Building visualization skills through investigating the Journal of the Medical Library Association coauthorship network from 2006–2017

Objective: The primary objective of this study was to explore different dimensions of Journal of the Medical Library Association (JMLA) authorship from 2006-2017. Dimensions that were evaluated using coauthorship networks and affiliation data included collaboration, geographical reach, and relationship between Medical Library Association (MLA) member and nonmember authors. A secondary objective was to analyze the practice and practical application of data science skills. Methods: A team of librarians who attended the 2017 Data Science and Visualization Institute used JMLA bibliographic metadata extracted from Scopus, together with select MLA membership data from 2006-2017. Data cleaning, anonymization, analysis, and visualization were done collaboratively by the team members to meet their learning objectives and to produce insights about the nature of collaborative authorship at JMLA. Results: Sixty-nine percent of the 1,351 JMLA authors from 2006-2017 were not MLA members. MLA members were more productive and collaborative, and tended to author articles together. The majority of the authoring institutions in JMLA are based in the United States. Global reach outside of the United States and Canada shows higher authorship in English-speaking countries (e.g., Australia, United Kingdom), as well as in Western Europe and Japan. Conclusions: MLA support of JMLA may benefit a wider network of health information specialists and medical professionals than is reflected in MLA membership. Conducting coauthorship network analyses can create opportunities for health sciences librarians to practice applying emerging data science and data visualization skills

Aster yellows phytoplasma in grapevines: identification of vectors in South Africa

Abstract Since the discovery of aster yellows phytoplasma on grapevine in South Africa in 2006, a concerted effort by various research groups to identify the vector(s) was co-ordinated by Winetech. This included qualitative and quantitative surveys for two years of leaf-and planthoppers occurring in vineyards in affected areas, testing specimens of leaf-and planthopper species for the presence of aster yellows phytoplasma with PCR, transmission experiments, and relating presence of leaf-and planthoppers in the field to the time of disease transmission. Twenty-eight leaf-and planthopper species/species groups have been recorded from vineyards in aster yellows-infected regions. The four most abundant species/species groups were Acia lineatifrons (Naudé), Austroagallia spp., Cicadulina spp. and Mgenia fuscovaria (Stål) (Hemiptera: Cicadellidae). Austroagallia spp. and M. fuscovaria repeatedly tested positive for the presence of AY. Results of transmission experiments and a field trial to determine leaf-/planthopper abundance in vineyards along with time of transmission in the field suggest that M. fuscovaria is a vector of aster yellows phytoplasma in South Africa. The concerted effort between industry and researchers allowed for fast identification of a potential vector of aster yellows phytoplasma in South Africa

Developing fencing policies in dryland ecosystems

The daily energy requirements of animals are determined by a combination of physical and physiological factors, but food availability may challenge the capacity to meet nutritional needs. Western gorillas (Gorilla gorilla) are an interesting model for investigating this topic because they are folivore-frugivores that adjust their diet and activities to seasonal variation in fruit availability. Observations of one habituated group of western gorillas in Bai-Hokou, Central African Republic (December 2004-December 2005) were used to examine seasonal variation in diet quality and nutritional intake. We tested if during the high fruit season the food consumed by western gorillas was higher in quality (higher in energy, sugar, fat but lower in fibre and antifeedants) than during the low fruit season. Food consumed during the high fruit season was higher in digestible energy, but not any other macronutrients. Second, we investigated whether the gorillas increased their daily intake of carbohydrates, metabolizable energy (KCal/g OM), or other nutrients during the high fruit season. Intake of dry matter, fibers, fat, protein and the majority of minerals and phenols decreased with increased frugivory and there was some indication of seasonal variation in intake of energy (KCal/g OM), tannins, protein/fiber ratio, and iron. Intake of non-structural carbohydrates and sugars was not influenced by fruit availability. Gorillas are probably able to extract large quantities of energy via fermentation since they rely on proteinaceous leaves during the low fruit season. Macronutrients and micronutrients, but not digestible energy, may be limited for them during times of low fruit availability because they are hind-gut fermenters. We discuss the advantages of seasonal frugivores having large dietary breath and flexibility, significant characteristics to consider in the conservation strategies of endangered species

MIKE-SHE integrated groundwater and surface water model used to simulate scenario hydrology for input to DRIFT-ARID: the Mokolo River case study

