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

Determination and manipulation of the ploidy level of purple Asparagus officinalis L.

This thesis reports on the examination of purple asparagus (Asparagus officinalis L.). Purple asparagus is a novel asparagus genotype which originated in countryside around the Northern Italian town of Albenga, and was thus named Violetto d'Albenga. Selections from this population were termed Violet of Albenga. The original population segregated for colour from a normal green through to a deep purple/burgundy colour. Selections for deeper colour tones has led to the selection from and breeding of two cultivars, Purple Passion and Pacific Purple. Observations of purple asparagus had indicated that it was larger than green asparagus. Quantitative measurements of purple asparagus and green asparagus were made and compared. From this investigation it was found that purple asparagus was significantly larger than green asparagus. Previously published observations of the size of the nuclei of purple asparagus indicate that they are larger than green asparagus nuclei, indicating that an increase in the amount of DNA in purple asparagus cells had occurred. This hypothesis was firstly tested by the examination of asparagus nuclei by flow cytometry. The results form this investigation showed that purple asparagus nuclei contained a DNA content similar to that of a standard tetraploid green asparagus. Further investigation via conventional chromosome counting confirmed that purple asparagus was a tetraploid with 2n=40 chromosomes. Purple asparagus contains a number of traits that would be highly desirable to be transferred to diploid populations. The most desirable of these traits is the increased sweetness. Attempts to cross purple with regular green diploid asparagus have been unsuccessful, although the reasons for this are not clear but it may be due to the differing ploidy levels. In theory the production of a purple asparagus haploid could allow green and purple asparagus to be crossed. In this thesis haploid plants were produced via the screening of 113130 purple asparagus seedlings for the production of spontaneous haploid in the form of twin seedlings. The separation of these twin seedlings provided 15 putative haploid of which 4 were found to be haploids (2n=20). Unfortunately none of the haploids produced flowered during the course of this research and it was not possible to attempt crosses with green asparagus plants. To further understand the nature of tetraploid purple asparagus and the origin of its polyploid level an attempt was made to examine the segregation of molecular markers. It was hoped that an examination of the PCR products of RAPD and satellite sequences of parental tissue and progeny would provide sufficient information to determine whether purple asparagus is an allotetraploid or an autotetraploid. Unfortunately time constraints meant that this objective was not achieved. The results and findings from this research has conclusively proved that purple asparagus is a tetraploid and that it is significantly larger than green asparagus. Furthermore it is possible to produce a haploid of purple asparagus

The Challenges of Analysing Highly Diverse Picobirnavirus Sequence Data

The reliable identification and classification of infectious diseases is critical for understanding their biology and controlling their impact. Recent advances in sequencing technology have allowed insight into the remarkable diversity of the virosphere, of which a large component remains undiscovered. For these emerging or undescribed viruses, the process of classifying unknown sequences is heavily reliant on existing nucleotide sequence information in public databases. However, due to the enormous diversity of viruses, and past focus on the most prevalent and impactful virus types, databases are often incomplete. Picobirnaviridae is a dsRNA virus family with broad host and geographic range, but with relatively little sequence information in public databases. The family contains one genus, Picobirnavirus, which may be associated with gastric illness in humans and animals. Little further information is available due in part to difficulties in identification. Here, we investigate diversity both within the genus Picobirnavirus and among other dsRNA virus types using a combined phylogenetic and functional (protein structure homology-modelling) approach. Our results show that diversity within picobirnavirus exceeds that seen between many other dsRNA genera. Furthermore, we find that commonly used practices employed to classify picobirnavirus, such as analysis of short fragments and trimming of sequences, can influence phylogenetic conclusions. The degree of phylogenetic and functional divergence among picobirnavirus sequences in our study suggests an enormous undiscovered diversity, which contributes to the undescribed “viral dark matter„ component of metagenomic studies

Genomic Characterisation of Canis Familiaris Papillomavirus Type 24, a Novel Papillomavirus Associated with Extensive Pigmented Plaque Formation in a Pug Dog

