Miracle-dz/UniFAR-FTUs huggingface dataset:
Applying Design Science research as a methodology in post graduate studies: A South African perspective

The purpose of the paper is to identify minimum design element requirements from various Design Science Research (DSR) papers that have to be considered when applying the methodology. Then to demonstrate how these were addressed in various South African postgraduate studies. Applying this methodology allows for new opportunities for future needs. The focus will be to provide this from a South African perspective. The methodology applied in this paper to analyze the literature to determine the minimum list, as well as the studies, is a qualitative descriptive exploratory study. Relevant and recent papers on DSRM were identified that provided various concepts for the minimum design elements requirements and specifically selected South African postgraduate studies (five graduated PhDs from 2017-2020) were analyzed to determine if and how these address the requirements list. It was found that all of the studies did address the identified minimum design element requirements for it to be regarded as a DSRM study. During the findings, some challenges experienced by the students and from the literature support the minimum design elements requirements. New opportunities that emerged are multi- and transdisciplinary implementations of artefacts and allowing students to develop methodological dexterity.
Motor and Predictive Processes in Auditory Beat and Rhythm Perception

In this article, we review recent advances in research on rhythm and musical beat perception, focusing on the role of predictive processes in auditory motor interactions. We suggest that experimental evidence of the motor system’s role in beat perception, including in passive listening, may be explained by the generation and maintenance of internal predictive models, concordant with the Active Inference framework of sensory processing. We highlight two complementary hypotheses for the neural underpinnings of rhythm perception: The Action Simulation for Auditory Prediction hypothesis (Patel and Iversen, 2014) and the Gradual Audiomotor Evolution hypothesis (Merchant and Honing, 2014) and review recent experimental progress supporting each of these hypotheses. While initial formulations of ASAP and GAE explain different aspects of beat-based timing–the involvement of motor structures in the absence of movement, and physical entrainment to an auditory beat respectively–we suggest that work under both hypotheses provide converging evidence toward understanding the predictive role of the motor system in the perception of rhythm, and the specific neural mechanisms involved. We discuss future experimental work necessary to further evaluate the causal neural mechanisms underlying beat and rhythm perception.
Matching Fingerprints with a Toroidal Iterative Closest Point Algorithm

We develop a generalisable Cartesian-toroidal Iterative Closest Points (ICP) fingerprint matcher. Both 2D and 3D minutiae are cast as point clouds that we augment with additional features. Iterative Closest Points (ICP) is immediately applicable to these data structures, yet nonetheless relatively unexplored in the fingerprinting domain. We apply our ICP-based method to conventional 2D minutiae and 3D features extracted from Optical Coherence Tomography (OCT) scans of fingertips. We show that ICP is a viable strategy to fingerprint matching using the diverse features in the internal fingerprint skin. Using 3D minutiae alone gave an Area Under the Curve (AUC) of 0.961, and 3D minutiae augmented with mean local OCT intensity gave an AUC of 0.973. Regarding 2D minutiae, our method offers a significant improvement over the baseline NIST Bozorth3 algorithm: an AUC of 0.94 versus 0.86 on an artificial dataset generated with SFinGe. In addition, ICP incurs only nominal computation cost when additional features are added.
Characterization of embryonic muscle migration in Caenorhabditis elegans and of the role of unc-54 and mem-1 in inhibiting ectopic muscle membrane extensions.

