Cheerfulness in the history of psychiatry.

In 1762, Louis-Antoine Marquis de Caraccioli (1719-1803), a prolific writer of the eighteenth century, dedicated a book to a psychological theme that medicine has forgotten: 'gaité' in French, which we will translate as 'cheerfulness'. At the beginning of the nineteenth century, this work inspired two doctoral theses in medicine, one defended in Montpellier, the other in Paris. In their texts, Louis Monferran (1785-?) and Vincent Rémi Giganon (1794-1857) explored the therapeutic benefits of the medical prescription of cheerfulness. In addition to lifestyle recommendations, they focused on the psychotropic substances available to them: alcohol, coca, hemp and opiates. In an original and novel way, Giganon introduced and recommended 'le gaz oxydule d'azote inspiré', or inhaled nitrous oxide gas.

Alzheimer's disease heterogeneity revealed by neuroanatomical normative modeling.

INTRODUCTION: Overlooking the heterogeneity in Alzheimer's disease (AD) may lead to diagnostic delays and failures. Neuroanatomical normative modeling captures individual brain variation and may inform our understanding of individual differences in AD-related atrophy. METHODS: We applied neuroanatomical normative modeling to magnetic resonance imaging from a real-world clinical cohort with confirmed AD (n = 86). Regional cortical thickness was compared to a healthy reference cohort (n = 33,072) and the number of outlying regions was summed (total outlier count) and mapped at individual- and group-levels. RESULTS: The superior temporal sulcus contained the highest proportion of outliers (60%). Elsewhere, overlap between patient atrophy patterns was low. Mean total outlier count was higher in patients who were non-amnestic, at more advanced disease stages, and without depressive symptoms. Amyloid burden was negatively associated with outlier count. DISCUSSION: Brain atrophy in AD is highly heterogeneous and neuroanatomical normative modeling can be used to explore anatomo-clinical correlations in individual patients.

Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria.

Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20-40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research.

The effects of hormonal contraceptive use on sleep patterns in women of reproductive age.

PURPOSE: Hormonal contraceptives alter hormone levels in women and have been linked to alterations in sleep patterns; however, previous studies yielded inconsistent results and lacked generalizability. This study examines hormonal contraceptive use and its impact on sleep outcomes, including sleep duration and sleep disturbances. METHODS: Women self-reported their sleep patterns and use of contraceptives in the 2017 population-based Behavioral Risk Factor Surveillance System Survey (n=1,970). Participants were categorized by use of hormonal or non-hormonal contraceptives for the purpose of pregnancy prevention. Sleep duration was defined as having met the recommended sleep levels of 7-9 hours per 24 hours. Sleep disturbances were defined as trouble falling asleep, staying asleep, or sleeping too much ≥ 6 days within a 14-day period. Prevalence ratios (PRs) and 95% confidence intervals (CIs) were calculated to examine the association between contraceptive use and each sleep outcome. SAS-callable SUDAAN was used for analyses to account for the complex sampling design. RESULTS: Women who used hormonal contraceptives had 6% higher prevalence of sleep disturbances (PR: 1.06, 95% CI: 0.99, 1.14) and 17% lower prevalence of not meeting sleep duration recommendations (PR: 0.83, 95% CI: 0.71, 0.98) compared to those who used non-hormonal contraceptives after adjustment for age. CONCLUSION: These findings suggest the use of hormonal contraceptives may have negative impacts on sleep disturbances, and positive effects on sleep duration among women using contraceptives for preventing pregnancy. Future studies should be conducted in diverse populations utilizing objective measurements of sleep patterns.

Prevalence of Depressive Symptoms in a Memory Clinic Cohort: A Retrospective Study.