A fully integrated, physically-based MIKE SHE/MIKE11 model was developed for the Mokolo River basin flow system to simulate key hydraulic and hydrologic indicator inputs to the Downstream Response to Imposed Flow Transformation for Arid Rivers (DRIFT-ARID) decision support system (DSS). The DRIFT-ARID tool is used in this study to define environmental water requirements (EWR) for non-perennial river flow systems in South Africa to facilitate ecosystembased management of water resources as required by the National Water Act (Act No. 36 of 1998). Fifty years of distributed daily climate data (1950 to 2000) were used to calibrate the model against decades of daily discharge data at various gauges, measurements of Mokolo Dam stage levels, and one-time groundwater level measurements at hundreds of wells throughout the basin. Though the calibrated model captures much of the seasonal and post-event stream discharge response characteristics, lack of sub-daily climate and stream discharge data limits the ability to calibrate the model to event-level system response (i.e. peak flows). In addition, lack of basic subsurface hydrogeologic characterisation and transient groundwater level data limits the ability to calibrate the groundwater flow model, and therefore baseflow response, to a high level. Despite these limitations, the calibrated model was used to simulate changes in hydrologic and hydraulic indicators at five study sites within the basin for five 50-year land-use change scenarios, including a present-day (with dam), natural conditions (no development/irrigation), and conversion of present-day irrigation to game farm, mine/city expansion, and a combination of the last two. Challenges and recommendations for simulating the range of non-perennial systems are presented.Keywords: hydrology, non-perennial, MIKE SHE, integrated surface and groundwater modellin

DRIFT-ARID: A method for assessing environmental water requirements (EWRs) for non-perennial rivers

Environmental water requirement (EWR) assessment methods, for ascertaining how much water should be retained in rivers to sustain ecological functioning and desired levels of biodiversity, have mostly been developed for perennial rivers. Despite non-perennial rivers comprising about 30–50% of the world’s freshwater systems, data on their hydrology, biota and ecological functioning are sparse. Current EWR assessments require hydrological and other data that may not be available for such rivers and some adaptation in the methods used seems necessary. DRIFT is an EWR method for perennial (or near-perennial) rivers that has been developed in South Africa over the past two decades and is now widely applied nationally and internationally. When applied to the semi-permanent Mokolo River, challenges particular to, or accentuated by, non-perennial rivers included the reliable simulation of hydrological data, the extent of acceptable extrapolation of data, difficulties in predicting surface-water connectivity along the river, and the location and resilience of pools, as well as whether it was possible to identify a reference (natural) condition. DRIFT-ARID, reported on here, is an adaptation of the DRIFT approach to begin addressing these and other issues. It consists of 11 phases containing 29 activities.Keywords: EWR, non-perennial, DRIFT, DS

450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy

Background: Epigenetic modifications, such as DNA methylation, due to in utero exposures may play a critical role in early programming for childhood and adult illness. Maternal smoking is a major risk factor for multiple adverse health outcomes in children, but the underlying mechanisms are unclear. Objective: We investigated epigenome-wide methylation in cord blood of newborns in relation to maternal smoking during pregnancy. Methods: We examined maternal plasma cotinine (an objective biomarker of smoking) measured during pregnancy in relation to DNA methylation at 473, 844 CpG sites (CpGs) in 1, 062 newborn cord blood samples from the Norwegian Mother and Child Cohort Study (MoBa) using the Infinium HumanMethylation450 BeadChip (450K). Results: We found differential DNA methylation at epigenome-wide statistical significance (p-value < 1.06 × 10–7) for 26 CpGs mapped to 10 genes. We replicated findings for CpGs in AHRR, CYP1A1, and GFI1 at strict Bonferroni-corrected statistical significance in a U.S. birth cohort. AHRR and CYP1A1 play a key role in the aryl hydrocarbon receptor signaling pathway, which mediates the detoxification of the components of tobacco smoke. GFI1 is involved in diverse developmental processes but has not previously been implicated in responses to tobacco smoke. Conclusions: We identified a set of genes with methylation changes present at birth in children whose mothers smoked during pregnancy. This is the first study of differential methylation across the genome in relation to maternal smoking during pregnancy using the 450K platform. Our findings implicate epigenetic mechanisms in the pathogenesis of the adverse health outcomes associated with this important in utero exposure.publishedVersio

Holographic hierarchy in the Gaussian matrix model via the fuzzy sphere

81 pages, 33 figuresS.R. is supported by STFC Grant ST/J000469/1, String theory, gauge theory, and duality

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe