A comparative study into the effects of venous and arterial blood on clot microstructure in critically unwell patients. Assessment of the diagnostic potential of a biomarker of haemostasis.

Blood for coagulation analysis can be sampled from the arterial or venous system in intensive care units (ICU). The determination of clot microstructure and strength by fractal analysis (df) gives valuable information in a range of vascular haemostatic disease and sepsis. We aimed to determine if df could be measured equally and comparatively in arterial or venous blood, and 45 critically ill patients in an ICU were recruited. df was found to be readily measured in arterial blood with results comparable to those in venous blood and that add value of df as a potential marker of haemostasis in these patients.

From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes.

Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for genetic, genomic, and phenotypic data that result from research using D. rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity.

Natural Mycoplasma Infection Reduces Expression of Pro-Inflammatory Cytokines in Response to Ovine Footrot Pathogens.

Ovine footrot is a complex multifactorial infectious disease, causing lameness in sheep with major welfare and economic consequences. Dichelobacter nodosus is the main causative bacterium; however, footrot is a polymicrobial disease with Fusobacterium necrophorum, Mycoplasma fermentans and Porphyromonas asaccharolytica also associated. There is limited understanding of the host response involved. The proinflammatory mediators, interleukin (IL)-1ß and C-X-C Motif Chemokine Ligand 8 (CXCL8), have been shown to play a role in the early response to D. nodosus in dermal fibroblasts and interdigital skin explant models. To further understand the response of ovine skin to bacterial stimulation, and to build an understanding of the role of the cytokines and chemokines identified, primary ovine interdigital fibroblasts and keratinocytes were isolated, cultured and stimulated. The expression of mRNA and protein release of CXCL8 and IL-1ß were measured after stimulation with LPS, D. nodosus or F. necrophorum, which resulted in increased transcript levels of IL-1ß and CXCL8 in the M. fermentans-free cells. However, only an increase in the CXCL8 protein release was observed. No IL-1ß protein release was detected, despite increases in IL-1ß mRNA, suggesting the signal for intracellular pre-IL-1ß processing may be lacking when culturing primary cells in isolation. The keratinocytes and fibroblasts naturally infected with M. fermentans showed little response to the LPS, a range of D. nodosus preparations or heat-inactivated F. necrophorum. Primary single cell culture models complement ex vivo organ culture models to study different aspects of the host response to D. nodosus. The ovine keratinocytes and fibroblasts infected with M. fermentans had a reduced response to the experimental bacterial stimulation. However, in the case of footrot where Mycoplasma spp. are associated with diseased feet, this natural infection gives important insights into the impact of multiple pathogens on the host response.

The effects of combined action observation and motor imagery on corticospinal excitability and movement outcomes: Two meta-analyses.

Motor simulation interventions involving motor imagery (MI) and action observation (AO) have received considerable interest in the behavioral sciences. A growing body of research has focused on using AO and MI simultaneously, termed 'combined action observation and motor imagery' (AOMI). The current paper includes two meta-analyses that quantify changes in corticospinal excitability and motor skill performance for AOMI compared to AO, MI and control conditions. Specifically, the first meta-analysis collated and synthesized existing motor evoked potential (MEP) amplitude data from transcranial magnetic stimulation studies and the second meta-analysis collated and synthesized existing movement outcome data from behavioral studies. AOMI had a positive effect compared to control and AO but not MI conditions for both MEP amplitudes and movement outcomes. No methodological factors moderated the effects of AOMI, indicating a robust effect of AOMI across the two outcome variables. The results of the meta-analyses are discussed in relation to existing literature on motor simulation and skill acquisition, before providing viable directions for future research on this topic.

Palmar/plantar oblique projections improve radiographic detection of fractures of the palmar/plantar processes of the equine distal phalanx.

Radiography is a standard diagnostic test for horses with suspected fractures of the palmar/plantar processes (PP) of the distal phalanx, however published studies evaluating the diagnostic utility for radiography are currently lacking. The objectives of this retrospective, diagnostic case-control study were to determine the sensitivity of radiographs for the detection of PP fractures, and determine the diagnostic utility of the palmar/plantar oblique projections of the PP for the identification of PP fractures compared to standard radiographic series. The medical records of horses undergoing MRI examination were reviewed and 23 horses diagnosed with a PP fracture were included as cases for analysis. Forty-six control horses were selected. Radiographs, including palmar/plantar oblique (palmaro/plantaro50o -proximal 45o -medial(lateral)-dorsodistolateral (medial) oblique (PPrM(L)-DDiL(M)O) projections, and MRI images were assessed independently for the presence or absence of PP fractures and the sensitivity and specificity of radiographs for their detection were calculated, using MRI as the gold-standard. A second, blinded, radiographic evaluation excluding the palmar/plantar oblique views was performed. Twenty-seven PP fractures were identified in the 23 case horses on MRI examination. Twenty-two fractures were identified in 20/23 horses on examination of the full radiographic series (sensitivity and specificity of 81.5% and 100% respectively). Fractures were most frequently identified on the palmar/plantar oblique projections (19/22 fractures), followed by the lateromedial projection. Radiographic assessment excluding the palmar/plantar oblique projections identified 18 PP fractures in 16/23 horses. Careful assessment of a standard radiographic series of the foot will allow identification of PP fractures but palmar/plantar oblique projections will improve the detection of these fractures.

Zebrafish information network, the knowledgebase for Danio rerio research.

The Zebrafish Information Network (zfin.org) is the central repository for Danio rerio genetic and genomic data. The Zebrafish Information Network has served the zebrafish research community since 1994, expertly curating, integrating, and displaying zebrafish data. Key data types available at the Zebrafish Information Network include, but are not limited to, genes, alleles, human disease models, gene expression, phenotype, and gene function. The Zebrafish Information Network makes zebrafish research data Findable, Accessible, Interoperable, and Reusable through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. Recently, the Zebrafish Information Network and 6 other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of model organisms to understand the genetic and genomic basis of human biology and disease. Here, we provide an overview of the data available at the Zebrafish Information Network including recent updates to the gene page to provide access to single-cell RNA sequencing data, links to Alliance web pages, ribbon diagrams to summarize the biological systems and Gene Ontology terms that have annotations, and data integration with the Alliance of Genome Resources.

A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions.

Footrot is a polymicrobial infectious disease in sheep causing severe lameness, leading to one of the industry's largest welfare problems. The complex etiology of footrot makes in situ or in vitro investigations difficult. Computational methods offer a solution to understanding the bacteria involved and how they may interact with the host, ultimately providing a way to identify targets for future hypothesis-driven investigative work. Here, we present the first combined global analysis of bacterial community transcripts together with the host immune response in healthy and diseased ovine feet during a natural polymicrobial infection state using metatranscriptomics. The intratissue and surface bacterial populations and the most abundant bacterial transcriptomes were analyzed, demonstrating that footrot-affected skin has reduced diversity and increased abundances of not only the causative bacterium Dichelobacter nodosus but also other species such as Mycoplasma fermentans and Porphyromonas asaccharolytica. Host transcriptomics reveals the suppression of biological processes related to skin barrier function, vascular functions, and immunosurveillance in unhealthy interdigital skin, supported by histological findings that type I collagen (associated with scar tissue formation) is significantly increased in footrot-affected interdigital skin compared to outwardly healthy skin. Finally, we provide some interesting indications of host and pathogen interactions associated with virulence genes and the host spliceosome, which could lead to the identification of future therapeutic targets.

Progressive hyperthermia elicits distinct responses in maximum and rapid torque production.

OBJECTIVES: To investigate the effect of progressive whole-body hyperthermia on maximal, and rapid voluntary torque production, and their neuromuscular determinants. DESIGN: Repeated measures, randomised. METHODS: Nine participants performed sets of neuromuscular assessments in HOT conditions (∼50°C, ∼35% relative humidity) at rectal temperatures (Tre) of 37, 38.5 and 39.5°C and in CON conditions (∼22°C, ∼35% relative humidity) at a Tre of ∼37°C and pre-determined comparative time-points. Electrically evoked twitch (single impulse) and octet (8 impulses at 300Hz) responses were measured at rest. Maximum voluntary torque (MVT), surface electromyography (EMG) normalised to maximal M-wave, and voluntary activation (VA) were measured during 3-5s isometric maximal voluntary contractions. Rate of torque development (RTD) and normalised EMG were measured during rapid voluntary isometric contractions from rest. RESULTS: All neuromuscular variables were unaffected by time in CON. In HOT, MVT, normalised EMG at MVT and VA were lower at 39.5°C compared to 37°C (p<0.05). Early- (0-50ms) and middle- (50-100ms) phase voluntary RTD were unaffected by increased Tre (p>0.05), despite lower normalised EMG at Tre 39.5°C (p<0.05) in rapid contractions. In contrast, late-phase (100-150ms) voluntary RTD was lower at 38.5°C and 39.5°C compared to 37°C (p<0.05) in HOT. Evoked twitch and octet RTD increased with increased Tre (p<0.05). CONCLUSIONS: Hyperthermia reduced late-phase voluntary RTD, likely due to reduced neural drive and the reduction in MVT. In contrast, early- and middle-phase voluntary RTD were unaffected by hyperthermia, likely due to the conflicting effects of reduced neural drive but faster intrinsic contractile properties.

