<i>Salmonella</i> Enteritidis infection levels in spleen, liver and reproductive tract following challenge of vaccinated and naïve hens four days following intravenous challenge at varying ages through sexual development.

<p>Data are presented as median values with ranges based on five birds per group at each age and number positive for <i>Salmonella</i> out of total number challenged per group. Quantitation was not performed on pooled reproductive tract samples and are shown as <i>Salmonella</i> culture positive or negative following enrichment culture.</p>*<p>Positive only after enrichment.</p><p>ND = Not done.</p

Expression of Interleukin-4 (A) and Interleukin-6 (B) in the ovary.

<p>Data is expressed as 40-Ct values in ovarian tissue in comparison to expression in breast muscle tissue as a control for no expression (40-Ct = 0). RNA levels are normalised between tissues using 28S RNA expression. Data are shown as means based on expression levels of 5 birds at each time point (±SD).</p

Changes in cell populations in the chicken reproductive tract as determined by immunohistological examination.

<p>2A shows T lymphocyte populations in the infundibulum (upper oviduct), 2B in the magnum (mid oviduct) and 2Cthe ovary. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048195#pone-0048195-g002" target="_blank">Figure 2D</a> shows the changes in macrophage populations in the ovary and oviduct. Data are based on 10 fields of view for two sections of each tissue from each animal. Between five to seven birds were examined at each time point. Data are given as a mean (±SD).</p

Changes to CD4+ lymphocyte populations in the reproductive tract.

<p>At 102 days of age CD4+ populations are primarily organised into aggregates in the ovary (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048195#pone-0048195-g003" target="_blank">Figure 3A</a>) and oviduct. Birds lack lymph nodes and form more loose lymphoid structures. At 130 days (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048195#pone-0048195-g003" target="_blank">Figure 3B</a>) these structures are no longer found, with smaller populations of cells found throughout the ovary. At 165 days (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048195#pone-0048195-g003" target="_blank">Figure 3C</a>) CD4+ numbers increase slightly, but remain scattered throughout the tissue. Photomicrographs taken at a magnification of ×400.</p

Antibody responses in persistently infected cattle during pregnancy.

<p><i>N. caninum</i>-specific antibody responses were measured weekly in eight naturally, persistently infected cattle (n1–n8) during gestation. Results are expressed as percent positivity (PP) values which are calculated as a ratio of test optical density to the optical density of a high positive control <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015799#pone.0015799-Williams3" target="_blank">[36]</a>. A cut off value of 25PP was used to indicate an infected cow. All eight cows had positive values (>25PP) prior to artificial insemination. Antibody values were measured weekly as soon as pregnancy was confirmed at 6 weeks gestation. For each individual animal, antibody levels were considered to be rising when the PP value increased above the mean +95% confidence intervals calculated for the PP values for the first six serum samples taken (6–12 weeks gestation). Each cow was killed when the PP value increased to >50% higher than the mean (6–12 weeks) PP value. This ranged from two to five weeks from the time when an increase in PP value was first detected. The control represents the PP values for one uninfected sentinel cow, housed with the infected group.</p

Evidence that <i>N. caninum</i> infection was present in the foetuses and placentae of all eight cows following parasite recrudescence.

<p>Detection of parasites or parasite-associated necrosis in the placenta and foetal tissues of ten foetuses obtained from eight naturally persistently <i>N. caninum</i>-infected cattle killed two to five weeks after first detection of evidence indicating parasite recrudescence had occurred. All ten foetuses were alive when the dams were euthanized as shown by ultrasound scanning to detect foetal heartbeat. Tissues were obtained within one hour of death. For histology and immunohistology, 10 full-thickness pieces of placentome from each animal were collected and brain, heart, spinal column and liver were collected from the foetuses. Two cows were carrying twins thus ten foetuses were examined. No parasite DNA was detected by PCR in any placental tissue samples analysed.</p><p>*where two symbols are given this denotes a value for each twin.</p

Histology and immunohistology of foetal tissues after parasite recrudescence.

<p>Foetus after parasite recrudescence. A, B. Foetus from animal no. 2, 25 weeks of gestation, skeletal muscle. A. Focal interstitial mononuclear (lymphocytes, plasma cells, macrophages) infiltration is seen (arrow; non-suppurative myosistis). B. <i>Neospora</i> antigen is seen within an intact myocyte immediately adjacent to the inflammatory infiltrate (arrow). C, D. Foetus from animal 6, 32 weeks of gestation. C. Spinal cord, exhibiting a moderate, focal extensive non-suppurative myelitis, represented by focal parenchymal (arrows) and perivascular (arrowheads) mononuclear inflammatory infiltrates. D. Dorsal root, spinal cord. Severe non-suppurative (mononuclear) radioculoneuritis (arrows). Inset: Staining for Neospora antigen identifies small extracellular cluster of tachyzoites within the inflammatory infiltrate (arrow). A, C, D. Haematoxylin-eosin stain. B, Inset D. Peroxidase anti-peroxidase method. Papanicolaou's haematoxylin counterstain.</p

DataSheet_1_Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19.docx

BackgroundThe COVID-19 pandemic has created pressure on healthcare systems worldwide. Tools that can stratify individuals according to prognosis could allow for more efficient allocation of healthcare resources and thus improved patient outcomes. It is currently unclear if blood gene expression signatures derived from patients at the point of admission to hospital could provide useful prognostic information.MethodsGene expression of whole blood obtained at the point of admission from a cohort of 78 patients hospitalised with COVID-19 during the first wave was measured by high resolution RNA sequencing. Gene signatures predictive of admission to Intensive Care Unit were identified and tested using machine learning and topological data analysis, TopMD.ResultsThe best gene expression signature predictive of ICU admission was defined using topological data analysis with an accuracy: 0.72 and ROC AUC: 0.76. The gene signature was primarily based on differentially activated pathways controlling epidermal growth factor receptor (EGFR) presentation, Peroxisome proliferator-activated receptor alpha (PPAR-α) signalling and Transforming growth factor beta (TGF-β) signalling.ConclusionsGene expression signatures from blood taken at the point of admission to hospital predicted ICU admission of treatment naïve patients with COVID-19.</p