University of the Free State

DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.

In this manuscript we proposed a new fractional derivative with non-local and\n no-singular kernel. We presented some useful properties of the new derivative\n and applied it to solve the fractional heat transfer model.

Abstract The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively 1–3 . In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function 4 . Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

BACKGROUND: Misconceptions about ADHD stigmatize affected people, reduce credibility of providers, and prevent/delay treatment. To challenge misconceptions, we curated findings with strong evidence base. METHODS: We reviewed studies with more than 2000 participants or meta-analyses from five or more studies or 2000 or more participants. We excluded meta-analyses that did not assess publication bias, except for meta-analyses of prevalence. For network meta-analyses we required comparison adjusted funnel plots. We excluded treatment studies with waiting-list or treatment as usual controls. From this literature, we extracted evidence-based assertions about the disorder. RESULTS: We generated 208 empirically supported statements about ADHD. The status of the included statements as empirically supported is approved by 80 authors from 27 countries and 6 continents. The contents of the manuscript are endorsed by 366 people who have read this document and agree with its contents. CONCLUSIONS: Many findings in ADHD are supported by meta-analysis. These allow for firm statements about the nature, course, outcome causes, and treatments for disorders that are useful for reducing misconceptions and stigma.

Summary Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.

A conceptually very simple but general algorithm for the estimation of the fixed effects, random effects, and components of dispersion in generalized linear models with random effects is proposed. Conditions are described under which the algorithm yields approximate maximum likelihood or quasi-maximum likelihood estimates of the fixed effects and dispersion components, and approximate empirical Bayes estimates of the random effects. The algorithm is applied to two data sets to illustrate the estimation of components of dispersion and the modelling of overdispersion.

Prostate cancer is one of the malignancies that affects men and significantly contributes to increased mortality rates in men globally. Patients affected with prostate cancer present with either a localized or advanced disease. In this review, we aim to provide a holistic overview of prostate cancer, including the diagnosis of the disease, mutations leading to the onset and progression of the disease, and treatment options. Prostate cancer diagnoses include a digital rectal examination, prostate-specific antigen analysis, and prostate biopsies. Mutations in certain genes are linked to the onset, progression, and metastasis of the cancer. Treatment for localized prostate cancer encompasses active surveillance, ablative radiotherapy, and radical prostatectomy. Men who relapse or present metastatic prostate cancer receive androgen deprivation therapy (ADT), salvage radiotherapy, and chemotherapy. Currently, available treatment options are more effective when used as combination therapy; however, despite available treatment options, prostate cancer remains to be incurable. There has been ongoing research on finding and identifying other treatment approaches such as the use of traditional medicine, the application of nanotechnologies, and gene therapy to combat prostate cancer, drug resistance, as well as to reduce the adverse effects that come with current treatment options. In this article, we summarize the genes involved in prostate cancer, available treatment options, and current research on alternative treatment options.

Stigma in health facilities undermines diagnosis, treatment, and successful health outcomes. Addressing stigma is fundamental to delivering quality healthcare and achieving optimal health. This correspondence article seeks to assess how developments over the past 5 years have contributed to the state of programmatic knowledge-both approaches and methods-regarding interventions to reduce stigma in health facilities, and explores the potential to concurrently address multiple health condition stigmas. It is supported by findings from a systematic review of published articles indexed in PubMed, Psychinfo and Web of Science, and in the United States Agency for International Development's Development Experience Clearinghouse, which was conducted in February 2018 and restricted to the past 5 years. Forty-two studies met inclusion criteria and provided insight on interventions to reduce HIV, mental illness, or substance abuse stigma. Multiple common approaches to address stigma in health facilities emerged, which were implemented in a variety of ways. The literature search identified key gaps including a dearth of stigma reduction interventions in health facilities that focus on tuberculosis, diabetes, leprosy, or cancer; target multiple cadres of staff or multiple ecological levels; leverage interactive technology; or address stigma experienced by health workers. Preliminary results from ongoing innovative responses to these gaps are also described.The current evidence base of stigma reduction in health facilities provides a solid foundation to develop and implement interventions. However, gaps exist and merit further work. Future investment in health facility stigma reduction should prioritize the involvement of clients living with the stigmatized condition or behavior and health workers living with stigmatized conditions and should address both individual and structural level stigma.