BACKGROUND: Depression has been suggested to be a cause of reversible cognitive impairment but also a risk factor for neurodegenerative disease. Studies suggest that depression prevalence may be high in early onset dementia, particularly Alzheimer's disease, but this has not been systematically assessed in a biomarker-validated clinical dementia cohort to date. OBJECTIVE: To examine the prevalence, features, and association with amyloid pathology of lifetime depressive symptoms in a memory clinic cohort meeting appropriate use criteria for amyloid PET imaging. METHODS: We included 300 patients from a single-center memory clinic cohort that received diagnostic biomarker evaluation with amyloid PET imaging according to appropriate use criteria. History of lifetime depressive symptoms was retrospectively assessed through structured review of clinical correspondence. RESULTS: One hundred forty-two (47%) patients had a history of significant depressive symptoms ('D+'). Of these, 89% had ongoing symptoms and 60% were on antidepressants at the time of presentation to our Clinic. Depressive symptoms were equally highly prevalent in the amyloid-positive and the heterogeneous group of amyloid-negative patients. CONCLUSION: Approximately half of patients who meet appropriate use criteria for amyloid PET have a history of depressive symptoms. We suggest that depression is an important feature of both neurodegenerative and non-neurodegenerative cognitive impairment and may contribute to the diagnostic uncertainty behind referral to amyloid PET.

Assessing Hospital Resource Utilization with Application to Imaging for Patients Diagnosed with Prostate Cancer.

Resource utilization measures are typically modeled by relying on clinical characteristics. However, in some settings, those clinical markers are not available, and hospitals are unable to explore potential inefficiencies or resource misutilization. We propose a novel approach to exploring misutilization that solely relies on administrative data in the form of patient characteristics and competing resource utilization, with the latter being a novel addition. We demonstrate this approach in a 2019 patient cohort diagnosed with prostate cancer (n = 51,111) across 1056 U.S. healthcare facilities using Premier, Inc.'s (Charlotte, NC, USA) all payor databases. A multivariate logistic regression model was fitted using administrative information and competing resources utilization. A decision curve analysis informed by industry average standards of utilization allows for a definition of misutilization with regards to these industry standards. Odds ratios were extracted at the patient level to demonstrate differences in misutilization by patient characteristics, such as race; Black individuals experienced higher under-utilization compared to White individuals (p < 0.0001). Volume-adjusted Poisson rate regression models allow for the identification and ranking of facilities with large departures in utilization. The proposed approach is scalable and easily generalizable to other diseases and resources and can be complemented with clinical information from electronic health record information, when available.

Antifungal Susceptibility Profiles and Drug Resistance Mechanisms of Clinical Lomentospora prolificans Isolates.

Lomentospora prolificans is an opportunistic fungal pathogen with low susceptibility to current antifungal drugs. Here, we tested the in vitro susceptibility of 8 drugs against 42 clinical L. prolificans isolates. All isolates showed high MICs to voriconazole (MIC90>16 µg/ml), itraconazole (MIC90>16 µg/ml), posaconazole (MIC90>16 µg/ml), isavuconazole (MIC90>16 µg/ml), amphotericin B (MIC90>16 µg/ml), and terbinafine (MIC90>64 µg/ml) and high minimum effective concentrations (MECs) to micafungin (MEC90>8 µg/ml), with the exception of miltefosine showing an MIC90 value of 4 µg/ml. We examined six different in vitro drug combinations and found that the combination of voriconazole and terbinafine achieved the most synergistic effort against L. prolificans We then annotated the L. prolificans whole genome and located its Cyp51 and Fks1 genes. We completely sequenced the two genes to determine if any mutation would be related to azole and echinocandin resistance in L. prolificans We found no amino acid changes in Cyp51 protein and no tandem repeats in the 5' upstream region of the Cyp51 gene. However, we identified three intrinsic amino acid residues (G138S, M220I, and T289A) in the Cyp51 protein that were linked to azole resistance. Likewise, two intrinsic amino acid residues (F639Y, W695F) that have reported to confer echinocandin resistance were found in Fks1 hot spot regions. In addition, three new amino acid alterations (D440A, S634R, and H1245R) were found outside Fks1 hot spot regions, and their contributions to echinocandin resistance need future investigation. Overall, our findings support the notion that L. prolificans is intrinsically resistant to azoles and echinocandins.

Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative.

Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.

Circular linkages between soil biodiversity, fertility and plant productivity are limited to topsoil at the continental scale.

The current theoretical framework suggests that tripartite positive feedback relationships between soil biodiversity, fertility and plant productivity are universal. However, empirical evidence for these relationships at the continental scale and across different soil depths is lacking. We investigate the continental-scale relationships between the diversity of microbial and invertebrate-based soil food webs, fertility and above-ground plant productivity at 289 sites and two soil depths, that is 0-10 and 20-30 cm, across Australia. Soil biodiversity, fertility and plant productivity are strongly positively related in surface soils. Conversely, in the deeper soil layer, the relationships between soil biodiversity, fertility and plant productivity weaken considerably, probably as a result of a reduction in biodiversity and fertility with depth. Further modeling suggested that strong positive associations among soil biodiversity-fertility and fertility-plant productivity are limited to the upper soil layer (0-10 cm), after accounting for key factors, such as distance from the equator, altitude, climate and physicochemical soil properties. These findings highlight the importance of surface soil biodiversity for soil fertility, and suggest that any loss of surface soil could potentially break the links between soil biodiversity-fertility and/or fertility-plant productivity, which can negatively impact nutrient cycling and food production, upon which future generations depend.

Whole-genome landscapes of major melanoma subtypes.

Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. Here we report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. However, acral and mucosal melanomas were dominated by structural changes and mutation signatures of unknown aetiology, not previously identified in melanoma. The number of genes affected by recurrent mutations disrupting non-coding sequences was similar to that affected by recurrent mutations to coding sequences. Significantly mutated genes included BRAF, CDKN2A, NRAS and TP53 in cutaneous melanoma, BRAF, NRAS and NF1 in acral melanoma and SF3B1 in mucosal melanoma. Mutations affecting the TERT promoter were the most frequent of all; however, neither they nor ATRX mutations, which correlate with alternative telomere lengthening, were associated with greater telomere length. Most melanomas had potentially actionable mutations, most in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways. The whole-genome mutation landscape of melanoma reveals diverse carcinogenic processes across its subtypes, some unrelated to sun exposure, and extends potential involvement of the non-coding genome in its pathogenesis.

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.

BACKGROUND: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. FINDINGS: BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'. CONCLUSIONS: Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.

Absolute quantification of human tear lactoferrin using multiple reaction monitoring technique with stable-isotopic labeling.

The mass spectrometry technique of multiple reaction monitoring (MRM) was used to quantify and compare the expression level of lactoferrin in tear films among control, prostate cancer (CaP), and benign prostate hyperplasia (BPH) groups. Tear samples from 14 men with CaP, 15 men with BPH, and 14 controls were analyzed in the study. Collected tears (2 µl) of each sample were digested with trypsin overnight at 37 °C without any pretreatment, and tear lactoferrin was quantified using a lactoferrin-specific peptide, VPSHAVVAR, both using natural/light and isotopic-labeled/heavy peptides with MRM. The average tear lactoferrin concentration was 1.01 ± 0.07 µg/µl in control samples, 0.96 ± 0.07 µg/µl in the BPH group, and 0.98 ± 0.07 µg/µl in the CaP group. Our study is the first to quantify tear proteins using a total of 43 individual (non-pooled) tear samples and showed that direct digestion of tear samples is suitable for MRM studies. The calculated average lactoferrin concentration in the control group matched that in the published range of human tear lactoferrin concentration measured by enzyme-linked immunosorbent assay (ELISA). Moreover, the lactoferrin was stably expressed across all of the samples, with no significant differences being observed among the control, BPH, and CaP groups.

Tumour procurement, DNA extraction, coverage analysis and optimisation of mutation-detection algorithms for human melanoma genomes.