Cholinesterase inhibitors for vascular dementia and other vascular cognitive impairments: a network meta-analysis.

BACKGROUND: Vascular cognitive impairment (VCI) describes a broad spectrum of cognitive impairments caused by cerebrovascular disease, ranging from mild cognitive impairment to dementia. There are currently no pharmacological treatments recommended for improving either cognition or function in people with VCI. Three cholinesterase inhibitors (donepezil, galantamine, and rivastigmine) are licenced for the treatment of dementia due to Alzheimer's disease. They are thought to work by compensating for reduced cholinergic neurotransmission, which is also a feature of VCI. Through pairwise comparisons with placebo and a network meta-analysis, we sought to determine whether these medications are effective in VCI and whether there are differences between them with regard to efficacy or adverse events. OBJECTIVES: (1) To assess the efficacy and safety of cholinesterase inhibitors in the treatment of adults with vascular dementia and other VCI. (2) To compare the effects of different cholinesterase inhibitors on cognition and adverse events, using network meta-analysis. SEARCH METHODS: We searched ALOIS, the Cochrane Dementia and Cognitive Improvement Group's register, MEDLINE (OvidSP), Embase (OvidSP), PsycINFO (OvidSP), CINAHL (EBSCOhost), Web of Science Core Collection (ISI Web of Science), LILACS (BIREME), ClinicalTrials.gov, and the World Health Organization International Clinical Trials Registry Platform on 19 August 2020. SELECTION CRITERIA: We included randomised controlled trials in which donepezil, galantamine, or rivastigmine was compared with placebo or in which the drugs were compared with each other in adults with vascular dementia or other VCI (excluding cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL)). We included all drug doses and routes of administration. DATA COLLECTION AND ANALYSIS: Two review authors independently identified eligible trials, extracted data, assessed risk of bias, and applied the GRADE approach to assess the certainty of the evidence. The primary outcomes were cognition, clinical global impression, function (performance of activities of daily living), and adverse events. Secondary outcomes were serious adverse events, incidence of development of new dementia, behavioural disturbance, carer burden, institutionalisation, quality of life and death. For the pairwise analyses, we pooled outcome data at similar time points using random-effects methods. We also performed a network meta-analysis using Bayesian methods. MAIN RESULTS: We included eight trials (4373 participants) in the review. Three trials studied donepezil 5 mg or 10 mg daily (n= 2193); three trials studied rivastigmine at a maximum daily dose of 3 to 12 mg (n= 800); and two trials studied galantamine at a maximum daily dose of 16 to 24 mg (n= 1380). The trials included participants with possible or probable vascular dementia or cognitive impairment following stroke. Mean ages were between 72.2 and 73.9 years. All of the trials were at low or unclear risk of bias in all domains, and the evidence ranged from very low to high level of certainty. For cognition, the results showed that donepezil 5 mg improves cognition slightly, although the size of the effect is unlikely to be clinically important (mean difference (MD) -0.92 Alzheimer's Disease Assessment Scale-Cognitive Subscale (ADAS-Cog) points (range 0 to 70), 95% confidence interval (CI) -1.44 to -0.40; high-certainty evidence). Donepezil 10 mg (MD -2.21 ADAS-Cog points, 95% CI -3.07 to -1.35; moderate-certainty evidence) and galantamine 16 to 24 mg (MD -2.01 ADAS-Cog point, 95%CI -3.18 to -0.85; moderate-certainty evidence) probably also improve cognition, although the larger effect estimates still may not be clinically important. With low certainty, there may be little to no effect of rivastigmine 3 to 12 mg daily on cognition (MD 0.03 ADAS-Cog points, 95% CI -3.04 to 3.10; low-certainty evidence). Adverse events reported in the studies included nausea and/or vomiting, diarrhoea, dizziness, headache, and hypertension. The results showed that there was probably little to no difference between donepezil 5 mg and placebo in the number of adverse events (odds ratio (OR) 1.22, 95% CI 0.94 to 1.58; moderate-certainty evidence), but there were slightly more adverse events with donepezil 10 mg than with placebo (OR 1.95, 95% CI 1.20 to 3.15; high-certainty evidence). The effect of rivastigmine 3 to 12 mg on adverse events was very uncertain (OR 3.21, 95% CI 0.36 to 28.88; very low-certainty evidence). Galantamine 16 to 24 mg is probably associated with a slight excess of adverse events over placebo (OR 1.57, 95% CI 1.02 to 2.43; moderate-certainty evidence). In the network meta-analysis (NMA), we included cognition to represent benefit, and adverse events to represent harm. All drugs ranked above placebo for cognition and below placebo for adverse events. We found donepezil 10 mg to rank first in terms of benefit, but third in terms of harms, when considering the network estimates and quality of evidence. Galantamine was ranked second in terms of both benefit and harm. Rivastigmine had the lowest ranking of the cholinesterase inhibitors in both benefit and harm NMA estimates, but this may reflect possibly inadequate doses received by some trial participants and small trial sample sizes. AUTHORS' CONCLUSIONS: We found moderate- to high-certainty evidence that donepezil 5 mg, donepezil 10 mg, and galantamine have a slight beneficial effect on cognition in people with VCI, although the size of the change is unlikely to be clinically important. Donepezil 10 mg and galantamine 16 to 24 mg are probably associated with more adverse events than placebo. The evidence for rivastigmine was less certain. The data suggest that donepezil 10 mg has the greatest effect on cognition, but at the cost of adverse effects. The effect is modest, but in the absence of any other treatments, people living with VCI may still wish to consider the use of these agents. Further research into rivastigmine is needed, including the use of transdermal patches.

