Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel PCR method directly quantifies sequence features that block primer extension

Many quantitative polymerase chain reaction (qPCR) assays indirectly quantify a target of interest as a drop in amplification signal relative to a larger total signal. The targeted sequence features include: DNA strand breaks introduced by enzymes that cleave at specific sequences or modifications, or caused by ionizing radiation or other DNA-damaging agents; DNA damage that does not break the DNA but blocks the DNA polymerase; and deletions of various sizes that prevent one or both primers from annealing. All of these loss of signal (a.k.a. negative) assays share the drawback of low sensitivity, as compared to positive assays, which generate an amplification signal that directly reflects the copy numbers of the sequence feature. Here we present a novel qPCR strategy that converts all of the above negative assays into positive ones. A mixture of three primers is added to genomic DNA, one primer pair that targets a sequence for strand-specific PCR, and a third, longer primer that prevents initiation of that PCR, by annealing at high temperature and extending across the target sequence, rendering it doublestranded and inaccessible for priming. Any sequence feature that blocks the third primer’s annealing or extension, while leaving the target sequence intact, allows the PCR to proceed and quantify the copy number of the sequence feature. This Primer Extension Blockade Enabled qPCR (PEBE-qPCR) method will facilitate many high-throughput, low-cost qPCR-based investigations in biology and medicine. As a first example, we present direct qPCR of the unmethylated allele at a MspI/HpaII site in the promoter of the human 45S rDNA gene.
A 1280×960 Dynamic Vision Sensor with a 4.95-μm Pixel Pitch and Motion Artifact Minimization

This paper reports a 1280×960 DVS. A 4.95-μm pixel pitch is achieved with in-pixel Cu-Cu connection and the newly designed GIDL-suppression scheme. A sequential column selection scheme and a global event-holding function are implemented to minimize motion artifacts. The power consumption per pixel of 122 nW is 1.25× smaller and the maximum readout speed of 1.3 Geps is 4.33× faster than the previous state-of-the-art.
Complete mitochondrial genome sequence of Aspergillus oryzae RIB 127 and its comparative analysis with related species

Abstract Here, we determined the complete sequence and annotation of the mitochondrial genome of A. oryzae (strain RIB 127). The complete mitochondrial genome is 29,202 base pairs (bp), with low GC content of 26.2%. Conserved genes identified include 26 transfer RNAs, the small and large ribosomal RNA subunits, and 14 protein-coding genes. Phylogenetic analysis based on the complete mitochondrial genome revealed that RIB 127 formed a single clade with two other A. oryzae species.
The effects of bio-extract from water hyacinth (Eichhornia crassipes (C. Mart.) Solms) and golden apple snail (Pomacea canaliculata Lamarck) on photosynthetic pigment and ascorbic acid contents of Chinese cabbage (Brassica chinensis var. pekinensis Rupr.

This study was aimed to compare the effects of bio-extract from water hyacinth, bio-extract from golden apple snail and the mixture of bio-extract on growth and some physiological characteristics of Chinese cabbage that grown in Dynamic Root Floating Technique (DRFT) of hydroponic culture. The bio-extract that filled in nutrient solution was 1: 500 and 1:1000 levels. Data were recorded on days 0, 7, 14, 21, 28 and 35 days after bio-extract treatments. Results of the study revealed that Chinese cabbage that grown in bio-extract from golden apple snail at the ratio of 1: 1000 had the tendency of producing higher total dry weight. However, the bio-extract from golden apple snail at the ratio of 1: 500 had the tendency of producing higher total chlorophyll, carotenoids and β-carotene contents. On the other hand, bio-extract from water hyacinth at the ratio 1:500 resulted in increased ascorbic acid contents. Our results indicated that bio-extract affects the growth of Chinese cabbage and can be used as a source of nutrients for crops to reduce used chemicals in hydroponics culture.
Head-Direction drift in rat pups is consistent with an angular path-integration process