Gaps in research focusing on work related stress, burnout, job satisfaction and general health of nurses is evident within developing contexts like South Africa. This study identified the relationship between work related stress, burnout, job satisfaction and general health of nurses. A total of 1200 nurses from four hospitals were invited to participate in this cross-sectional study (75% response rate). Participants completed five questionnaires and multiple linear regression analysis was used to determine significant relationships between variables. Staff issues are best associated with burnout as well as job satisfaction. Burnout explained the highest amount of variance in mental health of nurses. These are known to compromise productivity and performance, as well as affect the quality of patient care. Issues, such as security risks in the workplace, affect job satisfaction and health of nurses. Although this is more salient to developing contexts it is important in developing strategies and intervention programs towards improving nurse and patient related outcomes.

Moringa (Moringa oleifera Lam. moringaceae) is a highly valued plant that is mostly cultivated in the tropics and subtropics. It is used for food, medication and industrial purposes. The objective of the study was to assess the nutritional value of Moringa leaves of the South African ecotype. Proximate and Van Soest methods were used to determine the nutritional value of Moringa leaves. The dried leaves had crude protein levels of 30.3% and 19 amino acids. The dried leaves had the following mineral contents: calcium (3.65%), phoshorus (0.3%), magnesium (0.5%), potassium (1.5%), sodium (0.164%), sulphur (0.63%), zinc (13.03 mg/kg), copper (8.25%), manganese (86.8 mg/kg), iron (490 mg/kg) and selenium (363 mg/kg). 17 fatty acids were observed with α-Linolenic acid (44.57%) having the highest value followed by heneicosanoic (14.41%), g-linolenic (0.20%) palmiteic (0.17%) and capric acid (0.07%). Vitamin E had the highest concentration of 77 mg/100 g than beta-carotene, which had 18.5 mg/100 g in the dried leaves. The fiber content was neutral detergent fibre (NDF) (11.4%), acid detergent fibre (ADF) (8.49%), acid detergent lignin (ADL) (1.8%) and (acid detergent cellulose (ADC) (4.01%). The condensed tannins had a value of 3.2%, while total polyphenols were 2.02%. The values of amino acids, fatty acids, minerals and vitamin profiles reflect a desirable nutritional balance.   Key words: South African, supplemental food, nutritional value, Moringa oleifera.

Life cycle assessment (LCA) has been used to assess freshwater-related impacts according to a new water footprint framework formalized in the ISO 14046 standard. To date, no consensus-based approach exists for applying this standard and results are not always comparable when different scarcity or stress indicators are used for characterization of impacts. This paper presents the outcome of a 2-year consensus building process by the Water Use in Life Cycle Assessment (WULCA), a working group of the UNEP-SETAC Life Cycle Initiative, on a water scarcity midpoint method for use in LCA and for water scarcity footprint assessments. In the previous work, the question to be answered was identified and different expert workshops around the world led to three different proposals. After eliminating one proposal showing low relevance for the question to be answered, the remaining two were evaluated against four criteria: stakeholder acceptance, robustness with closed basins, main normative choice, and physical meaning. The recommended method, AWARE, is based on the quantification of the relative available water remaining per area once the demand of humans and aquatic ecosystems has been met, answering the question “What is the potential to deprive another user (human or ecosystem) when consuming water in this area?” The resulting characterization factor (CF) ranges between 0.1 and 100 and can be used to calculate water scarcity footprints as defined in the ISO standard. After 8 years of development on water use impact assessment methods, and 2 years of consensus building, this method represents the state of the art of the current knowledge on how to assess potential impacts from water use in LCA, assessing both human and ecosystem users’ potential deprivation, at the midpoint level, and provides a consensus-based methodology for the calculation of a water scarcity footprint as per ISO 14046.