ii Preface . iv Table of Contents. vi List of Tables. viii List of Figures . ix List of Abbreviations . xi Acknowledgements . xiii 1 Introduction . 1 1.1 Caenorhabditis elegans as a model organism. 1 1.2 Membrane extension and adhesion . 2 1.3 C. elegans body wall muscle . 6 1.4 Embryonic striated muscle migration. 7 1.5 C. elegans muscle arms . 11 1.6 Thesis objectives . 15 2 Membrane Extensions are Associated with Proper Anterior Migration of Muscle Cells During Caenorhabditis elegans Embryogenesis . 17 2.1 Synopsis . 17 2.2 Introduction . 18 2.3 Materials and methods . 20 2.3. 1 C. elegans strains . 20 2.3. 2 Molecular biology . 21 2.3. 3 Microscopy . 21 2.4 Results . 22 2.4. 1 A detailed description of C. elegans embryonic muscle migration. 22 2.4. 2 Proper embryonic muscle migration in C. elegans requires laminin . 27 2.4. 3 Proper ventral muscle process extension requires the α -integrin INA-1, the ephrin VAB-2, and the ROBO receptor SAX-3. 30 2.4. 4 Improper ventral muscle process extension is not due to defects in ventral hypodermal morphogenesis. 35 2.4. 5 SAX-3 is required in the nervous system for proper extension of ventral anterior muscle processes . 37 2.4. 6 Mislocalized neurons are associated with ventral anterior muscle defects. 39 2.5 Discussion . 41 2.5. 1 C. elegans muscle as a model to study muscle cell migration in vivo. 41 2.5. 2 Embryonic muscle migrations in C. elegans require laminin. 42 2.5. 3 Multiple signaling pathways affect ventral anterior muscle processes. 45 2.5. 4 Anterior muscle processes are required for anterior migration . 47
Transport, Fate and Impacts of the Deep Plume of Petroleum Hydrocarbons Formed During the Macondo Blowout

The 2010 Macondo oil well blowout consisted in a localized, intense infusion of petroleum hydrocarbons to the deep waters of the Gulf of Mexico. A substantial amount of these hydrocarbons did not reach the ocean surface but remained confined at depth within subsurface plumes, the largest and deepest of which was found at ∼ 1000–1200 m of depth, along the continental slope (the deep plume). This review outlines the challenges the science community overcame since 2010, the discoveries and the remaining open questions in interpreting and predicting the distribution, fate and impact of the Macondo oil entrained in the deep plume. In the past 10 years, the scientific community supported by the Gulf of Mexico Research Initiative (GoMRI) and others, has achieved key milestones in observing, conceptualizing and understanding the physical oceanography of the Gulf of Mexico along its northern continental shelf and slope. Major progress has been made in modeling the transport, evolution and degradation of hydrocarbons. Here we review this new knowledge and modeling tools, how our understanding of the deep plume formation and evolution has evolved, and how research in the past decade may help preparing the scientific community in the event of a future spill in the Gulf or elsewhere. We also summarize briefly current knowledge of the plume fate – in terms of microbial degradation and geochemistry – and impacts on fish, deep corals and mammals. Finally, we discuss observational, theoretical, and modeling limitations that constrain our ability to predict the three-dimensional movement of waters in this basin and the fate and impacts of the hydrocarbons they may carry, and we discuss research priorities to overcome them.
The Greener the Better! Avian Communities Across a Neotropical Gradient of Urbanization Density

Urbanization has been recognized as one of the most widespread threats to biodiversity. However, the response of wildlife to urbanization differs among groups, with many species being able to persist, adapt, and even thrive in these novel ecosystems. With the aim of assessing the response of avian communities in a neotropical green city, we evaluated their species richness and composition across a gradient of urbanization density comprised by a citywide survey performed in two consecutive years and considering both breeding and non-breeding seasons. As expected, species richness decreased with urbanization. Species loss was drastic when considering data from both years and both seasons, and gradual when seasons were assessed separately. Avian composition for both years and seasons differed largely between the less urbanized and the more urbanized sites, whereas sites with intermediate built cover showed to be more similar to each other. When evaluating avian composition by season in both years, highest differences were recorded between more urbanized sites and all other studied sites, while less urbanized sites showed high similarity regardless of the surveyed season. Sites with intermediate built cover had higher similarity among seasons, showing that such conditions shelter similar species in both seasons. This study presents findings on one of the first citywide gradients of urbanization density from the urban Neotropics, showing both differences and similarities in relation to previous studies from the Global North. Briefly, our species richness results showed a punctuated decrease when considering both seasons and years, rather than a gradual decrease or humped-shaped relations with higher richness at intermediately urbanized sites. Also, our composition findings stress the high representation of insectivore birds as part of avian communities across a citywide gradient of urbanization density. Undoubtedly, identifying the similarities and differences in the urban ecology patterns across cities, together with the particularities of some urban systems, will allow for increased effectiveness of urban management and planning strategies in the transformation toward more livable, resilient, and biodiverse cities.
Identification of Metastasis-Associated Biomarkers in Synovial Sarcoma Using Bioinformatics Analysis

