation Using Patch Seams

In this paper, we propose a technique for video object segmentation using patch seams across frames. Typically, seams, which are connected paths of low energy, are utilised for retargeting, where the primary aim is to reduce the image size while preserving the salient image contents. Here, we adapt the formulation of seams for temporal label propagation. The energy function associated with the proposed video seams provides temporal linking of patches across frames, to accurately segment the object. The proposed energy function takes into account the similarity of patches along the seam, temporal consistency of motion and spatial coherency of seams. Label propagation is achieved with high fidelity in the critical boundary regions, utilising the proposed patch seams. To achieve this without additional overheads, we curtail the error propagation by formulating boundary regions as rough-sets. The proposed approach out-perform state-of-the-art supervised and unsupervised algorithms, on benchmark datasets.
The essential and beneficial roles of nickel In growth of soybean and wheat plants

Nickel (Ni), which is known to be the cofactor of urease, was the last element to be included in the list of essential micronutrients for higher plants. Although the Ni requirement of plants is very low, Ni deficiency was documented to occur under field conditions. However, most of the studies on plant Ni nutrition were conducted in hydroponics and focused on urea metabolism. In order to investigate the essential and beneficial roles of Ni in plant growth, several nutrient solution and soil culture studies were conducted on two major crops, namely soybean and wheat, under growth chamber and greenhouse conditions. Nickel deficiency reduced the seed yield in nitrate-fed soybean and caused impaired growth and toxicity symptoms upon foliar urea applications. Moreover, Ni deficiency resulted in physiological nitrogen (N) deficiency and reduced the N uptake and N use efficiency (NUE) of urea-fed plants. Using high-Ni seeds was a highly effective alternative to external Ni supply for alleviating the problems caused by urea. In wheat, soil and/or foliar applications of Ni improved the grain yield and NUE under ample N supply, indicating that Ni may be beneficial at levels much higher than required to fulfill its essential roles, depending on the conditions. Furthermore, foliar Ni applications were shown to provide protection against sublethal glyphosate, which can cause developmental abnormalities and dramatic yield losses in wheat. The use of Ni as a micronutrient may have great impacts on agricultural productivity, NUE and crop tolerance to glyphosate drift. These effects should be further investigated under field conditions.
SOIL PROPERTIES AFFECTED BY LAND USE SYSTEMS IN WESTERN CHITWAN, NEPAL

Field experiments were conducted in acidic soils of Mangalpur and Fulbari VDCs in western Chitwan, Nepal to study the effects of different land use systems on soil properties. Seven land use systems (cereal based lowland, cereal based upland, vegetable farm land, fruit orchard land, pasture land, forest land and farmer’s field) were used and they were replicated four times in randomized complete block designs. Composite soil samples were collected from each study sites and were analyzed in laboratory for soil physicochemical properties. The data obtained were analyzed using MSTAT-C. Soil properties were significantly affected by land use systems in western Chitwan condition. Soil organic matter and total soil nitrogen were significantly higher from pasture land (4.69 % and 0.23 %) and the lowest were from farmer’s field (2.40 % and 0.08 %). However, available soil phosphorous content was significantly higher from cereal based upland (448.3 kg ha -1 ) and it was the lowest from forest land (13.0 kg ha -1 ). Soil bulk density and pH were not significantly affected by land use systems. Since land use systems and management practices significantly affect soil physical and chemical properties, an appropriate and sustainable land use management option is necessary for fertile and healthy soil. Conservation tillage with the addition of sufficient organic inputs can be suggested based on this study to maintain soil health for sustained production and optimum activity of soil organisms under the western Chitwan land use systems. DOI: http://dx.doi. org/10.3126/ijasbt.v2i3. 10660 DOI: http://dx.doi. org/10.3126/ijasbt.v2i3. 10660 Int J Appl Sci Biotechnol, Vol. 2(3): 265-269
Quantifying Transmission Heterogeneity Using Both Pathogen Phylogenies and Incidence Time Series

Abstract Heterogeneity in individual-level transmissibility can be quantified by the dispersion parameter k of the offspring distribution. Quantifying heterogeneity is important as it affects other parameter estimates, it modulates the degree of unpredictability of an epidemic, and it needs to be accounted for in models of infection control. Aggregated data such as incidence time series are often not sufficiently informative to estimate k. Incorporating phylogenetic analysis can help to estimate k concurrently with other epidemiological parameters. We have developed an inference framework that uses particle Markov Chain Monte Carlo to estimate k and other epidemiological parameters using both incidence time series and the pathogen phylogeny. Using the framework to fit a modified compartmental transmission model that includes the parameter k to simulated data, we found that more accurate and less biased estimates of the reproductive number were obtained by combining epidemiological and phylogenetic analyses. However, k was most accurately estimated using pathogen phylogeny alone. Accurately estimating k was necessary for unbiased estimates of the reproductive number, but it did not affect the accuracy of reporting probability and epidemic start date estimates. We further demonstrated that inference was possible in the presence of phylogenetic uncertainty by sampling from the posterior distribution of phylogenies. Finally, we used the inference framework to estimate transmission parameters from epidemiological and genetic data collected during a poliovirus outbreak. Despite the large degree of phylogenetic uncertainty, we demonstrated that incorporating phylogenetic data in parameter inference improved the accuracy and precision of estimates.
Reliability-based automatic repeat request for short code modulation visual evoked potentials in brain computer interfaces