Whole genome sequencing (WGS) of cancer patients' tumours offers the most comprehensive method of identifying both novel and known clinically-actionable genomic targets. However, the practicalities of performing WGS on clinical samples are poorly defined.This study was designed to test sample preparation, sequencing specifications and bioinformatic algorithms for their effect on accuracy and cost-efficiency in a large WGS analysis of human melanoma samples.WGS was performed on melanoma cell lines (n = 15) and melanoma fresh frozen tumours (n = 222). The appropriate level of coverage and the optimal mutation detection algorithm for the project pipeline were determined.An incremental increase in sequencing coverage from 36X to 132X in melanoma tissue samples and 30X to 103X for cell lines only resulted in a small increase (1-2%) in the number of mutations detected, and the quality scores of the additional mutations indicated a low probability that the mutations were real. The results suggest that 60X coverage for melanoma tissue and 40X for melanoma cell lines empower the detection of 98-99% of informative single nucleotide variants (SNVs), a sensitivity level at which clinical decision making or landscape research projects can be carried out with a high degree of confidence in the results. Likewise the bioinformatic mutation analysis methodology strongly influenced the number and quality of SNVs detected. Detecting mutations in the blood genomes separate to the tumour genomes generated 41% more SNVs than if the blood and melanoma tissue genomes were analysed simultaneously. Therefore, simultaneous analysis should be employed on matched melanoma tissue and blood genomes to reduce errors in mutation detection.This study provided valuable insights into the accuracy of SNV with WGS at various coverage levels in human clinical cancer specimens. Additionally, we investigated the accuracy of the publicly available mutation detection algorithms to detect cancer specific SNVs which will aid researchers and clinicians in study design and implementation of WGS for the identification of somatic mutations in other cancers.

The prescription of addiction medications after implementation of chronic care management for substance dependence in primary care.

People with addictive disorders commonly do not receive efficacious medications. Chronic care management (CCM) is designed to facilitate delivery of effective therapies. Using data from the CCM group in a trial testing its effectiveness for addiction (N=282), we examined factors associated with the prescription of addiction medications. Among participants with alcohol dependence, 17% (95% CI 12.0-22.1%) were prescribed alcohol dependence medications. Among those with drug dependence, 9% (95% CI 5.5-12.6%) were prescribed drug dependence medications. Among those with opioids as a substance of choice, 15% (95% CI 9.3-20.9%) were prescribed opioid agonist therapy. In contrast, psychiatric medications were prescribed to 64% (95% CI 58.2-69.4%). Absence of co-morbid drug dependence was associated with prescription of alcohol dependence medications. Lower alcohol addiction severity and recent opioid use were associated with prescription of drug dependence medications. Better understanding of infrequent prescription of addiction medications, despite a supportive clinical setting, might inform optimal approaches to delivering addiction medications.

Bread matters: a national initiative to profile the genetic diversity of Australian wheat.

The large and complex genome of wheat makes genetic and genomic analysis in this important species both expensive and resource intensive. The application of next-generation sequencing technologies is particularly resource intensive, with at least 17 Gbp of sequence data required to obtain minimal (1×) coverage of the genome. A similar volume of data would represent almost 40× coverage of the rice genome. Progress can be made through the establishment of consortia to produce shared genomic resources. Australian wheat genome researchers, working with Bioplatforms Australia, have collaborated in a national initiative to establish a genetic diversity dataset representing Australian wheat germplasm based on whole genome next-generation sequencing data. Here, we describe the establishment and validation of this resource which can provide a model for broader international initiatives for the analysis of large and complex genomes.

New method for prefractionation of plasma for proteomic analysis.

The depth of proteome analysis is severely limited in complex samples with a wide dynamic range of protein abundance such as plasma. Removal of high-abundance proteins should reveal the signal of lower abundance plasma proteins. However, smaller proteins may be part of larger protein complexes and hence the removal of proteins involved in complexes with high-abundance proteins such as albumin may inhibit the search for disease biomarkers. Prefractionation of a sample divides it into fractions of reduced complexity, allowing improved detection of lower abundance proteins. Using a prefractionation device, which employs Gradiflow™ technology, we were able to separate small volume plasma samples into multiple fractions based on the molecular weight and/or charge. The resulting samples of reduced complexity were directly compatible with 2-DE. The use of this prefractionation machine may therefore be useful in the hunt for disease biomarkers.