The Zebrafish Information Network: major gene page and home page updates.

The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, gene and mutant nomenclature, and reagents. New features at ZFIN include major updates to the home page and the gene page, the two most used pages at ZFIN. Data including disease models, phenotypes, expression, mutants and gene function continue to be contributed to The Alliance of Genome Resources for integration with similar data from other model organisms.

Equine nutrition in the post-operative colic: Survey of Diplomates of the American Colleges of Veterinary Internal Medicine and Veterinary Surgeons, and European Colleges of Equine Internal Medicine and Veterinary Surgeons.

BACKGROUND: Evidence is lacking concerning re-introduction of feed and water following colic surgery. OBJECTIVES: To describe current approaches of European and American specialists to re-introduction of feed and water in adult horses following surgical treatment of common intestinal lesions, assuming an uncomplicated recovery. STUDY DESIGN: Cross-sectional survey. METHODS: Electronic invitations, with a link to the online survey, were sent to 1,430 large animal specialists, including Diplomates of the ECVS, ACVS, ECEIM and ACVIM colleges. RESULTS: The response rate was 12.6% including partial respondent data. Responses for each multiple-choice question were between 123 and 178. Results are expressed as the percentage of the total number of responses and as a range where specific lesions are grouped together. Respondents reported that horses with large intestinal displacements were offered free choice water (63%-65%) within 3 hours (55%-63%), whereas horses with a small intestinal strangulating lesion were offered < 2 L water (64%-74%) 12-24 hours (28%-34%) post-operatively. Horses with a large colon displacement were offered feed within 3 hours of surgery (16%) with the majority offered feed 6-12 hours (35%-36%) post-operatively. Horses with small intestinal strangulating lesions and small colon lesions were offered feed 24-48 hours (34%-42%) after surgery. Following small intestinal, small colon or caecal lesions, horses were re-introduced feed in handfuls (79%-93%) and initially with grass (41%-54%). Horses with large colon displacements were mostly fed handfuls (49%-50%) of forage initially, but a number of respondents would offer larger quantities such as a small bucket (35%-37%) and predominantly of hay (50%-51%). MAIN LIMITATIONS: Low response rate. This study did not take into account common post-operative complications that may alter the clinical approach. CONCLUSIONS: This post-operative colic nutrition survey is the first to describe current clinical practice. Further research is required to investigate nutritional strategies in post-operative colic cases.

Association Between Administration of Antacid Medication and Anastomotic Stricture Formation After Repair of Esophageal Atresia.

