Classifying Australian PhD bibliographic thesis records by ANZSRC field of research codes

This report provides a brief report detailing the methods and approach used to classify the 2007-2009 theses by ANZSRC Fields of Research codes and any recommendations

Insight on Estrogen Receptor Alpha Modulator from Indonesian Herbal Database: An in-silico analysis

Estrogen receptor α (ERα) is liable for regulating transcription factors which are an important part of hormonal signaling in breast cancer. This study intends to find hit compounds that are considered capable of inhibiting ERα by utilizing structure-based pharmacophores and molecular docking. Pharmacophore of the original ERα ligand (E4D600) has one hydrogen bond acceptor and three hydrogen bond donors which are used to select compounds from the Indonesian herbal database. This pharmacophore model had an Area under Curve of the Receiver Operating Characteristics (AUC-ROC) value is 0.80 and the Goodness of Hits (GH) value is 0.81. The selection process generated 330 compounds which proceed to the molecular docking stage to analyze their binding energy and interactions to ERα. The results indicated potential hit compounds seen from their binding energies in the range -5.42 to -10.01 kcal/mol. four of the best compounds including Lig57/(-)-Bidwillon A, Lig47/Quercetin 3-(6''-galloylgalactoside), Lig197/Multifloroside and Lig83/Erythrabyssin II provide promising information for their detailed analysis as ERα inhibitors

COVID-19 publications: Database coverage, citations, readers, tweets, news, Facebook walls, Reddit posts

© 2020 The Authors. Published by MIT Press. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1162/qss_a_00066The COVID-19 pandemic requires a fast response from researchers to help address biological, medical and public health issues to minimize its impact. In this rapidly evolving context, scholars, professionals and the public may need to quickly identify important new studies. In response, this paper assesses the coverage of scholarly databases and impact indicators during 21 March to 18 April 2020. The rapidly increasing volume of research, is particularly accessible through Dimensions, and less through Scopus, the Web of Science, and PubMed. Google Scholar’s results included many false matches. A few COVID-19 papers from the 21,395 in Dimensions were already highly cited, with substantial news and social media attention. For this topic, in contrast to previous studies, there seems to be a high degree of convergence between articles shared in the social web and citation counts, at least in the short term. In particular, articles that are extensively tweeted on the day first indexed are likely to be highly read and relatively highly cited three weeks later. Researchers needing wide scope literature searches (rather than health focused PubMed or medRxiv searches) should start with Dimensions (or Google Scholar) and can use tweet and Mendeley reader counts as indicators of likely importance

Variable clinical phenotype in TBK1 mutations: case report of a novel mutation causing primary progressive aphasia and review of the literature

TBK1 mutations are a recently discovered cause of disorders in the frontotemporal dementia (FTD)-amyotrophic lateral sclerosis (ALS) spectrum. We describe a novel L683* mutation, predicted to cause a truncated protein and therefore be pathogenic, in a patient presenting with nonfluent variant primary progressive aphasia (PPA) at the age of 65. Her disease progressed over the following years, leading to her being mute and wheelchair bound seven years into her illness. Brain imaging showed asymmetrical left-sided predominant atrophy affecting the frontal, insular and temporal cortices as well as the striatum in particular. Review of the literature found 60 different nonsense, frameshift, deletion or splice site mutations, including the newly described mutation, with data on clinical diagnosis available in 110 people: 58% of the cases presented with an ALS syndrome, 16% with an FTD-ALS overlap, 19% with a cognitive presentation (including behavioural variant FTD (bvFTD) and PPA) and 4% with atypical parkinsonism. Age at onset (AAO) data was available in 75 people: mean (standard deviation) AAO was 57.5 (10.3) in those with ALS, which was significantly younger than those with a cognitive presentation (AAO = 65.1 (10.5), p = 0.008), or atypical parkinsonism (AAO = 68.3 (8.7), p = 0.021), with a trend compared with the FTD-ALS group (AAO = 61.9 (7.0), p=0.065); there was no significant difference in AAO between the other groups. In conclusion, clinical syndromes across the whole FTD-ALS-atypical parkinsonism spectrum have been reported in conjunction with mutations in TBK1. It is therefore important to include TBK1 on future gene panels for each of these disorders, and to suspect such mutations particularly when there are multiple different phenotypes in the same family

