Miracle-dz/UniFAR-FTUs huggingface dataset:
Feather Morphology of Four Different Mutations in the Japanese Quail

Abstract Scanning electron microscopy and chemical analyses of feathers from four different Japanese quail mutants were carried out to correlate changes at the microscopic and molecular levels with the genetic analysis. All four mutants as well as the wild-type feathers contain similar polypeptides and share common filament-forming processes, a critical step in normal development. Thus, neither the structural genes nor the interaction of their products is abnormal. Both the gross and microscopic evidence demonstrates structural differences among mutants and between mutants and wild-type feathers. We suggest that the morphological abnormalities are the result of higher order processes, perhaps by mutation of some regulatory genes, which produces flaws in the function or organization of the follicle.
Irrigation Periods and Fe, Zn Foliar Application on Agronomic Characters of Borago officinalis, Calendula officinalis, Thymus vulgaris and Alyssum desertorum

ABSTRACT To evaluate the effects of irrigation period and iron (Fe), zinc (Zn) foliar application on agronomic characters in Borago officinalis, Calendula officinalis, Thymus vulgaris and Alyssum desertorum, investigations were performed in a complete randomized block design with three replications in 2014 and 2015. The factors applied were (a) Fe foliar application (0, 200, 400, 600 ppm), (b) Zn foliar application (0, 200, 400, 600 ppm) and (c) irrigation periods (3, 6, 9 days). Results showed that Fe and Zn had a significant effect on many factors including shoot dry matter, height, flower production (marigold, borage and thyme) and seed (alyssum). Interaction of 400 ppm of Zn and Fe with irrigation period every 3 days was the best and produced the best amounts in most of the measured characters. The lowest of the measured characters was 600 ppm of Fe and Zn by irrigation period of 9 days. Results showed that Zn micronutrient was more effective than Fe.
Book Review

Although the voices of African American intellectuals have been largely absent from the discussion on the so-called achievement gap, three esteemed scholars with different disciplinary backgrounds have collaborated to change the course of the conversation regarding the achievement of African American students. Young, Gifted, and Black: Promoting High Achievement Among African American Students, a book that will undoubtedly provoke thought and action, brings together three essays by Theresa Perry, Claude Steele, and Asa G. Hilliard III. Although their perspectives differ, they share the view that “African American students face challenges unique to them as students in American schools at all levels by virtue of their social identity as African Americans and of the way that identity can be a source of devaluation in contemporary American society” (p. vii). In the first essay, “Up from the Parched Earth: Toward a Theory of African American Achievement,” Theresa Perry places a theory of African American achievement in a historical perspective, critiques two theoretical models commonly used to explain the limited achievement of students of color (social mobility and cultural difference), juxtaposes the task of achievement in the pre– and post–civil rights eras, and presents an outline for African American achievement, which includes negotiating social identity and committing to achievement. In the second essay, “Stereotype Threat and African American Student Achievement,” Claude Steele discusses the detrimental effect of stereotype threat on typically underperforming groups, particularly African Americans. Steele
Differences in drought resistance among 3 deciduous oak species grown

pedunculate oak (Ouercus robur L) and the sessile oak (Q petraea Liebl) observed in the forest as a result of drought. In addition, northern red oak (Q rubra L) was compared with the 2 indigenous oaks. The effects of controlled soil water deficits on growth and water relations of young plants of these 3 species grown in large boxes have been studied. The plants were old enough to have developed normal root systems. Two species were planted in each box, and submitted to very similar patterns of water stress. Predawn leaf water potential, stomatal conductance, net assimilation rates, shoot elongation and mortality were monitored. The effect of an overall improvement in mineral nutrition on these parameters was also tested. During water deficit (decrease in predawn leaf water potential), the pattern of decrease of gas exchange was similar for the 3 species. Thus, their ability to limit water deficit by reduction of transpiration was similar. On the other hand, shoot growth of Q rubra was more reduced than that of Q robur for similar predawn leaf water potential; growth of Q petraea was the least sensitive. However, increase of mineral nutrition improved the growth of both Q robur and Q rubra, but not that of Q petraea. For the 3 species, no mortality was noted as long as predawn leaf water potentials remained > -3.6 MPa. Below this limit, the mortality rate was highest in Q robur, Q petraea and lowest in Q rubra. These differences in mortality between species are due to differences in tolerance to water stress, not in avoidance.
Comparison of Object Detection and Patch-Based Classification Deep Learning Models on Mid- to Late-Season Weed Detection in UAV Imagery

Mid- to late-season weeds that escape from the routine early-season weed management threaten agricultural production by creating a large number of seeds for several future growing seasons. Rapid and accurate detection of weed patches in field is the first step of site-specific weed management. In this study, object detection-based convolutional neural network models were trained and evaluated over low-altitude unmanned aerial vehicle (UAV) imagery for mid- to late-season weed detection in soybean fields. The performance of two object detection models, Faster RCNN and the Single Shot Detector (SSD), were evaluated and compared in terms of weed detection performance using mean Intersection over Union (IoU) and inference speed. It was found that the Faster RCNN model with 200 box proposals had similar good weed detection performance to the SSD model in terms of precision, recall, f1 score, and IoU, as well as a similar inference time. The precision, recall, f1 score and IoU were 0.65, 0.68, 0.66 and 0.85 for Faster RCNN with 200 proposals, and 0.66, 0.68, 0.67 and 0.84 for SSD, respectively. However, the optimal confidence threshold of the SSD model was found to be much lower than that of the Faster RCNN model, which indicated that SSD might have lower generalization performance than Faster RCNN for mid- to late-season weed detection in soybean fields using UAV imagery. The performance of the object detection model was also compared with patch-based CNN model. The Faster RCNN model yielded a better weed detection performance than the patch-based CNN with and without overlap. The inference time of Faster RCNN was similar to patch-based CNN without overlap, but significantly less than patch-based CNN with overlap. Hence, Faster RCNN was found to be the best model in terms of weed detection performance and inference time among the different models compared in this study. This work is important in understanding the potential and identifying the algorithms for an on-farm, near real-time weed detection and management.
An Application of a Modified Gappy Proper Orthogonal Decomposition on Complexity Reduction of Allen-Cahn Equation

This work considers model reduction techniques that can substantially decrease computational cost in simulating parmetrized Allen–Cahn equation. We first employ the proper orthogonal decomposition (POD) approach to reduce the number of unknowns in the full-order discretized system. Since POD cannot reduce the computational complexity of nonlinearity in Allen–Cahn equation, we also apply discrete empirical interpolation method (DEIM) to approximate the nonlinear term for a substantial reduction in overall simulation time. However, in general, the POD-DEIM approach is less accurate than the POD approach, since it further approximates the nonlinear term. To increase the accuracy of the POD-DEIM approach, this work introduces an extension of the DEIM approximation based on the concept of Gappy POD (GPOD), which is optimal in the least-squares sense. The POD-GPOD approach is tested and compared with the POD and POD-DEIM approaches on Allen–Cahn equation for both cases of fixed parameter value and varying parameter values. The modified GPOD approximation introduced in this work is demonstrated to improve accuracy of DEIM without sacrificing too much efficiency on the computational speedup, e.g., in one of our numerical tests, the POD-GPOD approach provides an approximate solution to the parmetrized Allen–Cahn equation 200 times faster than the full-order system with average error of order O ( 10 − 4 ) . The POD-GPOD approach is therefore shown to be a promising technique that compromises between the accuracy of POD approach and the efficiency of POD-DEIM approach.
Identification of a Domain within the Human T-Cell Leukemia Virus Type 2 Envelope Required for Syncytium Induction and Replication