BACKGROUND: Anastomotic stricture is a significant cause of morbidity after repair of esophageal atresia (EA). Exposure to gastric acid has been postulated to contribute to stricture development and severity leading to prophylactic antacid use by some surgeons. We investigated the association between administration of antacid medication and the development of anastomotic strictures. METHODS: Retrospective case-note review of consecutive infants undergoing repair of EA with distal tracheoesophageal fistula (type C) between January 1994 and December 2014. Only infants who underwent primary esophageal anastomosis at initial surgical procedure were included. Stricture-related outcomes were compared initially for infants who received prophylactic antacid medication (PAAM) versus no prophylaxis, and the role of PAAM in stricture prevention was explored in a multivariate model. Outcomes were also compared for infants grouped by antacid use at any stage. RESULTS: One hundred fourteen infants were included. Sixteen infants received PAAM at surgeon preference. Of the remaining 98 infants, 44 subsequently received antacid as treatment for gastroesophageal reflux (GER) and 54 never received antacid medication. There was no statistically significant association between incidence of stricture in the first year (10 of 16 versus 41 of 98; P = 0.18) nor time to first stricture (median, 57 d [41-268] versus 102 d [43-320]; P = 0.89) and administration of PAAM. Similarly, there were no statistically significant associations between incidence of stricture, age at first stricture and number of dilatations, and administration of antacid medication either as prophylaxis nor when given as treatment for symptoms or signs of GER. CONCLUSIONS: These data do not support the hypothesis that PAAM reduces the incidence or severity of anastomotic stricture after repair of EA. Treatment with antacids may be best reserved for those with symptoms or signs of GER. Further prospective investigation of the role of antacid prophylaxis on stricture formation after EA repair is warranted.

Automated generation of gene summaries at the Alliance of Genome Resources.

Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult for knowledgebases to sustain. We developed an algorithm that uses curated, structured gene data at the Alliance of Genome Resources (Alliance; www.alliancegenome.org) to automatically generate gene summaries that simulate natural language. The gene data used for this purpose include curated associations (annotations) to ontology terms from the Gene Ontology, Disease Ontology, model organism knowledgebase (MOK)-specific anatomy ontologies and Alliance orthology data. The method uses sentence templates for each data category included in the gene summary in order to build a natural language sentence from the list of terms associated with each gene. To improve readability of the summaries when numerous gene annotations are present, we developed a new algorithm that traverses ontology graphs in order to group terms by their common ancestors. The algorithm optimizes the coverage of the initial set of terms and limits the length of the final summary, using measures of information content of each ontology term as a criterion for inclusion in the summary. The automated gene summaries are generated with each Alliance release, ensuring that they reflect current data at the Alliance. Our method effectively leverages category-specific curation efforts of the Alliance member databases to create modular, structured and standardized gene summaries for seven member species of the Alliance. These automatically generated gene summaries make cross-species gene function comparisons tenable and increase discoverability of potential models of human disease. In addition to being displayed on Alliance gene pages, these summaries are also included on several MOK gene pages.

Defining a role for lung function associated gene GSTCD in cell homeostasis.

Genome wide association (GWA) studies have reproducibly identified signals on chromosome 4q24 associated with lung function and COPD. GSTCD (Glutathione S-transferase C-terminal domain containing) represents a candidate causal gene in this locus, however little is currently known about the function of this protein. We set out to further our understanding of the role of GSTCD in cell functions and homeostasis using multiple molecular and cellular approaches in airway relevant cells. Recombinant expression of human GSTCD in conjunction with a GST activity assay did not identify any enzymatic activity for two GSTCD isoforms questioning the assignment of this protein to this family of enzymes. Protein structure analyses identified a potential methyltransferase domain contained within GSTCD, with these enzymes linked to cell viability and apoptosis. Targeted knockdown (siRNA) of GSTCD in bronchial epithelial cells identified a role for GSTCD in cell viability as proliferation rates were not altered. To provide greater insight we completed transcriptomic analyses on cells with GSTCD expression knocked down and identified several differentially expressed genes including those implicated in airway biology; fibrosis e.g. TGFBR1 and inflammation e.g. IL6R. Pathway based transcriptomic analyses identified an over-representation of genes related to adipogenesis which may suggest additional functions for GSTCD. These findings identify potential additional functions for GSTCD in the context of airway biology beyond the hypothesised GST activity and warrant further investigation.

The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources.

The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagents. New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more expressive Gene Ontology annotations. ZFIN has recently taken over maintenance of the zebrafish reference genome sequence as part of the Genome Reference Consortium. ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO). The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research.

Using ZFIN: Data Types, Organization, and Retrieval.

