Medical Stress and Fear of Death and Dying in a Medical Patient Population.

We explored the relationship between medical illness-related stress and fear of death and dying in a population of individuals with self-reported medical illnesses. Medically ill participants identified their level of stress related to their medical condition, their level of fear of death and dying, and what treatments they would most prefer for addressing any fear of death and dying as well as their medical illness-related stress. Participants' medical illness-related stress levels were high with an average endorsed score of 7.23 out of 10 (most extreme stress). The majority (70%) of participants endorsed "some," "a little," or "no fear" of death and dying. Overall, reported medical illness-related stress was not significantly correlated with fear of death and dying. Seventy-five percent of participants reported preferring psychotherapy or mindfulness interventions for addressing their stress. Psychotherapy, anti-anxiety medications, and meditation were the top three choices for addressing fear of death and dying.

Genomic and proteomic characterization of two novel siphovirus infecting the sedentary facultative epibiont cyanobacterium Acaryochloris marina.

Acaryochloris marina is a symbiotic species of cyanobacteria that is capable of utilizing far-red light. We report the characterization of the phages A-HIS1 and A-HIS2, capable of infecting Acaryochloris. Morphological characterization of these phages places them in the family Siphoviridae. However, molecular characterization reveals that they do not show genetic similarity with any known siphoviruses. While the phages do show synteny between each other, the nucleotide identity between the phages is low at 45-67%, suggesting they diverged from each other some time ago. The greatest number of genes shared with another phage (a myovirus infecting marine Synechococcus) was four. Unlike most other cyanophages and in common with the Siphoviridae infecting Synechococcus, no photosynthesis-related genes were found in the genome. CRISPR (clustered regularly interspaced short palindromic repeats) spacers from the host Acaryochloris had partial matches to sequences found within the phages, which is the first time CRISPRs have been reported in a cyanobacterial/cyanophage system. The phages also encode a homologue of the proteobacterial RNase T. The potential function of RNase T in the mark-up or digestion of crRNA hints at a novel mechanism for evading the host CRISPR system.

Automatic text classification of drug-induced liver injury using document-term matrix and XGBoost.

Introduction: Regulatory agencies generate a vast amount of textual data in the review process. For example, drug labeling serves as a valuable resource for regulatory agencies, such as U.S. Food and Drug Administration (FDA) and Europe Medical Agency (EMA), to communicate drug safety and effectiveness information to healthcare professionals and patients. Drug labeling also serves as a resource for pharmacovigilance and drug safety research. Automated text classification would significantly improve the analysis of drug labeling documents and conserve reviewer resources. Methods: We utilized artificial intelligence in this study to classify drug-induced liver injury (DILI)-related content from drug labeling documents based on FDA's DILIrank dataset. We employed text mining and XGBoost models and utilized the Preferred Terms of Medical queries for adverse event standards to simplify the elimination of common words and phrases while retaining medical standard terms for FDA and EMA drug label datasets. Then, we constructed a document term matrix using weights computed by Term Frequency-Inverse Document Frequency (TF-IDF) for each included word/term/token. Results: The automatic text classification model exhibited robust performance in predicting DILI, achieving cross-validation AUC scores exceeding 0.90 for both drug labels from FDA and EMA and literature abstracts from the Critical Assessment of Massive Data Analysis (CAMDA). Discussion: Moreover, the text mining and XGBoost functions demonstrated in this study can be applied to other text processing and classification tasks.

Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.

DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated nonorthologous displacement. Here, we present an analysis of two full-length homologues of this gene, which were found in the genomes of two bacteriophages, which infect the chlorophyll-d containing cyanobacterium Acaryochloris marina. Phylogenetic analyses of these phage DNA polymerase γ proteins show that they branch deeply within the DNA polymerase γ clade and therefore share a common origin with their eukaryotic homologues. We also found homologues of these phage polymerases in the environmental Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) database, which fell in the same clade. An analysis of the CAMERA assemblies containing the environmental homologues together with the filter fraction metadata indicated some of these assemblies may be of bacterial origin. We also show that the phage-encoded DNA polymerase γ is highly transcribed as the phage genomes are replicated. These findings provide data that may assist in reconstructing the evolution of mitochondria.

Successful use of a benchtop fluorescent enzyme immunoassay analyzer to measure serum cortisol concentration as a screening test for hypoadrenocorticism in dogs.

OBJECTIVE: To assess the diagnostic performance of a benchtop fluorescent enzyme immunoassay analyzer (AIA-360; Tosoh Bioscience Inc) for the measurement of serum cortisol concentration as a screening test for hypoadrenocorticism in dogs. ANIMALS: 173 client-owned dogs (20 with hypoadrenocorticism and 153 with nonadrenal illness). PROCEDURES: Medical records of all dogs that underwent an ACTH stimulation test between June 2015 and October 2019 were reviewed retrospectively. Dogs were excluded if the ACTH stimulation test was performed on the basis of a suspicion of hypercortisolism, serum cortisol concentrations were measured using an analyzer other than the one assessed in the present study, or dogs had received medication known to affect the pituitary-adrenal axis in the 4 weeks1,2 preceding ACTH stimulation testing. The diagnostic performance of the benchtop analyzer was evaluated by calculating sensitivity, specificity, and likelihood ratios at various cutoff points. RESULTS: Serum resting cortisol cutoff point concentrations of 0.8 µg/dL (22 nmol/L), 1 µg/dL (28 nmol/L), and 2 µg/dL (55 nmol/L) had a sensitivity of 100%. An optimal serum resting cortisol cutoff point of 0.58 µg/dL (16 nmol/L) had a sensitivity, specificity, and positive and negative likelihood ratios of 100%, 97%, and 30.6 and 0.0, respectively. CLINICAL RELEVANCE: Findings indicated that previously derived cutoff points could be used with excellent sensitivity to exclude hypoadrenocorticism in this population of dogs when serum cortisol concentration was measured with the evaluated benchtop analyzer. An ACTH stimulation test may need to only be performed to diagnose hypoadrenocorticism if resting serum cortisol concentration is ≤ 0.58 µg/dL when measured with the evaluated benchtop analyzer.

Milder phenotypes of glucose transporter type 1 deficiency syndrome.

Glucose transporter type 1 deficiency syndrome (GLUT1DS) is a treatable condition resulting from impaired glucose transport into the brain. The classical presentation is with infantile-onset epilepsy and severe developmental delay. Non-classical phenotypes with movement disorders and early-onset absence epilepsy are increasingly recognized and the clinical spectrum is expanding. The hallmark is hypoglycorrhachia (cerebrospinal fluid [CSF] glucose<2.2 mmol/l) in the presence of normoglycaemia with a CSF/blood glucose ratio of less than 0.4. GLUT1DS is due to a mutation in the solute carrier family 2, member 1 gene (SLC2A1). We present five individuals (four males, one female), all of whom had a mild phenotype, highlighting the importance of considering this diagnosis in unexplained neurological disorders associated with mild learning difficulties, subtle motor delay, early-onset absence epilepsy, fluctuating gait disorders, and/or dystonia. The mean age at diagnosis was 8 years 8 months. This paper also shows phenotypical parallels between GLUT1DS and paroxysmal exertion-induced dyskinesia.

Detailed analysis of the microdiversity of Prochlorococcus populations along a north-south Atlantic ocean transect.

In order to understand how environmental factors shape the diversity of Prochlorococcus in the Atlantic Ocean, we have elucidated the microdiversity along a north-south transect. The polymerase chain reaction-restriction fragment length polymorphism analysis of the genetic diversity of rpoC1 gene fragments of Prochlorococcus at 12 sampling sites revealed a latitudinal pattern in Prochlorococcus RFLP-type diversity in the samples collected from two depths. At the depth to which 14% of surface irradiance penetrated, HLII clones dominated the stations closest to the equator. The percentage of HLI clones increased with distance from the equator and LL clones were found only at the most northern and southern stations. In contrast, deeper (1% light depth) water samples did not show any overall trend in Prochlorococcus diversity or clade dominance. Multivariate statistical analyses indicated that Prochlorococcus diversity was linked to water temperature (partially an effect of latitude) and depth (which was linked to light penetration and turbidity). Phylogenetic analysis of the sequences obtained from the 423 different environmental RFLP-types detected in this study indicated that the HLII and HLI populations were composed of a wide range of genetically different clones, while the LL Prochlorococcus clade was less diverse, although half of the samples screened in this study derived from the 1% light depth.

T4 genes in the marine ecosystem: studies of the T4-like cyanophages and their role in marine ecology.

From genomic sequencing it has become apparent that the marine cyanomyoviruses capable of infecting strains of unicellular cyanobacteria assigned to the genera Synechococcus and Prochlorococcus are not only morphologically similar to T4, but are also genetically related, typically sharing some 40-48 genes. The large majority of these common genes are the same in all marine cyanomyoviruses so far characterized. Given the fundamental physiological differences between marine unicellular cyanobacteria and heterotrophic hosts of T4-like phages it is not surprising that the study of cyanomyoviruses has revealed novel and fascinating facets of the phage-host relationship. One of the most interesting features of the marine cyanomyoviruses is their possession of a number of genes that are clearly of host origin such as those involved in photosynthesis, like the psbA gene that encodes a core component of the photosystem II reaction centre. Other host-derived genes encode enzymes involved in carbon metabolism, phosphate acquisition and ppGpp metabolism. The impact of these host-derived genes on phage fitness has still largely to be assessed and represents one of the most important topics in the study of this group of T4-like phages in the laboratory. However, these phages are also of considerable environmental significance by virtue of their impact on key contributors to oceanic primary production and the true extent and nature of this impact has still to be accurately assessed.

Applications of Optically Controlled Gold Nanostructures in Biomedical Engineering.

Since their inception, optical tweezers have proven to be a useful tool for improving human understanding of the microscopic world with wide-ranging applications across science. In recent years, they have found many particularly appealing applications in the field of biomedical engineering which harnesses the knowledge and skills in engineering to tackle problems in biology and medicine. Notably, metallic nanostructures like gold nanoparticles have proven to be an excellent tool for OT-based micromanipulation due to their large polarizability and relatively low cytotoxicity. In this article, we review the progress made in the application of optically trapped gold nanomaterials to problems in bioengineering. After an introduction to the basic methods of optical trapping, we give an overview of potential applications to bioengineering specifically: nano/biomaterials, microfluidics, drug delivery, biosensing, biophotonics and imaging, and mechanobiology/single-molecule biophysics. We highlight the recent research progress, discuss challenges, and provide possible future directions in this field.

Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution.

The vast majority of cyanophages isolated to date are cyanomyoviruses, a group related to bacteriophage T4. Comparative genome analysis of five cyanomyoviruses, including a newly sequenced cyanophage S-RSM4, revealed a 'core genome' of 64 genes, the majority of which are also found in other T4-like phages. Subsequent comparative genomic hybridization analysis using a pilot microarray showed that a number of 'host' genes are widespread in cyanomyovirus isolates. Furthermore, a hyperplastic region was identified between genes g15-g18, within a highly conserved structural gene module, which contained a variable number of inserted genes that lacked conservation in gene order. Several of these inserted genes were host-like and included ptoX, gnd, zwf and petE encoding plastoquinol terminal oxidase, 6-phosphogluconate dehydrogenase, glucose 6-phosphate dehydrogenase and plastocyanin respectively. Phylogenetic analyses suggest that these genes were acquired independently of each other, even though they have become localized within the same genomic region. This hyperplastic region contains no detectable sequence features that might be mechanistically involved with the acquisition of host-like genes, but does appear to be a site specifically associated with the acquisition process and may represent a novel facet of the evolution of marine cyanomyoviruses.

Differential grazing of two heterotrophic nanoflagellates on marine Synechococcus strains.

Grazing of heterotrophic nanoflagellates on marine picophytoplankton presents a major mortality factor for this important group of primary producers. However, little is known of the selectivity of the grazing process, often merely being thought of as a general feature of cell size and motility. In this study, we tested grazing of two heterotrophic nanoflagellates, Paraphysomonas imperforata and Pteridomonas danica, on strains of marine Synechococcus. Both nanoflagellates proved to be selective in their grazing, with Paraphysomonas being able to grow on 5, and Pteridomonas on 11, of 37 Synechococcus strains tested. Additionally, a number of strains (11 for Paraphysomonas, 9 for Pteridomonas) were shown to be ingested, but not digested (and thus did not support growth of the grazer). Both the range of prey strains that supported growth as well as those that were ingested but not digested was very similar for the two grazers, suggesting a common property of these prey strains that lent them susceptible to grazing. Subsequent experiments on selected Synechococcus strains showed a pronounced difference in grazing susceptibility between wild-type Synechococcus sp. WH7803 and a spontaneous phage-resistant mutant derivative, WH7803PHR, suggesting that cell surface properties of the Synechococcus prey are an important attribute influencing grazing vulnerability.

The potential of phages to prevent MRSA infections.

This short review attempts to examine whether there is a potential for the use of phages capable of infecting Staphylococcus aureus to eradicate or reduce nasal colonisation, thereby reducing the overall infection burden in patient populations identified as being at risk from MRSA infections. There is clear evidence that nasal decolonisation may be of benefit to certain patient groups and also that phages can effectively combat experimentally induced S. aureus infections in animals. However, this is not in itself enough to validate the use of phages for decolonisation and, given the appearance of strains resistant to currently used topical antibiotics, there is a need for clinical trials of this prophylactic use of phages.

Exploring the prokaryotic virosphere.

The world of prokaryotic viruses, including the "traditional" bacteriophages and the viruses of Archaea, is currently in a period of renaissance, brought about largely by our new capabilities in (meta)genomics and by the isolation of diverse novel virus-host systems. In this review, we highlight some of the directions where we believe research on the prokaryotic virosphere will lead us in the near future.

Infection by the 'photosynthetic' phage S-PM2 induces increased synthesis of phycoerythrin in Synechococcus sp. WH7803.

Phycoerythrin-containing Synechococcus strains are unicellular cyanobacteria that are of great ecological importance in the marine environment. These organisms are known to be susceptible to infection by cyanophages (viruses that infect cyanobacteria). The infection cycle takes several hours and during this time the cyanophages may potentially modify the cyanobacterial light-harvesting apparatus. This study based on a model system consisting of Synechococcus sp. WH7803 and cyanophage S-PM2 revealed a progressive increase in the content of phycoerythrin per cell and per phycobilisome postinfection using absorption and emission spectrophotometry and sodium dodecyl sulphate-polyacrylamide gel electrophoresis. An increased cellular content of chlorophyll a was also revealed using absorption spectrophotometry. The transcript levels of the phycoerythrin-coding operons, mpeBA and cpeBA, were found to increase after phage infection using quantitative real-time PCR. This phage-induced increase in light-harvesting capacity could potentially increase the photosynthetic activity of the host to satisfy the phage's energy demand for reproduction.

Photosynthetic genes in viral populations with a large genomic size range from Norwegian coastal waters.

This study reports the diversity of uncultured environmental viruses harbouring photosynthetic genes (psbA and psbD) in samples from cold seawater (latitude above 60 degrees ). The viral community in coastal Norwegian waters was separated according to genome size using pulse field gel electrophoresis. Viral populations within a wide genome size range (31-380 kb) were investigated for the presence of the psbA and psbD genes using PCR, combined with cloning and sequencing. The results show the presence of photosynthetic genes in viral populations from all size ranges. Thus, valuable information could be obtained about the size class to which viral particles that encode photosynthesis genes belong. The wide genomic size range detected implies that a different cyanophage profile has been observed than has been reported previously. Thus, the method of phage gene detection applied here may represent a truer picture of phage diversity in general or that there is a larger range of size profile for viruses with psbA and psbD in higher latitudes than for the better-studied lower latitudes. Alternatively, a picture of diversity based on a different set of biases than that from either isolation-based research or from conventional metagenomic approaches may be observed.

The third age of phage.

The third age of phage has begun with the recognition that phages may be key to the great planetary biogeochemical cycles and represent the greatest potential genetic resource in the biosphere.

An alternative approach to projecting health expenditure in Australia.

OBJECTIVE: To introduce a large body of work that explores the modelling of expenditure on health services per person living with major causes of disease or injury as a valid basis for conclusions regarding future health expenditure in Australia. METHODS: Separate projections were calculated for important health conditions (or groups of conditions) by type of expenditure (hospital care, medical services, pharmaceuticals, aged care homes and other health services). Analyses accounted for expected changes in the number of affected cases, the proportion of cases treated, the volume of health services per treated case and excess health price inflation. RESULTS: Total health expenditure in Australia is expected to increase from 9.4% of GDP in 2002-03 to 10.8% of GDP in 2032-33. This represents a 15% increase in the "health : GDP" proportion over the projection period, or an annual growth of 0.5%. Two-thirds of this growth is accounted for by expected increases in population size and population ageing. CONCLUSIONS: The lower annual growth in the "health : GDP" proportion compared with other estimates for Australia (range, 0.9% to 1.7%) was attributed to different assumptions regarding non-demographic growth factors, particularly volume per case. Explicit modelling of these factors separately for each condition ensured that assumptions remained within plausible limits.

Pigment composition and adaptation in free-living and symbiotic strains of Acaryochloris marina.

Acaryochloris marina strains have been isolated from several varied locations and habitats worldwide demonstrating a diverse and dynamic ecology. In this study, the whole cell photophysiologies of strain MBIC11017, originally isolated from a colonial ascidian, and the free-living epilithic strain CCMEE5410 are analyzed by absorbance and fluorescence spectroscopy, laser scanning confocal microscopy, sodium dodecyl sulfate polyacrylamide gel electrophoresis and subsequent protein analysis. We demonstrate pigment adaptation in MBIC11017 and CCMEE5410 under different light regimes. We show that the higher the incident growth light intensity for both strains, the greater the decrease in their chlorophyll d content. However, the strain MBIC11017 loses its phycobiliproteins relative to its chlorophyll d content when grown at light intensities of 40 microE m(-2) s(-1) without shaking and 100 microE m(-2) s(-1) with shaking. We also conclude that phycobiliproteins are absent in the free-living strain CCMEE5410.

Phages of the marine cyanobacterial picophytoplankton.

Cyanobacteria of the genera Synechococcus and Prochlorococcus dominate the prokaryotic component of the picophytoplankton in the oceans. It is still less than 10 years since the discovery of phages that infect marine Synechococcus and the beginning of the characterisation of these phages and assessment of their ecological impact. Estimations of the contribution of phages to Synechococcus mortality are highly variable, but there is clear evidence that phages exert a significant selection pressure on Synechococcus community structure. In turn, there are strong selection pressures on the phage community, in terms of both abundance and composition. This review focuses on the factors affecting the diversity of cyanophages in the marine environment, cyanophage interactions with their hosts, and the selective pressures in the marine environment that affect cyanophage evolutionary biology.