Social Media Impact of Myopia Research

Myopia has become a public health issue worldwide. The fast increase in myopia prevalence in the last years has been accompanied by an increase in information through social and conventional media. This has led to the fight not only against a pandemic but also against the infodemic. The excess of information has made it increasingly difficult for health professionals to identify high-quality articles. Alternative Metrics are useful tools to identify publications that provoke attention to society. This research aims to study the impact that research on myopia has had on social media. Methods: Almetric Explorer was used to make a search using “myopia” as a keyword. The 100 outputs with the highest attention were analyzed and correlated with the number of cites on Web of Science using Spearman’s correlation coefficient. Results: The top 100 Altmetric Attention Score were published in 47 journals and had a mean value of Altmetric Attention Score of 437.61 ± 718.33. The outputs were mostly discussed on Twitter, with a mean of 296.36 ± 1585.58 tweets and retweets, and a mean of 185.18 ± 211.57 readers in Mendeley. There was a low correlation between Altmetric Attention Score and Web of Science Cites for the top-100 outputs. Conclusions: although myopia is a research topic with a high interest in society, most cited articles are not those with the most impact on social media. Myopia researchers should make more effort in promoting their goals, and social media is a useful tool to share them.Depto. de Optometría y VisiónFac. de Óptica y OptometríaTRUEpu

Clinicopathological and Genomic Characterization of a Simmental Calf with Generalized Bovine Juvenile Angiomatosis

Bovine juvenile angiomatosis (BJA) comprises a group of single or multiple proliferative vascular anomalies in the skin and viscera of affected calves. The purpose of this study was to characterize the clinicopathological phenotype of a 1.5-month-old Simmental calf with multiple cutaneous, subcutaneous, and visceral vascular hamartomas, which were compatible with a generalized form of BJA, and to identify genetic cause for this phenotype by whole-genome sequencing (WGS). The calf was referred to the clinics as a result of its failure to thrive and the presence of multiple cutaneous and subcutaneous nodules, some of which bled abundantly following spontaneous rupture. Gross pathology revealed similar lesions at the inner thoracic wall, diaphragm, mediastinum, pericardium, inner abdominal wall, and mesentery. Histologically, variably sized cavities lined by a single layer of plump cells and supported by a loose stroma with occasional acute hemorrhage were observed. Determined by immunochemistry, the plump cells lining the cavities displayed a strong cytoplasmic signal for PECAM-1, von Willebrand factor, and vimentin. WGS revealed six private protein-changing variants affecting different genes present in the calf and absent in more than 4500 control genomes. Assuming a spontaneous de novo mutation event, one of the identified variants found in the PREX1, UBE3B, PCDHGA2, and ZSWIM6 genes may represent a possible candidate pathogenic variant for this rare form of vascular malformation

Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome

Phylogenetic relationships of the Amblyomma cajennense complex (Acari: Ixodidae) at mitogenomic resolution