Numerous large dark plaques developed over the ventrum, legs and head of a 9-year-old pug dog over a 4-year-period. Histology confirmed a diagnosis of viral pigmented plaque and a short section of a novel papillomavirus (PV) type was amplified using consensus PCR primers. Taking advantage of the circular nature of PV DNA, ‘outward facing’ PCR primers allowed amplification of the full sequence. As this is the 24th PV known to infect dogs, the novel PV was designated canine papillomavirus (CPV) type 24. The CPV24 genome contained putative coding regions for 5 early proteins and 2 late ones. The CPV24 open reading frame L1 showed the highest (78.2%) similarity to CPV4 and phylogenetic analysis showed that CPV24 clustered with CPV4 and CPV16 suggesting CPV24 is the third species 2 Chipapillomavirus type identified in dogs. This is the third report of extensive pigmented plaques covering a high proportion of the skin. Both previous cases were caused CPV4 and, considering the high genetic similarity between CPV4 and CP24, infection by these CPV types may predispose to more severe clinical disease. In addition, as plaques caused by CPV16 appear more likely to progress to neoplasia, the detection of a species 2 Chipapillomavirus within a pigmented plaque may indicate the potential for more severe disease

Biofilm-Forming Potential of Staphylococcus aureus Isolated from Clinical Mastitis Cases in New Zealand

Biofilm formation is of growing concern in human and animal health. However, it is still unclear how biofilms are related to mastitis infections in dairy cattle. In this study, a comparison between two tests for biofilm formation and the association between biofilm and the presence of genes associated with biofilm formation were investigated for 92 Staphylococcus aureus isolates from clinical mastitis cases. Congo red agar (CRA) and microtitre test assay (MTA) in vitro phenotypic tests were used to evaluate biofilm formation. The presence of icaA, icaD, and bap genes associated with biofilm formation was confirmed using the polymerase chain reaction. Results show that most of the S. aureus isolates, though not possessing one of the biofilm-forming genes, were able to produce biofilms. MTA was more frequently positive in identifying biofilm-forming isolates than CRA

One dog’s waste is another dog’s wealth : a pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome

Canine acute hemorrhagic diarrhea syndrome (AHDS) has been associated in some studies with Clostridioides perfringens overgrowth and toxin-mediated necrosis of the intestinal mucosa. We aimed to determine the effect of a single fecal microbiota transplantation (FMT) on clinical scores and fecal microbiomes of 1 and 7 dogs with AHDS from New Zealand and South Africa. We hypothesized that FMT would improve AHDS clinical scores and increase microbiota alpha-diversity and short-chain fatty acid (SCFA)-producing microbial communities’ abundances in dogs with AHDS after FMT. We sequenced the V3-V4 region of the 16S-rRNA gene in the feces of AHDS FMT-recipients and sham-treated control dogs, and their healthy donors at admission, discharge, and 30 days post-discharge. There were no significant differences in median AHDS clinical scores between FMT-recipients and sham-treated controls at admission or discharge (P = 0.22, P = 0.41). At admission, the Shannon diversity index (SDI) was lower in AHDS dogs than healthy donors (P = 0.002). The SDI did not change from admission to 30 days in sham-treated dogs yet increased in FMT-recipients from admission to discharge (P = 0.04) to levels not different than donors (P = 0.33) but significantly higher than sham-treated controls (P = 0.002). At 30 days, the SDI did not differ between FMT recipients, sham-treated controls, and donors (P = 0.88). Principal coordinate analysis of the Bray-Curtis index separated post-FMT and donor dogs from pre-FMT and sham-treated dogs (P = 0.009) because of increased SCFA-producing genera’s abundances after FMT. A single co-abundance subnetwork contained many of the same OTUs found to be differentially abundant in FMT-recipients, and the abundance of this module was increased in FMT-recipients at discharge and 30 days, compared to shamtreated controls. We conclude in this small pilot study FMT did not have any clinical benefit.http://www.plosone.orgpm2022Companion Animal Clinical Studie

RNAseq Analysis of Brown Adipose Tissue and Thyroid of Newborn Lambs Subjected to Short-Term Cold Exposure Reveals Signs of Early Whitening of Adipose Tissue