Synovial sarcoma (SS) is a highly aggressive soft tissue tumor with high risk of local recurrence and metastasis. However, the mechanisms underlying SS metastasis are still largely unclear. The purpose of this study is to screen metastasis-associated biomarkers in SS by integrated bioinformatics analysis. Two mRNA datasets (GSE40018 and GSE40021) were selected to analyze the differentially expressed genes (DEGs). Using the Database for Annotation, Visualization and Integrated Discovery (DAVID) and gene set enrichment analysis (GSEA), functional and pathway enrichment analyses were performed for DEGs. Then, the protein-protein interaction (PPI) network was constructed via the Search Tool for the Retrieval of Interacting Genes (STRING) database. The module analysis of the PPI network and hub genes validation were performed using Cytoscape software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the hub genes were performed using WEB-based GEne SeT AnaLysis Toolkit (WebGestalt). The expression levels and survival analysis of hub genes were further assessed through Gene Expression Profiling Interactive Analysis (GEPIA) and the Kaplan-Meier plotter database. In total, 213 overlapping DEGs were identified, of which 109 were upregulated and 104 were downregulated. GO analysis revealed that the DEGs were predominantly involved in mitosis and cell division. KEGG pathways analysis demonstrated that most DEGs were significantly enriched in cell cycle pathway. GSEA revealed that the DEGs were mainly enriched in oocyte meiosis, cell cycle and DNA replication pathways. A key module was identified and 10 hub genes (CENPF, KIF11, KIF23, TTK, MKI67, TOP2A, CDC45, MELK, AURKB, and BUB1) were screened out. The expression and survival analysis disclosed that the 10 hub genes were upregulated in SS patients and could result in significantly reduced survival. Our study identified a series of metastasis-associated biomarkers involved in the progression of SS, and may provide novel therapeutic targets for SS metastasis.
A Protocol for Cancer-Related Mutation Detection on Exosomal DNA in Clinical Application

Background Recently, some genomic mutations in exosomal DNA have been found to be related to disease progress and clinical outcomes of patients in several cancers. Unfortunately, the methods for exosome isolation and exosomal DNA analysis are still lack of relevant research to ensure their optimal performance and the comparability. Here we aim to establish a protocol for cancer-related mutation detection on exosomal DNA in clinical application. Methods Taking KRAS mutation in pancreatic cancer as an example, we tested whether the types of blood samples, the potential factors in the courses of exosome isolation and exosomal DNA preparation, as well as the detail in mutation detection by droplet digital PCR (ddPCR) could influence the exosomal DNA analysis. Results We found that the concentration of exosomal DNA from serum was higher than that from plasma, whereas the mutant allele fraction (MAF) of KRAS in serum-derived exosomal DNA was obviously lower. The membrane-based method for exosome isolation showed no evident difference in both exosomal DNA yield and KRAS MAF from the classical ultracentrifugation method. DNase I pretreatment on exosomes could remove the wild-type DNA outside of exosomes and increase the KRAS MAF. PBS might interfere with the effect of DNase I and should not be recommended as resuspension buffer for exosomes if the subsequent experiments would be done with exosomal DNA. Besides, the denaturation of exosomal DNA before droplet generation during ddPCR could effectively improve the total KRAS copy number and mutation-positive droplet number. Conclusion This study provides some methodological evidences for the selection of the optimal experimental conditions in exosomal DNA analysis. We also suggest a protocol for mutation detection on exosomal DNA, which might be suitable for the clinical testing and could be helpful to the comparison of results from different laboratories.
Afferent and Efferent Visual Markers of Alzheimer’s Disease: A Review and Update in Early Stage Disease

