Miracle-dz/UniFAR-FTUs huggingface dataset:
1 Differential host response to a herpesvirus: Marek’s 2 disease virus peptides on chicken MHC class II 3 molecules are derived from only a few genes and 4 illustrate a new mode of peptide binding

31 Viral diseases pose major threats to humans and other animals, including the billions of 32 chickens that are an important food source as well as a public health concern due to 33 zoonotic pathogens. Unlike humans and other typical mammals, the major 34 histocompatibility complex (MHC) of chickens can confer decisive resistance or 35 susceptibility to many viral diseases. An iconic example is Marek’s disease, caused by an 36 oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules 37 present antigenic peptides to T lymphocytes, and it has been hard to understand how such 38 MHC molecules could be involved in susceptibility to Marek’s disease, given the potential 39 number of peptides from over 100 genes. We used a new in vitro infection system and 40 immunopeptidomics to determine peptide motifs for the two class II molecules expressed 41 by the MHC haplotype B2, which is known to confer resistance to Marek’s disease. 42 Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken 43 class II molecules arise from only four viral genes, nearly all having the peptide motif for 44 BL2, the dominantly-expressed class II molecule in chickens. We expressed BL2 linked to 45 several MDV peptides, and determined one X-ray crystal structure, showing how a single 46 small amino acid in the binding site causes a crinkle in the peptide, leading to core binding 47 peptide of ten amino acids, compared to the nine amino acids in all other reported class II 48 molecules. The limited number of potential T cell epitopes from such a complex virus can 49 explain the differential MHC-determined resistance to MDV, but raises questions of 50 mechanism and opportunities for vaccine targets in this important food species, as well as 51 providing a basis for understanding class II molecules in other species including humans.
A survey of earthquake damage detection and assessment of buildings using SAR imagery

Synthetic Aperture Radar(SAR) is one of the most important sensors for earthquake damage detection of buildings in building-up areas.With the development in the sensor technology,SAR has become research hotspots in urban damage detection and assessment.The purpose of this paper is to analyze the characteristics of buildings in SAR image,and to present an overview of the methods developed over the last 15 years and their applications.For each type of method,the merits and the limitations are discussed.Finally,for the new high resolution and full polarization SAR image,some topics which are worth studying further are proposed.
Research Article: Near-Remote Sensing of Water Turbidity Using Small Unmanned Aircraft Systems

This report describes the field demonstration of a near-remote sensing method to measure water turbidity over large areas, in a high-resolution, spatial context. Our interdisciplinary method used a novel multispectral imaging sensor deployed by a hand-launched small unmanned aircraft system (sUAS). The measurement of turbidity is a useful indicator of water quality. Current turbidity measurement tools, such as the Secchi disc, are labor-intensive and often limit coverage such that available samples are extrapolated unrealistically when representing large water resources. This handicaps computer models' ability to predict run-off, and these models produce the best results if supplied with high-resolution, fine time-increment measurements. This first study of the method developed operated the sUAS below 200 m over the surface of a 9.3-ha lake, capturing visible and near-infrared imagery at resolutions of ~0.2 m/pixel and capturing spectral bands matching those captured by the Landsat 4-5 satellites. The study established the spectral sensitivity and spatial coverage of the instrumentation and correlated turbidity estimates against traditional Secchi disc readings taken across the lake. This study also differentiated turbidity contribution from suspended organics vs. suspended sediments. To manage glare, this new technique required strategically positioned sunlight, thus sharing some operational limitations with the Secchi disc method. Plans have been made to extend the technique to be suitable for deeper, clearer lakes. The technique represents an improved monitoring tool for environmental scientists, watershed managers, and civil engineers.
Boosting Adversarial Training in Safety-Critical Systems Through Boundary Data Selection

AI-enabled collaborative robots are designed to be used in close collaboration with humans, thus requiring stringent safety standards and quick response times. Adversarial attacks pose a significant threat to the deep learning models of these systems, making it crucial to develop methods to improve the models' robustness against them. Adversarial training is one approach to improve their robustness: it works by augmenting the training data with adversarial examples. This, unfortunately, comes with the cost of increased computational overhead and extended training times. In this work, we balance the need for additional adversarial data with the goal of minimizing the training costs by selecting the most ‘valuable’ data for adversarial training. In particular, we propose a robustness-oriented boundary data selection method, RAST-AT, which stands for robust and fast adversarial training. RAST-AT selects training data near to the boundary by considering adversarial perturbations. Our method improves the speed of model training on CIFAR-10 by 68.67%, and compared to other data selection methods, has 10% higher accuracy with 10% training data selected, and 7% higher robustness with 4% training data selected. Our method also significantly improves efficiency by at least 25% in adversarial training, with the same performance. Finally, we evaluate our method on a cobot system, generating adversarial patches as attacks, and adopting RAST-AT as the defense. We find that RAST-AT can defend against 60% of untargeted attacks and 20% of targeted attacks. Our work highlights the benefits of developing effective defenses against adversarial attacks to ensure the security and reliability of AI-powered safety-critical systems.
Direct discrimination of palm oil as an adulterant in edible oils using a portable Raman spectrometer

Abstract The common adulteration process in oils involves mixing low-cost and high-cost edible oils. Palm oil has been widely used as an adulterant in the Indian market. In the present work, different ratios of palm oil were mixed with high-cost edible oils such as sunflower, groundnut, coconut, and gingelly. Raman peak intensity for all edible oils individually and after mixing palm oil as an adulterant was studied using a portable Raman spectrometer. The peaks at 838 cm−1, 868 cm−1, 973 cm−1, 1077 cm−1, 1262 cm−1,1300cm−1, 1438 cm−1, 1655 cm-1, and 1745 cm−1 represent vibration due to the (C–C) stretching, (CH) wagging from cis (–CH = CH–), δ(=CH), skeletal C–C stretching, (CH) deformation of (CH2), scissoring vibration of CH2 group, (C=C) stretching from cis –(CH=CH–), and (C=O) stretching vibration from (RC=OOR) for sunflower oil, groundnut oil, gingelly oil, and coconut oil. An attempt has been made to detect 12.5 mL of palm oil in 100 mL of high-cost edible oil. Raman peaks disappeared while adding more than 12.5 mL of adulterate oil. The disappearance of peaks in edible oils, 973 cm−1 for sunflower oil, 970 cm−1 for groundnut oil, 1122 cm−1 for coconut oil, and 1745 cm−1 for gingelly oil respectively. The obtained results will be used for futuristic data analysis to directly detect adulterants in the oils.
Different settling regimes in secondary settling tanks: experimental process analysis, model development and calibration

An improved 1-D model for the secondary clarifier, i.e. the Bürger-Diehl model, was recently presented. In this chapter, the impact of specific features of the BürgerDiehl model on settler underflow concentration predictions, plant sludge inventory and Mixed Liquor Suspended Solids (MLSS) based control actions is investigated by using the Benchmark Simulation Model No. 1. The numerical results show that by accounting for compression settling, the Bürger-Diehl model allows for more realistic predictions of the underflow sludge concentration and the Sludge Blanket Height (SBH), which are essential for more accurate wet weather modelling and sludge waste predictions. The choice of secondary settler model clearly has a profound impact on the operation and control of the entire treatment plant and it is recommended to use the Bürger-Diehl model as of now in any wastewater treatment plant modelling effort.
Changing Physic, Changing Pattern, and Conflicts of Rural-Urban Fringe Using a Combination Model