2008, Oxford University Press, Oxford. ISBN 978 0 19 442244 4, 287 pages

The present paper describes the mathematical modeling and dynamics of a novel corona virus (2019-nCoV). We describe the brief details of interaction among the bats and unknown hosts, then among the peoples and the infections reservoir (seafood market). The seafood marked are considered the main source of infection when the bats and the unknown hosts (may be wild animals) leaves the infection there. The purchasing of items from the seafood market by peoples have the ability to infect either asymptomatically or symptomatically. We reduced the model with the assumptions that the seafood market has enough source of infection that can be effective to infect people. We present the mathematical results of the model and then formulate a fractional model. We consider the available infection cases for January 21, 2020, till January 28, 2020 and parameterized the model. We compute the basic reproduction number for the data is R0≈2.4829. The fractional model is then solved numerically by presenting many graphical results, which can be helpful for the infection minimization.

The microbiology, epidemiology, diagnostics, and treatment of infective endocarditis (IE) have changed significantly since the Duke Criteria were published in 1994 and modified in 2000. The International Society for Cardiovascular Infectious Diseases (ISCVID) convened a multidisciplinary Working Group to update the diagnostic criteria for IE. The resulting 2023 Duke-ISCVID IE Criteria propose significant changes, including new microbiology diagnostics (enzyme immunoassay for Bartonella species, polymerase chain reaction, amplicon/metagenomic sequencing, in situ hybridization), imaging (positron emission computed tomography with 18F-fluorodeoxyglucose, cardiac computed tomography), and inclusion of intraoperative inspection as a new Major Clinical Criterion. The list of "typical" microorganisms causing IE was expanded and includes pathogens to be considered as typical only in the presence of intracardiac prostheses. The requirements for timing and separate venipunctures for blood cultures were removed. Last, additional predisposing conditions (transcatheter valve implants, endovascular cardiac implantable electronic devices, prior IE) were clarified. These diagnostic criteria should be updated periodically by making the Duke-ISCVID Criteria available online as a "Living Document."

Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.

In much of the world, resistance to stem rust in wheat, caused by Puccinia graminis f. sp. tritici, is based at least in part on the gene Sr31. During February 1999, high levels of stem rust infection were observed on entries in wheat (Triticum aestivum) grown in a nursery at Kalengyere Research Station in Uganda. Because several of the rusted entries were known to carry the 1BL-1RS chromosome translocation containing the Sr31, Lr26, and Yr9 genes for rust resistance, virulence to Sr31 was suspected. Urediniospores, collected in bulk from rusted stems of seven entries containing Sr31, were suspended in light mineral oil and sprayed on primary leaves of 7-day-old seedlings of South African wheat cv. Gamtoos (=Veery #3, pedigree: Kvz/Buho‘S’//Kal/BB). Plants were kept overnight at 19 to 21°C in a dew chamber before placement in a greenhouse at 18 to 25°C. After ≈14 days, urediniospores were collected from large, susceptible-type stem rust pustules and subsequently increased on Gamtoos, which served as a selective host for the new rust culture, designated Pgt-Ug99. Pathogenicity of Pgt-Ug99 was studied in seedling tests of available wheats containing Sr31, as well as other stem rust differential lines. All seedling tests were conducted at least three times in independent inoculations. Isolate Pgt-Ug99 was not virulent to Avocet‘S’/Yr9 (Australian line containing Sr26) or Oom Charl (South African cultivar) but was virulent to the other Sr31 testers: Alondra ‘S’, Bobwhite, Chokka, Clement, Federation/Kavkaz, Gamtoos, Grebe, Kavkaz, Letaba, Line E/Kavkaz, RL6078, and Veery ‘S’. Virulence to Sr31 (infection types [ITs] 3 - 3 to 3 ++ 4) was clearly contrasted by the low reactions (ITs 0; to 1) produced by UVPgt53, a South African pathotype avirulent to Sr31. According to the reactions of the differential lines, Pgt-Ug99 is avirulent to Sr21, -22, -24, -25, -26, -27, -29, -32, -33, -34, -35, -36, -39, -40, -42, and -43, Agi, and Em and virulent to Sr5, -6, -7b, -8a, -8b, -9b, -9e, -9g, -11, -15, -17, -30, -31, and -38. Virulence to the T. ventricosum-derived gene Sr38, which is linked to Lr37 and Yr17 and occurs in cultivars from Australia, the United Kingdom, and the United States, was not known previously (1). Both Pgt-Ug99 and UVPgt53 produced a continuum of ITs (; to 2+3) on Petkus rye (obtained from the USDA-ARS National Small Grains Collection, Aberdeen, ID), the original Sr31 donor source. Pgt-Ug99 did not appear more virulent than UVPgt53 on Petkus. All triticales tested, as well as oat cv. Overberg, were highly resistant to Pgt-Ug99. According to McIntosh et al. (1), Huerta-Espino mentioned a Sr31-virulent culture from Turkey, but this could not be confirmed. Should the Sr31-virulent pathotype migrate out of Uganda, it poses a major threat to wheat production in countries where the leading cultivars have resistance based on this gene. Reference: (1) R. A. McIntosh et al. 1995. Wheat Rusts: An Atlas of Resistance Genes. Kluwer Academic Publishers, Dordrecht, the Netherlands.

