Meal and food preferences of nutritionally at-risk inpatients admitted to two Australian tertiary teaching hospitals

Aim: To determine preferences for meals and snack of long-stay patients and hospitalised patients with increased energy and protein requirements.----- Methods: Using consistent methodology across two tertiary teaching hospitals, a convenience sample of adult public hospital inpatients with increased energy and protein requirements or longer stays (seven days or more) were interviewed regarding meal and snack preferences. Descriptive reporting of sample representativeness, preferred foods and frequency of meals and between meal snacks.----- Results: Of 134 respondents, 55% reported a decreased appetite and 28% rated their appetite as 'poor'. Most felt like eating either nothing (42%) or soup (15%) when unwell. The most desired foods were hot meal items, including eggs (31%), meat dishes (20%) and soup (69%). Of items not routinely available, soft drink (7.6%) and alcohol (6.7%) were most commonly desired during admission. Almost half (49%) reported difficulty opening packaged food and a majority (81%) indicated finger foods were easy to eat.----- Conclusion: Appetites during admission were frequently lower than usual. Responses encourage consideration of eggs, meat dishes and soups for long-stayers or those with high-energy, high-protein needs. Easy to consume but not routinely offered, between meal items, such as soup, juice, cake, soft drink or Milo could be explored further to enhance oral intakes

Hidden in plain sight: The importance of cryptic interactions in marine plankton

Here, we present a range of interactions, which we term “cryptic interactions.” These are interactions that occur throughout the marine planktonic foodweb but are currently largely overlooked by established methods, which mean large-scale data collection for these interactions is limited. Despite this, current evidence suggests some of these interactions may have perceptible impacts on foodweb dynamics and model results. Incorporation of cryptic interactions into models is especially important for those interactions involving the transport of nutrients or energy. Our aim is to highlight a range of cryptic interactions across the plankton foodweb, where they exist, and models that have taken steps to incorporate these interactions. Additionally, it is discussed where additional research and effort is required to continue advancing our understanding of these cryptic interactions. We call for more collaboration between ecologists and modelers in order to incorporate cryptic interactions into biogeochemical and foodweb models

High-Resolution Analysis of Cytosine Methylation in Ancient DNA

Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to participate in the rapid adaptation of species to changes in environment. Any direct test of this hypothesis would require the ability to measure epigenetic states over evolutionary timescales. Here we describe the first single-base resolution of cytosine methylation patterns in an ancient mammalian genome, by bisulphite allelic sequencing of loci from late Pleistocene Bison priscus remains. Retrotransposons and the differentially methylated regions of imprinted loci displayed methylation patterns identical to those derived from fresh bovine tissue, indicating that methylation patterns are preserved in the ancient DNA. Our findings establish the biochemical stability of methylated cytosines over extensive time frames, and provide the first direct evidence that cytosine methylation patterns are retained in DNA from ancient specimens. The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution

The LUMIERE dataset: Longitudinal Glioblastoma MRI with expert RANO evaluation.

Publicly available Glioblastoma (GBM) datasets predominantly include pre-operative Magnetic Resonance Imaging (MRI) or contain few follow-up images for each patient. Access to fully longitudinal datasets is critical to advance the refinement of treatment response assessment. We release a single-center longitudinal GBM MRI dataset with expert ratings of selected follow-up studies according to the response assessment in neuro-oncology criteria (RANO). The expert rating includes details about the rationale of the ratings. For a subset of patients, we provide pathology information regarding methylation of the O6-methylguanine-DNA methyltransferase (MGMT) promoter status and isocitrate dehydrogenase 1 (IDH1), as well as the overall survival time. The data includes T1-weighted pre- and post-contrast, T2-weighted, and fluid-attenuated inversion recovery (FLAIR) MRI. Segmentations from state-of-the-art automated segmentation tools, as well as radiomic features, complement the data. Possible applications of this dataset are radiomics research, the development and validation of automated segmentation methods, and studies on response assessment. This collection includes MRI data of 91 GBM patients with a total of 638 study dates and 2487 images

Evaluating automated longitudinal tumor measurements for glioblastoma response assessment.