The sense of direction is a vital computation, whose neural basis is considered to be carried out by head-direction cells. One way to estimate head-direction is by integrating head angular-velocity over time. However, this process results in error accumulation resembling a random walk, proportional to , which constitutes a mark for a path integration process. In the present study we analyzed previously recorded data to quantify the drift in head-direction cells of rat pups before and after eye-opening. We found that in rat pups before eye-opening the drift propagated as a random walk, while in rats after eye-opening the drift was lower. This suggests that a path-integration process underlies the estimation of head-direction, such that before eye-opening the head-direction system runs in an open-loop manner and accumulates error. After eye-opening, visual-input, such as arena shape, helps to correct errors and thus compute the sense of direction accurately.
Extra-field activity shifts the place field center of mass to encode aversion experience

The hippocampal place cells encode spatial representation but it remains unclear how they store concurrent positive or negative experiences. Here, we report on place field reconfiguration in response to an innately aversive odor trimethylthiazoline (TMT). The advantage of TMT is the absence of learning curve required for associative fear conditioning. Our study investigated if CA1 place cells, recorded from behaving rats, remap randomly or if their reconfiguration depends on the location of the aversive stimulus perception. Exposure to TMT increased the amplitude of hippocampal beta oscillations in two arms of a maze (TMT arms). We found that a population of place cells with fields located outside the TMT arms increased their activity (extra-field spiking) in the TMT arms during the aversive episodes. These cells exhibited significant shift of the center of mass towards the TMT arms in the subsequent post-TMT recording. The induction of extra-field plasticity was mediated by the basolateral amygdala complex (BLA). Photostimulation of the BLA triggered aversive behavior, synchronized response of hippocampal local field oscillations, augmented theta rhythm amplitude and increased the spiking of place cells for the first 100ms after the light delivery. This occurred only for the extra-field-but not for intra-field spikes. Optogenetic BLA-triggered an increase in extra-field spiking activity correlated to the degree of place field plasticity in the post-ChR2 recording session. Our findings demonstrate that the increased extra-field activity during aversive episodes mediates the degree of subsequent field plasticity.
Radiative and chemical implications of the size and composition of aerosol particles in the existing or modified global stratosphere

Abstract. The size of aerosol particles has fundamental effects on their chemistry and radiative effects. We explore those effects using aerosol size and composition data in the lowermost stratosphere along with calculations of light scattering. In the size range between about 0.1 and 1.0 µm diameter (accumulation mode), there are at least two modes of particles in the lowermost stratosphere. The larger mode consists mostly of particles produced in the stratosphere, and the smaller mode consists mostly of particles transported from the troposphere. The stratospheric mode is similar in the Northern and Southern Hemisphere, whereas the tropospheric mode is much more abundant in the Northern Hemisphere. The purity of sulfuric acid particles in the stratospheric mode shows that there is limited production of secondary organic aerosol in the stratosphere, especially in the Southern Hemisphere. Out of eight sets of flights sampling the lowermost stratosphere (four seasons and two hemispheres) there were three with large injections of specific materials: volcanic, biomass burning, or dust. The stratospheric and tropospheric modes have very different roles for radiative effects on climate and for heterogeneous chemistry. Because the larger particles are more efficient at scattering light, most of the radiative effect in the lowermost stratosphere is due to stratospheric particles. In contrast, the tropospheric particles can have more surface area, at least in the Northern Hemisphere. The surface area of tropospheric particles could have significant implications for heterogeneous chemistry because these particles, which are partially neutralized and contain organics, do not correspond to the substances used for laboratory studies of stratospheric heterogeneous chemistry. We then extend the analysis of size-dependent properties to particles injected into the stratosphere, either intentionally or from volcanoes. There is no single size that will simultaneously maximize the climate impact relative to the injected mass, infrared heating, potential for heterogeneous chemistry, and undesired changes in direct sunlight. In addition, light absorption in the far ultraviolet is identified as an issue requiring more study for both the existing and potentially modified stratosphere.
Macruropyxis fraxini on Fraxinus rhynchophylla: Confirmation in the Korean Peninsula after 82 Years and the First Record in South Korea

Abstract Macruropyxis fraxini has been recorded on several species of Fraxinus in China, Japan, Russia (Far East), and North Korea since its first recorded observation as a rust fungus on F. rhynchophylla in Jilin, China, in 1899. In the Korean Peninsula, the rust fungus was first recorded on F. rhynchophylla in 1935, based on four specimens collected at Mt. Kumgangsan, Gangwondo Province, in the North Korean territory. We confirmed this rust in the Korean Peninsula after 82 years. The rust fungus was identified based on morphological characteristics and a molecular phylogenetic analysis. This is the first record of M. fraxini in South Korea.
Sequencing and characterization of mitochondrial genome of Fusarium sp. (Hypocreales: Nectriaceae)

Abstract In this study, we presented the complete mitochondrial genome of Fusarium sp. It has a total length of 47, 74 bp, and the base composition of the mitogenome is as follows: A (34.1%), T (33.5%), C (14.7%), and G (17.7%). The mitogenome contains 23 protein-coding genes, 1 ribosomal RNA (rRNA), and 26 transfer RNA (tRNA) genes, all coded on the same strand of DNA. The gene order is identical to that of the other Fusarium mitogenomes. The taxonomic status of the Fusarium sp. mitogenome exhibits a closest relationship with F. oxysporum, but varied in the structure of mitochondrial genome.
The impact of even‐aged and uneven‐aged forest management on regional biodiversity of multiple taxa in European beech forests

For managed temperate forests, conservationists and policymakers favour fine-grained uneven-aged (UEA) management over more traditional coarse-grained even-aged (EA) management, based on the assumption that within-stand habitat heterogeneity enhances biodiversity. There is, however, little empirical evidence to support this assumption. We investigated for the first time how differently grained forest management systems affect the biodiversity of multiple above- and below-ground taxa across spatial scales. We sampled 15 taxa of animals, plants, fungi and bacteria within the largest contiguous beech forest landscape of Germany and classified them into functional groups. Selected forest stands have been managed for more than a century at different spatial grains. The EA (coarse-grained management) and UEA (fine-grained) forests are comparable in spatial arrangement, climate and soil conditions. These were compared to forests of a nearby national park that have been unmanaged for at least 20 years. We used diversity accumulation curves to compare γ-diversity for Hill numbers 0D (species richness), 1D (Shannon diversity) and 2D (Simpson diversity) between the management systems. Beta diversity was quantified as multiple-site dissimilarity. Gamma diversity was higher in EA than in UEA forests for at least one of the three Hill numbers for six taxa (up to 77%), while eight showed no difference. Only bacteria showed the opposite pattern. Higher γ-diversity in EA forests was also found for forest specialists and saproxylic beetles. Between-stand β-diversity was higher in EA than in UEA forests for one-third (all species) and half (forest specialists) of all taxa, driven by environmental heterogeneity between age-classes, while α-diversity showed no directional response across taxa or for forest specialists. Synthesis and applications. Comparing EA and uneven-aged forest management in Central European beech forests, our results show that a mosaic of different age-classes is more important for regional biodiversity than high within-stand heterogeneity. We suggest reconsidering the current trend of replacing even-aged management in temperate forests. Instead, the variability of stages and stand structures should be increased to promote landscape-scale biodiversity.
Secondary education spending and school attendance in South Africa: An ARDL approach

Abstract The education system in South Africa is perceived to be expensive, inefficient, and under-performing relative to its peers. Hence, this study aims to investigate the relationship between secondary education spending and school attendance in South Africa through econometric modelling. The ARDL Bounds test revealed that the variables have long-run relationship. Furthermore, the long run estimates indicate that both secondary education spending, household incomes, and urbanisation are statistically significant in explaining variations in school attendance. Granger Causality test indicates uni-directional causality from secondary education spending to secondary school attendance. Thus, to close the gap in providing quality education in SA, a wide range of interventions are needed. The focus should be on increasing enrolment rates and narrowing dropout rates, more especially those that are due to lack of funding. In addition, school officials should be provided with the necessary financial and administrative skills to receive, distribute, and utilise funds efficiently.
SQVDT: A scalable quantitative vulnerability detection technique for source code security assessment