ABSTRACT In vitro infection by human T-cell leukemia virus type 1 and 2 (HTLV-1 and HTLV-2) can result in syncytium formation, facilitating viral entry. Using cell lines that were susceptible to HTLV-2-mediated syncytium formation but were nonfusogenic with HTLV-1, we constructed chimeric envelopes between HTLV-1 and -2 and assayed for the ability to induce syncytia in BJAB cells and HeLa cells. We have identified a fusion domain composed of the first 64 amino acids at the amino terminus of the HTLV-2 transmembrane protein, p21, the retention of which was required for syncytium induction. Construction of replication-competent HTLV genomic clones allowed us to correlate the ability of HTLV-2 to induce syncytia with the ability to replicate in BJAB cells. Differences in the ability to induce syncytia were not due to differences in the levels of total or cell membrane-associated envelope or in the formation of multimers. Therefore, we have localized a fusion domain within the amino terminus of the transmembrane protein of HTLV-2 envelope that is necessary for syncytium induction and viral replication.
Direct and indirect effects of burrowing crab Chasmagnathus granulatus activities on erosion of southwest Atlantic Sarcocornia‐dominated marshes

Using field measurements and field experiments, we investigated the effect of a dominant Southwest Atlantic intertidal burrowing crab, Chasmagnathus granulatus, on the inland growth of tidal creeks and creek genesis in salt marshes. By burrowing intensively on marsh sediments, this crab changed sediment physical parameters, such as penetrability, water content, and shear strength, which are related to sediment resistance to erosion. There were positive relationships between crab density and activities occurring in the creek heads and creek growth rates. Field experiments show that the presence and activity of C. granulatus and the presence of their burrows enhance the growth rates of tidal creeks, promoting marsh erosion. When crabs were present, these creeks grew faster than did creeks in which crabs were excluded. Furthermore, the interaction (disturbance and herbivory) between crabs and the dominant halophyte marsh plant, Sarcocornia perennis, generate circular depressions that accumulate standing water (salt pans), which in turn facilitates the creation of new creeks in the marsh surface, which evolve, to a greater extent, into fully functional tidal creeks because of colonization by crabs, which in turn further enhances creek growth rates. These direct and indirect effects of crabs on marsh erosion provide strong evidence of the importance of bioturbation and biological processes to the erosion and geomorphology of marshes.
Epstein-Barr Virus BGLF4 Kinase Induces Premature Chromosome Condensation through Activation of Condensin and Topoisomerase II

Volume 81, no. 10, p. 5166–5180, 2007. Page 5178, column 2, lines 30 and 31: “Here we demonstrate that EBV BGLF4, but not UL13 or UL97, is able to dissolve and internalize nuclear lamina” should read “Here we demonstrate that EBV BGLF4, but not UL13 or UL97, is able to induce chromosome condensation. ” This correction is based on the results shown in Fig. 8: HSV UL13 and HCMV UL97 were compared with BGLF4 for their abilities to induce chromatin condensation but not their abilities to induce nuclear lamina disassembly. Therefore, we correct this sentence to avoid possible confusion.
Defective Replication in Human Immunodeficiency Virus Type 1 When Non-\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{tRNA}_{3}^{\mathrm{Lys}}\) \end{document}Primers Are Used for R

ABSTRACT \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{3}^{Lys}\) \end{document} , the primer for reverse transcriptase in human immunodeficiency virus type 1 (HIV-1), anneals to the primer binding site (PBS) in HIV-1 RNA. It has been shown that altering the PBS and U5 regions upstream of the PBS in HIV-1 so as to be complementary to sequences in tRNAMet or tRNAHis will allow these tRNA species to be stably used as primers for reverse transcription. We have examined the replication of these mutant viruses in Sup-T1 cells. When Sup-T1 cells are infected by cocultivation with HIV-1-transfected 293T cells, viruses using tRNAHis or tRNAMet are produced at rates that are approximately 1/10 or 1/100, respectively, of rates for wild-type virions that use \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{3}^{Lys}\) \end{document}. When Sup-T1 cells are directly infected with equal amounts of these different viruses isolated from the culture supernatant of transfected 293T cells, virions using tRNAMet are produced at 1/100 the rate of wild-type viruses, and production of virions using tRNAHis is not detected. Both wild-type and mutant virions selectively package tRNALys only, and examination of the ability of total viral RNA to prime reverse transcription in vitro indicates a >80% reduction in the annealing of tRNAHis or tRNAMet to the mutant viral RNAs. PCR analysis of which of the three primer tRNAs is used indicates that only \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{3}^{Lys}\) \end{document} is detected as primer in wild-type virions and only tRNAHis is detected as primer in virions containing a PBS complementary to tRNAHis, while the mutant viruses containing a PBS complementary to tRNAMet use both tRNAMet and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{1,2}^{Lys}\) \end{document} as primer tRNAs.
Enhanced Expression of α(1,3)-Fucosyltransferase Genes Correlates with E-selectin-mediated Adhesion and Metastatic Potential of Human Lung Adenocarcinoma Cells