Automated tumor segmentation tools for glioblastoma show promising performance. To apply these tools for automated response assessment, longitudinal segmentation, and tumor measurement, consistency is critical. This study aimed to determine whether BraTumIA and HD-GLIO are suited for this task. We evaluated two segmentation tools with respect to automated response assessment on the single-center retrospective LUMIERE dataset with 80 patients and a total of 502 post-operative time points. Volumetry and automated bi-dimensional measurements were compared with expert measurements following the Response Assessment in Neuro-Oncology (RANO) guidelines. The longitudinal trend agreement between the expert and methods was evaluated, and the RANO progression thresholds were tested against the expert-derived time-to-progression (TTP). The TTP and overall survival (OS) correlation was used to check the progression thresholds. We evaluated the automated detection and influence of non-measurable lesions. The tumor volume trend agreement calculated between segmentation volumes and the expert bi-dimensional measurements was high (HD-GLIO: 81.1%, BraTumIA: 79.7%). BraTumIA achieved the closest match to the expert TTP using the recommended RANO progression threshold. HD-GLIO-derived tumor volumes reached the highest correlation between TTP and OS (0.55). Both tools failed at an accurate lesion count across time. Manual false-positive removal and restricting to a maximum number of measurable lesions had no beneficial effect. Expert supervision and manual corrections are still necessary when applying the tested automated segmentation tools for automated response assessment. The longitudinal consistency of current segmentation tools needs further improvement. Validation of volumetric and bi-dimensional progression thresholds with multi-center studies is required to move toward volumetry-based response assessment

Two sides of the same coin? Patient and therapist experiences with a transdiagnostic blended intervention focusing on emotion regulation.

Introduction The combination of internet-based intervention and psychotherapy, commonly termed blended therapy (BT), has gained popularity in recent years. While advantages and disadvantages of BT have been identified from the patient and therapist perspective, the two perspectives have rarely been examined within the same treatment. Moreover, almost all available research on patient and therapist experiences with BT is disorder-specific. This study aimed to investigate patient and therapist experiences within the same transdiagnostic BT. Methods A qualitative analysis of semi-structured interviews with eight patients and eight therapists taking part in a transdiagnostic blended intervention focusing on the topic of emotion regulation was conducted. A qualitative content analysis approach was used. Category frequencies were calculated and similarities and differences between the patient and therapist experience were explored. Results Ten main themes and 59 subthemes were identified in the category system for patient interviews and ten main themes and 50 subthemes were identified in the category system for therapist interviews. Similarities and differences between the two perspectives were reported with regard to 1) expectations toward the intervention, 2) the internet-based intervention, 3) symptomatology and emotion regulation, 4) the therapeutic relationship and 5) the blended format. Conclusion This study provides first insights on the experiences with transdiagnostic BT focusing on emotion regulation. Based on the results, different recommendations for the improvement of transdiagnostic BT are made. Future research on patient and therapist experiences with transdiagnostic BT is necessary, in order to further improve the experience of those involved

An expert-driven framework for applying eDNA tools to improve biosecurity in the Antarctic

Signatories to the Antarctic Treaty System’s Environmental Protocol are committed to preventing incursions of non-native species into Antarctica, but systematic surveillance is rare. Environmental DNA (eDNA) methods provide new opportunities for enhancing detection of non-native species and biosecurity monitoring. To be effective for Antarctic biosecurity, eDNA tests must have appropriate sensitivity and specificity to distinguish non-native from native Antarctic species, and be fit-for-purpose. This requires knowledge of the priority risk species or taxonomic groups for which eDNA surveillance will be informative, validated eDNA assays for those species or groups, and reference DNA sequences for both target non-native and related native Antarctic species. Here, we used an expert elicitation process and decision-by-consensus approach to identify and assess priority biosecurity risks for the Australian Antarctic Program (AAP) in East Antarctica, including identifying high priority non-native species and their potential transport pathways. We determined that the priority targets for biosecurity monitoring were not individual species, but rather broader taxonomic groups such as mussels (Mytilus species), tunicates (Ascidiacea), springtails (Collembola), and grasses (Poaceae). These groups each include multiple species with high risks of introduction to and/or establishment in Antarctica. The most appropriate eDNA methods for the AAP must be capable of detecting a range of species within these high-risk groups (e.g., eDNA metabarcoding). We conclude that the most beneficial Antarctic eDNA biosecurity applications include surveillance of marine species in nearshore environments, terrestrial invertebrates, and biofouling species on vessels visiting Antarctica. An urgent need exists to identify suitable genetic markers for detecting priority species groups, establish baseline terrestrial and marine biodiversity for Antarctic stations, and develop eDNA sampling methods for detecting biofouling organisms