The Zebrafish Model Organism Database (ZFIN; zfin.org) was established in 1994 as the primary genetic and genomic resource for the zebrafish research community. Some of the earliest records in ZFIN were for people and laboratories. Since that time, services and data types provided by ZFIN have grown considerably. Today, ZFIN provides the official nomenclature for zebrafish genes, mutants, and transgenics and curates many data types including gene expression, phenotypes, Gene Ontology, models of human disease, orthology, knockdown reagents, transgenic constructs, and antibodies. Ontologies are used throughout ZFIN to structure these expertly curated data. An integrated genome browser provides genomic context for genes, transgenics, mutants, and knockdown reagents. ZFIN also supports a community wiki where the research community can post new antibody records and research protocols. Data in ZFIN are accessible via web pages, download files, and the ZebrafishMine (zebrafishmine.org), an installation of the InterMine data warehousing software. Searching for data at ZFIN utilizes both parameterized search forms and a single box search for searching or browsing data quickly. This chapter aims to describe the primary ZFIN data and services, and provide insight into how to use and interpret ZFIN searches, data, and web pages.

The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus.

Dichelobacter nodosus (D. nodosus) is the causative pathogen of ovine footrot, a disease that has a significant welfare and financial impact on the global sheep industry. Previous studies into the phylogenetics of D. nodosus have focused on Australia and Scandinavia, meaning the current diversity in the United Kingdom (U.K.) population and its relationship globally, is poorly understood. Numerous epidemiological methods are available for bacterial typing; however, few account for whole genome diversity or provide the opportunity for future application of new computational techniques. Multilocus sequence typing (MLST) measures nucleotide variations within several loci with slow accumulation of variation to enable the designation of allele numbers to determine a sequence type. The usage of whole genome sequence data enables the application of MLST, but also core and whole genome MLST for higher levels of strain discrimination with a negligible increase in experimental cost. An MLST database was developed alongside a seven loci scheme using publically available whole genome data from the sequence read archive. Sequence type designation and strain discrimination was compared to previously published data to ensure reproducibility. Multiple D. nodosus isolates from U.K. farms were directly compared to populations from other countries. The U.K. isolates define new clades within the global population of D. nodosus and predominantly consist of serogroups A, B and H, however serogroups C, D, E, and I were also found. The scheme is publically available at https://pubmlst.org/dnodosus/.

Predictors of post-traumatic stress disorder following critical illness: A mixed methods study.

PURPOSE: Post-traumatic stress disorder has been reported in survivors of critical illness. The aim of this study was to investigate the predictors of post-traumatic stress disorder in survivors of critical illness. MATERIALS AND METHODS: Patients attending the intensive care unit (ICU) follow-up clinic completed the UK-Post-Traumatic Stress Syndrome 14-Questions Inventory and data was collected from their medical records. Predictors investigated included age, gender, Apache II score, ICU length of stay, pre-illness psychopathology; delirium and benzodiazepine administration during ICU stay and delusional memories of the ICU stay following discharge. RESULTS: A total of 198 patients participated, with 54 (27%) patients suffering with post-traumatic stress disorder. On multivariable logistic regression, the significant predictors of post-traumatic stress disorder were younger age, lower Apache II score, pre-illness psychopathology and delirium during the ICU stay. CONCLUSIONS: The predictors of post-traumatic stress disorder in this study concur with previous research however a lower Apache II score has not been previously reported.

USP7 inhibition alters homologous recombination repair and targets CLL cells independently of ATM/p53 functional status.

The role of deubiquitylase ubiquitin-specific protease 7 (USP7) in the regulation of the p53-dependent DNA damage response (DDR) pathway is well established. Whereas previous studies have mostly focused on the mechanisms underlying how USP7 directly controls p53 stability, we recently showed that USP7 modulates the stability of the DNA damage responsive E3 ubiquitin ligase RAD18. This suggests that targeting USP7 may have therapeutic potential even in tumors with defective p53 or ibrutinib resistance. To test this hypothesis, we studied the effect of USP7 inhibition in chronic lymphocytic leukemia (CLL) where the ataxia telangiectasia mutated (ATM)-p53 pathway is inactivated with relatively high frequency, leading to treatment resistance and poor clinical outcome. We demonstrate that USP7 is upregulated in CLL cells, and its loss or inhibition disrupts homologous recombination repair (HRR). Consequently, USP7 inhibition induces significant tumor-cell killing independently of ATM and p53 through the accumulation of genotoxic levels of DNA damage. Moreover, USP7 inhibition sensitized p53-defective, chemotherapy-resistant CLL cells to clinically achievable doses of HRR-inducing chemotherapeutic agents in vitro and in vivo in a murine xenograft model. Together, these results identify USP7 as a promising therapeutic target for the treatment of hematological malignancies with DDR defects, where ATM/p53-dependent apoptosis is compromised.