Post-translation modification of proteins in tears.

This is the first 2-DE study using sequential dyes to analyse phospho-, glyco- and total tear protein profiles (Pro-Q Diamond for phosphoprotein, Pro-Q Emerald for glycoprotein and Sypro Ruby for total protein). This method minimised the gel-gel variations, allowing better comparisons among the three profiles and generated a whole map of PTM profiles of tear protein. A novel tear protein, dermcidin, was identified for the first time in this study. The identification of this antimicrobial protein suggests a new model of defence in tears. In addition, we are able to present the first experimental evidence of the presence of glycosylated lipocalin 1 and cystatin S. Nucleobindin 2 was only detected using phospho staining, suggesting it is only phosphorylated in tears. This study provides the groundwork for understanding the PTM of tear proteins and consequently these methods could be useful in the search for biomarkers in tears.

Candidate effector gene identification in the ascomycete fungal phytopathogen Venturia inaequalis by expressed sequence tag analysis.

The hemi-biotrophic fungus Venturia inaequalis infects members of the Maloideae, causing the economically important apple disease, scab. The plant-pathogen interaction of Malus and V. inaequalis follows the gene-for-gene model. cDNA libraries were constructed, and bioinformatic analysis of the resulting expressed sequence tags (ESTs) was used to characterize potential effector genes. Effectors are small proteins, secreted in planta, that are assumed to facilitate infection. Therefore, a cDNA library was constructed from a compatible interaction. To distinguish pathogen from plant sequences, the library was probed with genomic DNA from V. inaequalis to enrich for pathogen genes, and cDNA libraries were constructed from in vitro-grown material. A suppression subtractive hybridization library enriched for cellophane-induced genes was included, as growth on cellophane may mimic that in planta, with the differentiation of structures resembling those formed during plant colonization. Clustering of ESTs from the in planta and in vitro libraries indicated a fungal origin of the resulting non-redundant sequence. A total of 937 ESTs was classified as putatively fungal, which could be assembled into 633 non-redundant sequences. Sixteen new candidate effector genes were identified from V. inaequalis based on features common to characterized effector genes from filamentous fungi, i.e. they encode a small, novel, cysteine-rich protein, with a putative signal peptide. Three of the 16 candidates, in particular, conformed to most of the protein structural characteristics expected of fungal effectors and showed significant levels of transcriptional up-regulation during in planta growth. In addition to candidate effector genes, this collection of ESTs represents a valuable genomic resource for V. inaequalis.

Alterations to the protein profile of bladder carcinoma cell lines induced by plant extract MINA-05 in vitro.

Bladder cancer (BLCa) is a severe urological cancer of both men and women that commonly recurs and once invasive, is difficult to treat. MINA-05 (CK Life Sciences Int'l, Hong Kong) is a derivative of complex botanical extracts, shown to reduce cellular proliferation of bladder and prostate carcinomas. We tested the effects of MINA-05 against human BLCa cell sublines, B8, B8-RSP-GCK, B8-RSP-LN and C3, from a transitional cell carcinoma, grade IV, to determine the molecular targets of treatment by observing the cellular protein profile. Cells were acclimatised for 48 h then treated for 72 h with concentrations of MINA-05 reflecting 1/2 IC(50), IC(50) and 2 x IC(50) (n = 3) or with vehicle, (0.5% DMSO). Dose-dependant changes in protein abundance were detected and characterised using 2-dimensional electrophoresis and MS. We identified 10 proteins that underwent changes in abundance, pI and/or molecular mass in response to treatment. MINA-05 was shown to influence proteins across numerous functional classes including cytoskeletal proteins, energy metabolism proteins, protein degradation proteins and tumour suppressors, suggesting a global impact on these cell lines. This study implies that the ability of MINA-05 to retard cellular proliferation is attributed to its ability to alter cell cycling, metabolism, protein degradation and the cancer cell environment.