An expert-driven framework for applying eDNA tools to improve biosecurity in the Antarctic

Signatories to the Antarctic Treaty System’s Environmental Protocol are committed to preventing incursions of non-native species into Antarctica, but systematic surveillance is rare. Environmental DNA (eDNA) methods provide new opportunities for enhancing detection of non-native species and biosecurity monitoring. To be effective for Antarctic biosecurity, eDNA tests must have appropriate sensitivity and specificity to distinguish non-native from native Antarctic species, and be fit-for-purpose. This requires knowledge of the priority risk species or taxonomic groups for which eDNA surveillance will be informative, validated eDNA assays for those species or groups, and reference DNA sequences for both target non-native and related native Antarctic species. Here, we used an expert elicitation process and decision-by-consensus approach to identify and assess priority biosecurity risks for the Australian Antarctic Program (AAP) in East Antarctica, including identifying high priority non-native species and their potential transport pathways. We determined that the priority targets for biosecurity monitoring were not individual species, but rather broader taxonomic groups such as mussels (Mytilus species), tunicates (Ascidiacea), springtails (Collembola), and grasses (Poaceae). These groups each include multiple species with high risks of introduction to and/or establishment in Antarctica. The most appropriate eDNA methods for the AAP must be capable of detecting a range of species within these high-risk groups (e.g., eDNA metabarcoding). We conclude that the most beneficial Antarctic eDNA biosecurity applications include surveillance of marine species in nearshore environments, terrestrial invertebrates, and biofouling species on vessels visiting Antarctica. An urgent need exists to identify suitable genetic markers for detecting priority species groups, establish baseline terrestrial and marine biodiversity for Antarctic stations, and develop eDNA sampling methods for detecting biofouling organisms.This work was supported as a Science Innovation Project by the Department of Agriculture, Water and the Environment’s Science Innovation Program funding 2021–22 (project team: A.J.M., L.J.C., D.M.B., C.K.K., J.S.S. and L.S.). Support was also provided (to J.D.S, E.L.J., S.A.R., J.S.S., M.I.S., J.M.S., N.G.W.) from Australian Research Council SRIEAS grant SR200100005. P.C. and K.A.H. are supported by NERC core funding to the BAS Biodiversity, Evolution and Adaptation Team and Environment Office, respectively. L.R.P. and M.G. are supported by Biodiversa ASICS funding

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Gene expression profiling of rat spermatogonia and Sertoli cells reveals signaling pathways from stem cells to niche and testicular cancer cells to surrounding stroma

Background: Stem cells and their niches are studied in many systems, but mammalian germ stem cells (GSC) and their niches are still poorly understood. In rat testis, spermatogonia and undifferentiated Sertoli cells proliferate before puberty, but at puberty most spermatogonia enter spermatogenesis, and Sertoli cells differentiate to support this program. Thus, pre-pubertal spermatogonia might possess GSC potential and pre-pubertal Sertoli cells niche functions. We hypothesized that the different stem cell pools at pre-puberty and maturity provide a model for the identification of stem cell and niche-specific genes. We compared the transcript profiles of spermatogonia and Sertoli cells from pre-pubertal and pubertal rats and examined how these related to genes expressed in testicular cancers, which might originate from inappropriate communication between GSCs and Sertoli cells. Results: The pre-pubertal spermatogonia-specific gene set comprised known stem cell and spermatogonial stem cell (SSC) markers. Similarly, the pre-pubertal Sertoli cell-specific gene set comprised known niche gene transcripts. A large fraction of these specifically enriched transcripts encoded trans-membrane, extra-cellular, and secreted proteins highlighting stem cell to niche communication. Comparing selective gene sets established in this study with published gene expression data of testicular cancers and their stroma, we identified sets expressed genes shared between testicular tumors and pre-pubertal spermatogonia, and tumor stroma and pre-pubertal Sertoli cells with statistic significance. Conclusions: Our data suggest that SSC and their niche specifically express complementary factors for cell communication and that the same factors might be implicated in the communication between tumor cells and their micro-enviroment in testicular cancer