During the early postnatal period, lambs have the ability to thermoregulate body temperature via non-shivering thermogenesis through brown adipose tissue (BAT), which soon after birth begins to transform into white adipose tissue. An RNA seq approach was used to characterize the transcriptome of BAT and thyroid tissue in newborn lambs exposed to cold conditions. Fifteen newborn Romney lambs were selected and divided into three groups: group 1 (n = 3) was a control, and groups 2 and 3 (n = 6 each) were kept indoors for two days at an ambient temperature (20–22 °C) or at a cold temperature (4 °C), respectively. Sequencing was performed using a paired-end strategy through the BGISEQ-500 platform, followed by the identification of differentially expressed genes using DESeq2 and an enrichment analysis by g:Profiler. This study provides an in-depth expression network of the main characters involved in the thermogenesis and fat-whitening mechanisms that take place in the newborn lamb. Data revealed no significant differential expression of key thermogenic factors such as uncoupling protein 1, suggesting that the heat production peak under cold exposure might occur so rapidly and in such an immediate way that it may seem undetectable in BAT by day three of life. Moreover, these changes in expression might indicate the start of the whitening process of the adipose tissue, concluding the non-shivering thermogenesis period

One dog's waste is another dog's wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome.

Canine acute hemorrhagic diarrhea syndrome (AHDS) has been associated in some studies with Clostridioides perfringens overgrowth and toxin-mediated necrosis of the intestinal mucosa. We aimed to determine the effect of a single fecal microbiota transplantation (FMT) on clinical scores and fecal microbiomes of 1 and 7 dogs with AHDS from New Zealand and South Africa. We hypothesized that FMT would improve AHDS clinical scores and increase microbiota alpha-diversity and short-chain fatty acid (SCFA)-producing microbial communities' abundances in dogs with AHDS after FMT. We sequenced the V3-V4 region of the 16S-rRNA gene in the feces of AHDS FMT-recipients and sham-treated control dogs, and their healthy donors at admission, discharge, and 30 days post-discharge. There were no significant differences in median AHDS clinical scores between FMT-recipients and sham-treated controls at admission or discharge (P = 0.22, P = 0.41). At admission, the Shannon diversity index (SDI) was lower in AHDS dogs than healthy donors (P = 0.002). The SDI did not change from admission to 30 days in sham-treated dogs yet increased in FMT-recipients from admission to discharge (P = 0.04) to levels not different than donors (P = 0.33) but significantly higher than sham-treated controls (P = 0.002). At 30 days, the SDI did not differ between FMT recipients, sham-treated controls, and donors (P = 0.88). Principal coordinate analysis of the Bray-Curtis index separated post-FMT and donor dogs from pre-FMT and sham-treated dogs (P = 0.009) because of increased SCFA-producing genera's abundances after FMT. A single co-abundance subnetwork contained many of the same OTUs found to be differentially abundant in FMT-recipients, and the abundance of this module was increased in FMT-recipients at discharge and 30 days, compared to sham-treated controls. We conclude in this small pilot study FMT did not have any clinical benefit. A single FMT procedure has the potential to increase bacterial communities of SCFA-producing genera important for intestinal health up to 30 days post-FMT

Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic Biomass Crop

Prairie cordgrass (Spartina pectinata Bosc ex Link) is being developed as a cellulosic biomass crop. Development of this species will require numerous steps, including breeding, agronomy, and characterization of the species genome. The research in this paper describes the first investigation of the transcriptome of prairie cordgrass via Next Generation Sequencing Technology, 454 GS FLX. A total of 556,198 expressed sequence tags (ESTs) were produced from four prairie cordgrass tissues: roots, rhizomes, immature inflorescence, and hooks. These ESTs were assembled into 26,302 contigs and 71,103 singletons. From these data were identified, EST–SSR (simple sequence repeat) regions and cell wall biosynthetic pathway genes suitable for the development of molecular markers which can aid the breeding process of prairie cordgrass by means of marker assisted selection