This study evaluates the physical changes, the patterns, and the conflicts in the rural-urban fringe area based on the combination model and the comparative static analysis. The scope of physical changes focuses on the land use, the built-up, the infrastructure, the utilities and the home environment. The objective of this study was to identify the factors responsible for the physical changes, the patterns, and the conflicts in the rural-urban fringe between 1990 and 2010. Physical changes were mapped using GIS, while the changing pattern was identified using exploratory and population morphology. The results of the study showed that the physical facilities and the infrastructure in the rural-urban fringe area become better but the condition of the environmental healthy is in the bad-level. So, the environmental healthy and green spaces or agriculture-land also needs attention. The pattern of rural-urban fringe is changed by the transportation route and facilities, the land value, the land use and the building function, the distance, and the travel time. There has been an agriculture conflict because of the different commitment of the farmer in the rural-urban fringe: the majority of the farmer in the inner fringe does not want to maintain their agriculture-land and agriculture-activities. In contrast, the majority of the farmer in the outer fringe still wants to maintain their agriculture-land and their job as the farmer.
Seroprevalence of five diarrhea-related pathogens in bovine herds of scattered households in Inner Mongolia, China between 2019 and 2022

Bovine diarrhea is a multi-factorial disease and remains one of the biggest health problems in animal husbandry. The endemic trends of the main pathogens responsible for bovine diarrhea in Inner Mongolia have not been analyzed systematically before. Therefore, the purpose of this study was to estimate the prevalence of bovine diarrhea pathogens found in the scattered households of Inner Mongolia in China. Additionally, we assessed for differences in the prevalence of infection based on age and region, as well as determined local prevalence rates and the rates of mixed infections. Using a two-stage random sampling strategy, 3,050 serum samples were collected from 72 bovine herds in 11 leagues and cities in Inner Mongolia, and the positive rates of BVDV, BRV, BCoV, K99, and Mycobacterium paratuberculosis (M. paratuberculosis) antibodies in the samples were detected by ELISA to determine the epidemic trends and epidemic differences of the five pathogens in Inner Mongolia. The positive rates of antibodies based on serum samples were: BVDV, 18.79% (95% CI [17.44–20.22]); BRV, 12.39% (95% CI [11.27–13.61]); BCoV, 12.82% (95% CI [11.68–14.05]); K99, 13.80% (95% CI [12.62–15.07]); and M. paratuberculosis, 10.79% (95% CI [9.74–11.94]). The prevalence rates of BRV, BCoV and K99 at 0–2 months were significantly different from that at 2–6 months, 6–18 months and adult cattle (P < 0.05). The prevalence of BVDV and M. paratuberculosis was the highest in adult cattle, which was significantly different from that in other age groups (P < 0.05). Furthermore, obvious regional epidemiological differences among the five diseases were observed. There was a mixed infection of BRV+BCoV in each age stage, the highest mixed infection being BVDV+BRV+K99 at 0–2 months of age. Our results showed that the cattle of scattered households in the Inner Mongolia of China were endemicly infected with several important cattle pathogens. Most of the pathogens studied occurred between 0–2 months of age and were mixed infections, which greatly influences the health of the cattle and leads to economic loss. These findings are of practical significance for the future prevention and control of bovine diarrhea in the Inner Mongolia or other regions of China.
Impacts of a Solid Waste Disposal Site on Soil, Surface Water and Groundwater Quality in Dar es Salaam City, Tanzania

Solid waste disposal sites are potentially serious sources of pollution to the environment, especially when located very close to water sources and operated haphazardly. The high pollution potential of these sites is due to the fact that they usually contain almost all types of pollutants from the source community. The contaminants can leach out through the soil, contaminating the soil itself, ground water, and surface water. In the study reported here, environmental pollution impacts of a solid waste disposal site were investigated. Wet and dry seasons samples of soil, river sediments, groundwater, and surface water from sites suspected to be affected by the dumpsite were analysed for chemical, physical, and bacteriological parameters, including heavy metals such as Pb, Cd, Cr, and Zn, and nutrients (N and P). The dumpsite was found to be a significant (p<0.05) source of pollution to soil, groundwater, surface water and riverbed sediments in its neighbourhood. Concentrations of, among others, Pb and Cd in groundwater were as high as 15 and 35 mg/L, respectively. Seasons were also found to be an important factor in the occurrence and magnitude of pollution, and pollution was found to occur mostly through migration of leachate. This reasserts the notion that proper design, construction, and operation of dumpsites to reduce infiltration of rainwater and contain leachate can curtail pollution considerably.
Laboratory study on behaviour of static properties of saturated sand-gravel after liquefaction

By use of the medium scale dynamic triaxial apparatus(specimen size φ200 mm×510 mm),the laboratory tests on the sand-gravel after liquefaction were performed.The stress-strain responses and the main factors influencing the strength of liquefied sand-gravel were studied.It was shown that the strength of liquefied sand-gravel was mainly dependent on the confining pressure.
Residual strength of smectite-dominated soils from the Kamenose landslide in Japan

The residual strength of smectite-dominated soils from the main slip surfaces of the Kamenose landslide, Japan, was measured by ring shear test, and the relations of the residual strength to the clay fraction content and clay particle orientation were studied. The residual angles of shearing resistance, , were estimated assuming that the residual cohesion is zero. The magnitude of the residual angle of shearing resistance was dependent on the <2-μm clay fraction content, CF, and on the effective normal stress, , because of curved strength lines. At equivalent to the overburden pressures, the soils had of 6–8°. These residual angles of shearing resistance were fitted on the – CF line for sand–bentonite mixtures, and exhibited the sliding shear mode.The orientation of smectite particles on shear surfaces showing slickensides was assessed by X-ray diffraction technique. The orientation of smectite particles was found to reduce the residual strength considerably, and this orientation effect was revealed more .
Postnatal Maturation of the Blood–Brain Barrier in Senescence-Accelerated OXYS Rats, Which Are Prone to an Alzheimer’s Disease-like Pathology

Alzheimer’s disease (AD) is an old-age neurodegenerative disorder; however, AD predisposition may arise early in life. Vascular dysfunction makes a big contribution to AD development. Nonetheless, the possible role of early-life vascular dysfunction in AD development is still poorly investigated. Here, using OXYS rats as a suitable model of the most common (sporadic) type of AD, we investigated maturation of the blood–brain barrier (BBB) in the hippocampus and frontal cortex in the first 3 weeks of life. Using RNA-Seq data, we found an altered expression of BBB-associated genes in the middle of the first and second weeks of life in OXYS rats compared to control rats (Wistar strain). Moreover, by immunohistochemistry and electronic microscopy, we revealed a delay of vascularization and of subsequent pericyte coating of blood vessels in OXYS rats. These specific features were accompanied by an accelerated decrease in BBB permeability estimated using Evans blue dye. Notably, almost all of the observed differences from Wistar rats disappeared on postnatal day 20. Nonetheless, the observed features, which are characteristic of the postnatal period, may have long-term consequences and contribute to neurovascular dysfunction observed in OXYS rats late in life, thereby promoting early development of AD signs.
Economic and Climate Benefits from Utilization of Unused Farmlands for Eucalyptus Plantations and Charcoal Production in Thailand

Thai farmers plant eucalyptus trees on their unused farmlands with poor fertility soils to raise their incomes and in response to inducements from the Government. The conversion of unused farmlands to eucalyptus can contribute to climate change mitigation as the growing trees sequester carbon. To estimate the contribution of eucalyptus plantations to climate change mitigation requires not only accounting for the sequestered carbon, but also for the production of charcoal using eucalyptus wood residues from harvesting and from paper refineries. These by-products are the main raw materials used by rural communities in Thailand for charcoal making. This paper estimates the contribution of eucalyptus plantations on unused farmlands in Khon Kaen province in northeast Thailand, accounting for carbon sequestrated by the plantations, greenhouse gas emissions from eucalyptus charcoal production, and net avoided emissions from substituting fossil fuels with charcoal for heating. Carbon sequestration by the plantations was assessed for trees aged 1, 2 and 3 years by summing the aboveground biomass (stems, branches and leaves) and belowground biomass (roots). Three-year old eucalyptus trees are the main supply for the paper refineries. The amount of biomass and carbon stored in the eucalyptus plantations depend on age and productivity. The average carbon stored in 3-year old eucalyptus plantations at the study sites was 0.777 ton/ha. Eucalyptus growers received about 1,689 USD per ha from the harvesting of 3-4 year old eucalyptus plantations. Emissions from eucalyptus charcoal production were estimated by accounting for transportation of wood residues from the farms and refineries to kilns and charcoal processing. Emissions from charcoal production were estimated at 0.37 g CO2eq/MJ, meaning that substituting fossil fuels with eucalyptus charcoal reduces emissions for heat production by 99.5%. The eucalyptus plantation on unused land provided climate benefits and alternative income for local farmers. Based on these findings, the government should consider promoting eucalyptus plantation and eucalyptus charcoal production on unused suitable farmland under its policies on climate change mitigation, energy security and rural development.
Miospores and Cryptospores from the Silurian Section at Allenport, Pennsylvania, USA

Abstract Non-marine and marine palynomorphs were collected from a Telychian through Gorstian rock outcrop located near Allenport, Pennsylvania, USA in the east-central part of the Appalachian Foreland Basin. Close sampling of the section revealed six distinct palynological assemblages of spores, cryptospores, acritarchs and prasinophycean algae, likely deposited in nearshore marine settings. The Silurian Period is a critical time in plant evolution as megafossils found elsewhere indicate that vascular plants (tracheophytes) originated during this interval. Palynoflorules generally show a transition from cryptospore-dominated to miospore-dominated assemblages during the latter half of the Silurian. This transition is evident at Allenport, where over 30 species of miospores and cryptospores are recognized, including two new species: Vermiverruspora cottera and Rugosphaera falloambita. The sequential progression of innovations in exine structure and sculpture seen in the nonmarine palynomorphs at Allenport closely matches evolutionary patterns documented previously in the Appalachian Basin, Avalonia, and elsewhere around the world.
Nanogoethite is the dominant reactive oxyhydroxide phase in lake and marine sediments

Iron oxides affect many elemental cycles in aquatic sediments via numerous redox reactions and their large sorption capacities for phosphate and trace elements. The reactive ferric oxides and oxyhydroxides are usually quantified by operationally defined selective chemical extractions that are not mineral specific. We have used cryogenic 57Fe Mossbauer spectroscopy to show that the reactive iron oxyhydroxide phase in a large variety of lacustrine and marine environments is nanophase goethite (α-FeOOH), rather than the assumed surface-complex–stabilized, two-line ferrihydrite and accompanying mixture of clay and oxyhydroxide Fe-bearing phases. This result implies that the kinetic and stability parameters of the type of nanogoethite that we observe to be present in sediments should be first determined and then used in models of early diagenesis. The identity and characteristics of the reactive phase will also set constraints on the mechanisms of its authigenesis.
Nutrient removal by prairie filter strips in agricultural landscapes

Nitrogen (N) and phosphorus (P) from agricultural landscapes have been identified as primary sources of excess nutrients in aquatic systems. The main objective of this study was to evaluate the effectiveness of prairie filter strips (PFS) in removing nutrients from cropland runoff in 12 small watersheds in central Iowa. Four treatments with PFS of different spatial coverage and distribution (No-PFS, 10% PFS, 10% PFS with strips, and 20% PFS with strips) were arranged in a balanced incomplete block design across four blocks in 2007. A no-tillage two-year corn (Zea mays L.) –soybean (Glycine max [L.] Merr.) rotation was grown in row-cropped areas beginning in 2007. Runoff was monitored by H flumes, and runoff water samples were collected during the growing seasons to determine concentrations of nitrate-nitrogen (NO3-N), total nitrogen (TN) and total phosphorus (TP) through 2011. Overall, the presence of PFS reduced mean annual NO3-N, TN, and TP concentrations by 35%, 73%, and 82%, respectively, and reduced annual NO3-N, TN, and TP losses by 67%, 84%, and 90%, respectively. However, the amount and distribution of PFS had no significant impact on runoff and nutrient yields. The findings suggest that utilization of PFS at the footslope position of annual row crop systems provides an effective approach to reducing nutrient loss in runoff from small agricultural watersheds.