The genus Amblyomma is the third most diverse in the number of species within the Ixodidae, with practically half of its species distributed in the Americas, though there are also species occurring in Africa, Asia, and Australia. Within the genus, there are several species complexes with veterinary and public health importance. The Amblyomma cajennense complex, in the Americas, is represented by six species with a wide distribution, from Texas to northern Argentina. We combined two sequencing techniques to generate complete mitogenomes of species belonging to the Amblyomma cajennense complex: genome skimming and long-range PCRs sequencing methods. Thus, we generated seven new mitochondrial genomes for all species of the Amblyomma cajennense complex, except for Amblyomma interandinum. Genetic distances between the mitogenomes corroborate the clear differentiation between the five species of the Amblyomma cajennense complex. The phylogenetic relationships of these species had previously been evaluated by combining partial nuclear and mitochondrial genes and here these relationships are corroborated with a more robust framework of data, which demonstrates that the conjunction of mitochondrial and nuclear partial genes can resolve close relationships when entire genes or genomes are unavailable. The gene order, structure, composition, and length are stable across these mitogenomes, and they share the general characteristics of Metastriata. Future studies should increase the number of available mitogenomes for this genus, especially for those species from the Indo-Pacific region and Africa, by means of a better understanding of their relationships and evolutionary process.EEA RafaelaFil: Cotes-Perdomo, Andrea P. Museo Nacional de Ciencias Naturales (MNCN-CSIC), Departamento de Biodiversidad y Biología Evolutiva; EspañaFil: Cotes-Perdomo, Andrea P. University of South-Eastern. Faculty of Technology. Natural Sciences and Environmental Health Department. Natural Sciences and Maritime Sciences; NoruegaFil: Nava, Santiago. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; ArgentinaFil: Nava, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Nava, Santiago. Instituto Nacional de Tecnología Agropecuaria. Instituto de Investigación de la Cadena Láctea (IDICAL); ArgentinaFil: Castro, Lyda R. Universidad del Magdalena. Facultad de Ciencias Básicas. Grupo de investigación Evolución, Sistemática y Ecología Molecular (GIESEMOL); ColombiaFil: Rivera-Paéz, Fredy A. Universidad de Caldas. Facultad de Ciencias Exactas y Naturales. Departamento de Ciencias Biológicas. Grupo de Investigación en Genética, Biodiversidad y Manejo de Ecosistemas (GEBIOME); ColombiaFil: Cortés-Vecino, Jesús A. Universidad Nacional de Colombia. Facultad de Medicina Veterinaria y de Zootecnia. Grupo de Investigación Parasitología Veterinaria; ColombiaFil: Uribe, Juan E. Museo Nacional de Ciencias Naturales (MNCN-CSIC). Departamento de Biodiversidad y Biología Evolutiv; EspañaFil: Uribe, Juan E. Smithsonian Institution. National Museum of Natural History. Invertebrate Zoology Department; Estados Unido

Ranking cancer drivers via betweenness-based outlier detection and random walks

Background Recent cancer genomic studies have generated detailed molecular data on a large number of cancer patients. A key remaining problem in cancer genomics is the identification of driver genes. Results We propose BetweenNet, a computational approach that integrates genomic data with a protein-protein interaction network to identify cancer driver genes. BetweenNet utilizes a measure based on betweenness centrality on patient specific networks to identify the so-called outlier genes that correspond to dysregulated genes for each patient. Setting up the relationship between the mutated genes and the outliers through a bipartite graph, it employs a random-walk process on the graph, which provides the final prioritization of the mutated genes. We compare BetweenNet against state-of-the art cancer gene prioritization methods on lung, breast, and pan-cancer datasets. Conclusions Our evaluations show that BetweenNet is better at recovering known cancer genes based on multiple reference databases. Additionally, we show that the GO terms and the reference pathways enriched in BetweenNet ranked genes and those that are enriched in known cancer genes overlap significantly when compared to the overlaps achieved by the rankings of the alternative methods.This work has been supported by the Scientific and Technological Research Council of Turkey [117E879 to H.K. and C.E.

The climatic and genetic heritage of Italian goat breeds with genomic SNP data

Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo\u2011political situation preceding the country unification around two centuries ago. We leveraged the remarkable genetic and geographical diversity of the Italian goat populations and performed landscape genomics analysis to disentangle the relationship between genotype and environment, finding 64 SNPs intercepting genomic regions linked to growth, circadian rhythm, fertility, and inflammatory response. Lastly, we calculated the hypothetical future genotypic frequencies of the most relevant SNPs identified through landscape genomics to evaluate their long\u2011term effect on the genetic structure of the Italian goat populations. Our results provide an insight into the past and the future of the Italian local goat populations, helping the institutions in defining new conservation strategy plans that could preserve their diversity and their link to local realities challenged by climate change