We propose two methods to improve code modulation visual evoked potential brain computer interfaces (cVEP BCIs). Most of BCIs average brain signals from several trials in order to improve the classification performance. The number of averaging defines the trade-off between input speed and accuracy, and the optimal averaging number depends on individual, signal acquisition system, and so forth. Firstly, we propose a novel dynamic method to estimate the averaging number for cVEP BCIs. The proposed method is based on the automatic repeat request (ARQ) that is used in communication systems. The existing cVEP BCIs employ rather longer code, such as 63-bit M-sequence. The code length also defines the trade-off between input speed and accuracy. Since the reliability of the proposed BCI can be controlled by the proposed ARQ method, we introduce shorter codes, 32-bit M-sequence and the Kasami-sequence. Thanks to combine the dynamic averaging number estimation method and the shorter codes, the proposed system exhibited higher information transfer rate compared to existing cVEP BCIs.
Properties of silanized nypa fruticans filled polylactic acid/recycled low density polyethylene biocomposites

The biocomposites of Nypa Fruticans (NF) and Polylactic acid (PLA)/recycled low density polyethylene (rLDPE) were prepared using Brabender EC PLUS. The effect of NF content and silane coupling agent on mechanical, thermal, and morphological properties were studied. The results show that addition of NF in PLA/rLDPE biocomposites have decreased the tensile strength, elongation at break, and crystallinity of biocomposites. The Young's modulus of biocomposites and thermal stability increased with the increasing NF content. The surface of NF fillers were silanized to improved the interfacial adhesion between the NF filler and PLA/rLDPE matrix. It was found that the tensile strength, Young's modulus, crystallinity of PLA, and thermal stability of silanized biocomposites higher as compared to untreated biocomposites. The enhancement of the properties of biocomposites with silane treatment was proven by SEM studied. The silanized biocomposites showed better interfacial interaction and adhesion between NF and PLA/rLDPE matrix. POLYM. ENG. SCI., 55:1733–1740, 2015. © 2014 Society of Plastics Engineers
Numerical Modeling of the Subsoil-Structure Interaction

Numerical interaction model of reinforced concrete slab and subsoil was created in ANSYS. Input data for numerical analysis were obtained during experimental loading test of reinforced concrete slab. Loading test was performed using unique experimental equipment constructed in the area of Faculty of Civil Engineering, VŠB-TU Ostrava. Analysis of interaction of reinforced concrete slab with subsoil was solved with application of inhomogeneous half-space. Application of inhomogeneous half-space allows better capture the subsoil behaviour and its increasing modulus of deformability with increasing depth of subsoil model. Homogeneous half-space this takes no account. Reinforced concrete slab was cracked during an experiment. The effect of cracks was also taken into account in the numerical model of reinforced concrete slab using derived modulus of elasticity of cracked concrete. Values calculated by all types of interaction models were compared with values measured during the loading test of reinforced concrete slab.
Assembling 2-D Blocks Into 3-D Chips

Despite numerous advantages of 3-D integrated circuits (ICs), their commercial success remains limited. In part, this is due to the wide availability of trustworthy intellectual property (IP) blocks developed for 2-D ICs and proven through repeated use. Block-based design reuse is imperative for heterogeneous 3-D ICs where memory, logic, analog, and microelectromechanical systems dies are manufactured at different technology nodes and circuit modules cannot be partitioned among several dies. In this paper, we show how to integrate 2-D IP blocks into 3-D chips without altering their layout. Experiments indicate that the overhead of proposed integration is small, which can help accelerate industry adoption of 3-D integration.
What Are the Costs of Degraded Parafoveal Previews During Silent Reading?