Alpha(1,3)- and alpha(1,4)-fucosylated oligosaccharides such as sialyl-Lewis(x) (sialyl-Le(x)) and sialyl-Lewis(a) (sialyl-Le(a)) have been reported to participate in tumor cell adhesion to activated endothelium. We examined by cytofluorometry the expression of Le(x), sialyl-Le(x), sialyl-Le(x) dimeric, Le(a), and sialyl-Le(a) on the surface of two human lung adenocarcinoma cell lines with different lung colonization potential. High expression levels of all of these antigens were detected in the metastatic HAL-8Luc cells, whereas the closely related nonmetastatic HAL-24Luc cells only expressed the sialyl-Le(a) and sialyl-Le(x) dimeric antigens, both at lower level than in HAL-8Luc cells. Five alpha(1,3)-fucosyltransferases (alpha(1,3)-Fuc-T) controlling the synthesis of these molecules have been identified to date (Fuc-TIII-Fuc-IVII). The expression of these five genes was also higher in the metastatic cells than in the nonmetastatic counterparts as was shown by Northern blot analysis. In vitro adhesion assays showed that only the metastatic cell line adheres significantly to E-selectin-expressing human endothelial cells. Moreover, monoclonal antibody (mAb) blockade of E-selectin completely abolished tumor cell binding. Adhesion inhibition experiments using mAbs against sialylated fucosylated oligosaccharides expressed on tumor cells indicated that these antigens are involved in the binding. Anti-sialyl-Lex(x) mAb (CSLEX-1) inhibited adhesion by 85%; it had the most pronounced inhibitory effect. These findings suggest that the overexpression of alpha(1,3)-Fuc-T genes in the metastatic HAL-8Luc cells, compared with HAL-24Luc cells, results in an enhanced surface display of fucosylated oligosaccharides, which contributes to the adhesive capacity of these cells to the activated endothelium and correlates with their lung colonization potential.
Screening of Antioxidant, Antimutagenic, Antimicrobial Activities and Phytochemical Studies on Sphaeranthus amaranthoides (Burm).

The learn of Sphaeranthus amaranthoides Burn, were examined for their antioxidant, antimutagenic, antimicrobial and phytochemical activities. Preliminary evaluation of both crude and solvent fractions showed a broad spectrum of activity since the extracts inhibit the growth of both bacterial and fungal isolates. The inhibitory activity of plant extracts on the peroxidation of linolic acid were measured by fericthiocynate methodo. Ethonolic extract showed strong antioxidant activity and antimicrobial activity against to the bacteria, (K.pneumoniae, S. typhi, E.coli, P.aeroginosa, S.aureus) and fungus (A.nidulans, A.terreus, A.sulphureus, Candida albicans and Fusarium sp.) cultures. Due to the phytochemical diversity in the antioxidant phytocompounds, the above results were expected. It almost rich in carotenes, Neoxanthin, chlorophyll a and chlorophyll b, lutein, violexanthin, pheophytin, which may have been responsible for the antioxidant, antimicrobial and for phytochemical activity. For antimutagenic activity using sodium azide to induce the chemical compound of Sphaeranthus amaranthoides Burn, to prevent the degenerative cells and results further support the view that some Indian medicinal plants are source for potential antioxidants.
Using ALS Data to Improve Co-Registration of Photogrammetry-Based Point Cloud Data in Urban Areas