Vulnerability detection and exploit is becoming a very important part of security, especially in malware code delivery, hacking a system, efforts to create patches, improving the source code, or updating a software. Vulnerabilities in applications, including browsers, media players, online services, document readers, and so forth. are often exploited and cause a serious damage. In this article, we propose a vulnerability detection technique to detect vulnerabilities in software, as well as shared libraries at source code level. We crawl the vulnerable source code by tracing and locating the patch files from different web sources according to their CVE‐numbers and built a fingerprint index of 2931 vulnerable files. Then we developed a vulnerability detection approach based on code clone detection technique and detect hundreds of vulnerabilities in thousands of GitHub open source projects, which are not noticed before as vulnerable. We detected vulnerabilities in some very famous recently available software, including latest version of Linux, HTC‐kernel, FindX‐8.1‐kernel, and in 7‐TB of C/C++ source code (152,823 open source projects). In this study, we discuss some of the very high severity level (CVSS) vulnerabilities that are detected by our approach. Furthermore, we performed an empirical evaluation and verification on these vulnerabilities, including intraproject clone vulnerabilities, copied‐kernel clone vulnerabilities, and library‐used clone vulnerabilities. Our technique is very fast, efficient, reliable, practical, scalable, and can be implemented at industrial level. The comparison with the state‐of‐the‐art tools shows the effectiveness of our approach.
Comparison of releasing bound phenolic acids from wheat bran by fermentation of three Aspergillus species

Summary Wheat bran was fermented at 28 °C for 7 days under 70% humidity by Aspergillus niger, Aspergillus oryzae and Aspergillus awamori. Total phenolic content (TPC) of the unfermented sample was 1531.5 μg g−1 wheat bran. After the fermentation of Aspergillus awamori, Aspergillus oryzae and Aspergillus niger, TPC reached 5362.1, 7462.6 and 10 707.5 μg g−1, respectively. The antioxidant activity in the extractions of fermented wheat bran also increased significantly compared with the unfermented sample (P < 0.05). Aspergillus niger showed the greatest capacity to release bound ferulic acid (416.6 μg g−1). Aspergillus oryzae and Aspergillus awamori had the advantages of releasing more chlorogenic acid (84.0 μg g−1) and syringic acid (142.3 μg g−1), respectively. The destructive effect of Aspergillus niger on wheat bran structure was the strongest, followed by that of Aspergillus oryzae. This effect of Aspergillus niger may be due to its higher cellulase, xylanase, arabinofuranosidase and β-xylosidase activities. Besides, Aspergillus oryzae possessed higher β-glucosidase activity, and Aspergillus awamori had higher α-amylase and feruloyl esterase activities. Aspergillus niger may be the best to release bound phenolic acids in the three Aspergillus species. These will provide the helpful information for understanding mechanism of the fermentation by Aspergillus species releasing bound phenolic in wheat bran.
Green value and sustainable transportation engagement: The mediating role of attitude

Article history: Received: June18, 2020 Received in revised format: August 3 2020 Accepted: September 8, 2020 Available online: September 10, 2020 This study aims to investigate the effect of green value on attitude and sustainable transportation engagement and the mediating role of attitude on the relationship between green value and sustainable transportation engagement. A survey was carried out on students in a public university. A sample of 107 students was obtained for this study. The data was analyzed using Partial Least Squares Structural Equation Modelling (PLS-SEM). The findings show that green value and attitude had a significant influence on sustainable transportation engagement. In addition, attitude played a mediating role in the relationship between green value and sustainable transportation engagement. The study provides valuable contributions for both theory and practice in the area of eco-campus. Theoretically, the study extends the value-attitudebehavior model in the context of sustainable transportation and adds to the body of literature of ecocampus. This is among the first studies conducted in Malaysia that investigates factors that contribute towards sustainable transportation engagement among students. In terms of managerial significance, the results provide guidance to policymakers to help them plan for strategies to enhance students’ engagement in sustainable transportation in the future. © 2021 by the authors; licensee Growing Science, Canada
Artificial reefs create distinct fish assemblages