It has been suggested that the preview benefit effect is actually a combination of preview benefit and preview costs. Marx et al. (2015) proposed that visually degrading the parafoveal preview reduces the costs associated with traditional parafoveal letter masks used in the boundary paradigm (Rayner, 1975), thus leading to a more neutral baseline. We report 2 experiments of skilled adults reading silently. In Experiment 1, we found no compelling evidence that degraded previews reduced processing costs associated with traditional letter masks. Moreover, participants were highly sensitive to detecting degraded display changes. Experiment 2 used the boundary detection paradigm (Slattery, Angele, & Rayner, 2011) to explore whether participants were capable of detecting actual letter changes or if they were responding purely to changes in degradation. Half of the participants were instructed to respond to any noticed display changes; the other half were instructed to respond only to changes in letter identities. Participants were highly sensitive to degraded changes. In fact, these changes were so apparent that they reduced the sensitivity to letter masks. In the context of the model proposed by Angele, Slattery, and Rayner (2016), we suggest that degraded previews interfere with the attentional stage, as evidenced by the general lack of foveal load effects. In summary, we found that increasingly degrading parafoveal letter masks does not reduce their processing costs in adults, but that both degraded valid and invalid previews introduce additional costs in terms of greater display change awareness.
Polarimetric Decomposition for Soil Moisture Retrieval from Vegetated Soils in TERENO Observatories

A refined hybrid polarimetric decomposition and inversion method for soil moisture estimation under vegetation is investigated for its potential to retrieve soil moisture from vegetated soils in TERENO observatories. The refined algorithm is applied on Lband fully polarimetric data acquired by DLR’s novel F-SAR sensor. Two flight and field measurement campaigns were conducted in 2011 and 2012 for the TERENO Harz, Eifel and DEMMIN observatories, located all across Germany. The applied algorithm reveals distinct potential to invert soil moisture with inversion rates higher than >98% for a variety of crop types, phenological conditions and for pronounced topography. A quality assessment is conducted by validation with FDR, TDR and a wireless soil moisture network. The RMSE stays below 6.1vol. % for the different test sites and data takes including a variety of vegetation types in different phenological stages.
Genetic identification of source and likely vector of a widespread marine invader

Abstract The identification of native sources and vectors of introduced species informs their ecological and evolutionary history and may guide policies that seek to prevent future introductions. Population genetics provides a powerful set of tools to identify origins and vectors. However, these tools can mislead when the native range is poorly sampled or few molecular markers are used. Here, we traced the introduction of the Asian seaweed Gracilaria vermiculophylla (Rhodophyta) into estuaries in coastal western North America, the eastern United States, Europe, and northwestern Africa by genotyping more than 2,500 thalli from 37 native and 53 non‐native sites at mitochondrial cox1 and 10 nuclear microsatellite loci. Overall, greater than 90% of introduced thalli had a genetic signature similar to thalli sampled from the coastline of northeastern Japan, strongly indicating this region served as the principal source of the invasion. Notably, northeastern Japan exported the vast majority of the oyster Crassostrea gigas during the 20th century. The preponderance of evidence suggests G. vermiculophylla may have been inadvertently introduced with C. gigas shipments and that northeastern Japan is a common source region for estuarine invaders. Each invaded coastline reflected a complex mix of direct introductions from Japan and secondary introductions from other invaded coastlines. The spread of G. vermiculophylla along each coastline was likely facilitated by aquaculture, fishing, and boating activities. Our ability to document a source region was enabled by a robust sampling of locations and loci that previous studies lacked and strong phylogeographic structure along native coastlines.
Mucosa-Associated Bacterial Microbiome of the Gastrointestinal Tract of Weaned Pigs and Dynamics Linked to Dietary Calcium-Phosphorus

Dietary composition largely influences pig’s gastrointestinal microbiota and represents a useful prophylactic tool against enteric disturbances in young pigs. Despite the importance for host-microbe interactions and bacterial colonization, dietary responses of the mucosa-associated bacterial communities are less well investigated. In the present study, we characterized the mucosa-associated bacterial communities at the Pars non-glandularis of the stomach, ileum and colon, and identified shifts in these communities in response to different dietary calcium-phosphorus (Ca-P) contents (100% versus 190% of the Ca and P requirements) in combination with two basal diets (wheat-barley- or corn-based) in weaned pigs. Pyrosequencing of 16S rRNA genes from 93 mucosal samples yielded 447,849 sequences, clustering into 997 operational taxonomic units (OTUs) at 97% similarity level. OTUs were assigned to 198 genera belonging to 14 different phyla. Correlation-based networks revealed strong interactions among OTUs at the various gastrointestinal sites. Our data describe a previously not reported high diversity and species richness at the Pars non-glandularis of the stomach in weaned pigs. Moreover, high versus adequate Ca-P content significantly promoted Lactobacillus by 14.9% units (1.4 fold change) at the gastric Pars non-glandularis (P = 0.035). Discriminant analysis revealed dynamic changes in OTU composition in response to dietary cereals and Ca-P contents at all gastrointestinal sites which were less distinguishable at higher taxonomic levels. Overall, this study revealed a distinct mucosa-associated bacterial community at the different gut sites, and a strong effect of high Ca-P diets on the gastric community, thereby markedly expanding our comprehension on mucosa-associated microbiota and their diet-related dynamics in weaned pigs.