Vision, which requires extensive neural involvement, is often impaired in Alzheimer’s disease (AD). Over the last few decades, accumulating evidence has shown that various visual functions and structures are compromised in Alzheimer’s dementia and when measured can detect those with dementia from those with normal aging. These visual changes involve both the afferent and efferent parts of the visual system, which correspond to the sensory and eye movement aspects of vision, respectively. There are fewer, but a growing number of studies, that focus on the detection of predementia stages. Visual biomarkers that detect these stages are paramount in the development of successful disease-modifying therapies by identifying appropriate research participants and in identifying those who would receive future therapies. This review provides a summary and update on common afferent and efferent visual markers of AD with a focus on mild cognitive impairment (MCI) and preclinical disease detection. We further propose future directions in this area. Given the ease of performing visual tests, the accessibility of the eye, and advances in ocular technology, visual measures have the potential to be effective, practical, and non-invasive biomarkers of AD.
Melanism in the Uinta Ground Squirrel, Spermophilus armatus

Two melanistic specimens of Spermophilus armatus were described by A. H. Howell (N. Amer. Fauna No. 56, p. 79, May 18, 1938) as uniform blackish brown all over. " They were obtained on the same day (May 29, 1912) from one locality (Mountainview, Wyoming) by S. G. Jewett. One (USNM 179111) of the specimens was young, and the other (USNM 179288) was an adult, lactating female (Fig. 1). They merit further mention because the evidence indicates that the melanistic, lactating female survived to produce offspring and that dichromatism persisted in the population to which these melanistic squirrels belonged. The lactating female was possibly the mother of the young squirrel. No other melanistic individuals of Spermophilus armatus have been reported, although melanism in other sciurids is well known.
Bisphenols Threaten Male Reproductive Health via Testicular Cells

Male reproductive function and health are largely dependent on the testes, which are strictly regulated by their major cell components, i. e. , Sertoli, Leydig, and germ cells. Sertoli cells perform a crucial phagocytic function in addition to supporting the development of germ cells. Leydig cells produce hormones essential for male reproductive function, and germ cell quality is a key parameter for male fertility assessment. However, these cells have been identified as primary targets of endocrine disruptors, including bisphenols. Bisphenols are a category of man-made organic chemicals used to manufacture plastics, epoxy resins, and personal care products such as lipsticks, face makeup, and nail lacquers. Despite long-term uncertainty regarding their safety, bisphenols are still being used worldwide, especially bisphenol A. While considerable attention has been paid to the effects of bisphenols on health, current bisphenol-related reproductive health cases indicate that greater attention should be given to these chemicals. Bisphenols, especially bisphenol A, F, and S, have been reported to elicit various effects on testicular cells, including apoptosis, DNA damage, disruption of intercommunication among cells, mitochondrial damage, disruption of tight junctions, and arrest of proliferation, which threaten male reproductive health. In addition, bisphenols are xenoestrogens, which alter organs and cells functions via agonistic or antagonistic interplay with hormone receptors. In this review, we provide in utero, in vivo, and in vitro evidence that currently available brands of bisphenols impair male reproductive health through their action on testicular cells.
Selenium regulation of selenoproteome expression in rats

Glutathione peroxidase‐1 (Gpx1) mRNA levels as well as enzyme activity decrease dramatically in Se deficiency in rats, and both have been used to assess Se status and Se requirements. To determine the Se regulation of the complete selenoproteome, male weanling rats were supplemented with graded levels of Se (0 to 0.8 μg Se/g) for 28 d. There was no effect of Se deficiency on growth. Liver and kidney Se concentrations in Se‐deficient rats were 3 and 14% of Se‐adequate levels, respectively, and reached breakpoints at 0.1 μg Se/g. Se‐deficient plasma Gpx3 activity, and liver and kidney Gpx1 activities were 2, 2, and 6%, respectively, of Se‐adequate levels, with plateau breakpoints at 0.1 μg Se/g. Liver Gpx1, Sepw1, Selk, Selh, and Gpx3 mRNA levels were 11, 21, 28, 29, and 33%, respectively, of Se‐adequate plateau levels, with plateau breakpoints at 0.05–0.07 μg Se/g. In kidney, Gpx1, Sepw1, Selh, and Gpx3 were also highly regulated by Se status, with similar plateau breakpoints. In addition, 6 mRNAs in liver and 3 mRNAs in kidney were moderately down‐regulated by Se status. The majority of selenoprotein mRNAs in liver (12) and kidney (16) were not significantly down‐regulated by Se deficiency. The plateau breakpoints for Se‐regulated mRNAs are similar, and all are less than breakpoints for Gpx1 activity, suggesting a common mechanism for this regulation. (Supported by UW WIS04909 and by NIH T32‐DK07665)
Assisting teacher educators with constructive technology integration into curriculum delivery in the 21st Century