Globally, urban areas are rapidly expanding and high-quality remote sensing products are essential to help guide such development towards efficient and sustainable pathways. Here, we present an algorithm to address a common problem in digital aerial photogrammetry (DAP)-based image point clouds: vertical mis-registration. The algorithm uses the ground as inferred from airborne laser scanning (ALS) data as a reference surface and re-aligns individual point clouds to this surface. We demonstrate the effectiveness of the proposed method for the city of Kuopio, in central Finland. Here, we use the standard deviation of the vertical coordinate values as a measure of the mis-registration. We show that such standard deviation decreased substantially (more than 1.0 m) for a large proportion (23.2%) of the study area. Moreover, it was shown that the method performed better in urban and suburban areas, compared to vegetated areas (parks, forested areas, and so on). Hence, we demonstrate that the proposed algorithm is a simple and effective method to improve the quality and usability of DAP-based point clouds in urban areas.
Comparison of sample preparation methods for the determination of the rumen degradation characteristics of fresh and ensiled forages by the nylon bag technique

A study urns conducted to determine the best method of preparation of silage and freshly cut forage samples for the estimation of rumen degradability by the nylon bag technique. Three types of forage were evaluated: a grass silage, a fresh grass (ryegrass) and a fresh legume (white clover). For each forage, six preparation methods were compared: chopping fresh (FRS); chopping and macerating fresh (FMC); chopping, freezing, thawing and macerating (FRZ); freeze-drying (FD); low-temperature oven-drying (45°C, 72 h) (OVD); high-temperature oven-drying (160°C, 90 min) (DHD). Dried samples were hammer-milled (2·5-mm screen). Chemical composition and rumen degradability were affected by the method of preparation. Protein fractions were sensitive to drying method, and oven-drying reduced nitrogen (N) solubility and degradability as the severity of the heating was increased. OVD and DHD gave lower estimates of N and dry matter (DM) solubility and degradability than FD. The effect of drying method on DM degradability was to reduce solubility and effective degradability, calculated for an outflow rate of 0·033 per h, but not potential degradability. Silage DM degradability was less affected than that of fresh forages. Freshly prepared samples (FRS, FMC, FRZ) gave lower estimates of N and DM solubility and degradability than FD, the differences being least with silage and FRZ, which was the most effective at rupturing plant structures of the FRS, FMC and FRZ methods. Of the six preparation methods, freeze-drying was the most effective preparation method. FRZ and OVD were less effective, but similar to each other. The small particles (calculated) produced by grinding dried samples may result in an overestimation of zero time losses and hence the degradability of the sample. These undesirable effects might be minimized by coarser grinding (4-mm screen) and correction for particulate matter loss.
Thematic Classification Accuracy Assessment with Inherently Uncertain Boundaries: An Argument for Center-Weighted Accuracy Assessment Metrics

Accuracy assessment is one of the most important components of both applied and research-oriented remote sensing projects. For mapped classes that have sharp and easily identified boundaries, a broad array of accuracy assessment methods has been developed. However, accuracy assessment is in many cases complicated by classes that have fuzzy, indeterminate, or gradational boundaries, a condition which is common in real landscapes; for example, the boundaries of wetlands, many soil map units, and tree crowns. In such circumstances, the conventional approach of treating all reference pixels as equally important, whether located on the map close to the boundary of a class, or in the class center, can lead to misleading results. We therefore propose an accuracy assessment approach that relies on center-weighting map segment area to calculate a variety of common classification metrics including overall accuracy, class user’s and producer’s accuracy, precision, recall, specificity, and the F1 score. This method offers an augmentation of traditional assessment methods, can be used for both binary and multiclass assessment, allows for the calculation of count- and area-based measures, and permits the user to define the impact of distance from map segment edges based on a distance weighting exponent and a saturation threshold distance, after which the weighting ceases to grow. The method is demonstrated using synthetic and real examples, highlighting its use when the accuracy of maps with inherently uncertain class boundaries is evaluated.