: We conducted a before-after-control-impact (BACI) experiment to evaluate the effects of deploying small-scale artificial patch reefs on fish assemblages in a temperate bay (Port Phillip Bay) in south-eastern Australia. Three replicate artificial reef treatments were placed on sandy substratum and the response of the fish assemblage was compared with 3 control sites with no reef, and 3 nearby natural reef comparison sites. All habitats were sampled using baited re mote underwater video (BRUV) and underwater visual census (UVC) multiple times, 6 mo before and 22 mo after artificial reef deployment. Fish species rapidly colonised artificial reefs, with 30 new species detected in the first year post deployment and only 4 in the following year. Both sampling methods captured a shift in assemblage structure, albeit with different species compositions, as individual species numbers varied dependent upon method used. BRUV provided better esti-mates of the important recreational species snapper Chrysophrys auratus (family Sparidae), with more snapper recorded on artificial and natural reefs compared to sediment. The artificial reef assemblages were dominated by species that favour the reef/sediment interface. Several reef-associated species were detected in the juvenile stages; however, adults of obligate reef species were not observed on artificial reefs. Sediment-associated species present before artificial reef deployment persisted within the artificial patch reef area over the course of the study. Overall, the deployment of patchwork artificial reefs increased local species diversity and abundance of fish, and did not impact existing sediment fish assemblages.
The Role of Redox on Bridgmanite Crystal Chemistry and Calcium Speciation in the Lower Mantle

The amount of ferric iron Fe3+ in the lower mantle is largely unknown and may be influenced by the disproportionation reaction of ferrous iron Fe2+ into metallic Fe and Fe3+ triggered by the formation of bridgmanite. Recent work has shown that Fe3+ has a strong effect on the density and seismic wave speeds of bridgmanite and the incorporation of impurities such as aluminum. In order to further investigate the effects of ferric iron on mineral behavior at lower mantle conditions, we conducted laser‐heated diamond‐anvil cell (LHDAC) experiments on two sets of samples nearly identical in composition (an aluminum‐rich pyroxenite glass) except for the Fe3+ content; with one sample with more Fe3+ (“oxidized”: Fe3+/ΣFe ~ 55%) and the other with less Fe3+ (“reduced”: Fe3+/ΣFe ~ 11%). We heated the samples to lower mantle conditions, and the resulting assemblages were drastically different between the two sets of samples. For the reduced composition, we observed a multiphase assemblage dominated by bridgmanite and calcium perovskite. In contrast, the oxidized material yielded a single phase of Ca‐bearing bridgmanite. These Al‐rich pyroxenite samples show a difference in density and seismic velocities for these two redox states, where the reduced assemblage is denser than the oxidized assemblage by ~1.5% at the bottom of the lower mantle and slower (bulk sound speed) by ~2%. Thus, heterogeneities of Fe3+ content may lead to density and seismic wave speed heterogeneities in Earth's lower mantle.
Test framework and key challenges for virtual verification of automated vehicles: the VeriCAV project

Virtual simulation is considered a crucial step in assuring the safety of highly automated vehicles. Significant challenges however remain in producing valid evidence of real-world system performance from virtual simulation and doing so in a robust, efficient manner. A system architecture for virtual verification of highly automated vehicles is implemented in the VeriCAV project and described here, with a focus on the interfaces between system elements. The framework includes elements for test generation and assessment, virtual simulation, realistic virtual actors as well as the automated driving system being tested.
Detecting outliers in species distribution data

Species distribution data play a pivotal role in the study of ecology, evolution, biogeography and biodiversity conservation. Although large amounts of location data are available and accessible from public databases, data quality remains problematic. Of the potential sources of error, positional errors are critical for spatial applications, particularly where these errors place observations beyond the environmental or geographical range of species. These outliers need to be identified, checked and removed to improve data quality and minimize the impact on subsequent analyses. Manually checking all species records within large multispecies datasets is prohibitively costly. This work investigates algorithms that may assist in the efficient vetting of outliers in such large datasets.