This study analyses how teacher educators integrate technology into curriculum delivery and hence propose ways of assisting them to use the technologies into their teaching in a constructive manner. The conceptual model to understand the teacher educators’ technology integration was developed by combining constructivist teaching theory with Technological, Pedagogical and Content Knowledge (TPACK) complimented with Substitution Augmentation Modification Redefinition (SAMR) – both technology integration frameworks and the theory of constructivism. The researchers employed a qualitative research approach, gathered data using one-on-one semi-structured interviews and non-participant lecture observations. Eight teacher educators participated in the study. Analysis of the data collected shows that teacher educators in the study were limited in their knowledge of integrating technology into curriculum delivery in a way that enhanced teaching learning outcomes. The teacher educators need to be assisted on how to integrate the technologies following a constructivist approach to teach effectively in the 21st century.
ANTIMICROBIAL ACTIVITY OF ALSTONIA SCHOLARIS LEAF EXTRACTS

Alstonia scholaris leaf powder is extracted with petroleum ether, chloroform, ethyl acetate and methanol using soxhlet apparatus. All the extracts were screened for antibacterial and antifungal activity. The microorganisms used were Escherchia coli, Salmonella typhi, Staphylococcus aureus, Klebsiella pnuemoniae, Shigella dysenteriae, Aspergillus niger and Aspergillus flavus. Of the various extracts, chloroform extract showed promising antifungal activity against A. niger and A. flavus while petroleum ether and chloroform extracts showed moderate antibacterial activity against E. coli and K. pnuemoniae.
Status, management practices and performance in three strains of deoni breed of cattle

Deoni is an important medium heavy dual purpose cattle breed found mainly in Latur district and also distributed in small numbers in the neighboring districts viz. Parbhani, Nanded and Osmanabad of Maharashtra. Deoni cattle have three strains on the basis of coat colour variation viz. Wanner a (clear white with black colour at the sides of the face), Shevera (white body with irregular black spots) and Balankya (clear white with black spots on the lower side of the body). The information on 1682 Deoni cattle belonging to 579 owners from 48 villages of 5 talukas of Latur district of Maharashtra was collected randomly for studying morphometric characteristics as well as production and reproduction traits of three strains. The proportion of Wannera, Shevera and Balankya strains was 49.00%, 46.29% and 4.71%, respectively. In adult cattle, the Wannera strain had more chest girth (163 cm), body length (125 cm) and height at wither (126 cm) indicating heavier build-up than other two strains. Balankya strain of Deoni cattle had longer face length (50 cm), horn length (22 cm) and ear length (27 cm) than other two strains of Deoni. Balankya strain yielded more milk per lactation (973.63±55.18 kg) as compared to Wannera (830.80±40.38 kg) and Shevera (848.44±41.57 kg) strains and also had more lactation length (258.04±1 6.28 days). Balankya strain, also had higher fat % (4.08±0.60) and SNF % (8.45±0.19) than other two strains of Deoni cattle. The results revealed that Balankya strain of Deoni cattle had higher milk yield, lactation length and fat percent than Wannera and Shevera strains, but had slightly delayed age at first mating and age at first calving.
CERES Terra/Aqua Edition4A SYN1deg Observed TOA Fluxes – Accuracy and Validation

This section is devoted to the SYN1deg Ed4A observed TOA flux validation. The GEO accuracy and validation can be obtained in the CldTypHist Ed4A DQS. The SYN1deg Ed4A combines the CERES observed and GEO hourly derived fluxes. For accuracy and validation of the CERESonly TOA fluxes can be found in the SSF1deg Ed4A DQS. The solar incoming radiation data and associated uncertainty can be found in the EBAF Ed4.0 DQS. The incoming solar radiation is the same for the SSF1deg Ed4A and SYN1deg Ed4A products.