Wille (1996) proposed an item selection strategy which may be used to maximise, first, the internal consistency and, next, the convergent and discriminant validity of items in multi-dimensional Likert-type questionnaires or scales. In terms of his strategy, the latter aspects of validity are maximised by means of exploratory factor analyses. In this article, it is done by means of Tateneni, Mels, Cudeck and Browne’s (2001) Comprehensive Exploratory Factor Analysis (CEFA) program which implements exploratory factor analysis, but provides the advantages of standard confirmatory factor analysis (e.g., the computation of the standard errors of the rotated factor loadings and measures of “model" fit). The benefits that accrue by using this incremental approach are demonstrated in terms of Allport and Ross’ (1967) Religious Orientation Scale, a widely-used psychological instrument. Opsomming Wille (1996) het ’n itemseleksiestrategie voorgestel om eerstens die interne konsekwentheid, en tweedens die konvergente en divergente geldigheid van items in multidimensionele Likert-tipe vraelyste of skale te maksimeer. Volgens sy strategie word laasgenoemde aspekte van geldigheid deur middel van eksploratiewe faktorontledings gemaksimeer. In hierdie artikel, sal dit gedoen word deur Tateneni, Mels, Cudeck en Browne (2001) se program vir Omvattende Eksploratiewe Faktorontleding (CEFA) te gebruik, wat eksploratiewe faktorontleding aanwend, maar ook die voordele van gewone, bevestigende faktorontleding (bv., die berekening van die standaardfoute van die geroteerde faktorbeladings en indekse van modelpassing) bied. Die voordele wat spruit uit die toepassing van hierdie inkrementele benadering word gedemonstreer aan die hand van Allport en Ross (1967) se Religious Orientation Scale, ’n gewilde sielkundige meetintrument.

The yeast Saccharomyces cerevisiae responds to osmotic stress, i.e., an increase in osmolarity of the growth medium, by enhanced production and intracellular accumulation of glycerol as a compatible solute. We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. gpd1 delta mutants produced very little glycerol, and they were sensitive to osmotic stress. Thus, glycerol production is indeed essential for the growth of yeast cells during reduced water availability. hog1 delta mutants lacking a protein kinase involved in osmostress-induced signal transduction (the high-osmolarity glycerol response [HOG] pathway) failed to increase glycerol-3-phosphate dehydrogenase activity and mRNA levels when osmotic stress was imposed. Thus, expression of GPD1 is regulated through the HOG pathway. However, there may be Hog1-independent mechanisms mediating osmostress-induced glycerol accumulation, since a hog1 delta strain could still enhance its glycerol content, although less than the wild type. hog1 delta mutants are more sensitive to osmotic stress than isogenic gpd1 delta strains, and gpd1 delta hog1 delta double mutants are even more sensitive than either single mutant. Thus, the HOG pathway most probably has additional targets in the mechanism of adaptation to hypertonic medium.